CA2561742A1 - Methods for identifying risk of osteoarthritis and treatments thereof - Google Patents

Abstract

Provided herein are methods for identifying a risk of osteoarthritis in a subject, reagents and kits for carrying out the methods, methods for identifying candidate therapeutics for treating osteoarthritis, and therapeutic and preventative methods applicable to osteoarthritis. These embodiments are based upon an analysis of polymorphic variations in nucleotide sequences within the human genome.

Description

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METHODS FOR IDENTIFYING RISK OF OSTEOARTHRITIS AND
TREATMENTSTHEREOF
Field of the Invention [0001] The invention relates to genetic methods for identifying risk of osteoarthritis and treatments that specifically target such diseases.
Back r~ ound [0002] Osteoarthritis (OA) is a chronic disease usually affecting weight-bearing synovial joints.
There are approximately 20 million Americans affected by OA and it is the leading cause of disability in the United States. In addition to extensive human suffering, OA also accounts for nearly all knee replacements and more than half of all hip replacements in the United States.
Despite its prevalence, OA is poorly understood and there are few treatments available besides anti-inflammatory drugs and joint replacement.

[0003] Osteoarthritis (OA) is a disease caused by degeneration of articular cartilage and subsequent joint deformation. In addition to risk factors like body weight, joint injury and age, there is a strong hereditary component to OA, reflected by high heritability estimates from twin studies. So far, few of the genes responsible for this genetic component have been identified.
Summary [0004] It has been discovered that certain polymorphic variations in human genomic DNA are associated with osteoarthritis. In particular, polymorphic variants in loci containing PADI2, APOB;' ILIRL2, ILIRL1, WASPIP, ADAMTS2, BhES, TM7SF3, L~XLl, CASPR~ ahd APOL3 regions and other regions in Table B of human genomic DNA have been associated with risk of osteoarthritis.

[0005] Thus, featured herein are methods for identifying a subject at risk of osteoarthritis and/or a risk of osteoarthritis in a subject, which comprise detecting the presence or absence of one or more polymorphic variations associated with osteoarthritis in or around the loci described herein in a human nucleic acid sample. In an embodiment, two or more polymorphic variations are detected in two or more regions of which one is the PADI2, APOB, IL1RL2, ILIRLl, WASPIP, ADAMTS2, BYES, TM7SF3, LO~YZl, CASPR4 or APOL3 region or other region in Table B. In certain embodiments, 3 or more, or 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 or more polymorphic variants are detected.

[0006] Also featured are nucleic acids that include one or more polymorphic variations associated with occurrence of osteoarthritis, as well as polypeptides encoded by these nucleic acids. In addition, provided are methods for identifying candidate therapeutic molecules for treating osteoarthritis, as well as methods for treating osteoarthritis in a subject by identifying a subject at risk of osteoarthritis and treating the subject with a suitable prophylactic, treatment or therapeutic molecule.

[0007] Also provided are compositions comprising a cell from a subject having osteoarthritis or at risk of osteoarthritis and/or a PADI2, APOB, ILIRL2, IL1RL1, WASPIP, ADAMTS2, BhES, TM7SF3, LOXLl, CASPR4 or APOL3 nucleic acid or other nucleic acid referenced in Table B, with a RNAi, siRNA, antisense DNA or RNA, or ribozyme nucleic acid designed from a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLl, CASPR4 orAPOL3 nucleotide sequence or other nucleotide sequence referenced in Table B. In an embodiment, the RNAi, siRNA, antisense DNA
or RNA, or ribozyme nucleic acid is designed from a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BT~ES, TM7SF3, LOXLl, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B that includes one or more polymorphic variations associated with osteoarthritis, and in some instances, specifically interacts with such a nucleotide sequence. Further, provided are arrays of nucleic acids bound to a solid surface, in which one or more nucleic acid molecules ofthe array have a PADI2, APOB, ILIRL2, ILIRL1, WASPIP, ADAMTS2, BT~ES, TM7SF3, LOXL1, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B, or a fragment or substantially identical nucleic acid thereof, or a complementary nucleic acid of the foregoing. Featured also are compositions comprising a cell from a subject having osteoarthritis or at risk of osteoarthritis and/or a PADI2, .APOB, IL1RL2, ILIRL1, WASPIP, ADAMTS2, BT~ES, TM7SF3, LOXLl, CASPR4 or APOL3 polypeptide or other polypeptide referenced in Table B, with an antibody that specifically binds to the polypeptide. In an embodiment, the antibody specifically binds to an epitope in the polypeptide that includes a non-synonymous amino acid modification associated with osteoarthritis (e.g., results in an amino acid substitution in the encoded polypeptide associated with osteoarthritis). In certain embodiments, the antibody selectively binds to an epitope in the PADl2, APOB, ILIRL2, IL1RL1, WASPIP, ADAMTS2, BITES, TM7SF3, LOXL1, CASPR4 orAPOL3 polypeptide, or other polypeptide referenced in Table B, having an amino acid associated with osteoarthritis. Thus, featured is an antibody that binds an epitope having an amino acid encoded by rs1367117, rs1041973 and/or rs398829, such as a isoleucine or threonine encoded by rs1367117 (e.g., a threonine at position 98 in anAPOB polypeptide), a glutamic acid or alanine encoded by rs1041973 (e.g., an alanine at position 78 in a ILIRLI polypeptide), a valine or isoleucine encoded by rs398829 (e.g., a valine at position 245 in a AD~1MTS2 polypeptide), at the corresponding position in the polypeptide.
Brief Description of the Drawings [0008] Figures lA-1J show proximal SNPs in a 100-kb window in PADI2, APOB, IL1RL2, ILIRLI, WASPIP, ADAMTS2, BhES, TM7SF3, LOXLl, CASPR4 and APOL3 regions of genomic DNA, respectively, that were compared between pools of cases and controls. The x-axis corresponds to their chromosomal position and the y-axis to the test P-values (shown on the -logio scale). The continuous bold line presents the results of a goodness-of fit test for an excess of significance (compared to 0.05) in a 10 kb sliding window assessed at 1 kb increments.

Detailed Description [0009] It has been discovered that polyrnorphic variants in a locus containing a PADI2, APOB, ILIRL2, ILIRL1, WASPIP, ADAMTS2, BT~ES, TM7SF3, LOXLI, CASPR4 orAPOL3 region are associated with occurrence of osteoarthritis in subjects. Thus, detecting genetic determinants associated with an increased risk of osteoarthritis occurrence can lead to early identification of a predisposition to osteoarthritis and early prescription of preventative measures. Also, associating a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BITES, TM7SF3, LOXLl, CASPR4 orAPOL3 polymorphic variant and other variants referenced in Table B with osteoarthritis has provided new targets for screening molecules useful in treatments of osteoarthritis.
Osteoarthritis and Sample Selection [0010] Osteoarthritis (OA), or degenerative joint disease, is one of the oldest and most common types of arthritis. It is characterized by the breakdown of the joint's cartilage. Cartilage is the part of the joint that cushions the ends of bones, and its breakdown causes bones to rub against each other, causing pain and loss of movement. Type II collagen is the main component of cartilage, comprising 15-25% of the wet weight, approximately half the dry weight, and representing 90-95% of the total collagen content in the tissue. It forms fibrils that endow cartilage with tensile strength (Mayne, R. Arthritis Rhuem. 32:241-246 (1989)).

[0011] Most commonly affecting middle-aged and older people, OA can range from very mild to very severe. It affects hands and weight-bearing joints such as knees, hips, feet and the back. Knee OA
can be as disabling as any cardiovascular disease except stroke.

[0012] Osteoarthritis affects an estimated 20.7 million Americans, mostly after age 45, with women more commonly affected than men. Physicians make a diagnosis of OA based on a physical exam and history of symptoms. X-rays are used to confirm diagnosis. Most people over 60 reflect the disease on X-ray, and about one-third have actual symptoms.

[0013] There are many factors that can cause OA. Obesity may lead to 0steoarthritis of the knees.
In addition, people with joint injuries due to sports, work-related activity or accidents may be at increased risk of developing OA.

[0014] Genetics has a role in the development of OA too. Some people may be born with defective cartilage or with slight defects in the way that joints fit together. As a person ages, these defects may cause early cartilage breakdown in the joint or the inability to repair damaged or deteriorated cartilage in the joint.

[0015] Inclusion or exclusion of samples for an osteoarthritis pool may be based upon the following criteria: ethnicity (e.g., samples derived from an individual characterized as Caucasian);
parental ethnicity (e.g., samples derived from an individual of British paternal and maternal descent);
relevant phenotype information for the individual (e.g., case samples derived from individuals diagnosed with specific knee, hand or hip osteoarthritis (OA); case samples recruited from an OA knee replacement clinic). Control samples may be selected based on relevant phenotype information for the individual (e.g,, derived from individuals free of OA at several sites (knee, hand, hip etc)); and no family history of OA and/or rheumatoid arthritis. Additional phenotype information collected for both cases and controls may include age of the individual, gender, family history of OA, diagnosis with osteoarthritis (joint location of OA (e.g., knee, hips, hands and spine), date of primary diagnosis, age of individual as of primary diagnosis), knee history (current symptoms, any major knee injury, menisectomy, knee replacement surgery, age of surgery), HRT history, osteoporosis diagnosis.

[0016] Based in part upon selection criteria set forth above, individuals having osteoarthritis can be selected for genetic studies. Also, individuals having no history of osteoarthritis often are selected for genetic studies, as described hereafter.
Pol~phic Variants Associated with Osteoarthritis [0017] A genetic analysis provided herein linked osteoarthritis with polymorphic variant nucleic acid sequences in the human genome. As used herein, the term "polymorphic site" refers to a region in a nucleic acid at which two or more alternative nucleotide sequences are observed in a significant number of nucleic acid samples from a population of individuals. A polymorphic site may be a nucleotide sequence of two or more nucleotides, an inserted nucleotide or nucleotide sequence, a deleted nucleotide or nucleotide sequence, or a microsatellite, for example. A
polymorphic site that is two or more nucleotides in length may be 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more, 20 or more, 30 or more, 50 or more, 75 or more, 100 or more, 500 or more, or about 1000 nucleotides in length, where all or some of the nucleotide sequences differ within the region. A
polymorphic site is often one nucleotide in length, which is referred to herein as a "single nucleotide polymorphism" or a "SNP."

[0018] Where there are two, three, or four alternative nucleotide sequences at a polymorphic site, each nucleotide sequence is referred to as a "polymorphic variant" or "nucleic acid variant." Where two polymorphic variants exist, for example, the polymorphic variant represented in a minority of samples from a population is sometimes referred to as a "minor allele" and the polymorphic variant that is more prevalently represented is sometimes referred to as a "major allele." Many organisms possess a copy of each chromosome (e.g., humans), and those individuals who possess two major alleles or two minor alleles are often referred to as being "homozygous" with respect to the polymorphism, and those individuals who possess one major allele and one minor allele are normally referred to as being "heterozygous" with respect to the polymorphism. Individuals who are homozygous with respect to one allele are sometimes predisposed to a different phenotype as compared to individuals who are heterozygous or homozygous with respect to another allele.

[0019] In genetic analysis that associate polymorphic variants with osteoarthritis, samples from individuals having osteoarthritis and individuals not having osteoarthritis often are allelotyped and/or genotyped. The term "allelotype" as used herein refers to a process for determining the allele frequency for a polymorphic variant in pooled DNA samples from cases and controls. By pooling DNA from each group, an allele frequency for each SNP in each group is calculated. These allele frequencies are then compared to one another. The term "genotyped" as used herein refers to a process for determining a genotype of one or more individuals, where a "genotype" is a representation of one or more polymorphic variants in a population.

[0020] A genotype or polymorphic variant may be expressed in terms of a "haplotype," which as used herein refers to two or more polymorphic variants occurring within genomic DNA in a group of individuals within a population. For example, two SNPs may exist within a gene where each SNP
position includes a cytosine variation and an adenine variation. Certain individuals in a population may carry one allele (heterozygous) or two alleles (homozygous) having the gene with a cytosine at each SNP position. As the two cytosines corresponding to each SNP in the gene travel together on one or both alleles in these individuals, the individuals can be characterized as having a cytosine/cytosine haplotype with respect to the two SNPs in the gene.

[0021] As used herein, the term "phenotype" refers to a trait which can be compared between individuals, such as presence or absence of a condition, a visually observable difference in appearance between individuals, metabolic variations, physiological variations, variations in the function of biological molecules, and the like. An example of a phenotype is occurrence of osteoarthritis.

[0022] Researchers sometimes report a polymorphic variant in a database without determining whether the variant is represented in a significant fraction of a population.
Because a subset of these reported polymorphic variants are not represented in a statistically significant portion of the population, some of them are sequencing errors and/or not biologically relevant. Thus, it is often not known whether a reported polymorphic variant is statistically significant or biologically relevant until the presence of the variant is detected in a population of individuals and the frequency of the variant is determined. Methods for detecting a polymorphic variant in a population are described herein, specifically in Example 2. A polymorphic variant is statistically significant and often biologically relevant if it is represented in 5% or more of a population, sometimes 10% or more, 15% or more, or 20% or more of a population, and often 25% or more, 30% or more, 35% or more, 40% or more, 45% or more, or 50% or more of a population.

[0023] A polymorphic variant may be detected on either or both strands of a double-stranded nucleic acid. Also, a polymorphic variant may be located within an intron or exon of a gene or within a portion of a regulatory region such as a promoter, a S' untranslated region (UTR), a 3' UTR, and in DNA (e.g., genomic DNA (gDNA) and complementary DNA (cDNA)), RNA (e,g., mRNA, tRNA, and rRNA), or a polypeptide. Polymorphic variations may or may not result in detectable differences in gene expression, polypeptide structure, or polypeptide function.

[0024] It was determined that polymorphic variations associated with an increased risk of osteoarthritis existed in SEQ ID NO: 1-13 or a nucleotide sequence referenced in Table B. In certain embodiments, polymorphic variants at positions rs910223, rs1367117, rs1024791, rs1041973, rs1465621, rs398829, rs1018810, rs1484086, rs242392, rs8818, rs1395486, rs512294 and/or rs132659 in the human genome were associated with an increased risk of osteoarthritis, and in specific embodiments, the corresponding allele in the right-most column in Table B for each position is associated with an increased ride of osteoarthritis. In other embodiments polymorphic variants at positions rs1367117, rs1041973 and rs398829 were associated with an increased risk of osteoarthritis, and in specific embodiments, a threonine encoded by rs1367117, an alanine encoded by rs1041973, and a valine encoded by rs398829 were associated with an increased risk of osteoarthritis.

[0025] Polymorphic variants in and around the APOB locus were tested for association with osteoarthritis. These include polymorphic variants at positions in SEQ ID NO:
2 selected from the group consisting of 238, 294, 295, 347, 1425, 4891, 5087, 7041, 7121, 7219, 7443, 7485, 10939, 11367, 11571, 11839, 12551, 12646, 13469, 14913, 15205, 15246, 15695, 17473, 17610, 17828, 18130, 18281, 18623, 18890, 21561, 23100, 23872, 24581, 24582, 24983, 27540, 30846, 31415, 31453, 31899, 37000, 38681, 39287, 42951, 45648, 46222, 46687, 47020, 47593, 48513, 49723, 49986, 53018, 53296, 53547, 53899, 53916, 53933, 54305, 55327, 55895, 56143, 56640, 58486, 59576, 63048, 64008, 64018, 64859, 65995, 66905, 67183, 67942, 68101, 68521, 68664, 68988, 69178, 72143, 74183, 74312, 74407, 75518, 76153, 77398, 77615, 79092, 80000, 80125, 80595, 81061, 81151, 81918, 83072, 83137, 83235, 83263, 83279, 83280, 83533, 86856, 87186, 87189, 87727, 87978, 89129, 89556, 89702, 90233, 93060, 94779, 95367, 95844, 95942, 96884 , 96938, 97627, 97777, 97871, 98746 and 99663.
Polymorphic variants at the following positions in SEQ ID NO: 2 in particular were associated with an increased risk of osteoarthritis: 7219, 7485, 11839, 31899, 37000, 48513, 49986, 56640, 74407, 77398, 93060 and 97627. In particular, the following polymorphic variants in SEQ ID NO: 2 were associated with risk of osteoarthritis: an adenine at position 7219, a guanine at position 7~1-85, an adenine at position 11839, a thymine at position 31899, an adenine at position 37000, a cytosine at position 48513, a guanine at position 49986, a guanine at position 56640, a cytosine at position 74407, a guanine at position 77398, an adenine at position 93060 and an adenine at position 97627. A threonine at amino acid position 98 in an APOB polypeptide was associated with increased risk of osteoarthritis (i.e., an isoleucine to threonine non-synonymous variation).

[0026] Polymorphic variants in and around the IL1RL2 locus were tested for association with osteoarthritis. These include polymorphic variants at positions in SEQ ID NO:
3 selected from the group consisting of 225, 509, 860, 874, 939, 1483, 1798, 2189, 2215, 2282, 2340, 2963, 3369, 3481, 3564, 3653, 4860, 4941, 4975, 5321, 5346, 5541, 5633, 6007, 6317, 6378, 6382, 6426, 6479, 6641, 6703, 6705, 7963, 8525, 8526, 8598, 8624, 8883, 8980, 13578, 16135, 16141, 16642, 16931, 17004, 17009, 17010, 18713, 18853, 20783, 21335, 22180, 22268, 22285, 25378, 25906, 26015, 26475, 26798, 27042, 27649, 27827, 27873, 28122, 28202, 28232, 28240, 29546, 29748, 30054, 30646, 31149, 36912, 36936, 37184, 39064, 39343, 40868, 40917, 41113, 47343, 47806, 47911, 48009, 48621, 49245, 49247, 49299, 49302, 49514, 49626, 49791, 50010, 50294, 51482, 51556, 51855, 51956 ,52155, 52448, 52458, 52511, 52607, 54049, 54224, 54567, 55052, 55857, 55941, 56120, 56349, 56727, 57232, 58806, 61181, 63808, 64526, 64865, 64928, 64966, 65080, 65690, 66228, 66982, 72511, 74170, 74264, 74333, 74502, 74741, 75321, 82558, 85366, 85469, 86485, 87687, 89463, 89660, 95718 and 95821. Polymorphic variants at the following positions in SEQ ID NO: 3 in particular were associated with an increased risk of osteoarthritis: 2215, 3369, 16642, 20783, 52155, 55052, 55941, 74333, 74741, 85366, 85469, 87687, 89660 and 95718, where specific embodiments are directed to position 52155. In particular, the following polymorphic variants in SEQ ID NO: 3 were associated with risk of osteoarthritis: an adenine at position 2215, a deletion at position 3369, a deletion at position 16642, a cytosine at position 20783, a cytosine at position 52155, a cytosine at position 55052, a cytosine at position 55941, a thymine at position 74333, an adenine at position 74741, a deletion at position 85366, a thymine at position 85469, a thymine at position 87687, an adenine at position 89660 and a cytosine at position 95718.

[0027] Polymorphic variants in and around the ILIRLl locus were tested for association with osteoarthritis. These include polymorphic variants at positions in SEQ ID NO:
4 selected from the group consisting of 207, 6019, 6414, 7341, 10984, 12351, 13335, 16584, 16737, 23897, 24057, 25145, 25300, 26262, 26312, 26589, 27302, 27358, 27451, 27552, 30731, 32085, 32139, 33184, 42382, 42569, 44823, 45217, 45548, 45601, 45722, 45967 ,47367, 47642, 48126, 49218, 49274, 49433, 49610, 51282, 51466, 53757, 53960, 54031, 54574, 55679, 56100, 56182, 59817, 60533, 60656, 72209, 72778, 74293, 77335, 78029, 78374, 78421, 78434, 79174, 79397, 79562, 79700, 79730, 79904, 79920, 79938, 79972, 80125, 80368, 83484, 85536, 85829, 86425, 88083, 88770, 90622, 90924, 91634, 92029, 95152, 95348, 96145, 96793, 97015, 97064, 9771 l, 97855 and 98708. Polymorphic variants at the following positions in SEQ ID NO: 4 in particular were associated with an increased risk of osteoarthritis: 6414, 51282, 54574, 78374, 92029 and 96793, where specific embodiments are directed to position 54574. In particular, the following polymorphic variants in SEQ ID NO: 4 were associated with risk of osteoarthritis: an adenine at position 6414, an adenine at positoin 51282, a cytosine at position 54574, a thymine at position 92029 and an adenine at position 96793.

[0028] Polymorphic variants in and around the WASPIP locus were tested for association with osteoarthritis. These include polymorphic variants at positions in SEQ ID NO:
5 selected from the group consisting of 209, 5908, 7460, 7733, 7855, 7904, 8869, 9480, 13820, 15152, 17713, 17804, 18220, 19083, 19123, 19605, 20247, 20592, 21907, 23273, 23299, 23623, 23669, 23844, 24190, 24486, 24896, 25118, 30551, 30844, 30900, 30942, 31699, 32081, 35078, 36196, 36541, 38356, 45578, 49634, 49774, 51119, 51181, 51652, 54467, 55762, 55999, 57865, 66613, 68377, 69754, 72859, 76512, 76717, 77722, 80998, 82033, 89658, 89960, 94155 and 95679. Polymorphic variants at the following positions in SEQ ID NO: 5 in particular were associated with an increased risk of osteoarthritis: 19083, 30900, 38356, 76512 and 94155, where specific embodiments are directed to positions 30900, 76512 and/or 94155. In particular, the following polymorphic variants in SEQ ID NO: 5 were associated with risk of osteoarthritis: a thymine at position 19083, a guanine at position 30900, an adenine at position 38356, an adenine at position 76512 and an adenine at position 94155.

[0029] Polymorphic variants in and around the ADAMTS2 locus were tested for association with osteoarthritis. These include polymorphic variants at positions in SEQ ID NO:
6 selected from the group consisting of 210, 3608, 3609, 4318, 5593, 5629, 5639, 5640, 8943, 17968, 19887, 21034, 21085, 21596, 23379, 23432, 24007, 26121, 26273, 26755, 27411, 27710, 27842, 28379, 29603, 31232, 31504, 32583, 32794, 32840, 33044, 33150, 33218, 33513, 33959, 34486, 36289, 36570, 38247, 38477, 38518, 38529, 38667, 39781, 39856, 39927, 40506, 41869, 42452, 44788, 46059, 46846, 47712, 48796, 49441, 49602, 49723, 50050, 50171, 50477, 50818, 50833, 50881, 50882, 51386, 51534, 52317, 52368, 52970, 53023, 53356, 53882, 54553, 55475, 55530, 55691, 55848, 55879, 56316, 56911, 57320, 57391, 57437, 57478, 57500, 59111, 59333, 59715, 59804, 59851, 59929, 60052, 60240, 60359, 60381, 60456, 60724, 60875, 60968, 60978, 60998, 61557, 62091, 62645, 62943, 63131, 63145, 63406, 63427, 63554, 63661, 64093, 64153, 64409, 64544, 65257, 65626,65739 , 66392, 66720, 69177, 69336, 69636, 69823, 69928, 70547, 70633, 71805, 72181, 72200, 72474, 72567, 72973, 73468, 73889, 75730, 75970, 76114, 76342, 76449, 76465, 76791, 78042, 80758, 80778, 81356, 81576, 81689, 81759, 81950, 82562, 83591, 83700, 83821, 83842, 83923, 83929, 84021, 84175, 84417, 84747, 85746, 86129, 86335, 87315, 87648, 87764, 87770, 88221, 90474, 91148, 91150, 91160, 91733, 91772, 91785, 93140, 93148, 96080, 96157, 96313, 96759, 97026, 97320, 97732, 98713, 99707, 99959, 100009, 100020, 100065, 100086, 101270, 101276, 101371, 101376, 101439, 101820, 102392, 102602, 102604, 102896, 189104, 189134 and 189205. Polymorphic variants at the following positions in SEQ ID NO: 6 in particular were associated with an increased risk of osteoarthritis: 5640, 33150, 38247, 38529, 46846, 49723, 50050, 63427, 73889, 189104 and rs428901, where specific embodiments are directed to positions 46846, 73889, 189104 and/or rs428901. In particular, the following polymorphic variants in SEQ ID NO: 6 were associated with risk of osteoarthritis: a cytosine at position 5640, a cytosine at position 33150, an adenine at position 38247, a thymine at position 38529, an adenine at position 46846, a cytosine at position 49723, a cytosine at position 50050, a cytosine a position 63427, a guanine at position 73889, a thymine at position 189104, and an adenine at position rs428901.

[0030] Polymorphic variants in and around the BT~ES locus were tested for association with osteoarthritis. These include polymorphic variants at positions in SEQ ID NO:
7 selected from the group consisting of 241, 801, 899, 2091, 2290, 2440, 4959, 7914, 7969, 7972, 10831, 12399, 13841, 14461, 14680, 16808, 18231, 18394, 18505, 18684, 19257, 20263, 20656, 21499, 21563, 21612, 21834, 22406, 22408, 22685, 23303, 23306, 25139, 25211, 25364, 25381, 25414, 25835, 26214, 27224, 27526, 27934, 28550, 29015, 29879, 29979, 30030, 30585, 31753, 31934, 33227, 33228, 35172, 36901, 36921, 36932, 37061, 37570, 38745, 38970, 39725, 40070, 40460, 41470, 41562, 41956, 42047, 42280, 42358, 42629, 43075, 43387, 43393, 43438, 44115, 44537, 45642, 46629,47496, 47515, 48329, 48862, 48908, 49038, 49080, 50204, 50404, 50426, 50531, 50840, 50964, 50971,51378, 52610, 53906, 53951, 54111, 54149, 55563, 55999, 58415, 58961, 60447, 61377, 61528, 61606, 62140, 62461, 63826, 64950, 65076, 66121, 66406, 67051, 68860, 69014, 70796, 72325, 73414, 75258, 76347, 76839, 77358, 77822, 77946, 80002, 80024, 80285, 80397, 82075, 82153, 83981, 84184, 85089, 85288, 85330, 85581, 85642, 86433, 86904, 88391, 89042, 90828, 92676, 92881, 94227, 94585, 94616, 94712, 94738, 95253, 95522, 95869 and 97856. Polymorphic variants at the following positions in SEQ ID NO: 7 in particular were associated with an increased risk of osteoarthritis: 25414, 25835, 38970, 41470, 44115, 47496, 49038, 50204, 50840, 50964, 50971, 53906, 54149, 58415, 70796, 72325, 75258, 77822, 80002, 85288, 85581, 86904, 90828, 94616, 94712, 95869 and 97856. In particular, the following polymorphic variants in SEQ )D NO: 7 were associated with risk of osteoarthritis: an adenine at position 25414, a cytosine at position 25835, an adenine at position 38970, an adenine at position 41470, an adenine at position 44115, a guanine at position 47496, a cytosine at position 49038, an adenine at position 50204, a thymine at position 50840, a cytosine at position 50964, a cytosine at position 50971, an adenine at position 53906, a guanine at position 54149, a guanine at position 58415, a thymine at position ?0796, a guanine at position 72325, a cytosine at position 75258, an adenine at position 77822, an adenine at position 80002, an adenine at position 85288, an adenine at position 85581, a guanine at position 86904, a guanine at position 90828, an adenine thymine adenine adenine sequence at position 94616, a cytosine at position 94712, a guanine at position 95869 and a cytosine at position 97856.

[0031] Polymorphic variants in and around the TM7SF3 locus were tested for association with osteoarthritis. These include polymorphic variants at positions in SEQ ID NO:
8 selected from the group consisting of 230, 231, 5330, 6334, 11372, 11456, 11501, 13393, 16666, 17596, 19710, 19800, 20297, 20967, 32514, 33159, 37600, 41259, 41329, 50060, 53292, 53393, 56417, 56435, 58847, 59595, 59661, 60355, 60407, 62357, 68230, 68516, 69055, 72603, 73928, 85897 and 91554. Polymorphic variants at the following positions in SEQ ID NO: 8 in particular were associated with an increased risk of osteoarthritis: 56435, 59595, 53292, 33159 and 41329, with specific embodiments directed to positions 56435 and/or 59595. In particular, the following polymorphic variants in SEQ ID NO: 8 were associated with risk of osteoarthritis: a thymine thymine repeat at position 56435, a thymine at position 59595, a cytosine at position 53292, a guanine at position 33159 and a thymine at position 41329.

[0032] Polymorphic variants in and around the LOXLI locus were tested for association with osteoarthritis. These include polymorphic variants at positions in SEQ ID NO:
10 selected from the group consisting of 213, 249, 1824, 2057, 2306, 2869, 3976, 4288, 4290, 4434, 5298, 5467, 8486, 8487, 8831, 9036, 9058, 9131, 9732, 9862, 10191, 10270, 16167, 17620, 17751, 17764, 17787, 19401 ~ 21021, 21902, 22173, 22416, 22653, 24945, 2501 l, 28563, 48574, 48710, 48880, 50194, 56343, 56455, 56729, 56759, 56895, 57036, 57702, 62515, 62629, 63501, 63547, 64876, 65073, 67149, 67549, 71660, 71906 and 71911. A polymorphic variant at position 65073 in SEQ ID NO: 10, often a guanine, in particular was associated with. an increased risk of osteoarthritis.

[0033] Polymorphic variants in and around the ~'ASPR4 locus were tested for association with osteoanhritis. These include polymorphic variants at positions in SEQ ID NO:
11 selected from the group consisting of 205, 866, 4212, 5934, 11486, 16969, 22509, 22796, 28097, 28626, 28853, 28873, 30155, 30827, 31956, 32404, 32944, 35205, 35227, 35781, 41052, 45051, 46039, 47276, 47678, 47716, 51014, 54408, 54596, 56853, 61851, 62016, 62461, 68257, 69793, 73976, 73999, 74053, 75315 75729, 76466, 77216, 77217, 79239, 80825, 81060, 81097, 81426, 84787, 84896, 85165, 86502, 86753, 86941, 88787 and 95598. Polymorphic variants at the following positions in SEQ ID NO:
11 in particular were associated with an increased risk of osteoarthritis: 47716 and 69793. In particular, the following polymorphic variants in SEQ ID NO: 11 were associated with risk of osteoarthritis: an adenine at position 47716 and a thymine at position 69793.

[0034] Polymorphic variants in and around the APOL3 locus were tested for association with osteoarthritis. These include polymorphic variants at positions in SEQ ID NO:
13 selected from the group consisting of 201, 425, 1095, 2201, 7879, 8395, 8461, 9503, 10304, 10695, 16300, 16444 17591, 17988, 19116, 19358, 20300, 20669, 20891, 21451, 21978, 22785, 24248, 24770, 24844, 25066, 25096, 25309, 25344, 25529, 25537, 25554, 27963, 28134, 28356, 29648, 29986, 30217, 30267, 30315, 30585, 30724, 30897, 30931, 31080, 31246, 31373, 31463, 31467, 32188, 32288, 32520, 32594, 32657, 32677, 32764, 32784, 32830, 32872, 33121, 33348, 33952, 34184, 34361, 35026, 35192, 35600, 36033, 36289, 38869, 39629, 40530, 41621, 42379, 42802, 42865, 43644, 45051, 45828, 45829, 46257, 47286, 47427, 47963, 48013, 48229, 48282, 48376, 48404, 49900, 52699, 52897, 53414, 53487, 54112, 55492, 59766, 60307, 60701, 60952, 61401, 62379, 62870, 62879, 63499, 64284, 64408, 64760, 65230, 66127, , 6634, 66686, 66694, 67113, 67257, 67403, 67609, 68418, 68610, 69629, 70024, 70848, 71428, 71553, 71633, 71768 ,71769, 73039, 73325, 73412, 73547, 73769, 73806, 74467, 74472, 74473, 74482, 74494, 74592, 74670, 74672, 74714, 74723, 74749, 74861, 74892, 74893, 75176, 75705, 75989, 76027, 77949, 77974, 78167, 78310, 78415, 78575, 78590, 78709, 78875, 79864, 81316, 81320, 81409, 81737, 81843, 82102, 82833, 83461, 83624, 83660, 83701, 83708, 83782, 85707, 85717, 86486, 86833, 87115, 87234, 87479, 87561, 87604, 87674, 87958, 87992, 88019, 88074, 88079, 88115, 88118, 88120, 88135, 88142 ,88143, 88149, 88340, 88344, 88512, 88521, 88650, 88827, 89230, 89236, 90754, 90984, 91110, 92026, 92954, 93375, 93794, 94937, 95068, 96188, 97092 and 98812. Polymorphic variants at the following positions in SEQ m NO: 13 in particular were associated with an increased risk of osteoarthritis: 203 00, 46257, 87958, 89236, 30267, 32657, 36289, 38869, 45051, 54112, 60307, 63499, 20891, 52699, 71768, with specific embodiments directed to position 46257. In particular, the following polymorphic variants in SEQ ID NO: 13 were associated with risk of osteoarthritis: an adenine at position 20300, a thymine at position 46257, an adenine at position 89236, a guanine at position 30267, an adenine at position 32657, a cytosine at position 36289, a guanine at position 38869, a thymine at position 45051, a guanine at position 54112, an adenine at position 60307, a thymine at position 63499, a guanine at position 20891, a guanine at position 52699, and a cytosine at position 71768.

[0035] Based in part upon analyses summarized in Figures lA-1J, regions with significant association have been identified in regions associated with osteoarthritis.
Any polymorphic variants associated with osteoarthritis in a region of significant association can be utilized for embodiments described herein. For example, polymorphic variants in a region spanning positions 21233000 to 21243000 (approximately 10,000 nucleotides in length) in aAPOB locus, a region spanning chromosome positions 102456500 to 102471500 (approximately 15,000 nucleotides in length) in a ILIRL2 locus, a region spanning chromosome positions 102570000 to 102583000 (approximately 13,000 nucleotides in length) in a ILIRLI locus, a region spanning chromosome positions 175647734 to 175655734 (approximately 8,000 nucleotides in length) in a WASPIP locus, a region spanning chromosome positions 178746000 to 178751000 (approximately 5,000 nucleotides in length) in a ADAMTS2 locus, a region spanning chromosome positions 105595000 to 105615000 (approximately 20,000 nucleotides in length) in a BT~ES locus, in a region approximately 14,000 nucleotides in length spanning chromosome positions 27052000 to 27066000 in a TM7SF3 locus, a region spanning chromosome positions 71957600 to 71962600 (approximately 5,000 nucleotides in length) in a LOXLI
locus, a region spanning chromosome positions 76221000 to 76226000 (approximately 5,000 nucleotides in length) in a CASPR4 locus, and a region approximately 5000 nucleotides in length and spanning chromosome positions 3 4828750 and 34833750 in an APOL3 locus, have significant association (chromosome positions are within NCBI's Genome build 34).
Additional Polymorphic Variants Associated with Osteoarthritis [0036] Also provided is a method for identifying polymorphic variants proximal to an incident, founder polymorphic variant associated with osteoarthritis. Thus, featured herein are methods for identifying a polymorphic variation associated with osteoarthritis that is proximal to an incident polymorphic variation associated with osteoarthritis, which comprises identifying a polymorphic variant proximal to the incident polymorphic variant associated with osteoarthritis, where the incident polymorphic variant is in a PADI~, APOB, ILIRL2, ILIRLI, WASPIP, ADAMTS2, BYES, Ti117SF3, LOXL1, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B.
The nucleotide sequence often comprises a polynucleotide sequence selected from the group consisting of (a) a polynucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B;
(b) a polynucleotide sequence that encodes a polypeptide having an amino acid sequence encoded by a polynucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B; and (c) a polynucleotide sequence that encodes a polypeptide having an amino acid sequence that is 90% or more identical to an amino acid sequence encoded by a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B
or a polynucleotide sequence 90% or more identical to the polynucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B. The presence or absence of an association of the proximal polymorphic variant with osteoarthritis then is determined using a known association method, such as a method described in the Examples hereafter. In an embodiment, the incident polymorphic variant is a polymorphic variant associated with osteoarthritis described herein. In another embodiment, the proximal polymorphic variant identified sometimes is a publicly disclosed polymorphic variant, which for example, sometimes is published in a publicly available database. In other embodiments, the polymorphic variant identified is not publicly disclosed and is discovered using a known method, including, but not limited to, sequencing a region surrounding the incident polymorphic variant in a group of nucleic samples. Thus, multiple polymorphic variants proximal to an incident polymorphic variant are associated with osteoarthritis using this method.

[0037] The proximal polymorphic variant often is identified in a region surrounding the incident polymorphic variant. In certain embodiments, this surrounding region is about 50 kb flanking the first polymorphic variant (e.g. about 5 O kb 5' of the first polymorphic variant and about 50 kb 3' of the first polymorphic variant), and the region sometimes is composed of shorter flanking sequences, such as flanking sequences of about 40 kb, about 30 kb, about 25 kb, about 20 kb, about 15 kb, about 10 kb, about 7 kb, about 5 kb, or about 2 kb 5' and 3' of the incident polymorphic variant. In other embodiments, the region is composed of longer flanleing sequences, such as flanking sequences of about 55 kb, about 60 kb, about 65 kb, about 70 kb, about 75 kb, about 80 kb, about 85 kb, about 90 kb, about 95 kb, or about 100 kb 5' and 3' of the incident polymorphic variant.

[0038] In certain embodiments, polymorphic variants associated with osteoarthritis are identified iteratively. For example, a first proximal polymorphic variant is associated with osteoarthritis using the methods described above and then another polymorphic variant proximal to the first proximal polymorphic variant is identified (e.g., publicly disclosed or discovered) and the presence or absence of an association of one or more other polymorphic variants proximal to the first proximal polymorphic variant with osteoarthritis is determined.

[0039] The methods described herein are useful for identifying or discovering additional polymorphic variants that may be used to further characterize a gene, region or loci associated with a condition, a disease (e.g., osteoarthritis), or a disorder. For example, allelotyping or genotyping data from the additional polymorphic variants may be used to identify a functional mutation or a region of linkage disequilibrium. In certain embodiments, polymorphic variants identified or discovered within a region comprising the first polymorphic variant associated with osteoarthritis are genotyped using the genetic methods and sample selection techniques described herein, and it can be determined whether those polymorphic variants are in linkage disequilibrium with the first polymorphic variant. The size of the region in linkage disequilibrium with the first polymorphic variant also can be assessed using these genotyping methods. Thus, provided herein are methods for determining whether a polymorphic variant is in linkage disequilibrium with a first polymorphic variant associated with osteoarthritis, and such information can be used in prognosis/diagnosis methods described herein.
Isolated Nucleic Acids [0040] Featured herein are isolated PA.17I2, APOB, ILIRL2, IL1RL1, WASPIP, ADAMTS2, BITES, TM7SF3, LOXL1, CASPR4 or APOL3 nucleic acid variants depicted in SEQ ID NO: 1-13, SEQ ID NO:
14-36 or referenced in Table B, and substantially identical nucleic acids thereof. A nucleic acid variant may be represented on one or both strands in a double-stranded nucleic acid or on one chromosomal complement (heterozygous) or both chromosomal complements (homozygous).

[0041] ADAMTS2 exists in two forms, a "long" form comprising a molecule approximately 130 kDa in length (e.g., SEQ ID NO: 21 for cDNA sequence and SEQ ID NO: 44 for amino acid sequence), and a "short" form comprising a molecule approximately 70 kDa in length (e.g., SEQ ID NO: 22 for cDNA sequence and SEQ ID NO: 45 for amino acid sequence). Provided herein are polynucleotide sequences encoding both the short and long forms of ADAMTS2.

[0042] As used herein, the term "nucleic acid" includes DNA molecules (e.g., a complementary DNA (cDNA) and genomic DNA (gDNA)) and RNA molecules (e.g., mRNA, rRNA, siRNA
and tRNA) and analogs of DNA or RNA, for example, by use of nucleotide analogs.
The nucleic acid molecule can be single-stranded and it is often double-stranded. The term "isolated or purified nucleic acid" refers to nucleic acids that are separated from other nucleic acids present in the natural source of the nucleic acid. For example, with regard to genomic DNA, the term "isolated"
includes nucleic acids which are separated from the chromosome with which the genomic DNA is naturally associated. An "isolated" nucleic acid is often free of sequences which naturally flank the nucleic acid (i. e., sequences located at the 5' and/or 3' ends of the nucleic aci d) in the genomic DNA of the organism from which the nucleic acid is derived. For example, in various embodiments, the isolated nucleic acid molecule can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 lcb, 0.5 kb or 0.1 kb of 5' and/or 3' nucleotide sequences which flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived. Moreover, an "isolated" nucleic acid molecule, such as a cDNA
molecule, can be substantially free of other cellular material, or culture medimn when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. As used herein, the term "gene" refers to a nucleotide sequence that encodes a polypeptide.

[0043] Also included herein are nucleic acid fragments. These fragments often have a nucleotide sequence identical to a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B, a nucleotide sequence substantially identical to a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B, or a nucleotide sequence that is complementary to the foregoing. The nucleic acid fragment may be identical, substantially identical or homologous to a nucleotide sequence in an exon or an intron in a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B, and may encode a domain or part of a domain of a polypeptide. Sometimes, the fragment will comprises one or more of the polymorphic variations described herein as being associated with osteoarthritis. The nucleic acid fragment is often 50, 100, or 200 or fewer base pairs in length, and is sometimes about 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 2000, 3000, 4000, 5000, 10000, 15000, or 20000 base pairs in length.
A nucleic acid fragment that is complementary to a nucleotide sequence identical or substantially identical to a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B and hybridizes to such a nucleotide sequence under stringent conditions is often referred to as a "probe." Nucleic acid fragments often include one or more polymorphic sites, or sometimes have an end that is adjacent to a polymorphic site as described hereafter.

[0044] An example of a nucleic acid fragment is an oligonucleotide. As used herein, the term "oligonucleotide" refers to a nucleic acid comprising about 8 to about 50 covalently linked nucleotides, often comprising from about 8 to about 35 nucleotides, and more often from about 10 to about 25 nucleotides. The backbone and nucleotides with in an oligonucleotide may be the same as those of naturally occurring nucleic acids, or analogs or derivatives of naturally occurring nucleic acids, provided that oligonucleotides having such analogs or derivatives retain the ability to hybridize specifically to a nucleic acid comprising a targeted polymorphism.
Oligonucleotides described herein may be used as hybridization probes or as components of prognostic or diagnostic assays, for example, as described herein.

[0045] Oligonucleotides are typically synthesized using standard methods and equipment, such as the ABITM3900 High Throughput DNA Synthesizer and the EXPEDITETM 8909 Nucleic Acid Synthesizer, both of which are available from Applied Biosystems (Foster City, CA). Analogs and derivatives are exemplified in U.S. Pat. Nos. 4,469,863; 5,536,821; 5,541,306;
5,637,683; 5,637,684;
5,700,922; 5,717,083; 5,719,262; 5,739,308; 5,7'73,601; 5,886,165; 5,929,226;
5,977,296; 6,140,482;

46; WO 01/14398, and related publications. Methods for synthesizing oligonucleotides comprising such analogs or derivatives are disclosed, for example, in -the patent publications cited above and in U.S. Pat. Nos. 5,614,622; 5,739,314; 5,955,599; 5,962,674; 6,1 17,992;
in WO 00/75372; and in related publications.
[0046] Oligonucleotides may also be linked to a second moiety. The second moiety may be an additional nucleotide sequence such as a tail sequence (e.g., a polyadenosine tail), an adapter sequence (e.g., phage M13 universal tail sequence), and others. Alternatively, the second moiety may be a non-nucleotide moiety such as a moiety which facilitates linleage to a solid support or a label to facilitate detection of the oligonucleotide. Such labels include, without limitation, a radioactive label, a fluorescent label, a chemiluminescent label, a paramagnetic label, and the like. The second moiety may be attached to any position of the oligonucleotide, provided the oligonucleotide can hybridize to the nucleic acid comprising the polymorphism.
Uses for Nucleic Acid Sequence [0047] Nucleic acid coding sequences may be used for diagnostic purposes for detection and control of polypeptide expression. Also, included herein are oligonucleotide sequences such as antisense RNA, small-interfering RNA (siRNA) and DNA molecules and ribozymes that function to inhibit translation of a polypeptide. Antisense techniques and RNA
interference techniques are known in the art and are described herein.

[0048] Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA. The mechanism of ribozyme action involves sequence specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage.
For example, hammerhead motif ribozyme molecules may be engineered that specifically and efficiently catalyze endonucleolytic cleavage of RNA sequences corresponding to or corriplementary to PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BhES, TM7SF3, LOXLl, CAS'PR4 orAPOL3 nucleotide sequences or other nucleotide sequences referenced in Table B. Specific ribozyme cleavage sites within any potential RNA target are initially identified by scanning the target molecule for ribozyme cleavage sites which include the following sequences, GUA, GUU and GUC. Once identified, short RNA
sequences of between fifteen (15) and twenty (20) ribonucleotides corresponding to the region of the target gene containing the cleavage site may be evaluated for predicts d structural features such as secondary structure that may render the oligonucleotide sequence unsuitable.
The suitability of candidate targets may also be evaluated by testing their accessibility to hybridization with complementary oligonucleotides, using ribonuclease protection assays.

[0049] Antisense RNA and DNA molecules, siRNA and ribozyrnes may be prepared by any method known in the art for the synthesis of RNA molecules. These include techniques for chemically synthesizing oligodeoxyribonucleotides well known in the art such as solid phase phosphoramidite chemical synthesis. Alternatively, RNA molecules may be generated by ih vit~~o and in vivo transcription of DNA sequences encoding the antisense RNA molecule. Such DNA
sequences may be incorporated into a wide variety of vectors which incorporate suitable RNA
polymerase promoters such as the T7 or SP6 polymerase promoters. Alternatively, mtisense cDNA constructs that synthesize antisense RNA constitutively or inducibly, depending on the promoter used, can be introduced stably into cell lines.

[0050] DNA encoding a polypeptide also may have a number of uses for the diagnosis of diseases, including osteoarthritis, resulting from aberrant expression of a target gene described herein. For example, the nucleic acid sequence may be used in hybridization as says of biopsies or autopsies to diagnose abnormalities of expression or function (e.g., Southern or Northern blot analysis, in situ hybridization assays).

[0051] In addition, the expression of a polypeptide during embryonic development may also be determined using nucleic acid encoding the polypeptide. As addressed, infra, production of functionally impaired polypeptide is the cause of various disease states, such as osteoarthritis. In situ hybridizations using polypeptide as a probe may be employed to predict problems related to osteoarthritis. Further, as indicated, infra, administration of human active polypeptide, recorrlbinantly produced as described herein, may be used to treat disease states related to functionally irrlpaired polypeptide. Alternatively, gene therapy approaches may be employed to remedy deficiencies of functional polypeptide or to replace or compete with dysfunctional polypeptide.
Expression Vectors, Host Cells, and Genetically Engineered Cells [0052] Provided herein are nucleic acid vectors, often expressi on vectors, which contain a PADI2, APOB, IL1RL2, ILIRL1, WASPIP, ADAMTS2, BhES, TM7SF3, LOxLl, CASPR4 orAPOL3 nucleotide sequence or other nucleotide sequence referenced in Table B, or a substantially identical sequence thereof. As used herein, the term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked and can include a p lasmid, cosmid, or viral vector. The vector can be capable of autonomous replication or it can integrate into a host DNA. Viral vectors may include replication defective retroviruses, adenoviruses and adeno-associated viruses for example.

[0053] A vector can include a PADI2, APOB, ILIRL2, ILIRLI, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLl, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B in a form suitable for expression of an encoded target polypeptide or target nucleic acid in a host cell. A "target polypeptide" is a polypeptide encoded by a PADI2, APOB, ILIRL~, ILIRLI, WASPIP, ADAMTS2, BYES, TM7SF3, LO~Ll, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B, or a substantially identical nucleotide sequence thereof. The recombinant expression vector typically includes one or more regul atory sequences operatively linked to the nucleic acid sequence to be expressed. The term "regulatory sequence"
includes promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Regulatory sequences include those that direct constitutive expression of a nucleotide sequence, as well as tissue-specific regulatory and/or inducible sequences. The design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of polypeptide desired, and the like. Expression vectors can be introduced into host cells to produce target polypeptides, including fusion polypeptides.

[0054] Recombinant expression vectors can be designed for expression of target p olypeptides in prokaryotic or eukaryotic cells. For example, target polypeptides can be expressed in E. coli, insect cells (e.g., using baculovirus expression vectors), yeast cells, or mammalian cells. Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.

[0055] Expression of polypeptides in prokaryotes is most often carried out in E. coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion polypeptides. Fusion vectors add a number of amino acids to a polypeptide encoded therein, usually to the amino terminus of the recombinant polypeptide. Such fusion vectors typically serve three purposes:
1) to increase expression of recombinant polypeptide; 2) to increase the solubility of the recombinant polypeptide; and 3) to aid in the purification of the recombinant polypeptide by acting as a ligand in affinity purification. Often, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant polypeptide to enable separation of the recombinant polypeptide from the fusion moiety subsequent to purification of the fusion polypeptide. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase. Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith ~ Johnson, Gene 67: 31-40 (198; 8)), pMAL (New England Biolabs, Beverly, MA) and pRITS (Pharmacia, Piscataway, NJ) which fuse glutathione S-transferase (GST), maltose E binding polypeptide, or polypeptide A, respectively, to the target recombinant polypeptide.

[0056] Purified fusion polypeptides can be used in screening assays and to generate antibodies specific for target polypeptides. In a therapeutic embodiment, fusion polypeptide expressed in a retroviral expression vector is used to infect bone marrow cells that are subsequently transplanted into irradiated recipients. The pathology of the subject recipient is then examined after sufficient time has passed (e.g., six (6) weeks).

[0057] Expressing the polypeptide in host bacteria with an impaired capacity to pr-oteolytically cleave the recombinant polypeptide is often used to maximize recombinant polypeptidc expression (Gottesman, S., Gebze Expressioh Technology: Methods in Enzyfraology, Academic Press, Say Diego, California I85: 119-128 (1990)). Another strategy is to alter the nucleotide sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (Wada et al., Nueleic Acids Res. 20: 2111-2118 (1992]). Such alteration of nucleotide sequences can be carried out by standard DNA
synthesis techniques.

[0058] When used in mammalian cells, the expression vector's control functions axe often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40. Recombinant mammalian expression vectors are often capable of directing expression of the nucleic acid in a particular cell type (e.g,, tis sue-specific regulatory elements are used to express the nucleic acid). Non-limiting examples of suitable tissue-speciFc promoters include an albumin promoter (liver-specific; Pinkert et al., Genes Dev. 1: 268-277 (1987)), lymphoid-specific promoters (Calame & Eaton, Adv. Imnaunol. 43: 235-275 (1988)), promoters of T cell receptors (Winoto & Baltimore, EMBO J. 8: 729-733 (1989)) promoters of immunoglobulins (Banerji et al., Cell 33: 729-740 (1983); Queen & Baltimore, Cell 33. 741-748 (1983)), neuron-specific promoters (e.g., the neurofilament promoter; Byrne &
Ruddle, P~oe. Natl.
Acad. Sci. USA 86.' 5473-5477 (1989)), pancreas-specific promoters (Edlund et al., Sciehce 230: 912-916 (1985)), and mammary gland-specific promoters (e.g., milk whey promoter;
U.S. Patent No.
4,873,316 and European Application Publication No. 264,166). Developmentally-regulated promoters are sometimes utilized, for example, the murine hox promoters (I~essel &
Gruss, Seience 249: 374-379 (1990)) and the a-fetopolypeptide promoter (Campes & Tilghman, Genes Dev. 3:
537-5 46 (1989)).

[0059] APADI2, APOB, IL1RL2, ILIRLl, WASPIP, ADAMTS2, BITES, TM7SF3, LOdTLl, CASPR4 or APOL3 nucleic acid or other nucleic acid referenced in Table B also may be cloned into an expression vector in an antisense orientation. Regulatory sequences (e.g., viral promoters and/or enhancers) operatively linked to a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS~, BT~ES, TM7SF3, LOXLI, CASPR4 or APOL3 nucleic acid or other nucleic acid referenced in Table B cloned in the antisense orientation can be chosen for directing constitutive, tissue specific or cell type specific expression of antisense RNA in a variety of cell types. Antisense expression vectors can be in the form of a recombinant plasmid, phagemid or attenuated virus. For a discussion of the regulation of gene expression using antisense genes see, e.g., Weintraub et al., Antisense RNA as a molecu..lar tool for genetic analysis, Reviews - Trends in Genetics, Vol. 1(1) (1986).

[0060] Also provided herein are host cells that include a PADI2, APOB, ILIRL2, IL1RL1, WASPIP, ADAMTS2, BIIES, TM7SF3, LOXLl, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B within a recombinant expression vector or a fragment of such a nucleotide sequence which facilitate homologous recombination into a specific site of -the host cell genome. The terms "host cell" and "recombinant host cell" are used interchangeably herein. Such terms refer not only to the particular subject cell but rather also to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent ce 11, but are still included within the scope of the term as used herein. A host cell can be any prokaryotic or eukaryotic cell. For example, a target polypeptide can be expressed in bacterial cells such as E. colt, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS
cells). ether suitable host cells are known to those skilled in the art.

[0061] Vectors can be introduced into host cells via conventional transformation or transfection techniques. As used herein, the terms "transformation" and "transfection" are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) int~ a host cell, including calcium phosphate or calcium chloride co-precipitation, transduction/infection, DEAE-dextran-mediated transfection, lipofection, or electroporation.

[0062] A host cell provided herein can be used to produce (i. e., express) a target polypeptide: or a substantially identical polypeptide thereof. Accordingly, further provided are methods for producing a target polypeptide using host cells described herein. In one embodiment, the method includes culturing host cells into which a recombinant expression vector encoding a target polypeptide has been introduced in a suitable medium such that a target polypeptide is produced. In another embodiment, the method further includes isolating a target polypeptide from the medium or the host cell.

[0063] Also provided are cells or purified preparations of cells which include a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLl, CASPR4 orAPOL3 transgene, or other transgene in Table B, or which otherwise misexpress target polypeptide. Cell preparations can consist of human or non-human cells, e.g., rodent cells, e.g., mouse or rat cells, rabbit cells, or pig cells. In preferred embodiments, the cell or cells include a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BhES, TM7SF3, LOXLl, CASPR4 or APOL3 transgene or other transgene referenced in Table B (e.g., a heterologous form of a PADI2, APOB, ILIRL2, IL1RL1, WASPIP, ADAMTS2, BTIES, TM7SF3, LOXLl, CASPR4 or APOL3 gene or other gene referenced in Table B, such as a human gene expressed in non-human cells). The transgene can be misexpressed, e.g., overexpressed or underexpressed. In other preferred embodiments, the cell or cells include a gene which misexpress an endogenous target polypeptide (e.g., expression of a gene is disrupted, also known as a knockout,. Such cells can serve as a model for studying disorders which are related to mutated or mis-expressed alleles or for use in drug screening. Also provided are human cells (e.g., a hematopoietic stem cells) transfected with a PADI2, APOB, ILIRL2, ILIRLI, WASPIP, ADAMTS2, BT~ES, TM7SF3, LOXL 1, CASPR4 or APOL3 nucleic acid or other nucleic acid referenced in Table B.

[0064] Also provided are cells or a purified preparation thereof (e.g., human cells) in which an endogenous PAD12, APOB, ILIRL2, IL1RLI, WASPIP, ADAMTS2, BYES, TM7SF3, LOXL1, CAS'PR4 or APOL3 nucleic acid or other nucleic acid referenced in Table B is under the control of a regulatory sequence that does not normally control the expression of the endogenous gene.
The expression characteristics of an endogenous gene within a cell (e.g., a cell line or microorganism) can be modified by inserting a heterologous DNA regulatory element into the genome of the cell such that the inserted regulatory element is operably linked to the corresponding endogenous gene.
For example, an endogenous corresponding gene (e.g., a gene which is "transcriptionally silent," not normally expressed, or expressed only at very low levels) may be activated by inserting a regulatory element which is capable of promoting the expression of a normally expressed gene product in that cell. Techniques such as targeted homologous recombinations, can be used to insert the heterologous DNA as described in, e.g., Chappel, US 5,272,071; WO 91/06667, published on May 16, 1991.
1~

Trans~enic Animals [0065] Non-human transgenic animals that express a heterologous target polypeptide (e.g., expressed from a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLI, CASPR4 or APOL3 nucleic acid or other nucleic acid referenced in Table B, or substantially identical sequence thereof) can be generated. Such animals are useful for studying the function and/or activity of a target polypeptide and for identifying and/or evaluating modulators of the activity of PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BhES, TM7SF3, LOXL1, CASPR4 orAPOL3 nucleic acids, other nucleic acids referenced in Table B, and encoded polypeptides. As used herein, a "transgenic animal" is a non-human animal such as a mammal (e.g., a non-human primate such as chimpanzee, baboon, or macaque; an ungulate such as an equine, bovine, or caprine; or a rodent such as a rat, a mouse, or an Israeli sand rat), a bird (e.g., a chicken or a turkey), an amphibian (e.g., a frog, salamander, or newt), or an insect (e.g., Drosophila naela~ogaster), in which one or more of the cells of the animal includes a transgene. A transgene is exogenous DNA or a rearrangement (e.g., a deletion of endogenous chromosomal DNA) that is often integrated into or occurs in the genome of cells in a transgenic animal. A transgene can direct expression of an encoded gene product in one or more cell types or tissues of the transgenic animal, and other transgenes can reduce expression (e.g., a knockout).
Thus, a transgenic animal can be one in which an endogenous nucleic acid homologous to a PADI2, APOB, ILIRL2, ILIRL1, WASPIP, ADAMTS2, BhES, TM7SF3, LOXL1, CASPR~ orAPOL3 nucleic acid or other nucleic acid referenced in Table B has been altered by homologous recombination between the endogenous gene and an exogenous DNA molecule introduced into a cell of the animal (e.g., an embryonic cell of the animal) prior to development of the animal.

[0066] Intronic sequences and polyadenylation signals can also be included in the transgene to increase expression efficiency of the transgene. One or more tissue-specific regulatory sequences can be operably linked to a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BhES, TM7SF3, LOXLI, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B to direct expression of an encoded polypeptide to particular cells. A transgenic founder animal can be identified based upon the presence of a PADI2, APOB, ILIRL2, IL1RL1, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLl, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B in its genome and/or expression of encoded mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene.
Moreover, transgenic animals carrying a PADI2, APOB, ILIRL2, IL1RL1, WASPIP, ADAMTS2, BhES, TM7SF3, LOXL1, CASPR~ or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B can further be bred to other transgenic animals carrying other transgenes.

[0067] Target polypeptides can be expressed in transgenic animals or plants by introducing, for example, a PADI2, APOB, ILIRL2, ILIRLI, WASPIP, ADAMTS2, BTpES, TM7SF3, LOXLl, CASPR4 or APOL3 nucleic acid or other nucleic acid referenced in Table B into the genome of an animal that encodes the target polypeptide. In preferred embodiments the nucleic acid is placed under the control of a tissue specific promoter, e.g., a milk or egg specific promoter, and recovered from the milk or eggs produced by the animal. Also included is a population of cells from a transgenic animal.
Tar-eg t Polypeptides [0068] Also featured herein are isolated target polypeptides, which are encoded by a PADl2, APOB, ILIRL2, IL1RL1, WASPIP, ADAMTS2, BITES, TM7SF3, LO~Ll, CASPR4 orAPOL3 nucleotide sequence or a nucleotide sequence referenced in Table B (e.g., SEQ ID NO: 14-36 or a sequence referenced in Table B), or a substantially identical nucleotide sequence thereof. Examples of PAD12, APOB, ILIRL2, IL1RL1, WASPIP, ADAMTS2, BhES, TM7SF3, LOXLl, CASPR~ orAPOL3 polypeptides are set forth in SEQ ID NO: 37-55. The term "polypeptide" as used herein includes proteins and peptides. An "isolated" or "purified" polypeptide or protein is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized. In one embodiment, the language "substantially free" means preparation of a target polypeptide having less than about 30%, 20%, 10% and more preferably 5% (by dry weight), of non-target polypeptide (also referred to herein as a "contaminating protein"), or of chemical precursors or non-target chemicals.
When the target polypeptide or a biologically active portion thereof is reeombinantly produced, it is also preferably substantially free of culture medium, specifically, where culture medium represents less than about 20%, sometimes less than about 10%, and often less than about 5% of the volume of the polypeptide preparation. Isolated or purified target polypeptide preparations are sometimes 0.01 milligrams or more or 0.1 milligrams or more, and often 1.0 milligrams or more and 10 milligrams or more in dry weight. In certain embodiments, the APOL3 polypeptide or polypeptide fragment has APOL3 biological activity, for example, apolipoprotein activity.

[0069] Further included herein are target polypeptide fragments. The polypeptide fragment may be a domain or part of a domain of a target polypeptide. The polypeptide fragment may have increased, decreased or unexpected biological activity. The polypeptide fragment is often 50 or fewer, 100 or fewer, or 200 or fewer amino acids in length, and is sometimes 300, 400, 500, 600, 700, or 900 or fewer amino acids in length. In certain embodiments, the polypeptide fragment sometimes is amino acids 90-396 of SEQ D? NO: 53; amino acids 19-325 of SEQ ID NO: 54; or amino acids 1-196 of SEQ ID NO: 55. Shown in Table A below are examples of polypeptide fragments, where approximate amino acid positions are shown in parenthesis (e.g., a Pellino domain starts at about amino acid 3 and ends at about amino acid 412).
Amino acid sequences can be accessed using information in Table B and in SEQ
117 NO: 37-55.
TABLE A
RS ID Locus SEQ SignalDomain (amino acid ranges) ID

- NO. Peptide 910223 PAD12 37 none 1367117 PO~ 38 1-27 Apolipoprotein B48 mature peptide (1-2151) Lipoprotein amino terminal region (46-597) RS ID Locus SEQ SignalDomain (amino acid ranges) ID

NO. Peptide ATPase involved in DNA repair (2077-2583) 1024791 IL1RL2 39 1-19 Immunoglobulin C-2 Type (36-100;
137-197) TIR Domain (385-535) Neural cell adhesion molecule L1 (<53->295) Transmembrane Domain (336-358) 1465621 WASPIP 43 none WASP-interacting protein VRP1/WIP
(14->63) 1018810 BYES 46 none Popeye protein conserved region (123-266) 242392 PEL12 48 none Pellino (3-412) 8818 LOXL1 49 none Lysyl oxidase (370-574) 1395486 CASPR4 50 none Neurexin IV domain (3-1308) F5/8 type C domain (57-177) Laminin G domains (374-524; 475->750;
797-941; 1037-1176) 51 none Neurexin IV domain (1->721) F5/8 type C domain (29-149) Laminin G domains (169-314; 346-496;
579->662) 512294 GPR50 52 none 7 transmembrane receptor (rhodopsin family) (45..294) Microtubule-associated protein dynactin DCTN1/Glued (462..>587) Syndecan domain (485..>595) [0070] Interleukin 1 receptor-like 1 isoform 1 (SEQ ID NO: 40) is a member of the interleukin 1 receptor family with no known ligand (orphan receptor). ILIRLI exists in soluble (SEQ 117 NO: 41-42) and transmembrane forms, suggesting that it may have ligand or ligand scavenging activity. In an embodiment, ILIRLI protein agents may be administered to treat or prevent the occurrence of OA.
IL1RL1 protein agents include ILIRLI polypeptides or fragments thereof that have ILIRLI ligand activity (e.g., recombinant polypeptides of SEQ ID NO: 41-42). In a related embodiment, ILIRLI
protein agents include ILIRLl polypeptides or fragments thereof that have IL1RL1 ligand scavenging activity (e.g., recombinant polypeptide of SEQ ID NO: 40). Isolated ILIRLI
polypeptides featured herein include the full-length polypeptide, the mature polypeptide (i.e., the polypeptide without the signal sequence MGFWILAILTILMYSTAA) or a polypeptide fragment containing a domain or part of a IL1RL1 domain. The polypeptide fragment may have increased, decreased or unexpected biological activity.

[0071] In another embodiment, provided herein are ADAMTS~ polypeptides having an ADAMTSZ
activity (e.g., a zinc binding activity, a metalloprotease activity, a procollagen II processing or synthesis activity, or a collagen II synthesis activity in vitro or in vivo). In certain embodiments, the polypeptides are ADAMTS2 proteins including at least one propeptide domain, at least one metalloproteinase domain, at least one disintegrin-like domain, at least one, two, three, and often four thrombospondin domains, and sometimes having a ADAMTS2 activity, e.g., a ADAMTS2 activity as described herein. ADAMTS2 polypeptides and fragments thereof often have biological activity, such as excising the N-propeptide of type II procollagens. Methods for monitoring and quantifying this biological activity are known (e.g., Colige et al., J. Biol. Chem. 270: 16724-16730 (1995)).

[0072] Human ADAMTS2 protein (SEQ ID NO: 44-45) includes a signal sequence of about 29 amino acids (from amino acid 1 to about amino acid 29 of SEQ ID NO: 44-45).
The ADAMTS2 protein without the signal sequence can be approximately 1182 amino acid residues in length (from about amino acid 30 to amino acid 1211 of SEQ ID NO: 44) or approximately 485 amino acid residues in length (from about amino acid 30 to amino acid 514 of SEQ ID NO: 45). Human ADAMTS2 protein includes a "pro" region homologous to the reprolysin family propeptide, which is typically post-translationally cleaved upon conversion of the inactive (or pro-domain containing) protein to the catalytically active metalloprotease. The prodomain region of human ADAMTS2 protein corresponds to about amino acids 30 to 251, 30 to 252, 30 to 253, 30 to 254, 30 to 255, 30 to 256, 30 to 257, 30 to 258 or 30 to 259 of SEQ ID NO: 44-45, where it is understood that the active form ofADAMTS2 does not contain the propeptide domain.

[0073] Upon cleavage, catalytically active mature protein can be approximately 960, 959, 958, 957, 956, 955, 954, 953 or 952 amino acids in length (from about amino acid 252, 253, 254, 255, 256, 257, 258, 259 or 260 to amino acid 1211 of SEQ ID NO: 44) or approximately 261, 260, 259, 258, 257, 256, 255, 254 or 253 amino acid residues in length (from about amino acid 252, 253, 254, 255, 256, 257, 258, 259 or 260 to amino acid 514 of SEQ ID NO: 45).

[0074] Human ADAMTS2 contains the following regions or other structural features: a signal sequence at about amino acids 1-29 of SEQ ID NO: 44-45; a reprolysin family propeptide domain located at about amino acid residues 30 to 251, 30 to 252, 30 to 253, 30 to 254, 30 to 255, 30 to 256, 30 to 257, 30 to 258 or 30 to 259 of SEQ ID NO: 44-45; a zinc-metalloprotease catalytic domain at about amino acids 251 to 479, 252 to 479, 253 to 479, 254 to 479, 255 to 479, 256 to 479, 257 to 479, 258 to 479 or 259 to 479 of SEQ ID NO: 44-45; a disintegrin domain at about amino acids 480 to 560 of SEQ
ID NO: 44; a cysteine-rich domain at about amino acids 618 to 722 of SEQ ID
NO: 44; four thrombospondin motifs-2 motifs at about amino acids 561 to 616, 854 to 912, 914 to 971, and 975 to 1029 of SEQ ID NO: 44; and eight N-glycosylation sites located at about amino acids 112, 251, 949, 993, 1031, 1098, 1145, and 1150 of SEQ ID NO: 44.

[0075] In other embodiments, provided are methods of increasing the synthesis of procollagen II
comprising providing or administering to individuals in need of increasing levels of type II collagen the pharmaceutical or physiologically acceptable composition comprising active human ADAMTS2 protein or fragment thereof, where ADAMTS2 polypeptide fragments having activity are selected from amino acids 252-1211, 253-1211, 254-1211, 255-1211, 256-1211, 257-1211, 258-1211, 259-1211 or 260-1211 of SEQ ID NO: 4, where it is understood that the active form ofADAMTS2 does not contain the propeptide domain.

[0076] Substantially identical target polypeptides may depart from the amino acid sequences of target polypeptides in different manners. For example, conservative amino acid modifications may be introduced at one or more positions in the amino acid sequences of target polypeptides. A "conservative amino acid substitution" is one in which the amino acid is replaced by another amino acid having a similar structure and/or chemical function. Families of amino acid residues having similar structures and functions are well known. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Also, essential and non-essential amino acids may be replaced. A "non-essential" amino acid is one that can be altered without abolishing or substantially altering the biological function of a target polypeptide, whereas altering an "essential" amino acid abolishes or substantially alters the biological function of a target polypeptide. Amino acids that are conserved among target polypeptides are typically essential amino acids. In certain embodiments, the polypeptide includes one or more non-synonymous polymorphic variants associated with osteoarthritis, as described above (e.g., a threonine encoded by rs1367117 in an AP~B polypeptide).

[0077] Also, target polypeptides may exist as chimeric or fusion polypeptides.
As used herein, a target "chimeric polypeptide" or target "fusion polypeptide" includes a target polypeptide linked to a non-target polypeptide. A "non-target polypeptide" refers to a polypeptide having an amino acid sequence corresponding to a polypeptide which is not substantially identical to the target polypeptide, which includes, for example, a polypeptide that is different from the target polypeptide and derived from the same or a different organism. The target polypeptide in the fusion polypeptide can correspond to an entire or nearly entire target polypeptide or a fragment thereof. The non-target polypeptide can be fused to the N-terminus or C-terminus of the target polypeptide.

[0078] Fusion polypeptides can include a moiety having high affinity for a ligand. For example, the fusion polypeptide can be a GST-target fusion polypeptide in which the target sequences are fused to the C-terminus of the GST sequences, or a polyhistidine-target fusion polypeptide in which the target polypeptide is fused at the N- or C-terminus to a string of histidine residues. Such fusion polypeptides can facilitate purification of recombinant target polypeptide. Expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide), and a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B, or a substantially identical nucleotide sequence thereof, can he cloned into an expression vector such that the fusion moiety is linked in-frame to the target polypeptide. Further, the fusion polypeptide can be a target polypeptide containing a heterologous signal sequence at its N-terminus. In certain host cells (e.g., mammalian host cells), expression, secretion, cellular internalization, and cellular localization of a target polypeptide can be increased through use of a heterologous signal sequence. Fusion polypeptides can also include all or a part of a serum polypeptide (e.g., an IgG constant region or human serum albumin).

[0079] Target polypeptides can be incorporated into pharmaceutical compositions and administered to a subject in vivo. Administration of these target polypeptides can be used to affect the bioavailability of a substrate of the target polypeptide and may effectively increase target polypeptide biological activity in a cell. Target fusion polypeptides may be useful therapeutically for the treatment of disorders caused by, for example, (i) aberrant modification or mutation of a gene encoding a target polypeptide; (ii) mis-regulation of the gene encoding the target polypeptide;
and (iii) aberrant post-translational modification of a target polypeptide. Also, target polypeptides can be used as immunogens to produce anti-target antibodies in a subject, to purify target polypeptide ligands or binding partners, and in screening assays to identify molecules which inhibit or enhance the interaction of a target polypeptide with a substrate.

[0080] In addition, polypeptides can be chemically synthesized using techniques known in the art (See, e.g., Creighton, 1983 Proteins. New York, N.Y.: W. H. Freeman and Company; and Hunkapiller et al., (1984) Nature July 12 -18;310(5973):105-11). For example, a relative short fragment can be synthesized by use of a peptide synthesizer. Furthermore, if desired, non-classical amino acids or chemical amino acid analogs can be introduced as a substitution or addition into the fragment sequence.
Non-classical amino acids include, but are not limited to, to the D-isomers of the common amino acids, 2,4-diaminobutyric acid, a-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, g-Abu, e-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosine, citrulline, homocitrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, b-alanine, fluoroamino acids, designer amino acids such as b-methyl amino acids, Ca-methyl amino acids, Na-methyl amino acids, and amino acid analogs in general. Furthermore, the amino acid can be D (dextrorotary) or L
(levorotary).

[0081] Polypeptides and polypeptide fragments sometimes are differentially modified during or after translation, e.g., by glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to an antibody molecule or other cellular ligand, etc. Any of numerous chemical modifications may be carried out by known techniques, including but not limited, to specific chemical cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8 protease, NaBH4; acetylation, formylation, oxidation, reduction;
metabolic synthesis in the presence of tunicamycin; and the like. Additional post-translational modifications include, for example, N-linked or O-linked carbohydrate chains, processing of N-terminal or C-terminal ends), attachment of chemical moieties to the amino acid backbone, chemical modifications of N-linked or O-linked carbohydrate chains, and addition or deletion of an N-terminal methionine residue as a result of prokaryotic host cell expression. The polypeptide fragments may also be modified with a detectable label, such as an enzymatic, fluorescent, isotopic or affinity label to allow for detection and isolation of the polypeptide.

[0082] Also provided are chemically modified derivatives of polypeptides that can provide additional advantages such as increased solubility, stability and circulating time of the polypeptide, or decreased immunogenicity (see e.g., U.S. Pat. No: 4,179,337. The chemical moieties for derivitization may be selected from water soluble polymers such as polyethylene glycol, ethylene glycol/propylene glycol copolymers, carboxymethylcellulose, dextran, polyvinyl alcohol and the like. The polypeptides may be modified at random positions within the molecule, or at predetermined positions within the molecule and may include one, two, three or more attached chemical moieties.

[0083] The polymer may be of any molecular weight, and may be branched or unbranched. For polyethylene glycol, the preferred molecular weight is between about 1 kDa and about 100 kDa (the term "about" indicating that in preparations of polyethylene glycol, some molecules will weigh more, some less, than the stated molecular weight) for ease in handling and manufacturing. Other sizes may be used, depending on the desired therapeutic profile (e.g., the duration of sustained release desired, the effects, if any on biological activity, the ease in handling, the degree or lack of antigenicity and other known effects of the polyethylene glycol to a therapeutic protein or analog).

[0084] The polymers should be attached to the polypeptide with consideration of effects on functional or antigenic domains of the polypeptide. There are a number of attachment methods available to those skilled in the art (e.g., EP 0 401 384 (coupling PEG to G-CSF) and Malik et al. (1992) Exp Hematol. September;20(8):1028-35 (pegylation of GM-CSF using tresyl chloride)). For example, polyethylene glycol may be covalently bound through amino acid residues via a reactive group, such as a free amino or carboxyl group. Reactive groups are those to which an activated polyethylene glycol molecule may be bound. The amino acid residues having a free amino group may include lysine residues and the N-terminal amino acid residues; those having a free carboxyl group may include aspartic acid residues, glutamic acid residues and the C-terminal amino acid residue. Sulfhydryl groups may also be used as a reactive group for attaching the polyethylene glycol molecules. For therapeutic purposes, the attachment sometimes is at an amino group, such as attachment at the N-terminus or lysine group.

[0085] Proteins can be chemically modified at the N-terminus. Using polyethylene glycol as an illustration of such a composition, one may select from a variety of polyethylene glycol molecules (by molecular weight, branching, and the like), the proportion of polyethylene glycol molecules to protein (polypeptide) molecules in the reaction mix, the type of pegylation reaction to be performed, and the method of obtaining the selected N-terminally pegylated protein. The method of obtaining the N-terminally pegylated preparation (i.e., separating this moiety from other monopegylated moieties if necessary) may be by purification of the N-terminally pegylated material from a population of pegylated protein molecules. Selective proteins chemically modified at the N-terminus may be accomplished by reductive alkylation, which exploits differential reactivity of different types of primary amino groups (lysine versus the N-terminal) available for derivatization in a particular protein. Under the appropriate reaction conditions, substantially selective derivatization of the protein at the N-terminus with a carbonyl group containing polymer is achieved.
Substantially Identical Nucleic Acids and Polypeptides [0086] Nucleotide sequences and polypeptide sequences that are substantially identical to a PADI2, APOB, ILIRL2, ILIRL1, WASPIP, ADAMTS2, BYES, TM7SF3, LOdYLl, CASPR4 orAPOL3 nucleotide sequence or other nucleotide sequence referenced in Table B and the target polypeptide sequences 2,5 encoded by those nucleotide sequences, respectively, are included herein. The term "substantially identical" as used herein refers to two or more nucleic acids or polypeptides sharing one or more identical nucleotide sequences or polypeptide sequences, respectively.
Included are nucleotide sequences or polypeptide sequences that are 55% or more, 60% or more, 65% or more, 70% or more, 75% or more, 80°!0 or more, 85% or more, 90% or more, 95% or more (each often within a 1%, 2%, 3%
or 4% variability) identical to a PADl2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLl, CASPR4 or APOL3 nucleotide sequence, or other nucleotide sequence referenced in Table B, or the encoded target polypeptide amino acid sequences. One test for determining whether two nucleic acids are substantially identical is to determine the percent of identical nucleotide sequences or polypeptide sequences shared between the nucleic acids or polypeptides.

[0087] Calculations of sequence identity are often performed as follows.
Sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). The length of a reference sequence aligned for comparison purposes is sometimes 30% or more, 40% or more, 50% or more, often 60% or more, and more often 70% or more, 80% or more, 90°!0 or more, or 100% of the length of the reference sequence. The nucleotides or amino acids at corresponding nucleotide or polypeptide positions, respectively, are then compared among the two sequences. When a position in the first sequence is occupied by the same nucleotide or amino acid as the corresponding position in the second sequence, the nucleotides or amino acids are deemed to be identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, introduced for optimal alignment of the two sequences.

[0088] Comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. Percent identity between two amino acid or nucleotide sequences can be determined using the algorithm of Meyers & Miller, CABIOS 4: 11-17 (1989), which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4. Also, percent identity between two amino acid sequences can be determined using the Needleman & Wunsch, J. Mol.
Biol. 48: 444-453 (1970) algorithm which has been incorporated into the GAP program in the GCG
software package (available at the http address www.gcg.com), using either a Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6. Percent identity between two nucleotide sequences can be determined using the GAP program in the GCG software package (available at http address www.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6. A set ~f parameters often used is a Blossum 62 scoring matrix with a gap open penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.

[0089] Another manner for determining if two nucleic acids are substantially identical is to assess whether a polynucleotide homologous to one nucleic acid will hybridize to the other nucleic acid under stringent conditions. As use herein, the term "stringent conditions" refers to conditions for hybridization and washing. Stringent conditions are known to those skilled in the art and can be found in Current Pr~otoeols in Molecular Biology, John Wiley & Sons, N.Y. , 6.3.1-6.3.6 (1989). Aqueous and non-aqueous methods are described in that reference and either can be used. An example of stringent hybridization conditions is hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45°C, followed by one or more washes in 0.2X SSC, 0.1% SDS at 50°C. Another example of stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45°C, followed by one or more washes in 0.2X SSC, 0.1% SDS at 55°C. A further example of stringent hybridization conditions is hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45°C, followed by one or more washes in 0.2X SSC, 0.1% SDS at 60°C. Often, stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45°C, followed by one or more washes in 0.2X SSC, 0.1% SDS at 65°C. More often, stringency conditions are O.SM
sodium phosphate, 7% SDS at 65°C, followed by one or more washes at 0.2X SSC, 1% SDS at 65°C.

[0090] An example of a substantially identical nucleotide sequence to a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B is one that has a different nucleotide sequence but still encodes the same polypeptide sequence encoded by the nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B. Another example is a nucleotide sequence that encodes a polypeptide having a polypeptide sequence that is more than 70% or more identical to, sometimes more than 75% or more, 80% or more, or 85% or more identical to, and often more than 90% or more and 95% or more identical to a polypeptide sequence encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B.

[0091] Nucleotide sequences in SEQ ID NO: 1-13 or referenced in Table B and amino acid sequences of encoded polypeptides can be used as "query sequences" to perform a search against public databases to identify other family members or related sequences, for example.
Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul et al., J. Mol. Biol.
215: 403-10 (1990). BLAST nucleotide searches can be performed with the NBLAST
program, score =
100, wordlength = 12 to obtain nucleotide sequences homologous to nucleotide sequences in SEQ ID
NO: 1-13, SEQ ID NO: 14-36 or referenced in Table B. BLAST polypeptide searches can be performed with the XBLAST program, score = 50, wordlength = 3 to obtain amino acid sequences homologous to polypeptides encoded by the nucleotide sequences of SEQ ff~ NO: 14-36 or referenced in Table B. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., Nucleic Acids Res. 25(17): 3389-3402 (1997). When utilizing BLAST and Gapped BLAST programs, default parameters of the respective programs (e.g., XBLAST
and NBLAST) can be used (see the http address www.ncbi.nlm.nih.gov).

[0092] A nucleic acid that is substantially identical to a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B may include polymorphic sites at positions equivalent to those described herein when the sequences are aligned. For example, using the alignment procedures described herein, SNPs in a sequence substantially identical to a sequence in SEQ ID NO: 1-13 or referenced in Table B can be identified at nucleotide positions that match (i.e., align) with nucleotides at SNP positions in each nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B. Also, where a polymorphic variation results in an insertion or deletion, insertion or deletion of a nucleotide sequence from a reference sequence can change the relative positions of other polymorphic sites in the nucleotide sequence.

[0093] Substantially identical nucleotide and polypeptide sequences include those that are naturally occurring, such as allelic variants (same locus), splice variants, homologs (different locus), and orthologs (different organism) or can be non-naturally occurring. Non-naturally occurring variants can be generated by mutagenesis techniques, including those applied to polynucleotides, cells, or organisms.
The variants can contain nucleotide substitutions, deletions, inversions and insertions. Variation can occur in either or both the coding and non-coding regions. The variations can produce both conservative and non-conservative amino acid substitutions (as compared in the encoded product).
Orthologs, homologs, allelic variants, and splice variants can be identified using methods known in the art. These variants normally comprise a nucleotide sequence encoding a polypeptide that is 50% or more, about 55% or more, often about 70-75% or more or about 80-85% or more, and sometimes about 90-95% or more identical to the amino acid sequences of target polypeptides or a fragment thereof.
Such nucleic acid molecules can readily be identified as being able to hybridize under stringent conditions to a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B or a fragment of this sequence. Nucleic acid molecules corresponding to orthologs, homologs, and allelic variants of a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B can further be identified by mapping the sequence to the same chromosome or locus as the nucleotide sequence in SEQ
ID NO: 1-13 or referenced in Table B.

[0094] Also, substantially identical nucleotide sequences may include codons that are altered with respect to the naturally occurring sequence for enhancing expression of a target polypeptide in a particular expression system. For example, the nucleic acid can be one in which one or more codons are altered, and often 10% or more or 20% or more of the codons are altered for optimized expression in bacteria (e.g., E. coli.), yeast (e.g., S. eervesiae), human (e.g., 293 cells), insect, or rodent (e.g., hamster) cells.
Methods for Identifying Risk of Osteoarthritis [0095] Methods for prognosing and diagnosing osteoarthritis are included herein. These methods include detecting the presence or absence of one or more polymorphic variations in a nucleotide sequence associated with osteoarthritis, such as variants in or around the loci set forth herein, or a substantially identical sequence thereof, in a sample from a subject, where the presence of a polymorphic variant described herein is indicative of a risk of osteoarthritis. Determining a risk of osteoarthritis sometimes refers to determining whether an individual is at an increased risk of osteoarthritis (e.g., intermediate risk or higher risk).

[0096] Thus, featured herein is a method for identifying a subject who is at risk of osteoarthritis, which comprises detecting an aberration associated with osteoarthritis in a nucleic acid sample from the subject. An embodiment is a method for detecting a risk of osteoarthritis in a subject, which comprises detecting the presence or absence of a polymorphic variation associated with osteoarthritis at a polymorphic site in a nucleotide sequence in a nucleic acid sample from a subject, where the nucleotide sequence comprises a polynucleotide sequence selected from the group consisting of: (a) a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B; (b) a nucleotide sequence which encodes a polypeptide consisting of an amino acid sequence encoded by a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B; (c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to an amino acid sequence encoded by a nucleotide sequence of SEQ ID
NO: 1-13 or referenced in Table B, or a nucleotide sequence about 90% or more identical to a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B; and (d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising the polymorphic site; whereby the presence of the polymorphic variation is indicative of a predisposition to osteoarthritis in the subject. In certain embodiments, polymorphic variants at the positions described herein are detected for determining a risk of osteoarthritis, and polymorphic variants at positions in linkage disequilibrium with these positions are detected for determining a risk of osteoarthritis. As used herein, the terms "SEQ ID NO: 1-13" and other nucleotide sequences "referenced in Table B" refers to individual sequences in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or 13 or any individual sequence referenced in Table B, or any individual nucleic acid sequence provided in the sequence listing, including SEQ ID NO: 14-36 each sequence being separately applicable to embodiments described herein.

[0097] Risk of osteoarthritis sometimes is expressed as a probability, such as an odds ratio, percentage, or risk factor. Risk often is based upon the presence or absence of one or more polymorphic variants described herein, and also may be based in part upon phenotypic traits of the individual being tested. Methods for calculating risk based upon patient data are well known (see, e.g., Agresti, Categorical Data Analysis, 2nd Ed. 2002. Wiley). Allelotyping and genotyping analyses may be carried out in populations other than those exemplified herein to enhance the predictive power of the prognostic method. These further analyses are executed in view of the exemplified procedures described herein, and may be based upon the same polymorphic variations or additional polymorphic variations.

[0098] In certain embodiments, determining the presence of a combination of two or more polymorphic variants associated with osteoarthritis in one or more genetic loci (e.g., one or more genes) of the sample is determined to identify, quantify and/or estimate, risk of osteoarthritis. The risk often is the probability of having or developing osteoarthritis. The risk sometimes is expressed as a relative risk with respect to a population average risk of osteoarthritis, and sometimes is expressed as a relative risk with respect to the lowest risk group. Such relative risk assessments often are based upon penetrance values determined by statistical methods, and are particularly useful to clinicians and insurance companies for assessing risk of osteoarthritis (e.g., a clinician can target appropriate detection, prevention and therapeutic regimens to a patient after determining the patient's risk of osteoarthritis, and an insurance company can fine tune actuarial tables based upon population genotype assessments of osteoarthritis risk). Risk of osteoarthritis sometimes is expressed as an odds ratio, which is the odds of a particular person having a genotype has or will develop osteoarthritis with respect to another genotype group (e.g., the most disease protective genotype or population average). In related embodiments, the determination is utilized to identify a subject at risk of osteoarthritis. In an embodiment, two or more polymorphic variations are detected in two or more regions in human genomic DNA associated with increased risk of osteoarthritis, such as a locus containing a PADI2, APOB, IL1RL2, ILIRLI, WASPIP, ADAMTS2, BhES, TM7SF3, LOXLl, CASPR4 or APOL3 or other locus referenced in Table B, for example. In certain embodiments, 3 or more, or 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 90, 100 or more polymorphic variants are detected in the sample. In specific embodiments, polymorphic variants are detected in a PAD12, APOB, ILIRL2, ILIRL1, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLl, CASPR4 or APOL3 region or other region referenced in Table B, for example. In another embodiment, polymorphic variants are detected at two or three positions in a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B. In certain embodiments, polymorphic variants are detected at other genetic loci (e.g., the polymorphic variants can be detected in a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BT~ES, TM7SF3, LOXLl, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B in addition to other loci or only in other loci), where the other loci include but are not limited to those described in patent applications 60/559,011; 60/559,202; 60/559,203; 60/559,042;
60/559,275; 60/559,040 and 60/559,225, each of which is entitled "Methods for Identifying Risk of Osteoarthritis and Treatments Thereof," each of which was filed on 1 April 2004 and each of which is incorporated herein by reference in its entirety in jurisdictions allowing incorporation by reference.

[0099] Results from prognostic tests may be combined with other test results to diagnose osteoarthritis. For example, prognostic results may be gathered, a patient sample may be ordered based on a determined predisposition to osteoarthritis, the patient sample is analyzed, and the results of the analysis may be utilized to diagnose osteoarthritis. Also osteoarthritis diagnostic method can be developed from studies used to generate prognostic methods in which populations are stratified into subpopulations having different progressions of osteoarthritis. In another embodiment, prognostic results may be gathered, a patient's risk factors for developing osteoarthritis (e.g., age, weight, occupational history, race, diet) analyzed, and a patient sample may be ordered based on a determined predisposition to osteoarthritis.

[0100] The nucleic acid sample typically is isolated from a biological sample obtained from a subject. For example, nucleic acid can be isolated from blood, saliva, sputum, urine, cell scrapings, and biopsy tissue. The nucleic acid sample can be isolated from a biological sample using standard techniques, such as the technique described in Example 2. As used herein, the term "subject" refers primarily to humans but also refers to other mamrnals such as dogs, cats, and ungulates (e.g., cattle, sheep, and swine). Subjects also include avians (e.g., chickens and turkeys), reptiles, and fish (e.g., salmon), as embodiments described herein can be adapted to nucleic acid samples isolated from any of these organisms. The nucleic acid sample may be isolated from the subject and then directly utilized in a method for determining the presence of a polymorphic variant, or alternatively, the sample may be isolated and then stored (e.g., frozen) for a period of time before being subjected to analysis.

[0101] The presence or absence of a polymorphic variant is determined using one or both chromosomal complements represented in the nucleic acid sample. Determining the presence or absence of a polymorphic variant in both chromosomal complements represented in a nucleic acid sample from a subject having a copy of each chromosome is useful for determining the zygosity of an individual for the polymorphic variant (i. e., whether the individual is homozygous or heterozygous for the polymorphic variant). Any oligonucleotide-based diagnostic may be utilized to determine whether a sample includes the presence or absence of a polymorphic variant in a sample.
For example, primer extension methods, ligase sequence determination methods (e.g., U.S. Pat. Nos.
5,679,524 and 5,952,174, and WO 01/27326), mismatch sequence determination methods (e.g., U.S. Pat. Nos.
5,851,770; 5,958,692; 6,110,684; and 6,183,958), microarray sequence determination methods, restriction fragment length polymorphism (RFLP), single strand conformation polymorphism detection (SSCP) (e.g., U.S. Pat. Nos. 5,891,625 and 6,013,499), PCR-based assays (e.g., TAQMAN~ PCR
System (Applied Biosystems)), and nucleotide sequencing methods may be used.

[0102] Oligonucleotide extension methods typically involve providing a pair of oligonucleotide primers in a polymerise chain reaction (PCR) or in other nucleic acid amplification methods for the purpose of amplifying a region from the nucleic acid sample that comprises the polymorphic variation.
One oligonucleotide primer is complementary to a region 3' of the polymorphism and the other is complementary to a region 5' of the polymorphism. A PCR primer pair may be used in methods disclosed in U.S. Pat. Nos. 4,683,195; 4,683,202, 4,965,188; 5,656,493;
5,998,143; 6,140,054; WO
01/27327; and WO 01/27329 for example. PCR primer pairs may also be used in any commercially available machines that perform PCR, such as any of the GENEAMP~ Systems available from Applied Biosystems. Also, those of ordinary skill in the art will be able to design oligonucleotide primers based upon a PAD12, APOB, IL1RL2, ILIRLI, WASPIP, ADAMTS2, BTdES, TM7SF3, LOXLI, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B
using knowledge available in the art.

[0103] Also provided is an extension oligonucleotide that hybridizes to the amplified fragment adjacent to the polymorphic variation. As used herein, the term "adjacent"
refers to the 3' end of the extension oligonucleotide being often 1 nucleotide from the 5' end of the polymorphic site, and sometimes 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from the 5' end of the polymorphic site, in the nucleic acid when the extension oligonucleotide is hybridized to the nucleic acid. The extension oligonucleotide then is extended by one or more nucleotides, and the number and/or type of nucleotides that are added to the extension oligonucleotide determine whether the polymorphic variant is present.
Oligonucleotide extension methods are disclosed, for example, in U.S. Pat.
Nos. 4,656,127; 4,851,331;
5,679,524; 5,834,189; 5,876,934; 5,908,755; 5,912,118; 5,976,802; 5,981,186;
6,004,744; 6,013,431;

6,017,702; 6,046,005; 6,087,095; 6,210,891; and WO 01/20039. Oligonucleotide extension methods using mass spectrometry are described, for example, in U.S. Pat. Nos.
5,547,835; 5,605,798; 5,691,141;
5,849,542; 5,869,242; 5,928,906; 6,043,031; and 6,194,144, and a method often utilized is described herein in Example 2.

[0104] A microarray can be utilized for determining whether a polymorphic variant is present or absent in a nucleic acid sample. A microarray may include any oligonucleotides described herein, and methods for making and using oligonucleotide microarrays suitable for diagnostic use are disclosed in U.S. Pat_ Nos. 5,492,806; 5,525,464; 5,589,330; 5,695,940; 5,849,483;
6,018,041; 6,045,996;
6,136,541; 6,142,681; 6,156,501; 6,197,506; 6,223,127; 6,225,625; 6,229,911;
6,239,273; WO
00/52625; WO 01/25485; and WO 01/29259. The microarray typically comprises a solid support and the oligonucleotides may be linked to this solid support by covalent bonds or by non-covalent interactions. The oligonucleotides may also be linked to the solid support directly or by a spacer molecule. A microarray may comprise one or more oligonucleotides complementary to a polymorphic site set forth herein.

[0105] A lcit also may be utilized for determining whether a polymorphic variant is present or absent in a nucleic acid sample. A kit often comprises one or more pairs of oligonucleotide primers useful for amplifying a fragment of a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B
or a substantially identical sequence thereof, where the fragment includes a polymorphic site. The kit sometimes comprises a polymerizing agent, for example, a thermostable nucleic acid polymerase such as one disclosed in U.S. Pat. Nos. 4,889,818 or 6,077,664. Also, the kit often comprises an elongation oligonucleotide that hybridizes to a PADI2, APOB, ILIRL2, ILIRL1, WASPIP, ADAMTS2, BYES, TM7SF3, LO~'Ll, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B in a nucleic acid sample adjacent to the polymorphic site. Where the kit includes an elongation oligonucleotide, it also often comprises chain elongating nucleotides, such as dATP, dTTP, dGTP, dCTP, and dITP, including analogs of dATP, dTTP, dGTP, dCTP and dITP, provided that such analogs are substrates for a thermostable nucleic acid polymerase and can be incorporated into a nucleic acid chain elongated from the extension oligonucleotide. Along with chain elongating nucleotides would be one or more chain terminating nucleotides such as ddATP, ddTTP, ddGTP, ddCTP, and the like. In an embodiment, the kit comprises one or more oligonucleotide primer pairs, a polymerizing agent, chain elongating nucleotides, at least one elongation oligonucleotide, and one or more chain terminating nucleotides. Kits optionally include buffers, vials, microtiter plates, and instructions for use.

[0106] An individual identified as being at risk of osteoarthritis may be heterozygous or homozygous with respect to the allele associated with a higher risk of osteoarthritis. A subject homozygous for an allele associated with an increased risk of osteoarthritis is at a comparatively high risk of osteoarthritis, a subject heterozygous for an allele associated with an increased risk of osteoarthritis is at a comparatively intermediate risk of osteoarthritis, and a subject homozygous for an allele associated with a decreased risk of osteoarthritis is at a comparatively low risk of osteoarthritis. A

genotype may be assessed for a complementary strand, such that the complementary nucleotide at a particular position is detected.

[0107] Also featured are methods for determining risk of osteoarthritis and/or identifying a subject at risk of osteoarthritis by contacting a polypeptide or protein encoded by a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BITES, TM7SF3, LOXLl, CASPR4 or AI'OL3 nucleotide sequence or other nucleotide sequence referenced in Table B from a subject with an antibody that specifically binds to an epitope associated with increased risk of osteoarthritis in the polypeptide (e.g., an epitope comprising a valine at position 245 in an IRILRI polypeptide).
Applications of Prognostic and Diagnostic Results to Pharmaco~enomic Methods [0108] Pharmacogenomics is a discipline that involves tailoring a treatment for a subject according to the subject's genotype as a particular treatment regimen may exert a differential effect depending upon the subject's genotype. For example, based upon the outcome of a prognostic test described herein, a clinician or physician may target pertinent information and preventative or therapeutic treatments to a subject who would be benefited by the information or treatment and avoid directing such information and treatments to a subject who would not be benefited (e.g., the treatment has no therapeutic effect and/or the subject experiences adverse side effects).

[0109] The following is an example of a pharmacogenomic embodiment. A
particular treatment regimen can exert a differential effect depending upon the subject's genotype.
Where a candidate therapeutic exhibits a significant interaction with a major allele and a comparatively weak interaction with a minor allele (e.g., an order of magnitude or greater difference in the interaction), such a therapeutic Typically would not be administered to a subject genotyped as being homozygous for the minor allele, and sometimes not administered to a subject genotyped as being heterozygous for the minor allele. In another example, where a candidate therapeutic is not significantly toxic when administered to subjects who are homozygous for a major allele but is comparatively toxic when administered to subjects heterozygous or homozygous for a minor allele, the candidate therapeutic is not typically administered to subjects who are genotyped as being heterozygous or homozygous with respect to the minor allele.

[0110] The methods described herein are applicable to pharmacogenomic methods for preventing, alleviating or treating osteoarthritis. For example, a nucleic acid sample from an individual may be subjected to a prognostic test described herein. Where one or more polymorphic variations associated with increased risk of osteoarthritis are identified in a subject, information for preventing or treating osteoarthritis and/or one or more osteoarthritis treatment regimens then may be prescribed to that subject.

[0111] In certain embodiments, a treatment or preventative regimen is specifically prescribed and/or administered to individuals who will most benefit from it based upon their risk of developing osteoarthritis assessed by the methods described herein. Thus, provided are methods for identifying a subject predisposed to osteoarthritis and then prescribing a therapeutic or preventative regimen to individuals identified as having a predisposition. Thus, certain embodiments are directed to a method for reducing osteoarthritis in a subject, which comprises: detecting the presence or absence of a polymorphic variant associated with osteoarthritis in a nucleotide sequence in a nucleic acid sample from a subject, where the nucleotide sequence comprises a polynucleotide sequence selected from the group consisting of (a) a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B; (b) a nucleotide sequence which encodes a polypeptide consisting of an amino acid sequence encoded by a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B; (c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to an amino acid sequence encoded by a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B, or a nucleotide sequence about 90% or more identical to a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B; and (d) a fragment of a polynucleotide sequence of (a), (b), or (c); and prescribing or administering a treatment regimen to a subj ect from whom the sample originated where the presence of a polymorphic variation associated with osteoarthritis is detected in the nucleotide sequence. In these methods, predisposition results may be utilized in combination with other test results to diagnose osteoarthritis.

[0112] Certain preventative treatments often are prescribed to subjects having a predisposition to osteoarthritis and where the subject is diagnosed with osteoarthritis or is diagnosed as having symptoms indicative of an early stage of osteoarthritis. The treatment sometimes is preventative (e.g., is prescribed or administered to reduce the probability that osteoarthritis arises or progresses), sometimes is therapeutic, and sometimes delays, alleviates or halts the progression of osteoarthritis. Any known preventative or therapeutic treatment for alleviating or preventing the occurrence of osteoarthritis is prescribed and/or administered. For example, the treatment often is directed to decreasing pain and improving joint movement. Examples of OA treatments include exercises to keep joints flexible and improve muscle strength. Different medications to control pain, including corticosteroids and nonsteroidal anti-inflammatory drugs (NSAIDs, e.g., Voltaren); cyclooxygenase-2 (COX-2) inhibitors (e.g_ , Celebrex, Vioxx, Mobic, and Bextra); monoclonal antibodies (e.g., Remicade); tumor necrosis factor inhibitors (e.g., Enbrel); or injections of glucocorticoids, hyaluronic acid or chondrotin sulfate into joints that are inflamed and not responsive to NSAIDS. Orally administered chondroitin sulfate also may be used as a therapeutic, as it may increase hyaluronic acid levels and viscosity of synovial fluid, and decrease collagenase levels in synovial fluid. Also, glucosamine can serve as an OA
therapeutic as delivering it into joints may inhibit enzymes involved in cartilage degradation and enhance the production of hyaluronic acid. For mild pain without inflammation, acetaminophen may be used. Other treatments include: heat/cold therapy for temporary pain relief;
joint protection to prevent strain or stress on painful joints; surgery to relieve chronic pain in damaged joints; and weight control to prevent extra stress on weight-bearing joints.

[0113] As therapeutic approaches for treating osteoarthritis continue to evolve and improve, the goal of treatments for osteoarthritis related disorders is to intervene even before clinical signs first manifest. Thus, genetic markers associated with susceptibility to osteoarthritis prove useful for early diagnosis, prevention and treatment of osteoarthritis.

[0114] As osteoarthritis preventative and treatment information can be specifically targeted to subjects in need thereof (e.g., those at risk of developing osteoarthritis or those in an early stage of osteoarthritis), provided herein is a method for preventing or reducing the risk of developing osteoarthritis in a subject, which compris es: (a) detecting the presence or absence of a polymorphic variation associated with osteoarthritis at a polymorphic site in a nucleotide sequence in a nucleic acid sample from a subject; (b) identifying a subject with a predisposition to osteoarthritis, whereby the presence of the polymorphic variation is indicative of a predisposition to osteoarthritis in the subject;
and (c) if such a predisposition is identifi ed, providing the subject with information about nethods or products to prevent or reduce osteoarthritis or to delay the onset of osteoarthritis. Also provided is a method of targeting information or advertising to a subpopulation of a human population based on the subpopulation being genetically predisposed to a disease or condition, which comprises: (a) detecting the presence or absence of a polymorphic variation associated with osteoarthritis at a polyrnorphic site in a nucleotide sequence in a nucleic acid sample from a subject; (b) identifying the subpopulation of subjects in which the polymorphic variation is associated with osteoarthritis;
and (c) providing information only to the subpopulation of subjects about a particular product which may be obtained and consumed or applied by the subject to help prevent or delay onset of the disease or condition.

[0115] Pharmacogenomics methods also may be used to analyze and predict a response to osteoarthritis treatment or a drug. For example, if pharmacogenomics analysis indicates a likelihood that an individual will respond positively to osteoarthritis treatment with a particular drug, the drug may be administered to the individual. Conversely, if the analysis indicates that an individual is likely to respond negatively to treatment with a particular drug, an alternative course of treatment may be prescribed. A negative response may be defined as either the absence of an efficacious response or the presence of toxic side effects. The response to a therapeutic treatment can be predicted in a background study in which subjects in any of the following populations are genotyped: a population that responds favorably to a treatment regimen, a population that does not respond significantly to a treatment regimen, and a population that responds adversely to a treatment regimen (e.g., exhibits one or more side effects). These populations are provided as examples and other populations and subpopulations may be analyzed. Based upon the results of these analyses, a subject is genotyped to predict whether he or she will respond favorably to a treatment regimen, not respond significantly to a treatment regimen, or respond adversely to a treatment regimen.

[0116] The tests described herein also are applicable to clinical drug trials.
One or more polymorphic variants indicative of response to an agent for treating osteoarthritis or to side effects to an agent for treating osteoarthritis may be identified using the methods described herein. Thereafter, potential participants in clinical trials of such an agent may be screened to identify those individuals most likely to respond favorably to the drug and exclude those likely to experience side effects. In that way, the effectiveness of drug treatment rnay be measured in individuals who respond positively to the drug, without lowering the measurement as a result of the inclusion of individuals who are unlikely to respond positively in the study and without risking undesirable safety problems.

[0117] Thus, another embodiment is a method of selecting an individual for inclusion in a clinical trial of a treatment or drug comprising the steps of (a) obtaining a nucleic acid sample from an individual; (b) determining the identity of a polymorphic variation which is associated with a positive response to the treatment or the drug, or at least one polymorphic variation which is associated with a negative response to the treatment or the drug in the nucleic acid sample, and (c) including the individual in the clinical trial if the nucleic acid sample contains said polymorphic variation associated with a positive response to the treatment or the drug or if the nucleic acid sample lacks said polymorphic variation associated with a negative response to the treatment or the drug. In addition, the methods described herein for selecting an individual for inclusion in a clinical trial of a treatment or drug encompass methods with any further limitation described in this disclosure, or those following, specified alone or in any combination. The polymorphic variation may be in a sequence selected individually or in any combination from the group consisting of (i) a nucleotide sequence of SEQ ID
NO: 1-13 or referenced in Table B; (ii) a nucleotide sequence which encodes a polypeptide consisting of an amino acid sequence encoded by a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B; (iii) a nucleotide sequence which encodes a polypeptide that is 90°!° or more identical to an amino acid sequence encoded by a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B, or a nucleotide sequence about 90% or more identical to a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B; and (iv) a fragment of a polynucleotide sequence of (i), (ii), or (iii) comprising the polymorphic site. The including step (c) optionally comprises administering the drug or the treatment to the individual if the nucleic acid sample contains the polymorphic variation associated with a positive response to the treatment or the drug and the nucleic acid sample lacks said biallelic marker associated with a negative response to the treatment or the drug.

[0118] Also provided herein is a method of partnering between a diagnostic/prognostic testing provider and a provider of a consumable product, which comprises: (a) the diagnostic/prognostic testing provider detects the presence or absence of a polymorphic variation associated with osteoarthritis at a polymorphic site in a nucleotide sequence in a nucleic acid sample from a subject; (b) the diagnostic/prognostic testing provider identifies the subpopulation of subjects in which the polymorphic variation is associated with osteoarthritis; (c) the diagnostic/prognostic testing provider forwards information to the subpopulation of subjects about a particular product which may be obtained and consumed or applied by the subject to help prevent or delay onset of the disease or condition; and (d) the provider of a consumable product forwards to the diagnostic test provider a fee every time the diagnostic/prognostic test provider forwards information to the subject as set forth in step (c) above.
Compositions Comprising Osteoarthritis-Directed Molecules [0119] Featured herein is a composition comprising a cell from a subject having osteoarthritis or at risk of osteoarthritis and one or more molecules specifically directed and targeted to a nucleic acid comprising a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BT~ES, TM7SF3, LOXLl, CASPR4 orAPOL3 nucleotide sequence, other nucleotide sequence referenced in Table B, or an encoded amino acid sequence referenced herein. Such directed molecules include, but are not limited to, a compound that binds to a PADI2, APOB, IL1RL2, ILIRLl, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLI, CASPR4 or APOL3 nucleotide sequence, or other nucleotide sequence referenced in Table B, or encoded amino acid sequence; a RNAi or siRNA molecule having a strand complementary or substantially complementary to a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLI, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B (e.g., hybridizes to a PADI2, APOB, ILLRL2, IL1RL1, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLl, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B
under conditions of high stringency); an antisensa nucleic acid complementary or substantially complementary to an RNA encoded by a PADI2, APOB, IL1RL2, ILIRLI, WASPIP, ADAMTS2, BYES, TM7SF3, LO~YLl, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B (e.g., hybridizes to a PADI2, APOB, ILLRL2, ILIRLI, WASPIP, ADAMTS2, BYES, TM7SF3, LOXL1, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B
under conditions of high stringency); a ribozyme that hybridizes to a PADI2, APOB, ILIRL2, IL1RL1 WASPIP, ADAMTS2, BYES, TM7SF3, LOXLI, C~4SPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B (e.g., hybridizes to a PADI2, APOB, IL1RL2, ILIRLl, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLI, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B under conditions of high stringency); a nucleic acid aptamer that specifically binds a polypeptide encoded by a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLl, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B; and an antibody that specifically binds to a polypeptide encoded by a PADI2, APOB, ILIRL2, ILIRL1, WASPIP, ADAlIsITS2, BYES, TM7SF3, LO~Zl, CASPR4 orAPOL3 nucleotide sequence or other nucleotide sequence referenced in Table B or binds to a nucleic acid having such a nucleotide sequence. In an embodiment, the antibody selectively binds to an epitope comprising an amino acid encoded by rs1367117, rs1041973 and rs398829. In specific embodiments, the osteoarthritis directed molecule interacts with a nucleic acid or polypeptide variant associated with osteoarthritis, such as variants referenced herein. In other embodiments, the osteoarthritis directed molecule interacts with a polypeptide involved in a signal pathway of a polypeptide encoded by a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BYES, TM7SF3, LOXL1, CASPR4 orAPOL3 nucleotide sequence or other nucleotide sequence referenced in Table B, or a nucleic acid comprising such a nucleotide sequence.

[0120] Compositions sometimes include an adjuvant known to stimulate an immune response, and in certain embodiments, an adjuvant that stimulates a T-cell lymphocyte response. Adjuvants are known, including but not limited to an aluminum adjuvant (e.g., aluminum hydroxide); a cytokine adjuvant or adjuvant that stimulates a cytokine response (e.g., interleukin (IL)-12 and/or gamma-interferon cytokines); a Freund-Type mineral oil adjuvant emulsion (e.g., Freund's complete or incomplete adjuvant); a synthetic lipoid compound; a copolymer adjuvant (e.g., TitreMax); a saponin~
Quil A; a liposome; an oil-in-water emulsion (e.g_, an emulsion stabilized by Tween 80 and pluronic polyoxyethlene/polyoxypropylene block copolymer (Syntex Adjuvant Formulation);
TitreMax;
detoxified endotoxin (MPL) and mycobacterial cell wall components (TDW, CWS) in 2% squalene (Ribi Adjuvant System)); a muramyl dipeptide; an immune-stimulating complex (ISCOM, e.g., an Ag-modified saponin/cholesterol micelle that forms stable cage-like structure);
an aqueous phase adjuvant that does not have a depot effect (e.g., Gerbu adj uvant); a carbohydrate polymer (e.g., AdjuPrime); L-tyrosine; a manide-oleate compound (e.g., Montanide); an ethylene-vinyl acetate copolymer (e.g., Elvax 40W1,2); or lipid A, for example. Such compositions are useful for generating an immune response against osteoarthritis directed molecule (e.g., an I~LA-binding subsequence within a polypeptide encoded by a PADI2, APOB, ILIRL2, ILIRLI, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLI, CASPR4 or APOL3 nucleotide sequence). In such methods, a peptide having an amino acid subsequence of a polypeptide encoded by a PAD12, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS~, BYES, TM7SF3, LOXLl, CASPR4 or APOL3 nucleotide sequence is delivered to a subject, where the subsequence binds to an HLA molecule and induces a CTL lymphocyte response. The peptide sometimes is delivered to the subject as an isolated peptide or as a minigerie in a plasmid that encodes the peptide. Methods for identifying HLA-binding subsequences in such polypeptides are known (see e.g., publication W002/20616 and PCT application US98/01373 for methods of identifying such sequences).

[0121] The cell may be in a group of cells cultured i~ vitro or in a tissue maintained in vitro or present in an animal in vivo (e.g., a rat, mouse, ape or human). In certain embodiments, a composition comprises a component from a cell such as a nuc leic acid molecule (e.g., genomic DNA), a protein mixture or isolated protein, for example. The aforementioned compositions have utility in diagnostic, prognostic and pharmacogenomic methods described previously and in therapeutics described hereafter.
Certain osteoarthritis directed molecules are described in greater detail below.
Compounds [0122] Compounds can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; peptoid libraries (libraries of molecules having the functionalities of peptides, but with a novel, non-peptide backbone which are resistant to enzymatic degradation but which nevertheless remain bioactive (see, e.g., Zuckermann et al., J. Med. Chem.37:
2678-85 (1994)); spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; "one-bead one-compound" library methods; and synthetic library methods using affinity chromatography selection. Biological library and peptoid library approaches are typically limited to peptide libraries, while the other approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compourids (Lam, Anticancer Drug Des.
12: 145, (1997)).
Examples of methods for synthesizing molecular libraries are described, for example, in DeWitt et al., Proc. Natl. Acad. Sci. U.S.A. 90: 6909 (1993); Erb et al., Proc. Natl. Acad.
Sci. USA 91: 11422 (1994);
Zuckermann et al., J. Med. Chem. 37: 2678 (1994); Cho et al., Science 261:
1303 (1993); Carrell et al., Angew. Chem. Int. Ed. Engl. 33: 2059 (1994); Carell et al., Angew. Chem. Int.
Ed. Engl. 33: 2061 (1994); and in Gallop et al., J. Med. Chem. 37: 1233 (1994).

[0123] Libraries of compounds may be presented in solution (e.g,, Houghten, Biotechniques 13:
412-421 (1992)), or on beads (Lam, Nature 354: 82-84 ( 1991)), chips (Fodor, Nature 364: 555-556 (1993)), bacteria or spores (Ladner, United States Patent No. 5,223,409), plasmids (Cull et al., Proc.
Natl. Acad. Sci. USA 89: 1865-1869 (1992)) or on phaga (Scott and Smith, Science 249: 386-390 (1990); Devlin, Science 249: 404-406 (1990); Cwirla et al., Proc. Natl. Acad.
Sci. 87: 6378-6382 (1990); Felici, J. Mol. Biol. 222: 301-310 (1991); Ladner supra.).

[0124] A compound sometimes alters expression and sometimes alters activity of a polypeptide target and may be a small molecule. Small molecules include, but are not limited to, peptides, peptidomimetics (e.g., peptoids), amino acids, amino acid analogs, polynucleotides, polynucleotide analogs, nucleotides, nucleotide analogs, organic or inorganic compounds (i.e., including heteroorganic and organometallic compounds) having a molecular weight less than about 10,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 5,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 1,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 500 grams per mole, and salts, esters, and other pharmaceutically acceptable forms of such compounds.
Antisense Nucleic Acid Molecules, Ribozymes, RNAi, siRNA and Modified Nucleic Acid Molecules [0125] An "antisense" nucleic acid refers to a nucle otide sequence complementary to a "sense"
nucleic acid encoding a polypeptide, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence. The antisense nucleic acid can be complementary to an entire coding strand, or to a portion thereof or a substantially identical sequence thereof. In another embodiment, the antisense nucleic acid molecule is antisense to a "noncoding region" of the coding strand of a nucleotide sequence (e,g,, 5' and 3' untranslated regions in SEQ ID
NO: 1-13 or a nucleotide sequence referenced in Table $).

[0126] An antisense nucleic acid can be designed such that it is complementary to the entire coding region of an mRNA encoded by a nucleotide sequence (e.g., SEQ ID NO: 1-13, SEQ
ID NO: 14-36 or a nucleotide sequence referenced in Table B), and often the antisense nucleic acid is an oligonucleotide antisense to only a portion of a coding or noncoding region of the mRNA. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of the mRNA, e.g., between the -10 and +10 regions of the target gene nucleotide sequence of interest. An antisense oligonucleotide can be, for example, about 7, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, or more nucleotides in length. The antisense nucleic acids, which include the ribozymes described hereafter, can be designed to target a PADI2, APOB, IL11zL2, ILIRLl, WASPIP, ADAMTS2, BT~ES, TM7SF3, LOXLI, CASPR~ orAPOL3 nucleotide sequence, often a variant associated with osteoarthritis, or a substantially identical sequence thereof. Among the variants, minor alleles and major alleles can be targeted, and those associated with a higher risk of osteoarthritis are often designed, tested, and administered to subjects.

[0127] An antisense nucleic acid can be constructed using chemical synthesis and enzymatic ligation reactions using standard procedures. For example, an antisense nucleic acid (e.g., an antisense oligonucleotide) can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used.
Antisense nucleic acid also can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).
[012] When utilized as therapeutics, antisense nucleic acids typically are administered to a subject (e.g., by direct injection at a tissue site) or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a polypeptide and thereby inhibit expression of the polypeptide, for example, by inhibiting transcription and/or translation.
Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then are administered systemically. For systemic administration, antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, for example, by linking antisense nucleic acid molecules to peptides or antibodies which bind to cell surface receptors or antigens. Antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. Sufficient intracellular concentrations of antisense molecules are achieved by incorporating a strong promoter, such as a pol II
or pol III promoter, in the vector construct.
[0129] Antisense nucleic acid molecules sometimes are alpha-anoneric nucleic acid molecules.
An alpha-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual beta-units, the strands run parallel to each other (Gaultier et al., Nucleic Acids. Res. 15: 6625-6641 (1987)). Antisense nucleic acid molecules can also comprise a 2'-0-methylribonucleotide (moue et al., Nucleic Acids Res. 15: 6131-6148 ( 1987)) or a chimeric RNA-DNA
analogue (moue et al., FEBS Lett. 215: 327-330 (1987)). Antisense nucleic acids sometimes are composed of DNA or PNA or any other nucleic acid derivatives described previously.
[0130] In another embodiment, an antisense nucleic acid is a ribozyme. A
ribozyme having specificity for a PADI2, APOB, ILIRL2, ILIRLI, WASPIP, ADAMTS2, BYES, TM7SF3, LOXL1, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B can include one or more sequences complementary to such a nucleotide sequence, and a sequence having a known catalytic region responsible for mRNA cleavage (see e.g., U.S. Pat. No_ 5,093,246 or Haselhoff and Gerlach, Nature 334: 585-591 (1988)). For example, a derivative of a Tetrahymena L-19 IVS RNA is sometimes utilized in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in a mRNA (see e.g., Cech et al. U.S .
Patent No. 4,987,071; and Cech et al. U.S. Patent No. 5,116,742). Also, target mRNA sequences can ba used to select a catalytic RNA
having a specific ribonuclease activity from a pool of RNA molecules Csee e.g., Bartel ~ Szostak, Science 261: 1411-1418 (1993)).

[0131] Osteoarthritis directed molecules include in certain embodiments nucleic acids that can form triple helix structures with a PADI2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BhES, TM7SF3, LOXL1, CASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B, or a substantially identical sequence thereof, especially one that includes a regulatory region that controls expression of a polypeptide. Gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of a nucleotide sequence referenced herein or a substantially identical sequence (e.g., promoter and/or enhancers) to form triple helical structures that prevent transcription of a gene in target cells (see e.g., Helene, Anticancer Drug Des. 6(6): 569-84 (1991); Helene et al., Ann. N.Y. Acad. Sci. 660: 27-36 (1992); and Maher, Bioassays 14(12): 807-15 (1992). Potential sequences that can be targeted for triple helix formation can be increased by creating a so-called "switchback" nucleic acid molecule. Switchback molecules are synthesized in an alternating 5'-3', 3'-5' manner, such that they base pair with first one strand of a dup lex and then the other, eliminating the necessity for a sizeable stretch of either purines or pyrimidines to be present on one strand of a duplex.
[0132] Osteoarthritis directed molecules include RNAi and siRNA rmcleic acids.
Gene expression may be inhibited by the introduction of double-stranded RNA (dsRNA), which induces potent and specific gene silencing, a phenomenon called RNA interference or RNAi_ See, e.g., Fire et al., US
Patent Number 6,506,559; Tuschl et al. PCT International Publication No . WO
01/75164; Kay et al.
PCT International Publication No. WO 03/010180A1; or Bosher JM, Labouesse, Nat Cell Biol 2000 Feb;2(2):E31-6. This process has been improved by decreasing the size of the double-stranded RNA to 20-24 base pairs (to create small-interfering RNAs or siRNAs) that "switched off' genes in mammalian cells without initiating an acute phase response, i.e., a host defense mechanism that often results in cell death (see, e.g., Caplen et al. Proc Natl Acad Sci U S A. 2001 Aug 14;98 17):9742-7 and Elbashir et al.
Methods 2002 Feb;26(2):199-213). There is increasing evidence of post-rtranscriptional gene silencing by RNA interference (RNAi) for inhibiting targeted expression in mammalian cells at the mRNA level, in human cells. There is additional evidence of effective methods for inhibiting the proliferation and migration of tumor cells in human patients, and for inhibiting metastatic cancer development (see, e.g., U.S. Patent Application No. US2001000993183; Caplen et al. Proc Natl Acad Sci U S A; and Abderrahmani et al. Mol Cell Biol 2001 Nov21(21):7256-67).
[0133] An "siRNA" or "RNAi" refers to a nucleic acid that forms a double stranded RNA and has the ability to reduce or inhibit expression of a gene or target gene when the siRNA is delivered to or expressed in the same cell as the gene or target gene. "siRNA" refers to short double-stranded RNA
formed by the complementary strands. Complementary portions of the siRNA that hybridize to form the double stranded molecule often have substantial or complete identity to the target molecule sequence. In one embodiment, an siRNA refers to a nucleic acid that has substantial or complete identity to a target gene and forms a double stranded siRNA.
[0134] When designing the siRNA molecules, the targeted region often is selected from a given DNA sequence beginning 50 to 100 nucleotides downstream of the start c odon.
See, e.g., Elbashir et al,. Methods 26:199-213 (2002). Initially, 5' or 3' UTRs and regions nearby the start codon were avoided assuming that UTR-binding proteins and/or translation initiation complexes may interfere with binding of the siRNP or RISC endonuclease complex. Sometimes regions of the target 23 nucleotides in length conforming to the sequence motif AA(N19)TT (N, an nucleotide), and regions with approximately 30% to 70% G/C-content (often about 50% G/C-content) often are selected. If no suitable sequences are found, the search often is extended using the motif NA(N21 ). The sequence of the sense siRNA sometimes corresponds to (N19) TT or N21 (position 3 to 23 of the 23-nt motif), respectively. In the latter case, the 3' end of the sense siRNA often is converted to TT. The rationale for this sequence conversion is to generate a symmetric duplex with respect to the sequence composition of the sense and antisense 3' overhangs. The antisense siRNA is synthesized as the complement to position 1 to 21 of the 23-nt motif. Because position 1 of the 23-nt motif is not recognized sequence-specifically by the antisense siRNA, the 3'-most nucleotide residue of the antisense siRNA can be chosen deliberately. However, the penultimate nucleotide of the antisense siRNA (complementary to position 2 of the 23-nt motif) often is complementary to the targeted sequence. For simplifying chemical synthesis, TT often is utilized. siRNAs corresponding to the target motif NAR(N17)YNN, where R is purine (A,G) and Y is pyrimidine (C,U), often are selected.
Respective 21 nuc leotide sense and antisense siRNAs often begin with a purine nucleotide and can also be expressed from pol III
expression vectors without a change in targeting site. Expression of RNAs from pol III promoters often is efficient when the first transcribed nucleotide is a purine.
[0135] The sequence of the siRNA can correspond to the full length target gene, or a subsequence thereof. Often, the siRNA is about 15 to about 50 nucleotides in length (e.g., each complementary sequence of the double stranded siRNA is 15-50 nucleotides in length, and the double stranded siRNA
is about 15-50 base pairs in length, sometimes about 20-30 nucleotides in length or about 20-25 nucleotides in length, e.g., 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. The siRNA
sometimes is about 21 nucleotides in length. Methods of using siRNA are well known in -the art, and specific siRNA molecules may be purchased from a number of companies including Dharmacon Research, Inc.
[0136] Antisense, ribozyme, RNAi and siRNA nucleic acids can be altered to form modified nucleic acid molecules. The nucleic acids can be altered at base moieties, sugar moieties or phosphate backbone moieties to improve stability, hybridization, or solubility of the molecule. For example, the deoxyribose phosphate backbone of nucleic acid molecules can be modified to generate peptide nucleic acids (see Hyrup et al., Bioorganic & Medicinal Chemistry 4 (1): 5-23 (1996)).
As used herein, the terms "peptide nucleic acid" or "PNA" refers to a nucleic acid mimic such as a DNA mirrzic, in which the deoxyribose phosphate baclcbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained. The neutral backbone of a PNA can allow for specific hybridization to DNA
and RNA under conditions of low ionic strength. Synthesis of PNA oligomers can be performed using standard solid phase peptide synthesis protocols as described, for example, in Hyrup et al. ~ (1996) supra and Perry-O'Keefe et al., Proc. Natl. Acad. Sci. 93: 14670-675 (1996).

[0137] PNA nucleic acids can be used in prognostic, diagnostic, and therapeutic applications. For example, PNAs can be used as antisense or antigene agents for sequence-specific modulation of gene expression by, for example, inducing transcription or translation arrest or inhibiting replication. PNA
nucleic acid molecules can also be used in the analysis of single base pair mutations in a gene, (e.g., by PNA-directed PCR clamping); as "artificial restriction enzymes" when used in combination with other enzymes, (e.g., Sl nucleases (Hyrup (1996) supra)); or as probes or primers for DNA sequencing or hybridization (Hyrup et al., (1996) supra; Perry-O'Keefe supra).
[0138] In other embodiments, oligonucleotides may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across cell membranes (see e.g., Letsinger et al., Proc. Natl. Acad. Sci. USA 86: 6553-6556 (1989); Lemaitre et al., Proc. Natl. Acad. Sci. USA 84: 648-652 (1987); PCT Publication No. W088/09810) or the blood-brain barrier (see, e.g., PCT Publication No. W089/10134). In addition, oligonucleotides can be modified with hybridization-triggered cleavage agents (See, e.g., Krol et al., Bio-Techniques 6: 958-976 [ 1988)) or intercalating agents. (See, e.g., Zon, Pharm. Res. 5: 539-549 (1988) ). To this end, the oligonucleotide may be conjugated to another molecule, (e.g., a peptide, hybridization triggered cross-linking agent, transport agent, or hybridization-triggered cleavage agent).
[0139] Also included herein are molecular beacon oligonucleotide primer and probe molecules having one or more regions complementary to a PAD12, APOB, ILIRL2, ILIRLl, WASPIP, AD~1MTS2, BT~ES, TM7SF3, LOXI,1, C'ASPR4 or APOL3 nucleotide sequence or other nucleotide sequence referenced in Table B, or a substantially identical sequence thereof, two complementary regions one having a fluorophore and one a quencher such that the molecular beacon is useful for quantifying the presence of the nucleic acid in a sample. Molecular beacon nucleic acids are described, for example, in Lizardi et al., U.S. Patent No. 5,854,033; Nazarenko et al., U.S. Patent No.
5,866,336, and Lival~ et al., U.S. Patent 5,876,930.
Antibodies [0140] The term "antibody" as used herein refers to an immunoglobulin molecule or immunologically active portion thereof, i.e., an antigen-binding portion.
Examples of immunologically active portions of immunoglobulin molecules include Flab) and F(ab')2 fragments which can be generated by treating the antibody with an enzyme such as pepsin. An antibody sometimes is a polyclonal, monoclonal, recombinant (e.g., a chimeric or humanized), fully human, non-human (e.g., murine), or a single chain antibody. An antibody may have effector function and can fix complement, and is sometimes coupled to a toxin or imaging agent.
[0141] A full-length polypeptide or antigenic peptide fragment encoded by a nucleotide sequence referenced herein can be used as an immunogen or can be used to identify antibodies made with other immunogens, e.g., cells, membrane preparations, and the like. An antigenic peptide often includes at least 8 amino acid residues of the amino acid sequences encoded by a nucleotide sequence referenced herein, or substantially identical sequence thereof, and encompasses an epitope. Antigenic peptides sometimes include 10 or more amino acids, 15 or more amino acids, 20 or more amino acids, or 30 or more amino acids. Hydrophilic and hydrophobic fragments of polypeptides sometimes are used as immunogens.
[0142] Epitopes encompassed by the antigenic peptide are regions located on the surface of the polypeptide (e.g., hydrophilic regions) as well as regions with high antigenicity. For example, an Emini surface probability analysis of the human polypeptide sequence can be used to indicate the regions that have a particularly high probability of being localized to the surface of the polypeptide and are thus likely to constitute surface residues useful for targeting antibody production. The antibody may bind an epitope on any domain or region on polypeptides described herein.
[0143] Also, chimeric, humanized, and completely human antibodies are useful for applications which include repeated administration to subjects. Chimeric and humanized monoclonal antibodies, comprising both human and non-human portions, can be made using standard recombinant DNA
techniques. Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods described in Robinson et al International Application No. PCT/US86/02269; Akira, et al European Patent Application 184,187; Taniguchi, M., European Patent Application 171,496; Morrison et al European Patent Application 173,494; Neuberge=r et al PCT International Publication No. WO 86/01533; Cabilly et al U.S. Patent No. 4,816,567; Cabilly et al European Patent Application 125,023; Better et al., Science 240: 1041-1043 (1988); Liu et al., Proc. Natl. Acad. Sci. USA 84: 3439-3443 (1987); Liu et al., J. Immunol. 139:
3521-3526 (1987); Sun et al., Proc. Natl. Acad. Sci. USA 84: 214-218 (1987); Nishimura et al., Canc.
Res. 47: 999-1005 (1987); Wood et al., Nature 314: 446-449 (1985); and Shaw et al., J. Natl.
Cancer Inst. 80: 1553-1559 (1988); Morrison, S. L., Science 229: 1202-1207 (1985); Oi et al., BioTechniques 4: 214 (1986);
Winter U.S. Patent 5,225,539; Jones et al., Nature 321: 552-525 (1986);
Verhoeyan et al., Science 239:
1534; and Beidler et al., J. Immunol. 141: 4053-4060 (1988).
[0144] Completely human antibodies are particularly desirable for therapeutic treatment of human patients. Such antibodies can be produced using transgenic mice that are incapable of expressing endogenous immunoglobulin heavy and light chains genes, but which can express human heavy and light chain genes. See, for example, Lonberg and Huszar, Int. Rev. Immunol.
13: 65-93 (1995); and U.S. PatentNos. 5,625,126; 5,633,425; 5,569,825; 5,661,016; and 5,545,806. In addition, companies such as Abgenix, Inc. (Fremont, CA) and Medarex, Inc. (Princeton, NJ), can be engaged to provide human antibodies directed against a selected antigen using technology similar to that described above.
Completely human antibodies that recognize a selected epitope also can be generated using a technique referred to as "guided selection." In this approach a selected non-human monoclonal antibody (e.g., a murine antibody) is used to guide the selection of a completely human antibody recognizing the same epitope. This technology is described for example by Jespers et al., Bio/Teclmology 12: 899-903 ( 1994).
[0145] An antibody can be a single chain antibody. A single chain antibody (scFV) can be engineered (see, e.g., Colcher et al., Ann. N Y Acad. Sci. 880: 263-80 (1999);
and Reiter, Clin. Cancer Res. 2: 245-52 (1996)). Single chain antibodies can be dimerized or multimerized to generate multivalent antibodies having specificities for different epitopes of the same target polypeptide.
[0146] Antibodies also may be selected or modified so that they exhibit reduced or no ability to bind an Fc receptor. For example, an antibody may be an isotype or subtype, fragment or other mutant, which does not support binding to an Fc receptor (e.g., it has a mutagenized or deleted Fc receptor binding region).
[0147] Also, an antibody (or fragment thereof) may be conjugated to a therapeutic moiety such as a cytotoxin, a therapeutic agent or a radioactive metal ion. A cytotoxin or cytotoxic agent includes any agent that is detrimental to cells. Examples include taxol, cytochalasin B, gramicidin D, ethidium bromide, emetine, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicin, doxorubicin, daunorubicin, dihydroxy anthracin dione, mitoxantrone, mithramycin, actinomycin D, 1 dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine, propranolol, and puromycin and analogs or homologs thereof. Therapeutic agents include, but are not limited to, antimetabolites (e.g., methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil decarbazine), alkylating agents (e.g., mechlorethamine, thiotepa chlorambucil, melphalan, carmustine (BCNU) and lomustine (CCNU), cyclophosphamide, busulfan, dibromomannitol, streptozotocin, mitomycin C, and cis-dichlorodiamine platinum (II) (DDP) cisplatin), anthracyclines (e.g., daunorubicin (formerly daunomycin) and doxorubicin), antibiotics (e.g., dactinomycin (formerly actinomycin), bleomycin, mithramycin, and anthramycin (AMC)), and anti-mitotic agents (e.g., vincristine and vinblastine).
[0148] Antibody conjugates can be used for modifying a given biological response. For example, the drug moiety may be a protein or polypeptide possessing a desired biological activity. Such proteins may include, for example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin; a polypeptide such as tumor necrosis factor, gamma-interferon, alpha-interferon, nerve growth factor, platelet derived growth factor, tissue plasminogen activator; or, biological response modifiers such as, for example, lymphokines, interleukin-1 ("IL,-1"), interleukin-2 ("II,-2"), interleukin-6 ("IL,-6"), granulocyte macrophage colony stimulating factor ("GM-CSF"), granulocyte colony stimulating factor ("G-CSF"), or other growth factors. Also, an antibody can be conjugated to a second antibody to form an antibody heteroconjugate as described by Segal in U.S. Patent No.
4,676,980, for example.
[0149] An antibody (e.g., monoclonal antibody) can be used to isolate target polypeptides by standard techniques, such as affinity chromatography or immunoprecipitation.
Moreover, an antibody can be used to detect a target polypeptide (e.g., in a cellular lysate or cell supernatant) in order to evaluate the abundance and pattern of expression of the polypeptide.
Antibodies can be used diagnostically to monitor polypeptide levels in tissue as part of a clinical testing procedure, e.g., to determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling (i.e., physically linking) the antibody to a detectable substance (i.e., antibody labeling). Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, (3-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescer>Et material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and.
aequorin, and examples of suitable radioactive material include l2sh 1311, sss or 3H. Also, an antibody can be utilized as a test molecule for determining whether it can treat osteoarthritis, and as a therapeutic for administration to a subject for treating osteoarthritis.
[0150] An antibody can be made by immunizing with a purified antigen, or a fragment thereof, e.g., a fragment described herein, a membrane associated antigen, tissues, e.g., crude tissue preparations, whole cells, preferably living cells, lysed cells, or cell fractions.
[0151] Included herein are antibodies which bind only a native polypeptide, only denatured or otherwise non-native polypeptide, or which bind both, as well as those having linear or conformational epitopes. Conformational epitopes sometimes can be identified by selecting antibodies that bind to native but not denatured polypeptide. Also featured are antibodies that specifically bind to a polypeptide variant associated with osteoarthritis.
Methods for Identifyin~ Candidate Therapeutics for Treating Osteoarthritis [0152] Current therapies for the treatment of osteoarthritis have limited efficacy, limited tolerability and significant mechanism-based side effects, and few of the available therapies adequately address underlying defects. Current therapeutic approaches were largely developed in the absenc a of defined molecular targets or even a solid understanding of disease pathogenesis. Therefore, provided are methods of identifying candidate therapeutics that target biochemical pathways related to the development of osteoarthritis.
[0153] Thus, featured herein are methods for identifying a candidate therapeutic for treating osteoarthritis. The methods comprise contacting a test molecule with a target molecule in a system. A
"target molecule" as used herein refers to a PADI2, APOB, IL1RL2, ILIRLl, WASPIP, ADAMTS~, BIdES, TM7SF3, LOXLI, CASPR4 or APOL3 nucleic acid or other nucleotide sequence referenced in Table B, a substantially identical nucleic acid thereof, or a fragment thereof, and an encoded polypeptide of the foregoing. The methods also comprise determining the presence or absence o~ an interaction between the test molecule and the target molecule, where the presence of an interaction between the test molecule and the nucleic acid or polypeptide identifies the test molecule as a candidate osteoarthritis therapeutic. The interaction between the test molecule and the target molecule may be quantified.
[0154] Test molecules and candidate therapeutics include, but are not limited to, compounds, antisense nucleic acids, siRNA molecules, ribozymes, polypeptides or proteins encoded by a PAI~I2, APOB, ILIRL2, ILIRLl, WASPIP, ADAMTS2, BhES, TM7SF3, LO~Ll, CASPR~ orAPOL3 nucleotide sequence or other nucleotide sequence referenced in Table B , or a substantially identical sequence or fragment thereof, and immunotherapeutics (e.g., antibodies and HLA-presented polypeptide fragments).

A test molecule or candidate therapeutic may act as a modulator of target molecule concentration or target molecule function in a system. A "modulator" may agonize (i.e., up-regulates) or antagonize (i.e., down-regulates) a target molecule concentration partially or completely in a system by affecting such cellular functions as DNA replication and/or DNA processing (e.g., DNA
methylation or DNA
repair), RNA transcription and/or RNA processing (e.g., removal of intronic sequences and/or translocation of spliced mRNA from the nucleus), polypeptide production (e.g., translation of the polypeptide from mRNA), and/or polypeptide post-translational modification (e.g., glycosylation, phosphorylation, and proteolysis of pro-polypeptides). A modulator may also agonize or antagonize a biological function of a target molecule partially or completely, where the function may include adopting a certain structural conformation, interacting with one or more binding partners, ligand binding, catalysis (e.g., phosphorylation, dephosphorylation, hydrolysis, methylation, and isomerization), and an effect upon a cellular event (e.g., effecting progression of osteoarthritis). Any modulator may be utilized, such as a peptidyl arginine deiminase modulator (e.g., PADI2 likely is a peptidyl arginine deiminase) described in WO-09851784 and WO0244360A2 or an apolipoprotein (e.g., APOB includes an apolipoprotein domain) modulatory compound (e.g., WO-2004017969, WO-03002533, US 6,369,075, WO-02098839, WO-02098871, WO-00177077, WO-00153260, WO-00105767), antibody (e.g., WO-9600903A1, US 6,309,844 and US 5,330,910) or antisense molecule (e.g., W003011887A2 and W003097662A1).
[0155] As used herein, the term "system" refers to a cell free in vitro environment and a cell-based environment such as a collection of cells, a tissue, an organ, or an organism.
A system is "contacted"
with a test molecule in a variety of manners, including adding molecules in solution and allowing them to interact with one another by diffusion, cell injection, and any administration routes in an animal. .As used herein, the term "interaction" refers to an effect of a test molecule on test molecule, where the effect sometimes is binding between the test molecule and the target molecule, and sometimes is an observable change in cells, tissue, or organism.
[0156] There are many standard methods for detecting the presence or absence of interaction between a test molecule and a target molecule. For example, titrametric, acidimetric, radiometric, NMR, monolayer, polarographic, spectrophotometric, fluorescent, and ESR assays probative of a target molecule interaction may be utilized. Examples of G protein-coupled receptor assays are known, fog example, and are described in WO-0242461 and WO-04013285.
[0157] ADAMTS2 activity and/or ADAMTS2 interactions can be detected and quantified using assays known in the art. For example, an immunoprecipitation assay or a kinase activity assay that employs a lcinase-inactivated MEI~ can be utilized. Kinase inactivated MEI~s are known in the art, such as a MEI~ that includes the mutation I~97M. In these assays, mammalian cells (e.g., COS or NIH-3T3) are transiently transfected with constructs expressing ADAMTS2, and in addition, the cells are co-transfected with oncogenic RAS or SRC or both. Oncogenic RAS or SRC activates ADAMTS2 kina_se activity. ADAMTS2 is immunoprecipitated from cell extracts using a monoclonal antibody (e.g., 9E 10) or a polyclonal antibody (e.g., from rabbit) specific for a unique peptide from ADAMTS2. ADAMI'S'2 is then resuspended in assay buffer containing GST-Mekl or GST-Mek2 and/or GST-ERI~2. In addition, [gamma 3zP] ATP can be added to detect and/or quantify phosphorylation activity. Samples are incubated for 5-30 minutes at 30°C, and then the reaction is terminated by addition of EDTA. The samples are centrifuged and the supernatant fractions are collected.
Phosphorylation activity is detected using one of two methods: (i) activity of GST-ERK2 kinase can be measured using MBP (myelin basic protein, a substrate for ERIC) as substrate, or (ii) following incubation of immunoprecipitated ADAMTS2 in reaction buffer containing GST-ERIC and [gamma 32P] ATP, transfer of labeled ATP to kinase-dead ERK can be quantified by a phosphor-imager or densitometer following PAGE
separation of polypeptide products (phosphorylated and non-phosphorylated forms). These types of assays are described in Weber et al., Oncogene 19: 169-176 (2000); Mason et al., EMBO J.
18: 2137-2148 (1999);
Marais et al., J. Biol. Chem. 272: 4378-4383 (1997); Marais et al., EMBO J.
14: 3136-3145 (1995).
[0158] As noted above, ADAMTS2 includes a domain having metalloprotease activity, and modulators of such activity are known. Examples of such modulators are set forth in W003063~62A2;
WO-09937625; WO-09918076; WO-09838163; WO-09837877; W09947550A1; W00177092A1;
WO0040577A1; W09942436A1; W09838163A1; W09837877A1; W004014379A1;
W003106381A2; WO03014098A1; W003014092A1 and W002096426A1.
[0159] Test molecule/target molecule interactions can be detected and/or quantified using assays known in the art. For example, an interaction can be determined by labeling the test molecule and/or the target molecule, where the label is covalently or non-covalently attached to the test molecule or target molecule. The label is sometimes a radioactive molecule such as l2sh 1311, ssS or 3H, which can be detected by direct counting of radioemission or by scintillation counting.
Also, enzymatic labels such as horseradish peroxidase, alkaline phosphatase, or luciferase may be utilized where the enzymatic label can be detected by determining conversion of an appropriate substrate to product. In addition, presence or absence of an interaction can be determined without labeling. For example, a microphysiometer (e.g., Cytosensor) is an analytical instrument that measures the rate at which a cell acidifies its environment using a light-addressable potentiometric sensor (LAPS). Changes in this acidificati on rate can be used as an indication of an interaction between a test molecule and target molecule (McConnell, H. M. et al., Science 257: 1906-1912 (1992)).
[0160] In cell-based systems, cells typically include a PADI2, APOB, ILIRL2, ILIRLl, T~YAS'PIP, ADAMTS~, BYES, TM7SF3, LOXL1, CASPR4 or APOL3 nucleic acid or other nucleotide sequence referenced in Table B, an encoded polypeptide, or substantially identical nucleic acid or polypeptide thereof, and are often of mammalian origin, although the cell can be of any origin. Whole cells, cell homogenates, and cell fractions (e.g., cell membrane fractions) can be subjected to analysis. Where interactions between a test molecule with a target polypeptide are monitored, soluble and/or membrane bound forms of the polypeptide may be utilized. Where membrane-bound forms of the polypeptide are used, it may be desirable to utilize a solubilizing agent. Examples of such solubilizing agents include non-ionic detergents such as n-octylglucoside, n-dodecylglucoside, n-dodecylmaltoside, octanoyl-N-methylglucamide, decanoyl-N-methylglucamide, Triton~ X-100, Triton~ X-114, Thesit~, Isotridecypoly(ethylene glycol ether)n, 3-[(3-cholamidopropyl)dimethylamminio]-1-propane sulfonate (CHAPS), 3-[(3-cholamidopropyl)dimethylamminio]-2-hydroxy-1-propane sulfonate (CHAPSO), or N-dodecyl-N,N-dimethyl-3-ammonio-1-propane sulfonate.
[0161] An interaction between a test molecule and target molecule also can be detected by monitoring fluorescence energy transfer (FET) (see, e.g., Lakowicz et al., U.S. Patent No. 5,631,169;
Stavrianopoulos et al. U.S. Patent No. 4,868,103). A fluorophore label on a first, "donor" molecule is selected such that its emitted fluorescent energy will be absorbed by a fluorescent label on a second, "acceptor" molecule, which in turn is able to fluoresce due to the absorbed energy. Alternately, the "donor" polypeptide molecule may simply utilize the natural fluorescent energy of tryptophan residues.
Labels are chosen that emit different wavelengths of light, such that the "acceptor" molecule label may be differentiated from that of the "donor". Since the efficiency of energy transfer between the labels is related to the distance separating the molecules, the spatial relationship between the molecules can be assessed. In a situation in which binding occurs between the molecules, the fluorescent emission of the "acceptor" molecule label in the assay.should be maximal. An FET binding event can be conveniently measured through standard fluorometric detection means well known in the art (e.g., using a fluorimeter).
[0162] In another embodiment, determining the presence or absence of an interaction between a test molecule and a target molecule can be effected by monitoring surface plasmon resonance (see, e.g., Sjolander & Urbaniczk, Anal. Clzem. 63: 2338-2345 (1991) and Szabo et al., Curr. Opin. Struet. Biol. S:
699-705 (1995)). "Surface plasmon resonance" or "biomolecular interaction analysis (BIA)" can be utilized to detect biospecific interactions in real time, without labeling any of the interactants (e.g., BIAcore). Changes in the mass at the binding surface (indicative of a binding event) result in alterations of the refractive index of light near the surface (the optical phenomenon of surface plasmon resonance (SPR)), resulting in a detectable signal which can be used as an indication of real-time reactions between biological molecules.
[0163] In another embodiment, the target molecule or test molecules are anchored to a solid phase, facilitating the detection of target molecule/test molecule complexes and separation of the complexes from free, uncomplexed molecules. The target molecule or test molecule is immobilized to the solid support. In an embodiment, the target molecule is anchored to a solid surface, and the test molecule, which is not anchored, can be labeled, either directly or indirectly, with detectable labels discussed herein.
[0164] It may be desirable to immobilize a target molecule, an anti-target molecule antibody, and/or test molecules to facilitate separation of target molecule/test molecule complexes from uncomplexed forms, as well as to accommodate automation of the assay. The attachment between a test molecule and/or target molecule and the solid support may be covalent or non-covalent (see, e.g., U.S.
Patent No. 6,022,688 for non-covalent attachments). The solid support may be one or more surfaces of the system, such as one or more surfaces in each well of a microtiter plate, a surface of a silicon wafer, a surface of a bead (see, e.g., Lam, Nature 354: 82-84- (1991)) that is optionally linked to another solid support, or a channel in a microfluidic device, for example. Types of solid supports, linker molecules for covalent and non-covalent attachments to solid supports, and methods for immobilizing nucleic acids and other molecules to solid supports are well known (see, e.g., U.S.
Patant Nos. 6,261,776;
5,900,481; 6,133,436; and 6,022,688; and WIPO publication WO 01/18234).
[0165] In an embodiment, target molecule may be immobilized to surfaces via biotin and streptavidin. For example, biotinylated target polypeptide can be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, IL), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical). In another embodiment, a target polypeptide can be prepared as a fusion polypeptide. For example, glutathione-S-transferaseltarget polypeptide fusion can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, MO) or glutathione derivitized microtiter plates, which are then combined with a test molecule under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the beads or microtiter plate wells are yvashed to remove any unbound components, or the matrix is immobilized in the case of beads, and complex formation is determined directly or indirectly as described above. Alternatively, the complexes can be dissociated from the matrix, and the level of target molecule binding or activity is determined using standard techniques.
[0166] In an embodiment, the non-immobilized component is added to the coated surface containing the anchored component. After the reaction is complete, unreacted components are removed (e.g., by washing) under conditions such that a significant percentage of complexes formed will remain immobilized to the solid surface. The detection of complexes anchored on the solid surface can be accomplished in a number of manners. Where the previously non-immobilized component is pre-labeled, the detection of label immobilized on the surface indicates that complexes were formed. Where the previously non-immobilized component is not pre-labeled, an indirect label can be used to detect complexes anchored on the surface, e.g., by adding a labeled antibody specific for the immobilized component, where the antibody, in turn, can be directly labeled or indirectly labeled with, e.g., a labeled anti-Ig antibody.
[0167] In another embodiment, an assay is performed utilizing antibodies that specifically bind target molecule or test molecule but do not interfere with binding of the target molecule to the test molecule. Such antibodies can be derivitized to a solid support, and unbound -target molecule may be immobilized by antibody conjugation. Methods for detecting such complexes ~ in addition to those described above for the GST-immobilized complexes, include immunodetection of complexes using antibodies reactive with the target molecule, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the target molecule.
[0168] Cell free assays also can be conducted in a liquid phase. In such an assay, reaction products are separated from unreacted components, by any of a number of standard techniques, including but not limited to: differential centrifugation (see, e.g., Rivas, G., and Minton, Ti~es~ds Biochern Sci Aug;18(8):
284-7 (1993)); chromatography (gel filtration chromatography, ion-exchange chromatography);

electrophoresis (see, e.g., Ausubel et al., eds. Current Protocols in Molecular Biology , J. Wil ey: New York (1999)); and immunoprecipitation (see, e.g., Ausubel et al., eds., supra). Media and chromatographic techniques are known to one skilled in the art (see, e.g., Heegaard, JMoI. Recognit.
Winter; 11 (1-6): 141-8 (1998); Hage & Tweed, J. Clzromatog~. B Biomed. Sci.
Appl. Oct 10; 699 (1-2):
499-525 (1997)). Further, fluorescence energy transfer may also be conveniently utilized, as described herein, to detect binding without further purification of the complex from solution.
[0169] In another embodiment, modulators of target molecule expression are identified. For example, a cell or cell free mixture is contacted with a candidate compound and the expression of target mRNA or target polypeptide is evaluated relative to the level of expression of target mRNA or target polypeptide in the absence of the cmdidate compound. When expression of target mRNA or target polypeptide is greater in the presence of the candidate compound than in its absence, the candidate compound is identified as an agonist of target mRNA or target polypeptide expression. Alternatively, when expression of target mRNA or target polypeptide is less (e.g., less with statistical significance) in the presence of the candidate compound than in its absence, the candidate compound is identified as an antagonist or inhibitor of target mRNA or target polypeptide expression. The level of target rnRNA or target polypeptide expression can be determined by methods described herein.
[0170] In another embodiment, binding partners that interact with a target molecule are detected.
The target molecules can interact with one or more cellular or extracellular macromolecules, such as polypeptides in vivo, and these interacting molecules are referred to herein as "binding partne:rs."
Binding partners can agonize or antagonize target molecule biological activity. Also, test mo lecules that agonize or antagonize interactions between target molecules and binding partners can be useful as therapeutic molecules as they can up-regulate or down-regulated target molecule activity in vzvo and thereby treat osteoarthritis.
[0171] Binding partners of target molecules can be identified by methods known in the art. For example, binding partners may be identified by lysing cells and analyzing cell lysates by elec-trophoretic techniques. Alternatively, a two-hybrid assay or three-hybrid assay can be utilized (see, e.g., U.S.
Patent No. 5,283,317; Zervos et al., Cell 72:223-232 (1993); Madura et al., J.
Biol. ChenZ. 2~SS: 12046-12054 (1993); Bartel et al., BioteclZniques 14: 920-924 (1993); Iwabuchi et al., Oncogene ~: 1693-1696 (1993); and Brent W094/10300). A two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains. The assay often utilizes two different DNA constructs. In one construct, a PAD12, APOB, ILIRL2, ILIRLI, WASPIP, ADAMTS2, BVES, TM7SF3, LOXLI, CASPR4 or APOL3 nucleic acid or other nucleic acid referenced in Table B (sometimes referred to as the "bait") is fused to a gene encoding the DNA binding domain of a known transcription factor (e.g., GAL-4). In another construct, a DNA
sequence from a library of DNA sequences that encodes a potential binding partner (sometimes referred to as the "prey") is fused to a gene that encodes an activation domain of the known transcription factor.
Sometimes, a PADI2, APOB, ILIRL2, IL1RL1, WASPIP, ADAMTS2, BVES, TM7SF3, LOXLl, CASPR4 orAPOL3 nucleic acid or other nucleic acid referenced in Table B can be fused to the activation domain. If the "bait" and the "prey" molecules interact in vivo, the DNA-binding and activation domains of the transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g., LacZ) which is operably linked to a transcriptional regulatory site responsive to the transcription factor.
Expression of the reporter gene can be detected and cell colonies containing the functional traps cription factor can be isolated and used to identify the potential binding partner.
[0172] In an embodiment for identifying test molecules that antagonize or agonize complex formation between target molecules and binding partners, a reaction mixture containing the target molecule and the binding partner is prepared, under conditions and for a time sufficient to allow complex formation. The reaction mixture often is provided in the presence or absence of the test molecule. The test molecule can be included initially in the reaction mixture, or can be added a-t a time subsequent to the addition of the target molecule and its binding partner.
Control reaction mixtures are incubated without the test molecule or with a placebo. Formation of any complexes between the target molecule and the binding partner then is detected. Decreased formation of a complex in the reaction mixture containing test molecule as compared to in a control reaction mixture indicates that the molecule antagonizes target molecule/binding partner complex formation.
Alternatively, increased formation of a complex in the reaction mixture containing test molecule as compared to in a control reaction mixture indicates that the molecule agonizes target molecule/binding partner complex formation. In another embodiment, complex formation of target molecule/binding partner can be compared to complex formation of mutant target molecule/binding partner (e.g., amino acid modifications in a target polypeptide). Such a comparison can be important in those cases where it is desirable to identify test molecules that modulate interactions of mutant but not non-mutated target gene products.
[0173] The assays can be conducted in a heterogeneous or homogeneous format.
In heterogeneous assays, target molecule and/or the binding partner are immobilized to a solid phase, and complexes are detected on the solid phase at the end of the reaction. In homogeneous assays, the entire reaction is carried out in a liquid phase. In either approach, the order of addition of reactants can be varied to obtain different information about the molecules being tested. For example, test compounds that agonize target molecule/binding partner interactions can be identified by conducting the reaction in the presence of the test molecule in a competition format. Alternatively, test molecules that agonize preformed complexes, e.g., molecules with higher binding constants that displace one of the components from the complex, can be tested by adding the test compound to the reaction mixture after complexes have been formed.
[0174] In a heterogeneous assay embodiment, the target molecule or the binding partner is anchored onto a solid surface (e.g., a microtiter plate), while the non-anchored species is labeled, either directly or indirectly. The anchored molecule can be immobilized by non-covalent or covalent attachments. Alternatively, an immobilized antibody specific for the molecule to be anchored can be used to anchor the molecule to the solid surface. The partner of the immobilized species is exposed to the coated surface with or without the test molecule. After the reaction is complete, unreacted components are removed (e.g., by washing) such that a significant portion of any complexes formed will remain immobilized on the solid surface. Where the non-immobilized species is pre-labeled, the detection of label immobilized on the surface is indicative of complex. Where the non-immobilized species is not pre-labeled, an indirect label can be used to detect complexes anchored to the surface;
e.g., by using a labeled antibody specific for the initially non-immobilized species. Depending upon the order of addition of reaction components, test compounds that inhibit complex formation or that disrupt preformed complexes can be detected.
[0175] In another embodiment, the reaction can be conducted in a liquid phase in the presence or absence of test molecule, where the reaction products are separated from unreacted components, and the complexes are detected (e.g., using an immobilized antibody specific for one of the binding components to anchor any complexes formed in solution, and a labeled antibody specific for the other partner to detect anchored complexes). Again, depending upon the order of addition of reactants to the liquid phase, test compounds that inhibit complex or that disrupt preformed complexes can be identified.
[0176] In an alternate embodiment, a homogeneous assay can be utilized. For example, a preformed complex of the target gene product and the interactive cellular or extracellular binding partner product is prepared. One or both of the target molecule or binding partner is labeled, and the signal generated by the labels) is quenched upon complex formation (e.g., U.S.
Patent No. 4,109,496 that utilizes this approach for immunoassays). Addition of a test molecule that competes with and displaces one of the species from the preformed complex will result in the generation of a. signal above background. In this way, test substances that disrupt target molecule/binding partner complexes can be identified.
[0177] Candidate therapeutics for treating osteoarthritis are identified from a group of test molecules that interact with a target molecule. Test molecules are normally ranked according to the degree with which they modulate (e.g., agonize or antagonize) a function associated with the target molecule (e.g., DNA replication and/or processing, RNA transcription and/or processing, polypeptide production and/or processing, and/or biological function/activity), and then top ranking modulators are selected. Also, pharmacogenomic information described herein can determine the rank of a modulator.
The top 10% of ranked test molecules often are selected for further testing as candidate therapeutics, and sometimes the top 15%, 20%, or 25% of ranked test molecules are selected for further testing as candidate therapeutics. Candidate therapeutics typically are formulated for administration to a subject.
Therapeutic Formulations [0178] Formulations and pharmaceutical compositions typically include in combina_-tion with a pharmaceutically acceptable carrier one or more target molecule modulators.
The modulator often is a test molecule identified as having an interaction with a target molecule by a screening method described above. The modulator may be a compound, an antisense nucleic acid, a ribozyme, an antibody, or a binding partner. Also, formulations may comprise a target polypeptide or fragment thereof in combination with a pharmaceutically acceptable carrier, where the polypeptide or fragment sometimes has an APOL3 biological activity (e.g., apolipoprotein activity), and sometimes includes all or part of an apolipoprotein domain.
[0179] Formulations or pharmaceutical compositions typically include in combination with a pharmaceutically acceptable carrier, a compound, an antisense nucleic acid, a ribozyme, an antibody, a binding partner that interacts with an ADAMTS2 polypeptide, a ADAMTS2 nucleic acid, or a fragment thereof. The formulated molecule may be one that is identified by a screening method described above.
Also, formulations may comprise a ADAMTS2 polypeptide or fragment thereof, where the ADAMTS2 polypeptide contains an isoleucine at position 245 of SEQ ID NO: 44, and a pharmaceutically acceptable carrier. Also, formulations may comprise an active ADAMTS2 polypeptide or fragment thereof, where ADAMTS2 polypeptide fragments having activity are selected from amino acids 252-1211, 253-1211, 254-1211, 255-1211, 256-1211, 257-1211, 258-1211, 259-1211 or 260-1211 of SEQ
ID NO: 44, where it is understood that the active form of ADAMTS2 does not contain the propeptide domain. As used herein, the term "pharmaceutically acceptable carrier"
includes solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. Supplementary active compounds can also be incorporated into the compositions.
[0180] As used herein, the term "pharmaceutically acceptable carrier" includes solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the lilee, compatible with pharmaceutical administration. Supplementary active compounds can also be incorporated into the compositions. Pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.
[0181] A pharmaceutical composition typically is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerin, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfate;
chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose.
pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
[0182] Oral compositions generally include an inert diluent or an edible carrier. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules, e.g., gelatin capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouthwash. Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.
l[0183] Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, NJ) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
[0184] Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
[0185] For administration by inhalation, the compounds are delivered in the form of an aerosol spray from pressured container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.
[0186] Systemic administration can also be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art. Molecules can also be prepared in the form of suppositories (e.g., with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.
[0187] In one embodiment, active molecules are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. Materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers.
These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Patent No. 4,522,811.
[0188] It is advantageous to formulate oral or parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
[0189] Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LDso (the dose lethal to 50% of the population) and the EDso (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LDso/EDso. Molecules which exhibit high therapeutic indices are preferred.
While molecules that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.
[0190] The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such molecules lies preferably within a range of circulating concentrations that include the EDso with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
For any molecules used in the methods described herein, the therapeutically effective dose can be estimated initially from cell culture assays. A dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the ICSO (i.e., the concentration of the test compound which achieves a half maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans.
Levels in plasma may be measured, for example, by high performance liquid chromatography.
[0191] As defined herein, a therapeutically effective amount of protein or polypeptide (i.e., an effective dosage) ranges from about 0.001 to 30 mg/kg body weight, sometimes about 0.01 to 25 mg/kg body weight, often about 0.1 to 20 mg/kg body weight, and more often about 1 to 10 mg/kg, 2 to 9 mg/kg, 3 to 8 mg/kg, 4 to 7 mg/kg, or 5 to 6 mg/kg body weight. The protein or polypeptide can be administered one time per week for between about 1 to 10 weeks, sometimes between 2 to 8 weeks, often between about 3 to 7 weeks, and more often for about 4, 5, or 6 weeks.
The skilled artisan will appreciate that certain factors may influence the dosage and timing required to effectively treat a subject, including but not limited to the severity of the disease or disorder, previous treatments, the general health and/or age of the subject, and other diseases present.
Moreover, treatment of a subject with a therapeutically effective amount of a protein, polypeptide, or antibody can include a single treatment or, preferably, can include a series of treatments.
[0192] With regard to polypeptide formulations, featured herein is a method for treating osteoarthritis in a subject, which comprises contacting one or more cells in the subject with a first polypeptide, where the subject comprises a second polypeptide having one or more polymorphic variations associated with cancer, and where the first polypeptide comprises fewer polymorphic variations associated with cancer than the second polypeptide. The first and second polypeptides are encoded by a nucleic acid which comprises a nucleotide sequence in SEQ ID NO:
1-13 or referenced in Table B; a nucleotide sequence which encodes a polypeptide consisting of an amino acid sequence encoded by a nucleotide sequence referenced in SEQ ID NO: 1-13 or referenced in Table B; a nucleotide sequence which encodes a polypeptide that is 90% or more identical to an amino acid sequence encoded by a nucleotide sequence of SEQ ID NO: 1-13 or referenced in Table B and a nucleotide sequence 90% or more identical to a nucleotide sequence in SEQ ID
NO: 1-13 or referenced in Table B. The subject often is a human.
[0193] For antibodies, a dosage of 0.1 mg/kg of body weight (generally 10 mg/kg to 20 mg/kg) is often utilized. If the antibody is to act in the brain, a dosage of 50 mg/kg to 100 mg/kg is often appropriate. Generally, partially human antibodies and fully human antibodies have a longer half life within the human body than other antibodies. Accordingly, lower dosages and less frequent administration is often possible. Modifications such as lipidation can be used to stabilize antibodies and to enhance uptake and tissue penetration (e.g., into the brain). A method for lipidation of antibodies is described by Cruikshank et al., J. Acquired Inamune Defieiency Syndromes and Human Retnovinology 14:193 (1997).
[0194] Antibody conjugates can be used for modifying a given biological response, the drug moiety is not to be construed as limited to classical chemical therapeutic agents. For example, the drug moiety may be a protein or polypeptide possessing a desired biological activity. Such proteins may include, for example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin; a polypeptide such as tumor necrosis factor, alpha-interferon, beta-interferon, nerve growth factor, platelet derived growth factor, tissue plasminogen activator; or, biological response modifiers such as, for example, lymphokines, interleukin-1 ("IL-1"), interleukin-2 ("IL-2"), interleukin-6 ("IL-6"), granulocyte macrophage colony stimulating factor ("GM-CSF"), granulocyte colony stimulating factor ("G-CSF"), or other growth factors. Alternatively, an antibody can be conjugated to a second antibody to form an antibody heteroconjugate as described by Segal in U.S. Patent No.
4,676,980.

[0195] For compounds, exemplary doses include milligram or microgram amounts of the compound per kilogram of subject or sample weight, for example, about 1 microgram per kilogram to about 500 milligrams per kilogram, about 100 micrograms per kilogram to about 5 milligrams per kilogram, or about 1 microgram per kilogram to about 50 micrograms per kilogram. It is understood that appropriate doses of a small molecule depend upon the potency of the small molecule with respect to the expression or activity to be modulated. When one or more of these small molecules is to be administered to an animal (e.g., a human) in order to modulate expression or activity of a polypeptide or nucleic acid described herein, a physician, veterinarian, or researcher may, for example, prescribe a relatively low dose at first, subsequently increasing the dose until an appropriate response is obtauied.
In addition, it is understood that the specific dose level for any particular animal subject will depend upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, gender, and diet of the subject, the time of administration, the route of administration, the rate of excretion, any drug combination, and the degree of expression or activity to be modulated.
[0196] With regard to nucleic acid formulations, gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (see, e.g., U.S.
Patent 5,328,470) or by stereotactic injection (see e.g., Chen et al., (1994) Pr~oc. Natl. Acad. Sci.
USA 91:3054-3057).
Pharmaceutical preparations of gene therapy vectors can include a gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded.
Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells (e.g., retroviral vectors) the pharmaceutical preparation can include one or more cells which produce the gene delivery system. Examples of gene delivery vectors are described herein.
Therapeutic Methods [0197] A therapeutic formulation described above can be administered to a subject in need of a therapeutic for inducing a desired biological response. Therapeutic formulations can be administered by any of the paths described herein. With regard to both prophylactic and therapeutic methods of treatment, such treatments may be specifically tailored or modified, based on knowledge obtained from pharmacogenomic analyses described herein.
[0198] As used herein, the term "treatment" is defined as the application or administration of a therapeutic formulation to a subject, or application or administration of a therapeutic agent to an isolated tissue or cell line from a subject with the purpose to cure, heal, alleviate, relieve, alter, remedy, ameliorate, improve or affect osteoarthritis, symptoms of osteoarthritis or a predisposition towards osteoarthritis. A therapeutic formulation includes, but is not limited to, small molecules, peptides, antibodies, ribozymes and antisense oligonucleotides. Administration of a therapeutic formulation can occur prior to the manifestation of symptoms characteristic of osteoarthritis, such that osteoarthritis is prevented or delayed in its progression. The appropriate therapeutic composition can be determined based on screening assays described herein.

[0199] As discussed, successful treatment of osteoarthritis can be brought about by techniques that serve to agonize target molecule expression or function, or alternatively, antagonize target molecule expression or function. These techniques include administration of modulators that include, but are not limited to, small organic or inorganic molecules; antibodies (including, for example, polyclonal, monoclonal, humanized, anti-idiotypic, chimerie or single chain antibodies, and Fab, F(ab')Z and Fab expression library fragments, scFV molecules, and epitope-binding fragments thereof); and peptides, phosphopeptides, or polypeptides.
[0200] Further, antisense and ribozyme molecules that inhibit expression of the target gene can also be used to reduce the level of target gene expression, thus effectively reducing the level of target gene activity. Still further, triple helix molecules can be utilized in reducing the level of target gene activity. Antisense, ribozyme and triple helix molecules are discussed above.
It is possible that the use of antisense, ribozyme, and/or triple helix molecules to reduce or inhibit mutant gene expression can also reduce or inhibit the transcription (triple helix) and/or translation (antisense, ribozyme) of mRNA
produced by normal target gene alleles, such that the concentration of normal target gene product present can be lower than is necessary for a normal phenotype. In such cases, nucleic acid molecules that encode and express target gene polypeptides exhibiting normal target gene activity can be introduced into cells via gene therapy method. Alternatively, in instances in that the target gene encodes an extracellular polypeptide, it can be preferable to eo-administer normal target gene polypeptide into the cell or tissue in order to maintain the requisite level of cellular or tissue target gene activity.
[0201] Another method by which nucleic acid molecules may be utilized in treating or preventing osteoarthritis is use of aptamer molecules specific for target molecules.
Aptamers are nucleic acid molecules having a tertiary structure which permits them to specifically bind to ligands (see, e.g., Osborne, et al., Cur. Opin. Chem. Biol. l (1): 5-9 (1997); and Patel, D. J., Curs. Opitz. Chem. Biol.
Jun; l (1): 32-46 (1997)).
[0202] Yet another method of utilizing nucleic acid molecules for osteoarthritis treatment is gene therapy, which can also be referred to as allele therapy. Provided herein is a gene therapy method for treating osteoarthritis in a subject, which comprises contacting one or more cells in the subject or from the subject with a nucleic acid having a first nucleotide sequence (e.g., the first nucleotide sequence is identical to or substantially identical to a nucleotide sequence of SEQ ID NO:
1-13 or other nucleotide sequence referenced in Table B). Genomic DNA in the subject comprises a second nucleotide sequence having one or more polymorphic variations associated with osteoarthritis (e.g., the second nucleotide sequence is identical to or substantially identical to a nucleotide sequence of SEQ ID NO: 1-13 or other nucleotide sequence referenced in Table B). The first and second nucleotide sequences typically are substantially identical to one another, and the first nucleotide sequence comprises fewer polymorphic variations associated with osteoarthritis than the second nucleotide sequence.
The first nucleotide sequence may comprise a gene sequence that encodes a full-length polypeptide or a fragment thereof.
The subject is often a human. Allele therapy methods often are utilized in conjunction with a method of first determining whether a subject has genomic DNA that includes polymorphic variants associated with osteoarthritis.
[0203] In a certain embodiment, the method often comprises supplementing arthritis-associated ADAMTS2 polypeptide with a non-arthritis-associated ADAMTS2 polypeptide or fragment thereof, where the non-arthritis-associated form ofADAMTS2 contains an isoleucine at position 245 of SEQ ID
NO: 44 having enzymatic activity. The arthritis-associated ADAMTS2 polypeptide sometimes contains a valine at position 245 of SEQ ID NO: 44 having an altered enzymatic activity varying from the non-arthritis-associated polypeptide.
[0204] In an embodiment, provided is a method of increasing the synthesis of procollagen II
comprising providing or administering to individuals in need of increasing levels of type II collagen the pharmaceutical or physiologically acceptable composition comprising active human ADAMTS2 protein or fragment thereof, where ADAMTS2 polypeptide fragments having activity are selected from amino acids 252-1211, 253-1211, 254-1211, 255-1211, 256-1211, 257-1211, 258-1211, 259-1211 or 260-1211 of SEQ B7 NO: 44, where it is understood that the active form ofADAMTS2 does not contain the propeptide domain.
[0205] In another embodiment, provided herein is a method of increasing the synthesis of procollagen II comprising providing or administering to individuals in need of increasing levels of type II collagen the pharmaceutical or physiologically acceptable composition comprising an enzyme or molecule capable of cleaving ADAMTS2 propeptide, e.g., a furin-type endopeptidase or N-ethylmaleimide described herein [0206] In another allele therapy embodiment, provided herein is a method which comprises contacting one or more cells in the subject or from the subject with a polypeptide encoded by a nucleic acid having a first nucleotide sequence (e.g., the first nucleotide sequence is identical to or substantially identical to the nucleotide sequence of SEQ ID NO: 1-13 or other nucleotide sequence referenced in Table B). Genomic DNA in the subject comprises a second nucleotide sequence having one or more polymorphic variations associated with osteoarthritis (e.g., the second nucleotide sequence is identical to or substantially identical to a nucleotide sequence of SEQ ID NO: 1-13 or other nucleotide sequence referenced in Table B). The first and second nucleotide sequences typically are substantially identical to one another, and the first nucleotide sequence comprises fewer polymorphic variations associated with osteoarthritis than the second nucleotide sequence. The first nucleotide sequence may comprise a gene sequence that encodes a full-length polypeptide or a fragment thereof.
The subject is often a human.
[0207] k'or antibody-based therapies, antibodies can be generated that are both specific for target molecules and that reduce target molecule activity. Such antibodies may be administered in instances where antagonizing a target molecule function is appropriate for the treatment of osteoarthritis.
[0208] In circumstances where stimulating antibody production in an animal or a human subject by injection with a target molecule is harmful to the subject, it is possible to generate an immune response against the target molecule by use of anti-idiotypic antibodies (see, e.g., Herlyn, Ann. Med.; 31 (1): 66-78 (1999); and Bhattacharya-Chatterjee & Foon, Cancer Treat. Res.; 94.' S1-68 (1998)). Introducing an anti-idiotypic antibody to a mammal or human subject often stimulates production of anti-anti-idiotypic antibodies, which typically are specific to the target molecule. Vaccines directed to osteoarthritis also may be generated in this fashion.
[0209] In instances where the target molecule is intracellular and whole antibodies are used, internalizing antibodies may be preferred. Lipofectin or liposomes can be used to deliver the antibody or a fragment of the Fab region that binds to the target antigen into cells.
Where fragments of the antibody are used, the smallest inhibitory fragment that binds to the target antigen is preferred. For example, peptides having an amino acid sequence corresponding to the Fv region of the antibody can be used. Alternatively, single chain neutralizing antibodies that bind to intracellular target antigens can also be administered. Such single chain antibodies can be administered, for example, by expressing nucleotide sequences encoding single-chain antibodies within the target cell population (see, e.g., Marasco et al., Px~oc. Natl. Acad. Sci. USA 90: 7889-7893 (1993)).
[0210] Modulators can be administered to a patient at therapeutically effective doses to treat osteoarthritis. A therapeutically effective dose refers to an amount of the modulator sufficient to result in amelioration of symptoms of osteoarthritis. Toxicity and therapeutic e~cacy of modulators can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LDSO (the dose lethal to 50% of the population) and the EDSO
(the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LDSO/EDso. Modulators that exhibit large therapeutic indices are preferred. While modulators that exhibit toxic side effects can be used, care should be taken to design a delivery system that targets such molecules to the site of affected tissue in order to minimize potential damage to uninfected cells, thereby reducing side effects.
[0211] Data obtained from cell culture assays and animal studies can be used in formulating a range of dosages for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the EDso with little or no toxicity.
The dosage can vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the methods described herein, the therapeutically effective dose can be estimated initially from cell culture assays. A dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the ICSO (i. e., the concentration of the test compound that achieves a half maximal inhibition of symptoms) as determined in cell culture.
Such information can be used to more accurately determine useful doses in humans. Levels in plasma can be measured, for example, by high performance liquid chromatography.
[0212] Another example of effective dose determination for an individual is the ability to directly assay levels of "free" and "bound" compound in the serum of the test subject.
Such assays may utilize antibody mimics and/or "biosensors" that have been created through molecular imprinting techniques.
Molecules that modulate target molecule activity are used as a template, or "imprinting molecule", to spatially organize polymerizable monomers prior to their polymerization with catalytic reagents. The subsequent removal of the imprinted molecule leaves a polymer matrix which contains a repeated "negative image" of the compound and is able to selectively rebind the molecule under biological assay conditions. A detailed review of this technique can be seen in Ansell et al., Cur~etzt Opihioh in Biotechnology 7.' 89-94 (1996) and in Shea, Trends in Polymer Science 2: 166-173 (1994). Such "imprinted" affinity matrixes are amenable to ligand-binding assays, whereby the immobilized monoclonal antibody component is replaced by an appropriately imprinted matrix. An example of the use of such matrixes in this way can be seen in Vlatakis, et al., Natut~e 361:
645-647 (1993). Through the use of isotope-labeling, the "free" concentration of compound which modulates target molecule expression or activity readily can be monitored and used in calculations of ICSO. Such "imprinted"
affinity matrixes can also be designed to include fluorescent groups whose photon-emitting properties measurably change upon local and selective binding of target compound. These changes readily can be assayed in real time using appropriate flberoptic devices, in turn allowing the dose in a test subject to be quickly optimized based on its individual ICSO. An example of such a "biosensor" is discussed in I~riz et al., Analytieal Chemistry 67: 2142-2144 (1995).
[0213] The examples set forth below are intended to illustrate but not limit the invention.
Examples [0214] In the following studies a group of subjects was selected according to specific parameters relating to osteoarthritis. Nucleic acid samples obtained from individuals in the study group were subjected to genetic analysis, which identified associations between osteoarthritis and certain polymorphic variants in the following genes: PADI2, APOB, ILIRL~, ILIRL1, WASPIP, ADAMTS2, BT~ES, TM7SF3, PELl2, LO~L'LI, CASPR4, GPR50 or APOL3 (herein referred to as "Targets"). The polymorphisms were genotyped again in two replication cohorts consisting of individuals selected for OA. In addition, SNPs proximal to the incident polymorphism in APOB, IL1RL2, IL1RL1, WASPIP, ADAMTS2, BYES, TM7SF3, LOXLl, CASPR4 and APOL3 regions were identified and allelotyped in OA case and control pools. Methods are described for producing target polypeptides encoded by the nucleic acids of Table B in vitro or in vivo, which can be utilized in methods that screen test molecules for those that interact with target polypeptides. Test molecules identified as interactors with target polypeptides can be screened further as osteoarthritis therapeutics.
Example 1 Samples and Poolin S~ trateaies Sample Selection [0215] Blood samples were collected from individuals diagnosed with knee osteoarthritis, which were referred to as case samples. Also, blood samples were collected from individuals not diagnosed with knee osteoarthritis as gender and age-matched controls. A database was created that listed all phenotypic trait information gathered from individuals for each case and control sample. Genomic DNA was extracted from each of the blood samples for genetic analyses.
DNA Extraction from Blood Samples [0216] Six to ten milliliters of whole blood was transferred to a 50 ml tube containing 27 ml of red cell lysis solution (RCL). The tube was inverted until the contents were mixed. Each tube was incubated for 10 minutes at room temperature and inverted once during the incubation. The tubes were then centrifuged for 20 minutes at 3 000 x g and the supernatant was carefully poured off. 100-200 p,l of residual liquid was left in the tube and was pipetted repeatedly to resuspend the pellet in the residual supernatant. White cell lysis solution (WCL) was added to the tube and pipetted repeatedly until completely mixed. While no incubation was normally required, the solution was incubated at 37°C or room temperature if cell clumps were visible after mixing until the solution was homogeneous. 2 ml of protein precipitation was added to the cell lysate. The mixtures were vortexed vigorously at high speed for 20 sec to mix the protein precipitation solution uniformly with the cell lysate, and then centrifuged for 10 minutes at 3000 x g. The supernatant containing the DNA was then poured into a clean 15 ml tube, which contained 7 ml of 100°fo isopropanol. The samples were mixed by inverting the tubes gently until white threads of DNA were visible. Samples were centrifuged for 3 minutes at 2000 x g and the DNA was visible as a small white pellet. The supernatant was decanted and 5 ml of 70% ethanol was added to each tube. Each tube was inverted several times to wash the DNA
pellet, and then centrifuged for 1 minute at 2000 x g. The ethanol was decanted and each tube was drained on clean absorbent paper. The DNA was dried in the tube by inversion for 10 minutes, and then 1000 wl of 1X TE was added. The size of each sample was estimated, and less TE buffer was added during the following DNA
hydration step if the sample was smaller. The DNA was allowed to rehydrate overnight at room temperature, and DNA samples were stored at 2-8°C.
[0217] DNA was quantified by placing samples on a hematology mixer for at least 1 hour. DNA
was serially diluted (typically 1:80, 1:160, 1:320, and 1:640 dilutions) so that it would be within the measurable range of standards. 125 ~l of diluted DNA was transferred to a clear U-bottom microtitre plate, and 125 pl of 1X TE buffer was transferred into each well using a multichannel pipette. The DNA and 1X TE were mixed by repeated pipetting at least 15 times, and then the plates were sealed. 50 pl of diluted DNA was added to wells AS-H12 of a black flat bottom microtitre plate. Standards were inverted six times to mix them, and then 50 p,l of 1X TE buffer was pipetted into well A1, 1000 ng/ml of standard was pipetted into well A2, 500 ng/ml of standard was pipetted into well A3, and 250 ng/ml of standard was pipetted into well A4. PicoGreen (Molecular Probes, Eugene, Oregon) was thawed and freshly diluted 1:200 according to the number of plates that were being measured. PicoGreen was vortexed and then SOp.I was pipetted into all wells of the black plate with the diluted DNA. DNA and PicoGreen were mixed by pipetting repeatedly at least 10 times with the multichannel pipette. The plate was placed into a Fluoroskan Ascent Machine (microplate fluorometer produced by Labsystems) and the samples were allowed to incubate for 3 minutes before the machine was run using filter pairs 485 nm excitation and 538 nm emission wavelengths. Samples having measured DNA
concentrations of greater than 450 ng/p,l were re-measured for conformation. Samples having measured DNA
concentrations of 20 ng/p.l or less were re-measured for confirmation.
Poolin Strate ies - Discoverer Cohort [0218] Samples were derived from the Nottingham knee OA family study (IJK) where index cases were identified through a knee replacement registry. Siblings were approached and assessed with knee x-rays and assigned status as affected or unaffected. In all 1,157 individuals were available. In order to create same-sex pools of appropriate sizes, 335 unrelated female individuals with OA from the Nottingham OA sample were selected for the case pool. The control pool was made up of unrelated female individuals from the St. Thomas twin study (England) with normal knee x-rays and without other indications of OA, regardless of anatomical location, as well as lacking family history of OA. The St. Thomas twin study consists of Caucasian, female participants from the St.
Thomas' Hospital, London, adult-twin registry, which is a voluntary registry of >4,000 twin pairs ranging from 18 to 76 years of age. The female case samples and female control samples are described further in Table 1 below.
[0219] A select set of samples from each group were utilized to generate pools, and one pool was created for each group. Each individual sample in a pool was represented by an equal amount of genomic DNA. For example, where 25 ng of genomic DNA was utilized in each PCR
reaction and there were 200 individuals in each pool, each individual would provide 125 pg of genomic DNA.
Inclusion or exclusion of samples for a pool was based upon the following criteria: the sample was derived from an individual characterized as Caucasian; the sample was derived from an individual of British paternal and maternal descent; case samples were derived from individuals diagnosed with specific knee osteoarthritis (OA) and were recruited from an OA knee replacement clinic. Control samples were derived from individuals free of OA, family history of OA, and rheumatoid arthritis.
Also, sufficient genomic DNA was extracted from each blood sample for all allelotyping and genotyping reactions performed during the study. Phenotype information from each individual was collected and included age of the individual, gender, family history of OA, general medical information (e.g., height, weight, thyroid disease, diabetes, psoriasis, hysterectomy), joint history (previous and current symptoms, joint-related operations, age at onset of symptoms, date of primary diagnosis, age of individual as of primary diagnosis and order of involvement), and knee-related findings (crepitus, restricted passive movement, bony swelling/deformity). Additional knee information included knee history, current symptoms, any major knee injury, menisectomy, knee replacement surgery, age of surgery, and treatment history (including hormone replace therapy (HRT)).
Samples that met these criteria were added to appropriate pools based on disease status.

[0220] The selection process yielded the pools set forth in Table 1, which were used in the studies that follow:

Female case Female control Pool size 335 335 (Number) Pool Criteria (ex: case/control)control case Mean Age 57 95 (ex: years) , .

Example 2 Association of Pol.~phic Variants with Osteoarthritis [0221] A whole-genome screen was performed to identify particular SNPs associated with occurrence of osteoarthritis. As described in Example 1, two sets of samples were utilized, which included samples from female individuals having knee osteoarthritis (osteoarthritis cases), and samples from female individuals not having knee osteoarthritis (female controls). The initial screen of each pool was performed in an allelotyping study, in which certain samples in each group were pooled. By pooling DNA from each group, an allele frequency for each SNP in each group was calculated. These allele frequencies were then compared to one another. Particular SNPs were considered as being associated with osteoarthritis when allele frequency differences calculated between case and control pools were statistically significant. SNP disease association results obtained from the allelotyping study were then validated by genotyping each associated SNP across all samples from each pool. The results of the genotyping then were analyzed, allele frequencies for each group were calculated from the individual genotyping results, and a p-value was calculated to determine whether the case and control groups had statistically significant differences in allele frequencies for a particular SNP. When the genotyping results agreed with the original allelotyping results, the SNP
disease association was considered validated at the genetic level.
SNP Panel Used for Genetic Anal_ [0222] A whole-genome SNP screen began with an initial screen of approximately 25,000 SNPs over each set of disease and control samples using a pooling approach. The pools studied in the screen are described in Example 1. The SNPs analyzed in this study were part of a set of 25,488 SNPs confirmed as being statistically polymorphic as each is characterized as having a minor allele frequency of greater than 10°fo. The SNPs in the set reside in genes or in close proximity to genes, and many reside in gene exons. Specifically, SNPs in the set are located in exons, introns, and within 5,000 base-pairs upstream of a transcription start site of a gene_ In addition, SNPs were selected according to the following criteria: they are located in ESTs; they are located in Locuslink or Ensembl genes; and they are located in Genomatix promoter predictions. SNPs in the set were also selected on the basis of even spacing across the genome, as depicted in Table 2.
[0223] A case-control study design using a whole genome association strategy involving approximately 28,000 single nucleotide polymorphisms (SNPs) was employed.
Approximately 25,000 SNPs were evenly spaced in gene-based regions of the human genome with a median inter-marker distance of about 40,000 base pairs. Additionally, approximately 3,000 SNPs causing amino acid substitutions in genes described in the literature as candidates for various diseases were used. The case-contr-of study samples were of female Caucasian origin (British paternal and maternal descent) 670 individuals were equally distributed in two groups: female controls and female cases. The whole genome association approach was first conducted on 2 DNA pools representing the 2 groups.
Significant markers were confirmed by individual genotyping.

General Statistics Suacin~ Statistics Total # of SNPs 25,488 Median 37,058 by # of Exonic SNPs >4,335 (17%)Minimum* 1,000 by # SNPs with refSNP20,776 (81%)Maximum* 3,000,000 ID by Gene Coverage >10,000 Mean 122,412 by Chromosome CoverageAll Std Deviation 373,325 by *E.~cludes outliers Allelotypi~n and Genotyping Results [0224] The genetic studies summarized above and described in more detail below identified allelic variants associated with osteoarthritis, which are summarized in Table B.
Assay for Veri ,ping, Alleloty~ing, and Genotyping SNPs [0225] A MassARRAYTM system (Sequenom, Inc.) was utilized to perform SNP
genotyping in a high-throughput fashion. This genotyping platform was complemented by a homogeneous, single-tube assay method (hMETM or homogeneous MassEXTENDTM (Sequenom, Inc.)) in which two genotyping primers anneal to and amplify a genomic target surrounding a polymorphic site of interest. A third primer (the MassEXTENDTM primer), which is complementary to the amplified target up to but not including the polymorphism, was then enzymatically extended one or a few bases through the polyrnorphic site and then terminated.
[0226] For each polymorphism, SpectroDESIGNERTM software (Sequenom, Inc.) was used to generate a set of PCR primers and a MassEXTENDTM primer which where used to genotype the polymorphism. Other primer design software could be used or one of ordinary skill in the art could manually design primers based on his or her knowledge of the relevant factors and considerations in designing such primers. Table 3 shows PCR primers and Table 4 shows extension primers used for analyzing polymorphisms. The initial PCR amplification reaction was performed in a 5 p.l total volume containing 1X PCR buffer with 1.5 mM MgClz (Qiagen), 200 p,M each of dATP, dGTP, dCTP, dTTP
(Gibco-BRL), 2.5 ng of genomic DNA, 0.1 units of HotStar DNA polymerase (Qiagen), and 200 nM
each of forward and reverse PCR primers specific for the polymorphic region of interest.
TABLE 3: PCR Primers SNP Forward PCR primer Reverse PCR primer Reference rs910223ACGTTGGATGACAGAGTGTCAGGGCTCAGAACGTTGGATGTGGTTTTTCCAGTGTCTTAC

rs1367117ACGTfGGATGTTGGTTTTCTTCAGCAAGGCACGTTGGATGAGCTTCATCCTGAAGACCAG

rs1024791ACGTTGGATGGTGTAAGGGACTGCAGATACACGTTGGATGAAACAGAACCAGGAGGTTGG

rs1041973ACGTTGGATGGGGACTTCTGACAATACAGGACGTTGGATGAATCGTGTGTTTGCCTCAGG

rs1465621ACGTTGGATGTTCTCCTCCCATTCTTCCTGACGTTGGATGGCGGGACTAGAAGTAGATTC

rs398829ACGTTGGATGTAGTCATCGTCCGCAGCATGACGTTGGATGAAGACGGTGTCCTCTCCTTG

rs1018810ACGTTGGATGTGCTGCTCCCATTfCTCATGACGTTGGATGAAGGAGTAGAGACCTTGCTG

rs1484086ACGTTGGATGTGTCACTCT1'CGGAAGTCTCACGTTGGATGCATGTACAGGGCATTCACAG

rs242392ACGTTGGATGTGTTTGGGCTGCTGTGGCTCTACGTTGGATGACCACTTCTCACGGTfACTG

rs8818 ACGTTGGATGAATCTCTCCCCTTCCAAAGCACGTTGGATGTCCCTGTGGTTTTCATCCAC

rs1395486ACGTTGGATGCTCATTTATTTCATGTTCACACGTTGGATGTGCTGGAATAATGATfGTTG

rs512294ACGTTGGATGTCTTGCTACCCACCTCCGAGACGTTGGATGAGAGCTCATGAGGGAATGGG

rs132659ACGTTGGATGGGCCCATAGTGGGTCATAACACGTTGGATGGTGGGGTGAGTGCCCAAAAG
~

[0227] Samples were incubated at 95°C for 15 minutes, followed by 45 cycles of 95°C for 20 seconds, 56°C for 30 seconds, and 72°C for 1 minute, finishing with a 3 minute final extension at 72°C.
Following amplification, shrimp alkaline phosphatase (SAP) (0.3 units in a 2 p,l volume) (Amersham Pharmacia) was added to each reaction (total reaction volume was 7 pl) to remove any residual dNTPs that were not consumed in the PCR step. Samples were incubated for 20 minutes at 37°C, followed by minutes at 85°C to denature the SAP.
[0228] Once the SAP reaction was complete, a primer extension reaction was initiated by adding a polymorphism-specific MassEXTENDTM primer cocktail to each sample. Each MassEXTENDTM
cocktail included a specific combination of dideoxynucleotides (ddNTPs) and deoxynucleotides (dNTPs) used to distinguish polymorphic alleles from one another. Methods for verifying, allelotyping and genotyping SNPs are disclosed, for example, in U.S. Pat. No. 6,258,538, the content of which is hereby incorporated by reference. In Table 4, ddNTPs are shown and the fourth nucleotide not shown is the dNTP.
TABLE 4: Extension Primers SNP Extend Probe Termination Reference Mix rs910223GGGTCTGCACTG GTCCCA ACT

rs1367117AGCCATACACCTCTTfCAGG ACT

rs1024791CTGGCTGATGTCAGAAAGCA ACG

rs 1041973ATACCAGAATCAGCAACT ACT

rs1465621CCATTCTTCCTGACATTCGCC CGT

rs398829TGGCGTGCTCCTCTAGGA ACG

rs1018810CTGCTTTTATACATGCCACAC ACT

rs1484086CTCTTCGGAAGTCTCTTTCTCA ACT

rs242392CTGCTGTGGCTCTACTGGT ACG
~

SNP Extend Probe Termination Reference Mix rs8818 AGCCCCCAACCCACAGGCA ACT

rs1395486TTTCATGTTCACAAAAAATCTTCT ACG

rs512294 AGCTGGAGAGCAAACCACC ACT

rs 132659AGAACTCCCCAAATCGTCCT ACG

[0229] The MassEXTENDTM reaction was performed in a total volume of 9 ~,1, with the addition of 1X ThermoSequenase buffer, 0.576 units of TherrnoSequenase (Amersham Pharmacia), 600 nM
MassEXTENDTM primer, 2 mM of ddATP and/or ddCTP and/or ddGTP and/or ddTTP, and 2 mM of dATP or dCTP or dGTP or dTTP. The deoxy nucleotide (dNTP) used in the assay normally was complementary to the nucleotide at the polymorphic site in the amplicon.
Samples were incubated at 94°C for 2 minutes, followed by 55 cycles of 5 seconds at 94°C, 5 seconds at 52°C, and 5 seconds at 72°C.
[0230] Following incubation, samples were desalted by adding 16 pl of water (total reaction volume was 25 ~1), 3 mg of SpectroCLEANTM sample cleaning beads (Sequenom, Inc.) and allowed to incubate for 3 minutes with rotation. Samples were then robotically dispensed using a piezoelectric dispensing device (SpectroJETTM (Sequenom, Inc.)) onto either 96-spot or 384-spot silicon chips containing a matrix that crystallized each sample (SpectroCHIPTM (Sequenom, Inc.)). Subsequently, MALDI-TOF mass spectrometry (Biflex and Autoflex MALDI-TOF mass spectrometers (Bruker Daltonics) can be used) and SpectroTYPER RTT"'i software (Sequenom, Inc.) were used to analyze and interpret the SNP genotype for each sample.
Genetic Analysis [0231] Minor allelic frequencies for the polymorphisms set forth in Table B
were verified as being 10% or greater using the extension assay described above in a group of samples isolated from 92 individuals originating from the state of Utah in the United States, Venezuela and France (Coriell cell repositories).
[0232] Genotyping results are shown for female pools in Table 5. In Table 5, "AF" refers to allelic frequency; and "F case" and "F control" refer to female case and female control groups, respectively.
TABLE 5: Genotyping Results SNP Reference P-~alue F c se F co trol rs910223 A = 0.148 A = 0.099 . 0 G=0.852 G=0.901 .

rs1367117 A = 0.339 A = 0.402 0 G=0.661 G=0.598 .

rs1024791 G = 0.129 G = 0.088 0 A=0.871 A=0.912 .

rs1041973 A = 0.189 A = 0.233 0 C=0.811 C=0.767 .

rs1465621 T = 0.071 T = 0.107 0 A = 0.929 A = 0.893 .

rs398829 G = 0.740 G = 0.652 0.0002 A = 0.260 A = 0.348 rs 1018810 A = 0.142 A = 0.094 0 G = 0.858 G = 0.906 .

rs1484086 T = 0.821 T = 0.753 0 C=0.179 C=0.247 .

rs242392 C = 0.100 C = 0.139 0 T = 0.900 T = 0.861 .

rs8818 G = 0.158 G = 0.213 0 C=0.842 C=0.787 .

rs1395486 C = 0.115 C = 0.158 0 T = 0.885 T = 0.842 .

rs512294 A = 0.078 A = 0.124 0 G=0.922 G=0.876 .

rs132659 C = 0.675 C = 0.589 0 T=0.325 T=0.411 .

[0233] All of the single marker alleles set forth in Table B were considered validated, since the genotyping data agreed with the allelotyping data and each SNP significantly associated with osteoarthritis. Particularly significant associations with osteoarthritis are indicated by a calculated p-value of less than 0.05 for genotype results.
Example 3 Association of Pol morphic Variants with Osteoarthritis in Replication Cohorts [0234] The single marker polymorphisms set forth in Table B were genotyped again in two replication cohorts consisting of individuals selected for OA.
Sample Selection and Poolin Strategies -Replication Sample 1 [0235] A second case control sample (replication sample #1) was created by using 100 Caucasian female cases from Chingford, UK, and 148 unrelated female cases from the St.
Thomas twin study.
Cases were defined as having Kellgren-Lawrence (KL) scores of at least 2 in at least one knee x-ray. In addition, 199 male knee replacement cases from Nottingham were included. (For a cohort description, see the Nottingham description provided in Example 1). The control pool was made up of unrelated female individuals from the St. Thomas twin study (England) with normal knee x-rays and without other indications of OA, regardless of anatomical location, as well as lacking family history of OA. The St. Thomas twin study consists of Caucasian, female participants from the St.
Thomas' Hospital, London, adult-twin registry, which is a voluntary registry of >4,000 twin pairs ranging from 18 to 76 years of age. The replication sample 1 cohort was used to replicate the initial results. Table 6 below summarizes the selected phenotype data collected from the case and control individuals.

Phenotype Female cases (n=248):Male cases (n=199):Female controls (n=313):

median (range)/ median (range)/ mean (range)/ (n,%) (n,%) (n,%) Age 59 (39- 73) 66 (45- 73) 55 (50- 72) Height (cm)162 (141- 178) 175 (152- 198) 162 (141- 176) Phenotype Female cases (n=248):Male cases (n=199):Female controls (n=313):

median (range)/ median (range)/ mean (range)/ (n,%) (n,%) (n,%) Weight (kg) 68 (51- 123) 86 (62- 127) 64 (40- 111) Body mass 2g (18-44) 29 (21-41) 24 (18-46) index (Ecglm ) Kellgren- 0 (63, 26%), 1 (20, 8%), 2 Lawrence* (105, 43%), 3 (58,NA NA
left 23%), 4 knee (1, 0%) Kellgren- 0 (43, 7%), 1 (18, 7%), 2 Lawrence* (127, 52%), 3 (57,NA NA
right 23%), 4 knee (1, 0%) KL* >2 both No (145, 59%), NA NA
Yes (101, knees 41 %) KL* >2 eitherNo (0, 0%), Yes NA NA
(248, 100%) knee * 0: normal, 1: doubtful, 2: definite osteophyte (bony protuberance), 3: joint space narrowing (with or without osteophyte), 4: joint deformity Sample Selection and Poolin Sg trate~ies - Replication Sample 2 [0236] A third case control sample (replication sample #2) was created by using individuals with symptoms of OA from Newfoundland, Canada. These individuals were recruited and examined by the umatologists. Affected joints were x-rayed and a f nal diagnosis of definite or probable OA was made according to American College of Rheumatology criteria by a single rheumatologist to avoid any inter-examiner diagnosis variability. Controls were recruited from volunteers without any symptoms from the musculoskeletal system based on a normal joint exam performed by a rheumatologist. Only cases with a diagnosis of definite OA were included in the study. Only individuals of Caucasian origin were included. The cases consisted of 228 individuals with definite knee OA, 106 individuals with definite hip OA, and 74 individuals with hip OA.

Phenotype Case Control Age at Visit 62.7 52.5 Sex (Female/Male) 227/119 174/101 Knee OA Xray: No 35% (120) 80% (16) Unknown 1% (4) 0% (0) Yes 64% (221 ) 20% (4) Hip OA Xray: No 63% (215) 80% (16) Unknown 2% (7) 0% (0) Yes 35% (121 ) 20% (4) Assay for Verifying, Allelotypin~, and Genotyping SNPs [0237] Genotyping of the replication cohorts described in Tables 6 and 7 was performed using the same methods used for the original genotyping, as described herein. A
MassARRAYTM system (Sequenom, Inc.) was utilized to perform SNP genotyping in a high-throughput fashion. This genotyping platform was complemented by a homogeneous, single-tube assay method (hMETM or homogeneous MassEXTENDTM (Sequenom, Inc.)) in which two genotyping primers anneal to and amplify a genomic target surrounding a polymorphic site of interest. A third primer (the MassEXTENDTM primer), which is complementary to the amplified target up to but not including the polymorphism, was then enzymatically extended one or a few bases through the polymorphic site and then terminated.
[0238] For each polymorphism, SpectroDESIGNERTM software (Sequenom, Inc.) was used to generate a set of PCR primers and a MassEXTENDTM primer which where used to genotype the polymorphism. Other primer design software could be used or one of ordinary skill in the art could manually design primers based on his or her knowledge of the relevant factors and considerations in designing such primers. Table 3 shows PCR primers and Table 4 shows extension probes used for analyzing (e.g., genotyping) polymorphisms in the replication cohorts. The initial PCR amplification reaction was performed in a 5 p,l total volume containing 1 X PCR buffer with 1.5 mM MgClz (Qiagen), 200 ~,M each of dATP, dGTP, dCTP, dTTP (Gibco-BRL), 2.5 ng of genomic DNA, 0.1 units of HotStar DNA polymerase (Qiagen), and 200 nM each of forward and reverse PCR primers specific for the polymorphic region of interest.
[0239] Samples were incubated at 95°C for 15 minutes, followed by 45 cycles of 95°C for 20 seconds, 56°C for 30 seconds, and 72°C for 1 minute, finishing with a 3 minute final extension at 72°C.
Following amplification, shrimp alkaline phosphatase (SAP) (0.3 units in a 2 ~,l volume) (Amersham Pharmacia) was added to each reaction (total reaction volume was 7 ~,l) to remove any residual dNTPs that were not consumed in the PCR step. Samples were incubated for 20 minutes at 37°C, followed by minutes at 85°C to denature the SAP.
[0240] Once the SAP reaction was complete, a primer extension reaction was initiated by adding a polymorphism-specific MassEXTENDTM primer cocktail to each sample. Each MassEXTENDTM
cocktail included a specific combination of dideoxynucleotides (ddNTPs) and deoxynucleotides (dNTPs) used to distinguish polymorphic alleles from one another. Methods for verifying, allelotyping and genotyping SNPs are disclosed, for example, in LT.S. Pat. No. 6,258,538, the content of which is hereby incorporated by reference. In Table 7, ddNTPs are shown and the fourth nucleotide not shown is the dNTP.
[0241] The MassEXTENDTM reaction was performed in a total volume of 9 ~,1, with the addition of 1X ThermoSequenase buffer, 0.576 units of ThermoSequenase (Amersham Pharmacia), 600 nM
MassEXTENDTM primer, 2 mM of ddATP and/or ddCTP and/or ddGTP and/or ddTTP, and 2 mM of dATP or dCTP or dGTP or dTTP. The deoxy nucleotide (dNTP) used in the assay normally was complementary to the nucleotide at the polymorphic site in the amplicon.
Samples were incubated at 94°C for 2 minutes, followed by 55 cycles of 5 seconds at 94°C, 5 seconds at 52°C, and 5 seconds at 72°C.

[0242] Following incubation, samples were desalted by adding 16 ~1 of water (total reaction volume was 25 wl), 3 mg of SpectroCLEANTM sample cleaning beads (Sequenom, Inc.) and allowed to incubate for 3 minutes with rotation. Samples were then robotically dispensed using a piezoelectric dispensing device (SpectroJETTM (Sequenom, Inc.)) onto either 96-spot or 384-spot silicon chips containing a matrix that crystallized each sample (SpectroCI-i11'TM (Sequenom, Inc.)). Subsequently, MALDI-TOF mass spectrometry (Biflex and Autoflex MALDI-TOF mass spectrometers (Bruker Daltonics) can be used) and SpectroTYPER RTTM software (Sequenom, Inc.) were used to analyze and interpret the SNP genotype for each sample.
Genetic Anal [0243] Genotyping results for replication cohorts #1 and #2 are provided in Tables 8 and 9, respectively.

Replication Meta-analysis rslD #1 Disc. + Rep (Mixed #1 MaleIFemale P-value cases and Female controls) AF OA Con AF OA
Cas Delta P-value rs910223 0.87 0.86 0.01 0.650 0.1800 rs1367117 0.67 0.64 0.03 0.182 0.9900 rs1024791 0.87 0.87 -0.01 0.718 0.5900 rs1041973 0.77 0.79 -0.02 0.357 Not calculated rs1465621 0.89 0.91 -0.02 0.209 0.0095 rs398829 0.30 0.28 0.02 0.307 0.0260 rs1018810 0.91 0.89 0.02 0.289 0.0062 rs1484086 0.23 0.20 0.03 0.287 0.0077 rs242392 0.87 0.87 0.00 0.927 0.2400 rs8818 0.78 0.81 -0.03 0.259 0.0150 rs1395486 0.87 0.88 -0.01 0.492 0.0390 rs512294 0.89 0.88 0.00 0.909 0.3600 rs132659 0.38 0.34 0.04 0.128 .0077 Replication Meta-analysis rslD #2 (Newfoundland) Disc. + Rep (MaleIFemale #2 cases Not Done and controls) AF OA Con AF OA
Cas Delta P-value rs910223 0.86 0.86 0.001 0.974 rs1367117 0.64 0.69 -0.049 0.081 rs1024791 0.87 0.87 0.006 0.767 rs 1041973 0.78 0.79 -0.016 0.510 rs1465621 0.92 0.92 0.003 0.837 rs398829 0.27 0.28 -0.013 0.627 rs1018810 rs1484086 0.23 0.21 0.026 0.280 _ rs242392 0.88 0.88 -0.005 0.813 Replication Meta-analysis rslD #2 (Newfoundland) Disc. + Rep (Male/Female #2 cases and Not Done controls) AF OA Con AF OA Cas Delta P-value rs8818 0.85 0.82 0.034 0.127 rs1395486 0.86 0.85 0.015 0.486 rs512294 0.90 0.93 -0.037 0.021 rs132659 0.36 0.36 -0.001 0.973 I

[0244] To combine the evidence for association from multiple sample collections, a meta-analysis procedure was employed. The allele frequencies were compared between cases and controls within the discovery sample, as well as within the replication cohort #1 using the DerSimian-Laird approach (DerSimonian, R. and N. Laird. 1986. Meta-analysis in clinical trials. Control Clin Trials 7: 177-188.) [0245] The absence of a statistically significant association in one or more of the replication cohorts should not be interpreted as minimizing the value of the original finding. There are many reasons why a biologically derived association identified in a sample from one population would not replicate in a sample from another population. The most important reason is differences in population history. Due to bottlenecks and founder effects, there may be common disease predisposing alleles present in one population that are relatively rare in another, leading to a lack of association in the candidate region. .Also, because common diseases such as arthritis-related disorders are the result of susceptibilities in many genes and many environmental risk factors, differences in population-specific genetic and environmental backgrounds could mask the effects of a biologically relevant allele. For these and other reasons, statistically strong results in the original, discovery sample that did not replicate in one or more of the replication samples may be further evaluated in additional replication cohorts and experimental systems.
[0246] APOS, ILIRL2, WASPIP, BT~ES, LO.~'Ll and C'ASPR4 regions were analyzed further, as shown in the examples below. PADI2, described above, is a peptidyl arginine deiminase enzyme, type II, that converts arginine residues within proteins to citrulline residues _ This gene is one of four known PADI genes that encode enzymes that catalyze conversion of arginine to citrulline in proteins.
Individuals with rheumatoid arthritis (RA) frequently have autoantibodies to citrullinated peptides, suggesting the involvement of the peptidylarginine deiminases citrullinating enzymes in RA (van Venrooij et al., A~t7~y~itis ReS.;2(4):249-51. Epub 2000 May 24).
[0247] Pellino homolog 2 from Drosophila (PELI2) is a a member of the Pellino gene family, which are involved in Toll-like signalling pathways. Pellino-2 associates with the pelle-like kinase/1L
1R-associated kinase protein to couple the pelle-like kinase/IL-1R-associated kinase protein to IL-1- or LPS-dependent signaling. PELI2 may act as a downstream effector of interleukin receptor signaling and may play a ro le in inflammation-mediated Osteoarthritis. Pathway members downstream of PELF
may be targetable (e.g., interleukin receptors).

[0248] G protein-coupled receptor 50 (GPRSO) is a member of the G protein-coupled receptor family. GPR50 has significant homology to melatonin receptors and was isolated by PCR of human genomic DNA with degenerate primers based on conserved regions of melatonin receptors.
Example 4 APOB Proximal SNPs [0249] It has been discovered that rs1367117 is associated with occurrence of osteoarthritis in subjects. The polymorphic variant lies within the APOB gene and codes for a I98T amino acid change.
The guanine allele of SNP rs1367117 is associated with osteoarthritis (see Table 5) and codes for a threonine at position 98 (see, for example, amino acid sequence in SEQ ID NO:
38).
[0250] Apolipoprotein B (ApoB) is the main apolipoprotein of chylomicrons and low density lipoproteins (LDL). ApoB binds to sulfated proteoglycans, especially chondroitin and dermatan sulfate, that are components of cartilage (Camejo et. al., AtlZerosclerosis. 1998 Aug;13 9(2):205-22). This may contribute to inflarnmation/joint damage by lipoprotein oxidation products. In addition, increased levels of ApoB is seen as a risk factor for osteonecrosis (Miyanishi et. al., Ann Rheum Dis. 1999 Aug;58(8):514-6) _ Lipoprotein deposition has been noted in inflammatory (rheumatoid) arthritis and may play a role in inflammation mediated osteoarthritis. ApoB function can be modulated by addition of an antibody or a decoy receptor for ApoB. Examples of antibodies and small molecules that specifically interact with ApoB are described in U.S. Patent Nos. 6,107,045;
6,309,844; 5,330,910; and 6,369,075.
[0251] One hundred twenty-two additional allelic variants proximal to rs 1367117 were identified and subsequently allelotyped in osteoarthritis case and control sample sets as described in Examples 1 and 2. The polymorphic variants are set forth in Table 10. The chromosome positions provided in column four of Table 10 are based on Genome "Build 34" of NCBI's GenBanlc.

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs1318006 2 238 21188688 C/T

rs1318005 2 294 21188744 C/T

rs1318004 2 295 21188745 A/G

rs1318003 2 347 21188797 A/C

rs4327259 2 1425 21189875 A/C

rs6756501 2 4891 21193341 C/T

rs6725189 2 5087 21193537 G/T

rs4665709 2 7041 21195491 A/G

rs4665710 2 7121 21195571 A/C

rs4371387 2 7219 21195669 A/G

rs952274 2 7443 21195893 G/T

rs952275 2 7485 21195935 G/T

rs1801695 2 10939 21199389 A/G

rs1042034 2 11367 21199817 A/G

rs1801702 2 11571 21200021 C/G

dbSNP Chromo- Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs10420312 11839 21200289 A/G

rs26783782 12551 21201001 A/G

rs26783792 12646 21201096 A/G

rs18004792 13469 21201919 G/C

rs18017012 14913 21203363 A/G

rs43625892 15205 21203655 G/T

rs57429042 15246 21203696 A/G

rs17998122 15695 21204145 G/A

rs21632042 17473 21205923 G/T

rs6762102 17610 21206060 A/G

rs10420062 17828 21206278 A/C

rs18016962 18130 21206580 AlG

rs693 2 18281 21206731 C/T

rs10419742 18623 21207073 C/G

rs10419682 18890 21207340 C/T

rs5684132 21561 21210011 C/T

rs28547262 23100 21211550 A/T

rs28547252 23872 21212322 A/C

rs20009982 24581 21213031 A/T

rs20009972 24582 21213032 A/T

rs4971662 24983 21213433 C/T

rs5629562 27540 21215990 A/T

rs75893002 30846 21219296 C/T

rs37919802 31415 21219865 G/T

rs37919812 31453 21219903 A/G

rs18017002 31899 21220349 T/C

rs6798992 37000 21225450 A/G

rs10419522 38681 21227131 C/G

rs67277062 39287 21227737 C/T

rs67192072 42951 21231401 A/T

rs14695132 45648 21234098 C/T

rs18004782 46222 21234672 C/T

rs5506192 46687 21235137 A/G

rs67520262 47020 21235470 A/G

rs5798262 47593 21236043 C/T

rs5973312 48513 21236963 C/T

rs13671162 49723 21238173 A/G

rs13671172 49986 21238436 A/G

rs18004802 53018 21241468 C/G

rs18004812 53296 21241746 C/T

rs9341972 53547 21241997 A/G

rs16257642 53899 21242349 C/T

rs16257142 53916 21242366 G/T

rs15603572 53933 21242383 A/C

rs6173142 54305 21242755 G/T

rs5471862 55327 21243777 A/T

rs5895662 55895 21244345 C/T

rs5882452 56143 21244593 CIT

rs5859672 56640 21245090 G/T

rs75627772 58486 21246936 A/G

rs75758402 59576 21248026 G/T

rs75676532 63048 21251498 A/G

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs65480102 64008 21252458 A/G

rs65480112 64018 21252468 C/T

rs934198 2 64859 21253309 A/C

rs634292 2 65995 21254445 G/T

rs10031772 66905 21255355 A/G

rs67261152 67183 21255633 A/G

rs481069 2 67942 21256392 C/T

rs13671152 68101 21256551 A/G

rs666126 2 68521 21256971 A/G

rs75660302 68664 21257114 ClG

rs75901352 68988 21257438 A/G

rs67185132 69178 21257628 C/G

rs515135 2 72143 21260593 A/G

rs13671142 74183 21262633 C/G

rs563290 2 74312 21262762 C/T

rs562338 2 74407 21262857 C/T

rs581411 2 75518 21263968 A/G

rs580889 2 76153 21264603 A/G

rs548145 2 77398 21265848 AlG

rs668948 2 77615 21266065 A/G

rs594677 2 79092 21267542 C/T

rs571468 2 80000 21268450 G/T

rs46654922 80125 21268575 A/C

rs622236 2 80595 21269045 G/T

rs541041 2 81061 21269511 C/T

rs540156 2 81151 21269601 A/G

rs13671132 81918 21270368 C/T

rs18970842 83072 21271522 C/T

rs18970832 83137 21271587 C/T

rs478588 2 83235 21271685 C/T

rs664894 2 83263 21271713 A/T

rs15942862 83279 21271729 A/G

rs74221682 83280 21271730 C/G

rs565202 2 83533 21271983 C/T

rs14299742 86856 21275306 G/T

rs58297692 87186 21275636 -/TATA

rs30565752 87189 21275639 -/ATAT

rs67081682 87727 21276177 A/T

rs67567432 87978 21276428 C/T

rs21955982 89129 21277579 A/G

rs75672172 89556 21278006 C/T

rs568938 2 89702 21278152 AIG

rs666416 2 90233 21278683 A/G

rs67613002 93060 21281510 A/G

rs58297702 94779 21283229 -/T

rs14299732 95367 21283817 A/G

rs14299722 95844 21284294 A/G

rs67562842 95942 21284392 A/G

rs749988 2 96884 21285334 C/T

rs749987 2 96938 21285388 A/G

rs754524 2 97627 21286077 A/C

rs754523 2 97777 21286227 C/T

dbSNP Chromo-Position Chromosome Allele in SEQ

rs# some ID NO: 2 Position Variants rs6754302 97871 21286321 A/C

rs6000122 98746 21287196 AlG

rs6143032 99663 21288113 A/G

Assay for Veri in~Land Allelotyping SNPs [0252] The methods used to verify and allelotype the 122 proximal SNPs of Table 10 are the same methods described in Examples 1 and 2 herein. The primers and probes used in these assays are provided in Table 11 and Table 12, respectively.

dbSNP Forward Reverse rs# PCR primer PCR primer rs1318006ACGTTGGATGTCTCATGGCCCATCCAAGGCACGTTGGATGAAGGAGCCCATGAAGGCAGC

rs1318005ACGTTGGATGACAGCCTTGGATGGGCCATGACGTTGGATGTCTCCCAGTCTGGTGGAAAG

rs1318004ACGTTGGATGACAGCCTTGGATGGGCCATGACGTTGGATGTCTCCCAGTCTGGTGGAAAG

rs1318003ACGTTGGATGTTTCCACCAGACTGGGAGACACGTTGGATGAGTGCCCAGCACAGAGTCTT

rs4327259ACGTTGGATGAACAAGCTTGCTCAGCCACTACGTTGGATGTGTGTTCTGTCCAGGAAGAG

rs6756501ACGTTGGATGATGCATTCATTCGCTGTTTGAGGTTGGATGGAGATCAATGAGAAAAATAGG

rs6725189ACGTTGGATGAAGAACAATAGAGAGGGCCGACGTTGGATGAGTATTGACTGCCTTGGTTC

rs4665709ACGTTGGATGGCACAACCTCATAGATGTGGACGTTGGATGCCACCTCCATCATTGTGGAT

rs4665710ACGTTGGATGAATCCACAATGATGGAGGTGACGTTGGATGGATAACTCACTCACTATCACG

rs4371387ACGTTGGATGTAAAAGTGTGTAGCACCTCCACGTTGGATGTCATGGCAGAAGTTAAAGGG

rs952274ACGTTGGATGCAGAAGGGTGACATGCATTGACGTTGGATGCTCATATCCAGATTCACCCC

rs952275ACGTTGGATGCACAATGCATGTCACCCTTCACGTTGGATGGACACTCTCTTTGCTGAAGG

rs1801695ACGTTGGATGGAAATTATTTTCTTCGTCGACGTTGGATGTGCTCAGGAAATAATTAAA

rs1042034ACGTTGGATGATCCAAGATGAGATCAACACACGTTGGATGGGCATAGGTTTTCTTTCAAC

rs1801702ACGTTGGATGTTTTGATAAATCTTTCAACACGTTGGATGCTAATAGATGTAATCTCGA

rs1042031ACGTTGGATGGTTTGATGGCTTGGTACGAGACGTTGGATGTTTCCCCGGAAACTGGAATC

rs2678378ACGTTGGATGGTTTTCAGTCCTAGGAAGGCACGTTGGATGTATCACATGCCCCAGAAAGG

rs2678379ACGTTGGATGCTTCCTAGGACTGAAAACTGACGTTGGATGTGGGCTCCAACTTGCCTTTT

rs1800479ACGTTGGATGAAGGGTATGGAGATGAAGAACGTTGGATGACCTTATACCTTTTGAAA

rs1801701ACGTTGGATGCTTGGTCATTGGAAAGCTCGACGTTGGATGGTGGCCCTGAATGCTAACAC

rs4362589ACGTTGGATGCTGCAGGGCACTTCCAAAATACGTTGGATGTATATGCGTTGGAGTGTGGC

rs5742904ACGTTGGATGATTTTGGAAGTGCCCTGCAGACGTTGGATGCTATTGCTAGTGAGGCCAAC

rs1799812ACGTTGGATGTTGTGGTGCCCTCTAATTTACGTTGGATGCATCTTCATCTGTCATTGA

rs2163204ACGTTGGATGTTTGGACTCTCCTTTGGCAGACGTTGGATGGCTGACATAGGGAATGGAAC

rs676210ACGTTGGATGCCCAACTCTCAACCTTAATGACGTTGGATGAATTGTGTGTGAGATGTGGG

rs1042006ACGTTGGATGCAGCATCTGGTCAATGGTTCACGTTGGATGACACCTTCCACATTCCTTCC

rs1801696ACGTTGGATGTGCTAAGAACCTTACTGACACGTTGGATGGCCCAATCTTGGATAGAAT

rs693 ACGTTGGATGCAGCATCTTTGGCTCACATGACGTTGGATGTCCTGCTGAATGTCCATTTG

rs1041974ACGTTGGATGTACTTTGAGAAATTGGTTGGACGTTGGATGGTTAACATCTTCAATGAATG

rs1041968ACGTTGGATGTCAGCTACTTCAAAATCCCCACGTTGGATGGGCTATTGATGTTAGAGTGC

rs568413ACGTTGGATGGAGACTGGGTTGTTTCCAAGACGTTGGATGCCACAAGAATACGTTCACAC

rs2854726ACGTTGGATGCTCTAGCTTAACAGCAAGCCACGTTGGATGGCAAATTCTCCCTCTGACTG

rs2854725ACGTTGGATGCATTCAGCTTTGTGTAACTGACGTTGGATGTTTCCAAAGACTGTATAAGG

rs2000998ACGTTGGATGTGAACCATCCTTGTATCTGGACGTTGGATGTGGCACCAATGATTTTGTCC

rs2000997ACGTTGGATGTGGCACCAATGATTTTGTCCACGTTGGATGTGAACCATCCTTGTATCTGG

rs497166ACGTTGGATGTCCCAAAGTGCTGGGATTACACGTTGGATGAAATCCAACTGGACATGCGC

rs562956ACGTTGGATGTAACAGTCTTACCACACGGCACGTTGGATGATAAGGGAAAGTCTCCCTGG

dbSNP Forward Reverse rs# PCR primer PCR primer rs7589300ACGTTGGATGTACCACGTATGTTGAGTGAGACGTTGGA-fGCCCTTACTCTATGATTACTGC

rs3791980ACGTTGGATGTCTGGAGAGATCATCTTTGGACGTTGGATGCTACCTAGCTACCTCAAATC

rs3791981ACGTTGGATGTGTTTTGAGAATGAAGAAACACGTTGGATGGTTCTTAGGTATTTTTTGGG

rs1801700ACGTTGGATGGACCCGACTCGTGGAAGAAACGTTGGATGTCGCTAGGAGTGGGGTCCA

rs679899ACGTTGGATGCTGAAGTCCATGACAGTTGGACGTTGGATGTTGTGGCTTCCCATATTGCC

rs1041952ACGTTGGATGCATGGAGCAGTTAACTCCAGACGTTGGATGTCTGGATCATCAGTGATGGC

rs6727706ACGTTGGATGGCACCACTTATTGAAAAGGGACGTTGGATGCACATACTTACAGTCAACGG

rs6719207ACGTTGGATGGTCCCAGTTGTAACCATGTCACGTTGGATGGGAATCCAGACTTGTCTGAG

rs1469513ACGTTGGATGCTTTTCTGCACAAGGACTCCACGTTGGATGACTCCACTTCATGGGATGAG

rs1800478ACGTTGGATGTGACGGTAAAGTGAGTGGAGACGTTGGATGCCCGTGTTGAATACATGTGG

rs550619ACGTTGGATGGCAAACACAGGTGAAGCATCACGTTGGATGGGCTTATCAGGTTGGGTCTA

rs6752026ACGTTGGATGCAGAAGGGAAGCAGGTTTTCACGTTGGATGCAGAAATGATGCCCCTCTTG

rs579826ACGTTGGATGAAAGTGCTGGGACTACAGGCACGTTGGATGATATGGGTGGAGAACAGAGC

rs597331ACGTTGGATGACACTCTCTCAGAAAGTTCCACGTTGGATGGTATGGTGATCAGATCAGAG

rs1367116ACGTTGGATGCAAGAAGTTTAAAGCATGAGACGTTGGATGATCATCAAAAAGAGAGAAGC

rs1367117ACGTTGGATGTTGGTTTTCTTCAGCAAGGCACGTTGGATGAGCTTCATCCTGAAGACCAG

rs1800480ACGTTGGATGCCGAGAAGGGCACTCAGCCACGTTGGATGCGCCGGCCGCGCATTCCCA

rs1800481ACGTTGGATGATCTGAAGAAGGCACCCCTGACGTTGGATGAAGCGTCTTCAGTGCTCTGG

rs934197ACGTTGGATGTGACTGGTCACTCACCAGACACGTTGGATGATCCTGATCAGAATCTGTGG

rs1625764ACGTTGGATGCAGAGGCATCGAGCGCTGGACGTTGGATGGACAGGACACGTCATGTTCC

rs1625714ACGTTGGATGAATTCCACTACCGCTGATTCACGTTGGe~TGATCGTTTCCTTCTCTTCTAG

rs1560357ACGTTGGATGGTCCCTGAAATTCCACTACCACGTTGGATGATTTCCCACCGGAAGCTTCA

rs617314ACGTTGGATGCAGTCTTCACCAGTAGCTTGACGTTGGATGTTGCAGAAGTCAGTGTGTGC

rs547186ACGTTGGATGCAGTTCAGGGAAGACTTGCCACGTTGGATGGAGAGGACTGTCACCATCTC

rs589566ACGTTGGATGCCCAGCAGACCAATATTCTGACGTTGGATGGGTATAGCTGAATGGTGCAG

rs588245ACGTTGGATGGCTCCAAAATCTCATCTGGCACGTTGGATGAGCTTCTGGGCATCATTTGC

rs585967ACGTTGGATGTGACAGGGAATCAGAGTCACACGTTGGATGCCACCTACTGCACTGAATCT

rs7562777ACGTTGGATGTTGGAGATTGCTCTTTGGGCACGTTGGATGTGACCTCAGGTTATCCACAC

rs7575840ACGTTGGATGCATAGACTGTCCATCACAGGACGTTGGATGGGTGTCAGAAAAACTTCCAC

rs7567653ACGTTGGATGAAAGTGGTGATGGATGCCTGACGTTGGATGGGGAGCAAATAGCTCATCTG

rs6548010ACGTTGGATGGCCTGGATTCGGGTTTTTAAACGTTGGATGCTATAAGCTGCTTATCAGAG

rs6548011ACGTTGGATGCTATAAGCTGCTTATCAGAGACGTTGGATGGCCTGGATTCGGGTTTTTAA

rs934198ACGTTGGATGACATGGAAGGAGGATGAGTGACGTTGGATGAGGTAGGACCCTCATGATTG

rs634292ACGTTGGATGGAGGCTTGTTTATGGCACAGACGTTGGATGCGTGCTTTTTCTCAAGTGCC

rs1003177ACGTTGGATGTACACAGACCCAGAAGATACACGTTGGATGGATGCATGAACAAAGGAAGC

rs6726115ACGTTGGATGATACAGATAAGGCACTTGGCACGTTGGATGAGGGAACTGAACGTGAAAGG

rs481069ACGTTGGATGTTTGAACTTCCTGAATGGTGACGTTGGATGATTGTGAGGGTTTACTTTCC

rs1367115ACGTTGGATGGGTTTGGAACAACTGATTGGACGTTGGA-T'GGGTAGGGAAATACTTTCAACG

rs666126ACGTTGGATGTTCTGCAGGATTCATCTCTCACGTTGGATGTTTTGTATGCCAGGTTAAGG

rs7566030ACGTTGGATGGATACAGAAGAGAGTGGTGGACGTTGGATGAGACTTGAGCCTTCAATGGC

rs7590135ACGTTGGATGACTGGTCTTAGGGTTACACCACGTTGGATGACAAAGCACCTGCTCCAAGA

rs6718513ACGTTGGATGCTTCCCTAGGTCTGAAGAACACGTTGGATGGCTTCTTTAGTGCCAAAGAG

rs515135ACGTTGGATGGGCTTACAGCCAAGTAACAGACGTTGGATGACCATCTTGTTACTGCACAG

rs1367114ACGTTGGATGGTTGGAGAATTATTTGCAGGACGTTGGATGGTGTGTGTGTATTTGTGTTTG

rs563290ACGTTGGATGGGGAAAATGCTGCAATGAACACGTTGGATGTCTGGGTATTCATCCAGAAG

rs562338ACGTTGGATGACCCAAGATGTAGAAACAGCACGTTGGATGCCATGGTTTGCATACATCAC

rs581411ACGTTGGATGACCTGGTGTGCTTAACTGTTACGTTGGATGGACAAGTGAAAAAGTTGGGC

rs580889ACGTTGGATGTGGGCTGACTCTCTTATCTCACGTTGGATGCCTCTGAACTGCAATAAGCC

rs548145ACGTTGGATGGAAGGAGGATGGTCAGAAACACGTTGGATGAGCTGTATCTCCCCTTTGTG

rs668948ACGTTGGATGATTGGAATAGGAAGGGCATGACGTTGGATGCTCTATCGTAATGGGGAAAAG

rs594677ACGTTGGATGGACTTGGTATTGAACAGGACACCTTGGATGTAGCAGGCATTTGCACTTTG

rs571468ACGTTGGATGGTGATGAAATTAAGGCCAGGACGTTGGATGATCTCACTGTTTCTCCAGGG

dbSNP Forward Reverse rs# PCR primer pCR primer rs4665492ACGTTGGATGAGTGCGTCACTTCTATTGACACGTTGGATGCCAACAAGCATGTAAGTCAC

rs622236ACGTTGGATGCGCTTTTCTGTACTGTTTGAGACGTTGGATGTCCCTTGTCACTACAAAGAC

rs541041ACGTTGGATGGAGAGGAAAAGGTCACATTCACGTTGGATGATGCAGTAAGAGTAAGTGGC

rs540156ACGTTGGATGCTTGTCTTTGAAATTCCATAGACGTTGGATGCTCTCCTCCATGAATAATTAC

rs1367113ACGTTGGATGATAATACTGCAGGAGGACAGACGTTGGATGAGAACAAATGTCCTTCTCTG

rs1897084ACGTTGGATGCTTCATCCTCTTAAAAGGTCACGTTGGATGCACAAAACTATGAAACTTCC

rs1897083ACGTTGGATGGTTCAACCTATCATTTTCTTCACGTTGGATGTAACTCAATATGGATTAGAC

rs478588ACGTTGGATGATCTCTTGAACCCAAGAGATACGTTGGATG'f-GTTTAAGGTTTATGTCTTG

rs664894ACGTTGGATGCTTGAACCCAAGAGATGGAGACGTTGGATGTGGATTCTCTTTCTGCTGCC

rs1594286ACGTTGGATGCTTGAACCCAAGAGATGGAGACGTTGGATGTGAATTCTCTTTCTGCTGCC

rs7422168ACGTTGGATGCTTGAACCCAAGAGATGGAGACGTTGGATGTGAATTCTCTTTCTGCTGCC

rs565202ACGTTGGATGGCAAAGGCAATTCCATGGAGACGTTGGATGCTCGCAGCCTATGTCTTGTT

rs1429974ACGTTGGATGCTTCATTCTGGTCTGATTTCAACGTTGGATGGAAAGAATTCTATCAAGAAG

rs5829769ACGTTGGATGGTTGGAGCAGATGTTAAGGGACGTTGGATGGATCATGCTTCTGCCTTAAG

rs3056575ACGTTGGATGGTTGGAGCAGATGTTAAGGGACGTTGGATGGATCATGCTTCTGCCTTAAG

rs6708168ACGTTGGATGATGGTTACAGTAGCACCCTGACGTTGGATGTTTTTTACGGCAGCCTGAGC

rs6756743ACGTTGGATGTGGAATCGCAAGTGTAAGTGACGTTGGATGT-fGCACATGTATCCCAGAAC

rs2195598ACGTTGGATGATGGGCAAAGACTTCTTGACACGTTGGATGTGCTGTCAGAAGCTCTTTAG

rs7567217ACGTTGGATGCTCAAAACTCTTCTGGCCTCACGTTGGATGAACAGATGCTGGAGAGGATG

rs568938ACGTTGGATGCTCCTCAGCTAAATATCCAGACGTTGGATGAAAGTGGCAAAGTACTTGGC

rs666416ACGTTGGATGACCCTTTGAAACTGAGGTGGACGTTGGATGTCAGAAGTCCTTAGGACTGC

rs6761300ACGTTGGATGCCTACGAAGTAATTTTTCTCCACGTTGGATGCTATATTGAATGACAAGAGG

rs5829770ACGTTGGATGCACCTAACTGAGAATACACAGACGTTGGATGGCTGTAATTTCCTTAGTGGC

rs1429973ACGTTGGATGAAATATGGCTTGAACCCAGGACGTTGGATGTGGAGTGCAGTGGCACGATCT

rs1429972ACGTTGGATGCTTTCTTTGCTAACCACTGCACGTTGGATGCAGAATCTCTCTGAAAGCTG

rs6756284ACGTTGGATGTGGGATTATAGGCATGAGCCACGTTGGATGT'TCAGCTTTCAGAGAGATTC

rs749988ACGTTGGATGTTTTCTATTTGCATCTACTGACGTTGGATGGTGACAAAACAAACCAAAGTC

rs749987ACGTTGGATGGTCTTCAAATATAGTATGGCACGTTGGATGATTTCCAGGGTTTGACTTTG

rs754524ACGTTGGATGGACTTTCTGGGATTTCTCATCACGTTGGATGCTTCCACTCTAAGCCTTAAG

rs754523ACGTTGGATGGTATTTGCAAAGTAGGTGACACGTTGGATGTCTTGAAAGTGAAAGCCTCC

rs675430ACGTTGGATGATGAGCATGACACAACAACCACGTTGGATGAGGTATCTTCAGAGACACAG

rs600012ACGTTGGATGACTCCAGCCTGGGAGACAGAACGTTGGATGGCCTTGAACTTACACTCAAG

rs614303ACGTTGGATGCAAAACTCACATTCTTTGACACGTTGGATG'1-TTAAATTCCTGCCATGCAC

dbSNP Extend Term rs# Primer Mix rs1318006 CCCTGACCTGTCACAGGG ACG

rs1318005 ATGAGAGCCCACCTCCTGT ACT

rs1318004 TGAGAGCCCACCTCCTGTA ACG

rs1318003 ACTGGGAGACTCACAGGGA ACT

rs4327259 GCCACTGGTCCAGCACAG ACT

rs6756501 GCCACTTTCTCCTCCTGCT ACG

rs6725189 AGAGAGGGCCGACTGCTG CGT

rs4665709 GTCCCCACCCAAATCTCAC ACT

rs4665710 GGCGGATTTCTCCTTTGGTG CGT

rs4371387 GTTCCAGCCATGTAGGTTGT ACT

rs952274 GGGTGACATGCATTGTGATTT CGT

rs952275 I CCTTCTGCTCAAAAACTTTTACI ACT

dbSNP Extend Term rs# Primer Mix rs1801695 ATTATTTTCTTCGTCGCAATGG ACG

rs1042034 GAGATCAACACAATCTTCA ACT

rs1801702 GATAAATCTTTCAACAGTTCC ACT

rs1042031 TTGGTACGAGTTACTCAA ACT

rs2678378 AGTCCTAGGAAGGCTTTAATTT ACG

rs2678379 AGTCAGGAAATGACAGATAGG ACT

rs1800479 GGTATGGAGATGAAGAAAATCA ACT

rs1801701 AAAGACCCAGAATGAATC ACG

rs4362589 GGGCACTTCCAAAATTGATGAT CGT

rs5742904 CCTGCAGCTTCACTGAAGAC ACG

rs1799812 GGTGCCCTCTAATTTGTACTG ACG

rs2163204 GCTGCGATACCTGCTTCGT ACT

rs676210 AAGTTCCTGACCTTCACATAC ACG

rs1042006 CTGATGATCTTTACTTTCATTTCACT

rs1801696 GAACCTTACTGACTTTGCA ACT

rs693 GGCCAAATTCCGAGAGAC ACG

rs1041974 GTTGGATTTATTGATGATGCTGTACT

rs1041968 TTTGACATGCTCAAGAAC ACT

rs568413 TGGCGTAGAGACCCATCA ACT

rs2854726 AGCCTGTAGTCAATAACGCC CGT

rs2854725 AGCTTTGTGTAACTGGGTAAC ACT

rs2000998 TATCTGGTTTTGATCACCACAT CGT

rs2000997 CAGGATTAAACAGAAGTTCCAA CGT

rs497166 AGTGCTGGGATTACAGGTGT ACT

rs562956 CGGCTTCTCCTCTTATTTCTG CGT

rs7589300 AAGGTCCCTGACCTTTGAAC ACT

rs3791980 GGAAAATTAATATTTTCCCCCC CGT

rs3791981 GAGAATGAAGAAACAATAGCTC ACG

rs1801700 GACTCGTGGAAGAAGTTGGT ACT

rs679899 AAGTTGAGATTCTTTCAGA ACT

rs1041952 CAGAACTCAAGTCTTCAATCCT ACT

rs6727706 TCCCTAGTGTATGTTTTTGTCA ACT

rs6719207 TGTAACCATGTCAACAGTAGC CGT

rs1469513 CAAGCCTCTGGCCTTTGAAG ACT

rs1800478 CATACACGGTATCCTATGGAG ACT

rs550619 GTGGCCAGGACTCCTCAAT ACT

rs6752026 GGGAAGCAGGTTTTCCTTTAC ACG

rs579826 TGAGCCACCAGGTCCAGC ACG

rs597331 CTCTCAGAAAGTTCCCAACAC ACT

rs1367116 TTAAAGGAACCTAACTAGGGAA ACT

rs1367117 AGCCATACACCTCTTTCAGG ACT

rs1800480 GGCACTCAGCCCCGCAG ACT

rs1800481 TCTCAGACCCTGAGGCGC ACG

rs934197 CTGCATCCCCCTTCTCTCT ACG

rs1625764 CATCGAGCGCTGGCTGAAG ACG

rs1625714 TCCAGCTGGGCAGAGGCA ACT

rs1560357 CCACTACCGCTGATTCCCT CGT

rs617314 GTAGCTTGTTACATCTGGGG ACT

rs547186 GGGAAGACTTGCCAAAGACC I CGT

~0 dbSNP Extend Term rs# Primer Mix rs589566 TCTGAGTTTAGTGCTGTTCAC ACT

rs588245 AGCCTATCTCGTTTCTGCCT ACT

rs585967 CTATGAAGTCTAACTGGGCTG ACT

rs7562777 ATGGTGCCTCGTGCCTGTA ACT

rs7575840 TCACAGGGAAAGCCAGGAAT ACT

rs7567653 ACTTCATTAATAACATCGCCGT ACT

rs6548010 GGTTTTTTGGTATACACATATTCACT

rs6548011 AAGGATAGAAAAAATATAGTCCCACT

rs934198 AGGAGGATGAGTGGGGAGA ACT

rs634292 CTTGTTTATGGCACAGAAGATG ACT

rs1003177 CACCATTTATGCAGGGCTAG ACT

rs6726115 CTGGTACTTGGTTAATAGTCC ACT

rs481069 CAGGACCCCAGCCCCCA ACT

rs1367115 TGGATTAGTGAATGGGAGGG ACT

rs666126 GCAGGATTCATCTCTCCATATA ACG

rs7566030 TGCCTGCCCCAACCCTCT ACT

rs7590135 CACCAGGCTGTTTTAGCAGC ACG

rs6718513 AAGAACAAAAAGAGGATTGGGA ACT

rs515135 ACAGCCAAAATGGAACCAAAG ACT

rs1367114 TTGCAGGTCACTTTTTTAAAGTTACT

rs563290 AACACAGAAATGCAGATATCTC ACG

rs562338 CATTGTCTTGACAGATGAATGC ACT

rs581411 TGATAGAGACAGTTATCAATTTCACT

rs580889 TCTCCGGCTGGGCCGTC ACT

rs548145 AGAAACAATGACAGAATACTAAGACT

rs668948 GGCATGCTGTCTCCTCTGC ACT

rs594677 GTATTGAACAGGACTGAGTAAT ACG

rs571468 GAAGAGAAGGCTGGCGCC CGT

rs4665492 CCTATAGATAAGACTTTTATTCCAACT

rs622236 GTGAATGAATGAATGAATGAACCCGT

rs541041 CTATTCATGTTTCAGGGCCCA ACG

rs540156 TACGAGTATATGTATACATTTGCACT

rs1367113 GGCTAGATAGGGAAGTGGG ACT

rs1897084 TCTTAAAAGGTCTTTTGCAAAGAACT

rs1897083 TCTATATTTTCTTTTGGAAGTTTCACT

rs478588 CTGGGCAGCAGAAAGAGAAT ACG

rs664894 GCCAAGATCATGCCACTGC CGT

rs1594286 ATGGAGGTTGCAGTGAGCC ACT

rs7422168 GATGGAGGTTGCAGTGAGC ACT

rs565202 CAGGAACAATTGGAAGTCTACA ACG

rs1429974 CTGGTCTGATTTCAGTTGCC ACT

rs5829769 GAGGATATATTCCAGGAGATATACGT

rs3056575 CAGAGGATATATTCCAGGAGA CGT

rs6708168 CCCTGCTTCTCAGTACCAAA CGT

rs6756743 CGCAAGTGTAAGTGATCAAAG ACG

rs2195598 ACTAAAACACCAAAAGCAATGG ACG

rs7567217 ACTCTTCTGGCCTCATCTAC ACT

rs568938 CCTCACACAAAACACCAGAAC ACT

rs666416 GCCTGTCCCACTGGGCC ACG

dbSNP Extend Term rs# Primer Mix rs6761300 GGAATTCTTCAATAATGACAACAACT

rs5829770 CTTGATAACATGTACCAAAAAAAACGT

rs1429973 CTTGAACCCAGGAGGCAGA ACT

rs1429972 GCTAACCACTGCAGCTCCT ACG

rs6756284 GGCATGAGCCACCGCGC ACG

rs749988 TCTATTTGCATCTACTGAATTTTTACG

rs749987 CGAATAAGGAGCTATCTGTGA ACG

rs754524 TAGAAAACAAGCTATACATTCATAACT

rs754523 TGCAAAGTAGGTGACAATTGC ACG

rs675430 GTGAAAAATGAACAGATTTGTCCACT

rs600012 CTGGGAGACAGAGCGAGATT ACG

rs614303 CTTTGACAATACATGAGCCCT I ACG

Genetic Analysis [0253] Allelotyping results from the discovery cohort are shown for cases and controls in Table 13.
The allele frequency for the A2 allele is noted in the fifth and sixth columns for osteoarthritis case pools and control pools, respectively, where "AF" is allele frequency. The allele frequency for the A1 allele can be easily calculated by subtracting the A2 allele frequency from 1 (A1 AF
= 1-A2 AF). For example, the SNP rs1318006 has the following case and control allele frequencies: case A1 (C) = 0.494;
case A2 (T) = 0.506; control Al (C) = 0.460; and control A2 (T) = 0.540, where the nucleotide is provided in paranthesis. Some SNPs are labeled "untyped" because of failed assays.

dbSNP PositionChromosomeAl/A2 F A2 F A2 F p-rs# in position AlleleCase Control Value SEQ D AF AF
NO:

rs1318006238 21188688 C/T 0.506 0.540 0.326 rs1318005294 21188744 C/T 0.044 0.034 0.643 rs1318004295 21188745 A/G

rs1318003347 21188797 A/C

rs43272591425 21189875 A/C 0.962 0.965 0.865 rs67565014891 21193341 C/T 0.195 0.141 0.061 rs67251895087 21193537 G/T 0.317 0.250 0.036 rs46657097041 21195491 A/G 0.683 0.757 0.014 rs46657107121 21195571 A/C 0.206 0.209 0.926 rs43713877219 21195669 A/G 0.579 0.688 0.0001 rs952274 7443 21195893 G/T 0.163 0.123 0.158 rs952275 7485 21195935 G/T 0.234 0.319 0.013 rs180169510939 21199389 A/G 0.047 0.071 0.319 rs104203411367 21199817 A/G 0.191 0.182 0.743 rs180170211571 21200021 C/G

rs104203111839 21200289 A/G 0.686 0.785 0.001 rs267837812551 21201001 A/G

rs267837912646 21201096 A/G 0.693 0.714 0.466 rs180047913469 21201919 G/C 0.144 0.130 0.687 rs180170114913 21203363 A/G 0.090 0.116 0.314 rs436258915205 21203655 G/T

rs574290415246 21203696 A/G

rs179981215695 21204145 G/A

rs216320417473 21205923 G/T

rs676210 17610 21206060 A/G 0.186 0.177 0.758 rs104200617828 21206278 A/C

dbSNP positionChromosomeAllA2 F A2 F A2 F p-rs# in position Allele Case Control Value SEQ ID AF AF
NO:

rs180169618130 21206580 A/G

rs693 18281 21206731 C/T 0.494 0.537 0.208 rs104197418623 21207073 CIG

rs104196818890 21207340 C/T

rs568413 21561 21210011 C/T

rs285472623100 21211550 A/T

rs285472523872 21212322 A/C

rs200099824581 21213031 A/T

rs200099724582 21213032 A/T

rs497166 24983 21213433 C/T

rs562956 27540 21215990 A/T

rs758930030846 21219296 C/T

rs379198031415 21219865 G/T

rs379198131453 21219903 A/G 0.964 0.968 0.849 rs180170031899 21220349 TIC 0.832 0.897 0.008 rs679899 37000 21225450 A/G 0.378 0.474 0.004 rs104195238681 21227131 ClG

rs672770639287 21227737 C/T

rs671920742951 21231401 A/T

rs146951345648 21234098 ClT 0.477 0.534 0.079 rs180047846222 21234672 C/T

rs550619 46687 21235137 A/G 0.053 0.062 0.656 rs675202647020 21235470 A/G

rs579826 47593 21236043 C/T 0.069 0.063 0.817 rs597331 48513 21236963 C/T 0.435 0.512 0.014 rs136711649723 21238173 A/G

rs136711749986 21238436 A/G 0.431 0.367 0.049 rs180048053018 21241468 C/G 0.978 NA NA

rs180048153296 21241746 C/T 0.100 0.082 0.487 rs934197 53547 21241997 A/G 0.338 0.398 0.075 rs162576453899 21242349 C/T

rs162571453916 21242366 G/T

rs156035753933 21242383 A/C

rs617314 54305 21242755 G/T 0.977 0.971 0.741 rs547186 55327 21243777 A/T 0.468 0.490 0.528 rs589566 55895 21244345 C/T 0.386 0.377 0.780 rs588245 56143 21244593 C/T 0.425 0.398 0.397 rs585967 56640 21245090 G/T 0.724 0.781 0.046 rs756277758486 21246936 A/G

rs757584059576 21248026 G/T 0.436 0.408 0.422 rs756765363048 21251498 A/G 0.918 0.910 0.739 rs654801064008 21252458 A/G 0.293 0.345 0.081 rs654801164018 21252468 C/T 0.530 0.482 0.135 rs934198 64859 21253309 A/C 0.526 0.484 0.225 rs634292 65995 21254445 G/T 0.456 0.492 0.256 rs100317766905 21255355 A/G

rs672611567183 21255633 A/G 0.293 0.342 0.119 rs481069 67942 21256392 C/T 0.138 0.104 0.167 rs136711568101 21256551 A/G 0,421 0.408 0.693 rs666126 68521 21256971 A/G 0.500 0.530 0.388 rs756603068664 21257114 C/G 0.397 0.416 0.536 rs759013568988 21257438 A/G 0.268 0.324 0.082 rs671851369178 21257628 CIG

rs515135 72143 21260593 A/G 0.726 0.747 0.455 rs136711474183 21262633 C/G

rs563290 74312 21262762 C/T 0.667 0.690 0.516 rs562338 74407 21262857 C/T 0.482 0.578 0.006 rs581411 75518 21263968 A/G 0.162 0.157 0.839 rs580889 76153 21264603 A/G 0.127 0.111 0.487 rs548145 77398 21265848 A/G 0.709 0.765 0.049 rs668948 77615 21266065 A/G 0.133 0.127 0.805 rs594677 79092 21267542 C/T

rs571468 80000 21268450 G/T 0.455 0.502 0.169 ~3 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in position Allele Case Control Value SEQ iD AF AF
NO:

rs466549280125 21268575 A/C 0.274 0.327 0.088 rs622236 80595 21269045 G/T

rs541041 81061 21269511 C/T 0.779 0.791 0.694 rs540156 81151 21269601 A/G 0.237 0.277 0.237 rs136711381918 21270368 C/T 0.394 0.366 0.370 rs189708483072 21271522 C/T

rs189708383137 21271587 C/T 0.279 0.326 0.139 rs478588 83235 21271685 C/T

rs664894 83263 21271713 A/T 0.319 0.343 0.467 rs159428683279 21271729 A/G

rs742216883280 21271730 CIG

rs565202 83533 21271983 C/T 0.483 0.514 0.373 rs142997486856 21275306 G/T 0.583 0.535 0.189 rs582976987186 21275636 -/TATA

rs305657587189 21275639 -/ATAT

rs670816887727 21276177 AIT 0.610 0.563 0.163 rs675674387978 21276428 C/T 0.051 0.051 0.978 rs219559889129 21277579 A/G

rs756721789556 21278006 C/T 0.100 0.087 0.547 rs568938 89702 21278152 A/G 0.177 0.150 0.304 rs666416 90233 21278683 A/G 0.421 0.364 0.093 rs676130093060 21281510 A/G 0.271 0.348 0.012 rs582977094779 21283229 -/T 0.036 0.037 0.971 rs142997395367 21283817 A/G

rs142997295844 21284294 A/G 0.422 0.443 0.533 rs675628495942 21284392 A/G 0.155 0.114 0.133 rs749988 96884 21285334 CIT

rs749987 96938 21285388 A/G

rs754524 97627 21286077 A/C 0.248 0.306 0.044 rs754523 97777 21286227 C/T 0.567 0.512 0.113 rs675430 97871 21286321 A/C 0.352 0.345 0.812 rs600012 98746 21287196 A/G

rs614303 99663 21288113 A/G 0.722 0.730 0.805 [0254] Allelotyping results were considered particularly significant with a calculated p-value of less than or equal to 0.05 for allelotype results. These values are indicated in bold. The allelotyping p-values were plotted in Figure lA for the discovery cohort. The position of each SNP on the chromosome is presented on the x-axis. The y-axis gives the negative logarithm (base 10) of the p-value comparing the estimated allele in the case group to that of the control group. The minor allele frequency of the control group for each SNP designated by an X or other symbol on the graphs in Figure 1 A can be determined by consulting Table 13. For example, the left-most X on the left graph is at position 21188688. By proceeding down the Table from top to bottom and across the graphs from left to right the allele frequency associated with each symbol shown can be determined.
(0255] To aid the interpretation, multiple lines have been added to the graph.
The broken horizontal lines are drawn at two common significance levels, 0.05 and 0.01.
The vertical broken lines are drawn every 20kb to assist in the interpretation of distances between SNPs. Two other lines are drawn to expose linear trends in the association of SNPs to the disease. The generally bottom-most curve is a nonlinear smoother through the data points on the graph using a local polynomial regression method (W.S. Cleveland, E. Grosse and W.M. Shyu (1992) Local regression models. Chapter 8 of Statistical Models in S eds J.M. Chambers and T.J. Hastie, Wadsworth &
Brooks/Cole.). The black line provides a local test for excess statistical significance to identify regions of association. This was created by use of a l0kb sliding window with lkb step sizes. Within each window, a chi-square goodness of fit test was applied to compare the proportion of SNPs that were significant at a test wise level of 0.01, to the proportion that would be expected by chance alone (0.05 for the methods used here). Resulting p-values that were less than 10-8 were truncated at that value.
[0256] Finally, the exons and introns of the genes in the covered region are plotted below each graph at the appropriate chromosomal positions. The gene boundary is indicated by the broken horizontal line. The exon positions are shown as thick, unbroken bars. An arrow is place at the 3' end of each gene to show the direction of transcription.
Example 5 ILIRL2 Proximal SNPs [0257] It has been discovered that rs1024791, which lies within the ILIRL2 gene, is associated with occurrence of osteoarthritis in subjects. Interleukin-1 receptor-like 2 is a member of the interleukin 1 receptor family. ILIRL2 inhibits IL-1 activity and contains immmunoglobulin domains. This gene and four other interleulcin 1 receptor family genes, including interleukin 1 receptor, type I (ILIRI), interleukin 1 receptor, type II (IL1R2), interleukin 1 receptor-like 1 (IL1RL1), and interleukin 18 receptor 1 (IL18R1), form a cytokine receptor gene cluster in a region mapped to chromosome 2q12.
ILIRL2 may mediate inflammatory responses that can contribute to the development of OA. ILIRL2 biological activity can be modulated by addition of an antibody, a recombinant binding partner, a binding agent, or a recombinant ILIRL2 protein or functional fragment thereof.
[025] One hundred forty additional allelic variants proximal to rs 1024791 were identified and subsequently allelotyped in osteoarthritis case and control sample sets as described in Examples 1 and 2.
The polymorphic variants are set forth in Table 14. The chromosome positions provided in column four of Table 14 are based on Genome "Build 34" of NCBI's GenBank.

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs39173042 225 102409525 G/T

rs20417472 509 102409809 C/T

rs39173052 860 102410160 C/T

rs37712002 874 102410174 C/T

rs39173062 939 102410239 A/G

rs39173072 1483 102410783 G/T

rs39173082 1798 102411098 C/T

rs39173102 2189 102411489 A/T

rs39173112 2215 102411515 A/G

rs39173122 2282 102411582 ClG

rs39173132 2340 640 C/T

~rs39173142 ~ 2963 ~ _ A/C
~ _ _ _ ~

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs39173162 3369 102412669 -/T

rs31718452 3481 102412781 A/G

rs31718462 3564 102412864 G/T

rs39173172 3653 102412953 -/TC

rs39173182 4860 102414160 A/G

rs39173192 4941 102414241 A/T

rs39173202 4975 102414275 A/C

rs39173212 5321 102414621 A/G

rs39173222 5346 102414646 A/G

rs39173232 5541 102414841 A/G

rs39173242 5633 102414933 C/G

rs39173252 6007 102415307 G/T

rs37321342 6317 102415617 C/G

rs37321332 6378 102415678 A/G

rs21107262 6382 102415682 C/T

rs39173262 6426 102415726 C/T

rs39173272 6479 102415779 C/G

rs39173282 6641 102415941 C/T

rs37321312 6703 102416003 C/T

rs37321302 6705 102416005 C/T

rs39173292 7963 102417263 G/T

rs39173302 8525 102417825 G/T

rs39173312 8526 102417826 A/T

rs39173442 8598 102417898 C/T

rs39173322 8624 102417924 A/T

rs39173332 8883 102418183 A/T

rs39173342 8980 102418280 G/T

rs10300212 13578 102422878 G/T

rs22411322 16135 102425435 G/T

rs22411312 16141 102425441 G/T

rs38350362 16642 102425942 -/TGG

rs19975042 16931 102426231 A/G

rs18052322 17004 102426304 A/G

rs19716962 17009 102426309 C/T

rs19716952 17010 102426310 AIG

rs37711992 18713 102428013 C/T

rs19223032 18853 102428153 C/T

rs32137342 20783 102430083 C/T

rs19975032 21335 102430635 A/G

rs15586492 22180 102431480 C/T

rs15586482 22268 102431568 A/C

rs15586472 22285 102431585 C/T

rs15586462 25378 102434678 C/T

rs18825142 25906 102435206 C/G

rs18825132 26015 102435315 A/G

rs867770 2 26475 102435775 A/G

rs23102352 26798 102436098 A/T

rs870684 2 27042 102436342 A/G

rs37711972 27649 102436949 A/G

rs37711962 27827 102437127 A/T

rs38212072 27873 102437173 A/G

rs37711952 28122 102437422 A/G

~6 dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs37711942 28202 102437502 A/G

rs37711932 28232 102437532 A/C

rs37711922 28240 102437540 G/T

rs37552902 29546 102438846 G/T

rs38212062 29748 102439048 A/G

rs23026232 30054 102439354 A/T

rs37552892 30646 102439946 G/T

rs19223022 31149 102440449 A/C

rs21107252 36912 102446212 A/C

rs14653262 36936 102446236 C/G

rs28714582 37184 102446484 C/T

rs20803102 39064 102448364 C/T

rs19222892 39343 102448643 G/T

rs19222902 40868 102450168 C/G

rs19222912 40917 102450217 A/G

rs19222922 41113 102450413 A/C

rs38155172 47343 102456643 A/T

rs22411302 47806 102457106 A/G

rs19222952 47911 102457211 A/G

rs19222942 48009 102457309 C/T

rs23026222 48621 102457921 C/G

rs23102402 49245 102458545 C/G

rs10247922 49247 102458547 CIG

rs38361122 49299 102458599 -/CTCT

rs30749692 49302 102458602 -/AGAG

rs9179942 49514 102458814 CIT

rs20417532 49626 102458926 G/T

rs20417522 49791 102459091 A/G

rs10247912 50010 102459310 A/G

rs10247902 50294 102459594 A/G

rs9955152 51482 102460782 AIG/T

rs9955142 51556 102460856 A/G

rs19222932 51855 102461155 A/G

rs37552872 51956 102461256 C/T

rs37295642 52155 102461455 A/G

rs37711882 52448 102461748 A/G

rs37711872 52458 102461758 C/T

rs37711862 52511 102461811 C/T

rs37711852 52607 102461907 A/G

rs23102412 54049 102463349 A/C

rs23026212 54224 102463524 A/C

rs23026202 54567 102463867 A/G

rs37711842 55052 102464352 C/T

rs38341612 55857 102465157 -/C

rs37552862 55941 102465241 C/G

rs37552852 56120 102465420 A/G

rs19975022 56349 102465649 C/T

rs37711822 56727 102466027 A/G

rs38361112 57232 102466532 -/CT

rs37711812 58806 102468106 C/T

rs9557542 _61_181 102470481 C/T

rs23026122 ~ 63808 _ ~ A/G
( 102473108 ~7 dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs37552842 64526 102473826 A/T

rs3821 2 64865 102474165 A/G

rs38155112 64928 102474228 C/T

rs22870412 64966 102474266 A/C

rs22870402 65080 102474380 A/G

rs22870392 65690 102474990 C/T

rs37552832 66228 102475528 AlG

rs37552822 66982 102476282 A/G

rs18123262 72511 102481811 A/G

rs15586262 74170 102483470 A/T

rs15586252 74264 102483564 C/T

rs15586242 74333 102483633 C/T

rs15586232 74502 102483802 A/T

rs10351312 74741 102484041 A/C

rs21106612 75321 102484621 C/T

rs142O0932 82558 102491858 A/G

rs30749712 85366 102494666 -/TTG

rs13453022 85469 102494769 C/T

rs14200922 86485 102495785 G/T

rs13453012 87687 102496987 C/T

rs23102422 89463 102498763 G/T

rs231 2 89660 102498960 A/G

rs18825102 95718 102505018 C/T

rs18825112 95821 102505121 A!G

Assay for Verifying and Allelotypin~ SNPs [0259] The methods used to verify and allelotype the 140 proximal SNPs of Table 14 are the same methods described in Examples 1 and 2 herein. The primers and probes used in these assays are provided in Table 15 and Table 16, respectively.

dbSNP Forward Reverse rs# PCR primer PCR primer rs3917304ACGTTGGATGCAGAGAAGATAAGGAATGAGACGTTGGATGAAGGAAAATTACCCTAAACC

rs2041747ACGTTGGATGGGGAAGACTATTACAGGTATGACGTTGGATGTAGGAGCAACTAACACTTGC

rs3917305ACGTTGGATGGTTGTGAAGGAGAGGTCATGACGTTGGATGCGAAAGCCTCTACTGGTTTC

rs3771200ACGTTGGATGCTGGTTTCCTACTGCTCATCACGTTGGATGAGTGCTTTGCAGGTGTTGTG

rs3917306ACGTTGGATGCACCTGCAAAGCACTTTGTCACGTTGGATGTGCATTGTGTTCTCCATGGG

rs3917307ACGTTGGATGCTGTAGTAAGATTCCATGACACGTTGGATGACCCAAGTAATGAGGAAGTG

rs3917308ACGTTGGATGCAGTGACTTCTGATGTCCTCACGTTGGATGAAGTTAGGTCTGGTACATTG

rs3917310ACGTTGGATGGAGAAGAACTAAATGGAAGGACGTTGGATGGGGAAGAACTGATATCTTCA

rs3917311ACGTTGGATGCCATAGATTCATTTGGGGAAGACGTTGGATGGAGAAGAACTAAATGGAAGG

rs3917312ACGTTGGATGCCATACAAACACTGACTCTCACGTTGGATGGAAGATATCAGTTCTTCCCC

rs3917313ACGTTGGATGCACCATGACTATACTTGGTCACGTTGGATGTCAGTGTTTGTATGGGTGTG

rs3917314ACGTTGGATGGGCCTGCATTCAGACAATATACGTTGGATGGAAACTTCATAGAATGCACC

rs3917316ACGTTGGATGAGTATTCTTGTATATGCCACACGTTGGATGGTTAGGAGATGTAGAAGATG

rs3171845ACGTTGGATGGAACTCATTAGGCTGAATATCACGTTGGATGACAGATGCTCTAAATACCTG

gg dbSNP . Forward Reverse rs# PCR primer PCR primer rs3171846ACGTTGGATGTGTCCTATTCATCACAGAGCACGTTGGATGCTGCCTCAACATTCATATTGG

rs3917317ACGTTGGATGTCTCAGCCCTGAATTCTATCACGTTGGATGGACTAGATCTTCATGCATCAG

rs3917318ACGTTGGATGAAAAGCCTTGTGTGGCTTTGACGTTGGATGGTCTGAAAAACAGGAAGCAC

rs3917319ACGTTGGATGGTGCTTCCTGTTTTTCAGACACGTTGGATGAAGCCTGATGTTTCTCTGAC

rs3917320ACGTTGGATGCGTAAAGAAAAGCAGAAGACACGTTGGATGTTGCTCTTCAGATGAACCAC

rs3917321ACGTTGGATGAGGAGAAACTGCAAAGAGAGACGTTGGATGACAGGAGGCACCTAAAGAAC

rs3917322ACGTTGGATGAGTCAGCATGAGGCATAACCACGTTGGATGAGCATGGAGAAGTTGCCAAG

rs3917323ACGTTGGATGACTTCAGAGTAGAGGGCTTGACGTTGGATGAAGTGCTGGGATTATAGGCG

rs3917324ACGTTGGATGATCACCAGAGGTCAGGAGTTACGTTGGATGCCACCATGCCTAGCTCATTT

rs3917325ACGTTGGATGTAGTTAAGTCATCCACAGCCACGTTGGATGTGTCAGTCTCACTTTGCCTG

rs3732134ACGTTGGATGTTAATGCTTTCCTCCCTGGCACGTTGGATGTAGGGAGCTGTTCCTCCAAA

rs3732133ACGTTGGATGAAGGATGGTTCATGTGTGGGACGTTGGATGTTACGTCTTTGGAGGAACAG

rs2110726ACGTTGGATGAAGGATGGTTCATGTGTGGGACGTTGGATGTACGTCTTTGGAGGAACAGC

rs3917326ACGTTGGATGTGCACAGCCCACACATGAACACGTTGGATGTTCAGCTCCTGAACAGGTGG

rs3917327ACGTTGGATGAAAGCATGGGCTTCAGCTCCACGTTGGATGATGCCGCTCTTCTGTCATCC

rs3917328ACGTTGGATGTAGGCAAAGGAGGAGGAAGGACGTTGGATGTGTGTGAATTCCCAGGTTGG

rs3732131ACGTTGGATGAGGCCTTCTCGCATTTTCTCACGTTGGATGTCCCAGAGACTGTGGAATTG

rs3732130ACGTTGGATGTCCCAGAGACTGTGGAATTGACGTTGGATGAGGCCTTCTCGCATTTTCTC

rs3917329ACGTTGGATGAAGTCAAAGGAAGTTCACGGACGTTGGATGGTGCAAAGTTATTCCCCATC

rs3917330ACGTTGGATGTAAGCCAATAGCCTCTGACCACGTTGGATGAACAAGGTGAGGAGACCTTC

rs3917331ACGTTGGATGAACAAGGTGAGGAGACCTTCACGTTGGATGTAAGCCAATAGCCTCTGACC

rs3917344ACGTTGGATGAGAGTTCTTCCTGTTGTGGGACGTTGGATGTAGAAGAAGGGAGTTAGGGC

rs3917332ACGTTGGATGATTGGCTTAACAGTGAGCCCACGTTGGATGAGAAGCAAATGAGCAGAGGG

rs3917333ACGTTGGATGTAAGAAGGAGGCACTGACTGACGTTGGATGGCTGTCCAAAATGCATGCTC

rs3917334ACGTTGGATGGACTCAGACTCTAAGCCAACACGTTGGATGAGTCAGTGCCTCCTTCTTAC

rs1030021ACGTTGGATGCATTGCTTCATGTTCTTACCACGTTGGATGAAAACTGGGCATAACCTCTC

rs2241132ACGTTGGATGAGGAGGATGGGCGAGGAGTAACGTTGGATGTCTGGACACCAGCCTGCTTC

rs2241131ACGTTGGATGAGGAGGATGGGCGAGGAGTAACGTTGGATGCTGTCAGGTGGCAGAAGCAG

rs3835036ACGTTGGATGTTCCGCGGAAGAGGAAACAGACGTTGGATGTCACCTCCAAGCTCAAAGGC

rs1997504ACGTTGGATGCCTGTAATCCCAGTACTTTGACGTTGGATGTGTTAGCCAGGATGGTCTAG

rs1805232ACGTTGGATGTTGAGTAGCTGGGACTACAGACGTTGGATGTAACACGGTGAAACCCCGTC

rs1971696ACGTTGGATGTAGACCATCCTGGCTAACACACGTTGGATGTTGAGTAGCTGGGACTACAG

rs1971695ACGTTGGATGTTGAGTAGCTGGGACTACAGACGTTGGATGTAGACCATCCTGGCTAACAC

rs3771199ACGTTGGATGTGAATAACACAGGCCTGCTGACGTTGGATGGCTTGACCTGAATAGACAGC

rs1922303ACGTTGGATGGTGGGGCCTGAATAAAACACACGTTGGATGTAAGGTCATGCAAGCCAGTG

rs3213734ACGTTGGATGAACCCACTGTTTTTTATAGGACGTTGGATGTGACTGCTAGCTAACTAATC

rs1997503ACGTTGGATGAAAACTCATGACCCAGAGGGACGTTGGATGGCACAGGCTAGTCATTTGAG

rs1558649ACGTTGGATGTGCATGGTGGTTCATGCCTGACGTTGGATGAATCTTGCTATGATGCCCAG

rs1558648ACGTTGGATGAGATTTCCTACAACCTTGTGACGTTGGATGAGGTACATTTTATACCCACC

rs1558647ACGTTGGATGGAAAAATGTGGTCAATCTCACACGTTGGATGCAACCTTGTGTTGAACTTTG

rs1558646ACGTTGGATGGGCCTTGGTTAGAGTTTAGGACGTTGGATGGCTTTAGGTTGGCATAAATGG

rs1882514ACGTTGGATGTTCCTTTCCTGTCCATCCTGACGTTGGATGCAGAGTTGAGGTACTGGAAG

rs1882513ACGTTGGATGAAAGTAGAGAGGTCAGGTGGACGTTGGATGGGGCATTACACTTTTCCACC

rs867770ACGTTGGATGGCAGGTGGTGTATTTCAGAGACGTTGGATGACACTGCAGAAGTAGCTTGC

rs2310235ACGTTGGATGGAGCTGGAATAGGGAATCAGACGTTGGATGGCCATTATCCAGAACCTCTG

rs870684ACGTTGGATGCCCAAATTACTCCTCAGCACACGTTGGATGAGAGCGCGAAGTAACTTCAG

rs3771197ACGTTGGATGTAAGCAGTTCCAGTCCACAGACGTTGGATGCCTTTGCTTACCTAAGACTG

rs3771196ACGTTGGATGCCTTTAAACTACACAGCAACACGTTGGATGAGAAGCTTTCTGAGCAAGAG

rs3821207ACGTTGGATGAAAACCATGAAGAGGAGACGACGTTGGATGGCAACTAAAGGATCTTTCTC

rs3771195ACGTTGGATGGTGGACGCTATTGTTCTTAACACGTTGGATGTAAACTCTCAATGAGCTTGG

rs3771194ACGTTGGATGATCTTAAAGTTCAGCCTTGCACGTTGGATGATAATGTTCCAGTGGATCAG

rs3771193ACGTTGGATGGTTCCAGTGGATCAGAATAGACGTTGGATGTTAAAGTTCAGCCTTGCAGC

~9 dbSNP Forward Reverse rs# PCR primer PCR primer rs3771192ACGTTGGATGGGGTTCATTCTTTCTTTCAAGACGTTGGATGATAGCAAAGCGACAGAATGG

rs3755290ACGTTGGATGCCCAATTACACTTTCTGCACACGTTGGATGTGATCACTGTTCAGACCTTC

rs3821206ACGTTGGATGAGAGTGGCCTACATGAGTTGACGTTGGATGCCTCCTGCAAAAAACTGACC

rs2302623ACGTTGGATGGAATACTTAGAAACCTGTGTGACGTTGGATGATCTGTTGTCTTCCAGTTAG

rs3755289ACGTTGGATGTCCAGAACTCTGAGCTCTGCACGTTGGATGCCTCAGCCTTCATTGTCGTG

rs1922302ACGTTGGATGGAGATCTTTCACTTCTTTGGACGTTGGATGGCCACACATAAAACCATATC

rs2110725ACGTTGGATGATTCTCTCCCCAAGCTATACACGTTGGATGCAATAACCAGGTTTGTGACC

rs1465326ACGTTGGATGTGTGTTTGGAAAAACCAATGACGTTGGATGTTTACAGAGTTCCAGGAGGG

rs2871458ACGTTGGATGAGATCCCCATAGGGATCCACACGTTGGATGCACACTTCAGAGTACTAGGG

rs2080310ACGTTGGATGGAATGATCCATTCCAGGGTGACGTTGGATGGACATCATGTTACCTGTGCC

rs1922289ACGTTGGATGTGAGTTTGGTCATTGCTACGACGTTGGATGATACAGGCCATGACCTACTC

rs1922290ACGTTGGATGACACCCAGTTTCCAGCTTTGACGTTGGATGCTTCGGCTCTCTGGTGTTTT

rs1922291ACGTTGGATGGACTTCTCTGCTACCACAACACGTTGGATGCTCATGGGGAGAGGAATCAA

rs1922292ACGTTGGATGATATTACCTCACAATGCAAGACGTTGGATGATGCTTATTGATCCTTTTCC

rs3815517ACGTTGGATGACAATGGTTGTCCTGGAAGGACGTTGGATGAATAGCCCCCTAGGCAAATG

rs2241130ACGTTGGATGGAGAAATGGATCTTACTGCTCACGTTGGATGCAATCCCACCTATCACATAG

rs1922295ACGTTGGATGGTTATATCATGAGCCATCGGACGTTGGATGGTGTCATTTCCAGTGTTTGC

rs1922294ACGTTGGATGCGGGCATACAAAGCAAACACACGTTGGATGACTGTCTTCCCTAAGAGTCC

rs2302622ACGTTGGATGTACTCCAGTGGGTTACACACACGTTGGATGGCATTTAGAGTCACTGCTCC

rs2310240ACGTTGGATGAAATTCAAGTCCTCTCTCTTACGTTGGATGGTGGTTTACCAAGACAGTTG

rs1024792ACGTTGGATGGCTGTGTGGTTTACCAAGACACGTTGGATGCCACACACGTGCGTGTCAAA

rs3836112ACGTTGGATGACGCACGTGTGTGGCTAGCTAACGTTGGATGGATGTATGCAAGCATAGG

rs3074969ACGTTGGATGACGTGTGTGGCTAGCTACATACGTTGGATGGGCTTTAGCTTGATGTATGC

rs917994ACGTTGGATGCCTCCCTTAGAATTGCAGTGACGTTGGATGAAGCAGAGAATGTGCACACC

rs2041753ACGTTGGATGTCCACATGTTGCAACCCAAGACGTTGGATGTAACTGTGAGTGAGCACAGC

rs2041752ACGTTGGATGGAACCTCTTAGAGGTACCAGACGTTGGATGTCCTTCTCCATCACTTTCCC

rs1024791ACGTTGGATGGTGTAAGGGACTGCAGATACACGTTGGATGAAACAGAACCAGGAGGTTGG

rs1024790ACGTTGGATGAGAAAATTCCAGCTGATTCTACGTTGGATGGACTCCTGCCCTACACTTTAA

rs995515ACGTTGGATGTGGGATGGAAATCGCTATTGACGTTGGATGTGTCCCAACCTAGAAGTTTG

rs995514ACGTTGGATGGCTTGGACTTGGCCTCAGAAACGTTGGATGCCAATAGCGATTTCCATCCC

rs1922293ACGTTGGATGGGACAGAGCTAAGGTTATAGACGTTGGATGGATTCAAATCTGGAGGTGTC

rs3755287ACGTTGGATGAAATTGGGTGTGCTCTTCCGACGTTGGATGGACTACTACCAGCCTTCAAC

rs3729564ACGTTGGATGCCTGAGTCCCTCTGAATGTAACGTTGGATGTGCCTTCGAGAGTACTGATG

rs3771188ACGTTGGATGAATCCAATCCTGGGCACTTGACGTTGGATGAGAGTAGAGGATGAGGAAGC

rs3771187ACGTTGGATGAGAGTAGAGGATGAGGAAGCACGTTGGATGAATCCAATCCTGGGCACTTG

rs3771186ACGTTGGATGAAGTGCCCAGGATTGGATTGACGTTGGATGGAGTAAGTCCCAATGCAGCC

rs3771185ACGTTGGATGATCTTGAGGCCCAAGATTTCACGTTGGATGGGCACCAAATGTGTTCTTAG

rs2310241ACGTTGGATGACCTTCTCCAGCTGGTTCTGACGTTGGATGTGGGAGTCCAGCTGTTCAAC

rs2302621ACGTTGGATGCGTCTACCACCGGAAACTAGACGTTGGATGGGAAACAAGTCAGCTCCTGG

rs2302620ACGTTGGATGGTCTCTGTAGAATGGAAGGCACGTTGGATGTGGCTGTGTCTGTTGTGTAC

rs3771184ACGTTGGATGTCTCTCTAGGCCCTGTACTTACGTTGGATGACTTGGTTTGATCTCTCTCC

rs3834161ACGTTGGATGAGGGAAACTGGTTGTCTGAGACGTTGGATGCAAAGCAAGCACTTGATGCC

rs3755286ACGTTGGATGGCATCAAGTGCTTGCTTTGCACGTTGGATGCAAGTTAGTGAATAGCCACG

rs3755285ACGTTGGATGTGCAGATGCCAGAGCCAAAAACGTTGGATGACCTGAAGTGCTGCTAGTAC

rs1997502ACGTTGGATGCGTATTCTTCCTGGAAGCTCACGTTGGATGTCACTGACAGAGTCAGTGAG

rs3771182ACGTTGGATGGCCAACACACAGAGATATTACACGTTGGATGGTATGTGTGCATTTTGTGATG

rs3836111ACGTTGGATGTCTACCCCGACTTGTTTTCCACGTTGGATGGGCTAAAACGAAGACAAGCC

rs3771181ACGTTGGATGTTCCTTCTCCAAAAGTTCAGACGTTGGATGGCCAGAGGATTTTTTTTCCG

rs955754ACGTTGGATGGTGATGTGGCCAGAAATGAGACGTTGGATGTATCCTCCTGCTTCAGCTTG

rs2302612ACGTTGGATGTGACAAACCTCGTGTCCTCCACGTTGGATGAAGGTGTCGGCCGTTTCCTC

rs3755284ACGTTGGATGGCTGCTCAGAATTCTGGTTGACGTTGGATGACCCTTCCATGTTTGAGAGG

rs3821205ACGTTGGATGATGCCATCCTAAGACCACAGACGTTGGATGCTTAGTAAGCAGTCAGTGGG

dbSNP Forward Reverse rs# PCR primer PCR primer rs3815511ACGTTGGATGTACCACCCATCGCCTGTGAAACGTTGGATGGTGGTCTTAGGATGGCATGG

rs2287041ACGTTGGATGTGAAAGTCCATCCCACACTGACGTTGGATGTGTGGTCTTAGGATGGCATG

rs2287040ACGTTGGATGATAAAGAGTGGACCAATGTCACGTTGGATGTTATGTTCCAAGGTGACCTC

rs2287039ACGTTGGATGTTCACAGGCACACCCTTCAGACGTTGGATGAGCCACAGTGTGGGGAGAGT

rs3755283ACGTTGGATGTTCTTGCTGCATTGCATCCCACGTTGGATGGGAGAGAGAAATCGAGATGC

rs3755282ACGTTGGATGGAGGACCAAGCAAGATGAAGACGTTGGATGATATTTTGGCAGGCCAGCTC

rs1812326ACGTTGGATGTTCAAGTGATTCTACTGCCGACGTTGGATGAACCCCCGTCTCTACTAAAC

rs1558626ACGTTGGATGACCTCCAAGCATGATCTCAGACGTTGGATGTGGTTTTCCCTTGGTACTCG

rs1558625ACGTTGGATGTCAGCAAAGCAGGACCGACCACGTTGGATGTGAGATCATGCTTGGAGGTC

rs1558624ACGTTGGATGGGAAAGAACGGCCTGTCTTCACGTTGGATGATCCACAGGGTTCGTGTTGT

rs1558623ACGTTGGATGAAGTCCCAAACCCAAGTGAGACGTTGGATGTTAGGAAGCGAAGGAAAAAC

rs1035131ACGTTGGATGACTCTTCCTACCTTGATGGCACGTTGGATGTAGGCTTCAGGATTGGATGG

rs2110661ACGTTGGATGTCCCTCCAAAACCCACCTTTACGTTGGATGTGGATGGTGACACCTTCATG

rs1420093ACGTTGGATGAAGAAATTTAAAGCCCAGAGACGTTGGATGTATCTCAATAGAGGCTCTAC

rs3074971ACGTTGGATGAAACAAACTGAACCGCTAGGACGTTGGATGCAGCGTTCTTCTGGGTATTT

rs1345302ACGTTGGATGGGTAATCAGAAAACAGAGTCACGTTGGATGTGCCAGTAGAAGTACAGTAG

rs1420092ACGTTGGATGGTGCTCAGAGATGGTTAAACACGTTGGATGACTGCACCCTAGTTGATTTG

rs1345301ACGTTGGATGGCTCAAGTCTGGAGAAATGAACGTTGGATGCATGGTTGGATTTTGTGTTG

rs2310242ACGTTGGATGCCACCACTCAAACCTTTGTCACGTTGGATGGACAGCAAGAGTGAAACTCC

rs2310243ACGTTGGATGTGTAGCTAAGCACTATAGCGACGTTGGATGGCTCCTTCTAGATATGCATG

rs1882510ACGTTGGATGCTCGCTAGTCACTGGAGCTGACGTTGGATGAAGTCCAGGTGGACCCTGGT

rs1882511ACGTTGGATGAAGGAACTGTCAGGGCCATGACGTTGGATGAATGGTGCAACTGCCTTGGG

dbSNP Extend Term rs# Primer Mix rs3917304 GGTTACTAATGGTGGTTTTCTCTGACT

rs2041747 ATGCTAAGAGTTATTCACATTTTGACT

rs3917305 GGAGATCCTTGTCCCATAGAT ACT

rs3771200 TACTGCTCATCTATGGGACAA ACT

rs3917306 GCACTTTGTCATCTGCCCCA ACT

rs3917307 AAGTTTGAAATGCCATTTCCTCT ACT

rs3917308 TAGTCTTACCCTATGCATCATCA ACT

rs3917310 ATGGAAGGATATACAATGTTCAT CGT

rs3917311 ATTCATTTGGGGAAGAACTGATA ACG

rs3917312 TACAAACACTGACTCTCACTTGTAACT

rs3917313 CTTGGTCCTTTACAGTTCCCT ACT

rs3917314 GGATACTAATGTACAAAGCAATGAACT

rs3917316 ATTTTAGAAACCCTCTTAGTAAAACGT

rs3171845 TGAATATCATTGTTTTCTAA ACT

rs3171846 ATCACAGAGCAAGGCCTA CGT

rs3917317 AGTTTAAACAAAGGAGAGAGAGA ACT

rs3917318 GTGTG GCTTTGGTTCAGGAG ACT

rs3917319 GTTGAGGTCATTAATGAAAACGT CGT

rs3917320 GAAGACTGATTATCATTTTAGTC CGT

rs3917321 ACGTGCCTCTCGGGTAGC ACT

rs3917322 CCATAAGACAGGAGGCACC ACG

rs3917323 GGGAAGATCTTTTAAAAAGGCA I ACT

dbSNP Extend Term rs# Primer Mix rs3917324 TCAGGAGTTCGAGACCAGC ACT

rs3917325 CCTGTAGAGTCACTGACCC ACT

rs3732134 TTCCTCCCTGGCATGACCAT ACT

rs3732133 CAAGGGACATTGCAGACGGA ACT

rs2110726 TGCAAGGGACATTGCAGA ACG

rs3917326 CCCACACATGAACCATCCTTCC ACG

rs3917327 GCTTCAGCTCCTGAACAGGTG ACT

rs3917328 GGAGGAAGGGTGCAGGCAA ACT

rs3732131 TCTCGCATTTTCTCTAGCTGATC ACT

rs3732130 GGATGTTCTGAATTTTGGTAAAATACG

rs3917329 CTTCTTCCTCCAGAATTCAAC CGT

rs3917330 TCCCCACAACAGGAAGAACT CGT

rs3917331 TGAGGAGACCTTCTGCAGAG CGT

rs3917344 GAGTGGAGGTCAGAGGCTAT ACG

rs3917332 ACAGTGAGCCCTAACTCCC CGT

rs3917333 GGGTGTCATCTCTGACCATC CGT

rs3917334 TCAGACTCTAAGCCAACCTGCCA CGT

rs1030021 CTTTTAAATTTTGCCAGTTTTGC ACT

rs2241132 CGGTGGGGACCGCGTGG ACT

rs2241131 CGGCGGCGGTGGGGACC ACT

rs3835036 GCGGAAGAGGAAACAGAGAACCA ACT

rs1997504 GCGGGCGGATCACGAGG ACG

rs1805232 CGCCCGCCACCGCGCCC ACT

rs1971696 ACATTAAAAAAATTAGCCGGGC ACT

rs1971695 TACAGGCGCCCGCCACC ACT

rs3771199 TGACTGTGGTCAGCTGGAAA ACT

rs1922303 GGGGCCTGAATA,AAACACATCTGTACT

rs3213734 TTTAAGGCAGAATTGGTAAAGAAAACT

rs1997503 AGAGGGGTGTGCTGGCAGGC ACT

rs1558649 GGTGGTTCATGCCTGTAATCC ACG

rs1558648 TGTTGAACTTTGTATTATAAGCC ACT

rs1558647 GGTACATTTTATACCCACCAAA ACG

rs1558646 CTTGGTTAGAGTTTAGGGCACAT ACT

rs1882514 GGATTCACGTGTCCATCACTT ACT

rs1882513 GTGGGCTAATTCCAGTTAAGA ACG

rs867770 AGAAGTAGCTTGCCCTGAGAGC ACG

rs2310235 GGGAATCAGTCAGAAAGTAATA CGT

rs870684 CACAGTGGTTTTGGGTCCC ACG

rs3771197 GTTCCAGTCCACAGAATTTAGT ACT

rs3771196 CTACACAGCAACTAAAGGATC CGT

rs3821207 AAGAGGAGACGAGCATCAGA ACT

rs3771195 TTAAATCTTGTTAGTGAGACATTAACG

rs3771194 TGTCGCTTTGCTATAACTTAGACTACT

rs3771193 GTTATAGCAAAGCGACAGAATG ACT

rs3771192 CATCTTAAAGTTCAGCCTTGCA ACT

rs3755290 TGCACTTATCAAGCATTGGAC ACT

rs3821206 GGAAGGAAGACTTCATGGAG ACT

rs2302623 GAAACCTGTGTGATCCCTAG CGT

rs3755289 TCAGCTGGAAGGCCCGCA ~CT

dbSNP Extend Term rs# Primer Mix rs1922302 TTAATTCCTAGGTATTTAATTTCGACT

rs2110725 CATTTTACAGAGTTCCAGGAGGG ACT

rs1465326 GGCTCTGTTTCTGACAATAACCAGACT

rs2871458 GGATCCACACCACCCAGAA ACT

rs2080310 GGTGGATCAGAAGTGCAGGT ACT

rs1922289 CATTGCTACGTTGAGTATGAG ACT

rs1922290 CCCAGTTTCCAGCTTTGGATATACACT

rs1922291 TCTGCTACCACAACTTTTCCA ACG

rs1922292 ACCTCACAATGCAAGATATATTA CGT

rs3815517 GCCACTTGCCCCTTGTGG CGT

rs2241130 GATCTTACTGCTCTCAGGGAT ACT

rs1922295 GCCTTCAAAGCTTAATGCCC ACG

rs1922294 GTTCTTTGCTATACTAAACAAGC ACT

rs2302622 CACACTGTTCAGAGTGTTCAAAACACT

rs2310240 TGCAAACACACACACACACACA ACT

rs1024792 CGTGTCAAACACACACACACACA ACT

rs3836112 TGGCTAGCTACATGCAAGAG ACT

rs3074969 TGGCTAGCTACATGCAAGAG ACT

rs917994 CAGTGAP;TAGGGATCTGTGC ACT

rs2041753 CCCATGTGCTCAGGGTGAG ACT

rs2041752 CTTAGAGGTACCAGAGAGAGA ACT

rs1024791 CTGGCTGATGTCAGAAAGCA ACG

rs1024790 CACAGAGAGGTTGAGTGACA ACT

rs995515 CTATTGGTCAGCTTCAGTCTAT ACT

rs995514 ACTTGGCCTCAGAATCCTTC ACT

rs1922293 GCTTCTCCATTTGACTTCCTTA ACG

rs3755287 GGTGTGCTCTTCCGTGAATTCGC ACT

rs3729564 TTCCAATTTCATTCTCTTTTAGCTACG

rs3771188 TGTGAGAACCCCTCACTTCA ACT

rs3771187 TCTGTCTTATGATTGAAGTGAG ACT

rs3771186 CGGTGTGTGGTGCAGTGC ACT

rs3771185 AGGCCCAAGATTTCTCATTTACT ACT

rs2310241 CAGCTGGTTCTGCTGCCC ACT

rs2302621 GGGCTCTGCAGACTTTTACTC ACT

rs2302620 CTGTAGAATGGAAGGCACTTCG ACT

rs3771184 CCCTGTACTTGGTGCCTGAAG ACT

rs3834161 GTTGTCTGAGAACGTTTTATGGG ACT

rs3755286 AGTACGGTTGTTGCCCACAT ACT

rs3755285 ACCCCCTCCCCATGCCC ACT

rs1997502 TCCTGGAAGCTCAGGCCCC ACT

rs3771182 GTTCTCGTAGACAGAGCTGT ACT

rs3836111 CCTTGGTTTCCCTTTGATCACT CGT

rs3771181 TCAGAAACATAAGAAACTTATGAAACT

rs955754 GCCAGAAATGAGAATTAAAGGCAGACT

rs2302612 GTAGCAAGGTGTGTGCTGC ACT

rs3755284 TGTCTAAAAGAGAGAGAAAAGG CGT

rs3821205 CCTCTGGCTCCCTCTCTC ACT

rs3815511 GGCACAGCACCTCCTAACC ACG

rs2287041 CATCCCACACTGGGTACCA I CGT

dbSNP Extend Term rs# Primer Mix rs2287040 TGGACCAATGTCAAGTCGAG ACT

rs2287039 CAGAGAGGACACGTCCCC ACT

rs3755283 CCTATTATTTCATTAGGAATTAGTACT

rs3755282 CATGTGAAAAGTGCTTGGCAAAC ACG

rs1812326 AGGTGCATGCCACCACACT ACG

rs1558626 TTCAGGCTAGTTTCACCCGA CGT

rs1558625 GCAGGACCGACCCTCCCT ACG

rs1558624 GGCCTGTCTTCAGGGCTC ACT

rs1558623 AAGTGAGGGCTCCAGCGAT CGT

rs1035131 GATGGCACATCTCTAGAAAAG CGT

rs2110661 GTCTCTCCTCAGATATGAGCC ACG

rs1420093 TTTAAAGCCCAGAGATTTTAAAAAACT

rs3074971 CTAGGAAAAAAGAAAGGCAACA CGT

rs1345302 GAAAACAGAGTCTTTACCAATC ACT

rs1420092 AGAGATGGTTAAACAGGCACA ACT

rs1345301 CACAAGTTTACACCTTTTCTTTA ACT

rs2310242 CTCTATAACCTTACAAATGTTATTCGT

rs2310243 TGCAGTTTGGGACACAAAGG ACG

rs1882510 AAAACTGAGCTGGGCCTGC ACT

rs1882511 GGGAGGCATTCAGGGATCA I ACG

Genetic Anal, [0260] Allelotyping results from the discovery cohort are shown for cases and controls in Table 17.
The allele frequency for the A2 allele is noted in the fifth and sixth columns for osteoarthritis case pools and control pools, respectively, where "AF" is allele frequency. The allele frequency for the A1 allele can be easily calcularted by subtracting the A2 allele frequency from 1 (A1 AF
= 1-A2 AF). For example, the SNP rs3917304 has the following case and control allele frequencies: case A1 (G) = 0.431;
case A2 (T) = 0.569, control Al (G) = 0.450; and control A2 (T) = 0.550, where the nucleotide is provided in paranthesis. Some SNPs are labeled "untyped" because of failed assays.

dbSNP position ChromosomeAl/A2 F A2 F A2 F p-rs# in position Allele Case Control Value SEQ D AF AF
NO:

rs3917304225 102409525G/T 0.569 0.550 0.460 rs2041747509 102409809C/T 0.027 0.023 0.800 rs3917305860 102410160C/T

rs3771200874 102410174C/T 0.467 0.473 0.809 rs3917306939 102410239A/G

rs39173071483 102410783G/T

rs39173081798 102411098C/T

rs39173102189 102411489A/T

rs39173112215 102411515A/G 0.945 0.964 0.193 rs39173122282 102411582CIG

rs39173132340 102411640C/T

rs39173142963 102412263A/C 0.025 0.028 0.881 rs39173163369 102412669-/T 0.785 0.856 0.004 rs31718453481 102412781A/G 0.904 0.894 0.624 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in position Allele Case Control Value SEQ D AF AF
NO:

rs31718463564 102412864G/T

rs39173'173653 102412953-/TC 0.320 0.325 0.824 rs39173184860 102414160A/G 0.151 0.151 0.978 rs39173'194941 102414241A/T

rs39173204975 102414275A/C 0.936 0.946 0.585 rs39173215321 102414621A/G

rs39173225346 102414646A/G 0.978 unt ed NA

rs39173235541 102414841A/G 0.977 unt ed NA

rs39173245633 102414933C/G

rs39173256007 102415307G/T 0.029 0.030 0.901 rs37321346317 102415617C/G

rs37321336378 102415678A/G

rs21107266382 102415682C/T 0.320 0.318 0.944 rs39173266426 102415726C/T

rs39173276479 102415779C/G

rs39173286641 102415941C/T 0.898 0.891 0.706 rs37321316703 102416003C/T 0.047 0.036 0.434 rs37321306705 102416005C/T

rs39173297963 102417263G/T 0.070 0.081 0.473 rs39173308525 102417825G/T

rs39173318526 102417826A/T

rs39173448598 102417898C/T

rs39173328624 102417924A/T 0.224 0.209 0.473 rs39173338883 102418183A/T

rs39173348980 102418280G/T

rs103002113578 102422878GIT 0.160 0.183 0.255 rs224113216135 102425435G/T 0.604 0.631 0.385 rs224113116141 102425441G/T 0.451 0.477 0.282 rs383503616642 102425942-/TGG 0.424 0.463 0.112 rs199750416931 102426231A/G

rs180523217004 102426304A/G

rs197169617009 102426309C/T

rs197169517010 102426310A/G

rs377119918713 102428013C/T 0.299 0.291 0.726 rs192230318853 102428153C/T

rs321373420783 102430083C/T 0.826 0.860 0.099 rs199750321335 102430635A/G 0.830 0.806 0.281 rs155864922180 102431480C/T

rs155864822268 102431568A/C 0.127 0.142 0.439 rs155864722285 102431585C/T 0.824 0.825 0.955 rs155864625378 102434678C/T 0.576 0.580 0.886 rs188251425906 102435206C/G 0.547 0.556 0.730 rs188251326015 102435315A/G 0.500 0.513 0.574 rs867770 26475 102435775A/G

rs231023526798 102436098A/T 0.608 0.573 0.252 rs870684 27042 102436342A/G 0.687 0.685 0.931 rs377119727649 102436949A/G 0.534 0.544 0.676 rs377119627827 102437127A/T 0.171 0.189 0.558 rs38212 27873 102437173A/G 0.029 0.033 0.751 rs377119528122 102437422A/G 0.342 0.326 0.480 rs377119428202 102437502A/G 0.474 0.465 0.725 rs37711 28232 102437532A/C

rs37711 28240 102437540G/T

rs375529029546 102438846G/T 0.348 0.329 0.428 rs38212 29748 102439048A/G 0.914 0.920 0.803 rs230262330054 102439354A/T 0.261 0.263 0.948 rs375528930646 102439946G/T 0.429 0.442 0.621 rs192230231149 102440449A/C 0.574 0.539 0.166 rs2110T2536912 102446212A/C

rs146532636936 102446236C/G 0.592 0.613 0.413 rs287145837184 102446484C/T 0.068 0.059 0.549 rs208031039064 102448364C/T 0.258 0.256 0.926 rs192228939343 102448643G/T 0.593 0.593 0.976 dbSNP PositionChromosomeAl/A2 F A2 F A2 F p-rs# in position Allele Case Control Value SEQ D AF AF
NO:

rs192229040868 102450168 C/G 0.577 0.595 0.489 rs192229140917 102450217 A/G 0.344 0.358 0.549 rs192229241113 102450413 A/C 0.226 0.221 0.874 rs381551747343 102456643 A/T 0.291 0.291 0.984 rs224113047806 102457106 A/G 0.112 0.088 0.153 rs192229547911 102457211 A/G 0.362 0.349 0.594 rs192229448009 102457309 C/T 0.075 0.065 0.581 rs230262248621 102457921 CIG

rs231024049245 102458545 C/G

rs102479249247 102458547 C/G

rs383611249299 102458599 -/CTCT 0.374 0.360 0.568 rs307496949302 102458602 -/AGAG 0.361 0.353 0.747 rs917994 49514 102458814 C/T 0.289 0.304 0.544 rs204175349626 102458926 G/T 0.330 0.329 0.981 rs204175249791 102459091 A/G 0.492 0.528 0.176 rs102479150010 102459310 A/G

rs102479050294 102459594 A/G 0.771 0.776 0.828 rs995515 51482 102460782 A/G/T 0.312 0.310 0.91 T

rs995514 51556 102460856 A/G 0.393 0.420 0.246 rs192229351855 102461155 A/G 0.597 0.608 0.653 rs375528751956 102461256 C/T 0.869 0.885 0.458 rs372956452155 102461455 A/G 0.331 0.315 0.511 rs377118852448 102461748 A/G

rs377118752458 102461758 C/T 0.280 0.258 0.332 rs377118652511 102461811 C/T 0.764 0.813 0.048 rs377118552607 102461907 A/G 0.429 0.395 0.160 rs231024154049 102463349 A/C 0.424 0.406 0.462 rs230262154224 102433524 A/C 0.323 0.340 0.473 rs230262054567 102433867 A/G 0.103 0.092 0.512 rs377118455052 102434352 C/T 0.779 0.809 0.173 rs383416155857 102435157 -/C 0.062 0.069 0.674 rs375528655941 102435241 CIG 0.786 0.817 0.150 rs375528556120 102435420 A/G 0.184 0.174 0.619 rs199750256349 102485649 C/T 0.580 0.564 0.559 rs377118256727 102466027 A/G 0.101 0.085 0.352 rs383611157232 102466532 -/CT 0.138 0.113 0.154 rs377118158806 102468106 C/T

rs955754 61181 102470481 C/T 0.194 0.172 0.29'1 rs230261263808 102473108 A/G 0.135 0.120 0.456 rs375528464526 102473826 A/T 0.757 0.789 0.147 rs382120564865 102474165 A/G 0.831 0.832 0.992 rs381551164928 102474228 C/T 0.022 unt ed NA

rs228704164966 102474266 A/C 0.118 0.100 0.346 rs228704065080 102474380 A/G 0.518 0.536 0.462 rs228703965690 102474990 C/T 0.975 0.970 0.752 rs375528366228 102475528 A/G

rs375528266982 102476282 A/G 0.312 0.295 0.452 rs181232672511 102481811 A/G 0.343 0.297 0.054 rs155862674170 102483470 A/T 0.536 0.551 0.643 rs155862574264 102483564 C/T 0.661 0.697 0.128 rs155862474333 102483633 C/T 0.322 0.278 0.074 rs155862374502 102483802 A/T 0.303 0.273 0.200 rs103513174741 102484041 A/C 0.543 0.595 0.046 rs211066175321 102484621 C/T 0.430 0.413 0.485 rs142009382558 102491858 A/G 0.381 0.388 0.826 rs307497185366 102494666 -/TTG 0.438 0.479 0.096 rs134530285469 1024J4769 C/T 0.428 0.397 0.223 rs142009286485 102495785 G/T 0.792 0.793 0.965 rs134530187687 102496987 C/T 0.514 0.477 0.139 rs231024289463 102498763 G/T 0.108 0.114 0.804 rs231024389660 1024J8960 A/G 0.490 0.523 0.194 rs188251095718 102505018 C/T 0.617 0.667 0.075 rs188251195821 102505121 A/G 0.664 0.652 0.599 [0261] The IL1RL2 proximal SNPs were also allelotyped in the replication cohorts using the methods described herein and the primers provided in Tables 15 and 16. The replication allelotyping results for replication cohort #1 and replication cohort #2 are provided in Tables 18 and 19, respectively.

dbSNP PositionChromosom Al/A2 F A2 F A2 F p-rs# in a Allele Case Control Value SEQ D position AF AF
NO:

rs3917304 225 102409525 G/T 0.599 0.592 0.843 rs2041747 509 102409809 C/T 0.021 0.026 0.845 rs3917305 860 102410160 C/T

rs3771200 874 102410174 C/T 0.442 0.482 0.207 rs3917306 939 102410239 A/G

rs3917307 1483 102410783 G/T

rs3917308 1798 102411098 C/T

rs3917310 2189 102411489 A/T

rs3917311 2215 102411515 AIG 0.933 0.974 0.042 rs3917312 2282 102411582 C/G

rs3917313 2340 102411640 C/T

rs3917314 2963 102412263 A/C 0.036 0.038 0.918 rs3917316 3369 102412669 -/T 0.904 0.963 0.072 rs3171845 3481 102412781 A/G 0.898 0.882 0.610 rs3171846 3564 102412864 G/T

rs3917317 3653 102412953 -/TC 0.313 0.323 0.759 rs3917318 4860 102414160 A/G 0.149 0.142 0.803 rs3917319 4941 102414241 A/T

rs3917320 4975 102414275 A/C 0.921 0.930 0.749 rs3917321 5321 102414621 A/G

rs3917322 5346 102414640 A/G

rs3917323 5541 10241484'1A/G

rs3917324 5633 102414933 C/G

rs3917325 6007 10241530 G/T 0.033 0.040 0.716 rs3732134 6317 10241561 C/G

rs3732133 6378 102415678 A/G

rs2110726 6382 102415682 C/T 0.334 0.339 0.880 rs3917326 6426 102415726 C/T

rs3917327 6479 102415779 C/G

rs3917328 6641 10241594'1C/T 0.885 0.867 0.523 rs3732131 6703 102416003 C/T 0.045 0.022 0.224 rs3732130 6705 102416005 C/T

rs3917329 7963 102417263 G/T 0.068 0.091 0.296 rs3917330 8525 102417825 G/T

rs3917331 8526 102417826 A/T

rs3917344 8598 102417898 C/T

rs3917332 8624 102417924 A/T 0.203 0.195 0.785 rs3917333 8883 102418183 A/T

rs3917334 8980 10241828 G/T
O

rs1030021 13578 102422878 G/T 0.148 0.174 0.325 rs2241132 16135 102425435 G/T 0.604 0.595 0.815 rs2241131 16141 10242544'1G/T 0.452 0.464 0.696 rs3835036 16642 102425942 -/TGG 0.402 0.479 0.017 rs1997504 16931 10242623'1AlG

rs1805232 17004 102426304 A/G

rs1971696 17009 102426309 C/T

rs1971695 17010 10242631 A/G
O

rs3771199 18713 102428013 C/T 0.317 0.310 0.818 rs1922303 18853 102428153 C/T

rs3213734 20783 102430083 C/T 0.824 0.892 0.012 rs1997503 21335 102430635 A/G 0.838 0.790 0.114 dbSNP PositionChromosomeAl/A2 F A2 F A2 F p-rs# in position Allele Case Control Value SEQ D AF AF
NO:

rs155864922180 102431480C/T

rs155864822268 102431568A/C 0.125 0.164 0.121 rs155864722285 102431585C/T 0.834 0.831 0.895 rs155864625378 102434678C/T 0.547 0.561 0.672 rs188251425906 102435206C/G 0.538 0.542 0.905 rs188251326015 102435315A/G 0.471 0.497 0.414 rs867770 26475 102435775A/G

rs231023526798 102436098AIT 0.562 NA 0.608 rs870684 27042 102436342A/G 0.657 0.680 0.509 rs377119727649 102436949A/G 0.502 0.534 0.351 rs377119627827 102437127A/T 0.171 0.189 0.558 rs382120727873 102437173A/G 0.033 0.038 0.821 rs377119528122 102437422A/G 0.374 0.342 0.311 rs377119428202 102437502A/G 0.493 0.480 0.696 rs377119328232 102437532A/C

rs377119228240 102437540G/T

rs375529029546 102438846G/T 0.364 0.346 0.602 rs382120629748 102439048A/G 0.940 NA 0.914 rs230262330054 102439354A/T 0.267 0.268 0.984 rs375528930646 102439946G/T 0.417 0.451 0.281 rs 192230231149 102440449A/C 0.600 0.559 0.245 rs211072536912 102446212A/C

rs146532636936 102446236C/G 0.573 0.614 0.296 rs287145837184 102446484C/T 0.085 0.070 0.530 rs208031039064 102448364C/T 0.277 0.268 0.776 rs192228939343 102448643G/T 0.580 0.576 0.924 rs192229040868 102450168C/G 0.558 0.579 0.556 rs192229140917 102450217A/G 0.322 0.348 0.401 rs192229241113 102450413A/C 0.235 un ed NA

rs381551747343 102456643A/T 0.310 0.312 0.950 rs224113047806 102457106A/G 0.110 0.068 0.071 rs 192229547911 102457211A/G 0.378 0.364 0.695 rs192229448009 102457309C/T 0.061 0.055 0.799 rs230262248621 102457921C/G

rs231024049245 102458545C/G

rs102479249247 102458547C/G

rs383611249299 102458599-/CTCT 0.407 0.378 0.382 rs307496949302 102458602-/AGAG 0.385 0.362 0.497 rs917994 49514 102458814C/T 0.271 0.281 0.757 rs204175349626 102458926G/T 0.357 0.342 0.672 rs204175249791 102459091A/G 0.459 0.511 0.155 rs102479150010 102459310A/G

rs102479050294 102459594A/G 0.781 0.773 0.769 rs995515 51482 102460782A/G/T 0.331 0.323 0.825 rs995514 51556 102460856A/G 0.373 0.412 0.221 rs192229351855 102461155A/G 0.568 0.597 0.376 rs375528751956 102461256C/T 0.867 0.907 0.138 rs372956452155 102461455A/G 0.362 0.320 0.212 rs377118852448 102461748AIG

rs377118752458 102461758C/T 0.308 0.276 0.288 rs377118652511 102461811C/T 0.761 0.847 0.003 rs377118552607 102461907A/G 0.445 0.385 0.069 rs231024154049 102463349A/C 0.446 0.400 0.161 rs230262154224 102463524A/C 0.304 0.326 0.499 rs230262054567 102463867A/G 0.100 0.074 0.236 rs377118455052 102464352C/T 0.785 0.853 0.014 rs383416155857 102465157-lC 0.068 0.081 0.596 rs375528655941 102465241C/G 0.791 0.850 0.038 rs375528556120 102465420A/G 0.194 0.173 0.446 rs199750256349 102465649C/T 0.604 0.577 0.536 rs377118256727 102466027A/G 0.107 0.070 0.117 rs383611157232 102466532-/CT 0.137 0.090 0.048 I

rs377118158806 102468106C/T I

dbSNP PositionChromosomeAl/A2 F A2 F A2 F p-rs# in position Allele Case Control Value SEQ )aD AF AF
NO:

rs955754 61181 102470481C/T 0.209 0.160 0.084 rs2302612 63808 102473108A/G 0.138 0.111 0.331 rs3755284 64526 102473826A/T 0.754 0.829 0.010 rs3821205 64865 102474165A/G 0.799 0.814 0.594 rs3815511 64928 102474228C/T

rs2287041 64966 102474266A/C 0.113 0.074 0.143 rs2287040 65080 102474380A/G 0.493 0.521 0.386 rs2287039 65690 102474990C/T 0.970 0.962 0.703 rs3755283 66228 102475528A/G

rs3755282 66982 102476282A/G 0.327 0.312 0.636 rs1812326 72511 102481811A/G 0.362 0.299 0.067 rs1558626 74170 102483470A/T 0.558 unt ed rs1558625 74264 102483564C/T 0.635 0.683 0.137 rs1558624 74333 102483633C/T 0.350 0.278 0.024 rs1558623 74502 102483802A/T 0.323 0.281 0.204 rs1035131 74741 102484041A/C 0.513 0.598 0.026 rs2110661 75321 102484621C/T 0.449 0.412 0.237 rs1420093 82558 102491858A/G 0.390 unt ed rs3074971 85366 102494666-ITTG 0.398 0.485 0.006 rs1345302 85469 102494769C/T 0.468 0.392 0.036 rs1420092 86485 102495785G/T 0.810 0.808 0.958 rs1345301 87687 102496987C/T 0.554 0.470 0.016 rs2310242 89463 102498763G/T 0.110 unt ed rs2310243 89660 102498960A/G 0.452 0.529 0.031 rs1882510 95718 102505018C/T 0.597 0.688 0.022 rs1882511 95821 102505121A/G 0.684 0.657 0.373 dbSNP PositionChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value Figure AF AF

rs3917304 225 102409525G/T 0.531 0.483 0.236 rs2041747 509 102409809CIT 0.034 unt ed rs3917305 860 102410160C/T

rs3771200 874 102410174C/T 0.500 0.460 0.282 rs3917306 939 102410239A/G

rs3917307 1483 102410783G/T

rs3917308 1798 102411098C/T

rs3917310 2189 102411489A/T

rs3917311 2215 102411515A/G 0.959 0.947 0.574 rs3917312 2282 102411582C/G

rs3917313 2340 102411640C/T

rs3917314 2963 102412263A/C

rs3917316 3369 102412669-/T 0.633 0.687 0.176 rs3171845 3481 102412781A/G 0.912 0.913 0.964 rs3171846 3564 102412864G/T

rs3917317 3653 102412953-/TC 0.329 0.329 0.999 rs3917318 4860 102414160A/G 0.153 0.165 0.696 rs3917319 4941 102414241A/T

rs3917320 4975 102414275A/C 0.955 0.971 0.463 rs3917321 5321 102414621A/G

rs3917322 5346 102414646A/G

rs3917323 5541 102414841A/G

rs3917324 5633 102414933C/G

rs3917325 6007 102415307G/T 0.023 unt ed rs3732134 6317 102415617C/G

rs3732133 6378 102415678A/G

rs2110726 6382 102415682CIT 0.301 0.285 0.632 rs3917326 6426 102415726C/T

rs3917327 6479 102415779C/G

rs3917328 6641 102415941C/T 0.915 0.929 0.621 dbSNP PositionChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value Figure AF AF

rs37321316703 102416003C/T 0.049 0.058 0.670 rs37321306705 102416005C/T

rs39173297963 102417263G/T 0.073 0.067 0.798 rs39173308525 102417825G/T

rs39173318526 102417826A/T

rs39173448598 102417898ClT

rs39173328624 102417924A/T 0.251 0.231 0.534 rs39173338883 102418183A/T

rs39173348980 102418280G/T

rs103002113578 102422878G/T 0.176 0.197 0.489 rs224113216135 102425435G/T unt 0.688 NA
ed rs224113116141 102425441G/T 0.451 0.498 0.204 rs383503616642 102425942-/TGG 0.453 0.439 0.715 rs199750416931 102426231A/G

rs180523217004 102426304A/G

rs197169617009 102426309C/T

rs197169517010 102426310A/G

rs377119918713 102428013C/T 0.277 0.262 0.665 rs192230318853 102428153C/T

rs321373420783 102430083C/T 0.827 0.809 0.573 rs199750321335 102430635A/G 0.821 0_ 832 0.740 rs155864922180 102431480C/T

rs155864822268 102431568A/C 0.130 0.105 0.368 rs155864722285 102431585C/T 0.810 0_ 815 0.861 rs155864625378 102434678ClT 0.613 0_ 608 0.893 rs188251425906 102435206C/G 0.558 0_ 578 0.630 rs188251326015 102435315A/G 0.537 0_ 539 0.952 rs867770 26475 102435775A/G

rs231023526798 102436098A/T 0.589 0_ 019 rs870684 27042 102436342A/G 0.726 0_ 693 0.392 rs377119727649 102436949A/G 0.574 0_ 561 0.725 rs377119627827 102437127A/T

rs382120727873 102437173A/G 0.023 0_026 0.884 rs377119528122 102437422A/G 0.303 0 _ 301 0.952 rs377119428202 102437502A/G 0.450 0 _ 442 0.832 rs377119328232 102437532A/C

rs377119228240 102437540G/T

rs375529029546 102438846G/T 0.328 0 _ 302 0.452 rs382120629748 102439048A/G 0.889 0_026 rs230262330054 102439354A/T 0.254 0 _ 255 0.962 rs375528930646 102439946G/T 0.444 0_429 0.744 rs 192230231149 102440449A/C 0.541 0 _ 507 0.364 rs211072536912 102446212A/C

rs146532ti36936 102446236C/G 0.616 0_612 0.919 rs287145837184 102446484C/T 0.046 0_041 0.775 rs208031039064 102448364C/T 0.235 0 _238 0.933 rs192228939343 102448643G/T 0.611 0_618 0.845 rs192229040868 102450168C/G 0.601 0 _619 0.631 rs192229140917 102450217A/G 0.372 0 _374 0.961 rs 192229241113 102450413A/C 0.215 0 _ 221 0.827 rs381551747343 102456643A/T 0.268 0 _257 0.766 rs224113047806 102457106A/G 0.115 0 _ 119 0.854 rs192229547911 102457211A/G 0.342 0 _325 0.632 rs192229448009 102457309C/T 0.092 0 _081 0.677 rs230262248621 102457921C/G

rs231024049245 102458545C/G

rs102479249247 102458547C/G

rs383611249299 102458599-/CTCT 0.332 0 _332 0.999 rs307496949302 102458602-/AGAG 0.330 0 _339 0.822 rs917994 49514 102458814C/T 0.312 0.339 0.456 rs204175349626 102458926G/T 0.296 0.310 0.737 rs204175249791 102459091A/G 0.534 ~ _556 0.587 rs102479150010 102459310A/G

rs102479050294 102459594A/G 0.759 0.780 0.498 dbSNP PositionChromosomeAl/A2 F A2 F A2 F p-rs# in Position AlleleCase Control Value Figure AF AF

rs995515 51482 102460782 A/G/T 0.288 0.288 0.992 rs995514 51556 102460856 A/G 0.417 0.434 0.657 rs192229351855 102461155 A/G 0.634 0.625 0.806 rs375528751956 102461256 C/T 0.873 0.850 0.471 rs372956452155 102461455 A/G 0.291 0.308 0.643 rs377118852448 102461748 A/G

rs377118752458 102461758 C/T 0.246 0.231 0.677 rs377118652511 102461811 C/T 0.766 0.759 0.850 rs377118552607 102461907 AIG 0.409 0.410 0.972 rs231024154049 102463349 AIC 0.396 0.416 0.591 rs230262154224 102463524 A/C 0.347 0.363 0.667 rs230262054567 102463867 A/G 0.107 0.121 0.605 rs377118455052 102464352 CIT 0.772 0.740 0.364 rs383416155857 102465157 -/C 0.054 0.051 0.860 rs375528655941 102465241 CIG 0.781 0.766 0.641 rs375528556120 102465420 AIG 0.172 0.175 0.897 rs199750256349 102465649 C/T 0.550 0.543 0.849 rs377118256727 102466027 AIG 0.094 0.109 0.562 rs383611157232 102466532 -!CT 0.139 0.148 0.750 rs377118158806 102468106 C/T

rs955754 61181 102470481 C/T 0.173 0.190 0.571 rs230261263808 102473108 A/G 0.132 0.135 0.909 rs375528464526 102473826 A/T 0.760 0.726 0.332 rs382120564865 102474165 A/G 0.873 0.859 0.629 rs381551164928 102474228 C/T

rs228704164966 102474266 A/C 0.124 0.141 0.517 rs228704065080 102474380 A/G 0.550 0.559 0.802 rs228703965690 102474990 C/T

rs375528366228 102475528 A/G

rs375528266982 102476282 A/G 0.293 0.268 0.452 rs181232672511 102481811 A/G 0.320 0.294 0.453 rs155862674170 102483470 A/T 0.541 unt ed rs 155862574264 102483564 C/T 0.694 0.719 0.473 rs155862474333 102483633 C/T 0.285 0.279 0.865 rs155862374502 102483802 A/T 0.277 0.261 0.615 rs103513174741 102484041 A/C 0.581 0.590 0.795 rs211066175321 102484621 C/T 0.405 0.414 0.800 rs142009382558 102491858 A/G 0.384 unt ed rs307497185366 102494666 -/TTG 0.488 0.469 0.619 rs134530285469 102494769 C/T 0.378 0.406 0.437 rs142009286485 102495785 G/T 0.769 0.768 0.980 rs134530187687 102496987 C/T 0.464 0.487 0.531 rs231024289463 102498763 G/T 0.120 unt ed rs231024389660 102498960 A/G 0.537 0.514 0.548 rs188251095718 102505018 C/T 0.642 0.635 0.875 rs188251195821 102505121 A/G 0.639 0.644 x.871 [0262] Allelotyping results were considered particularly significant with a calculatedL p-value of less than or equal to 0.05 for allelotype results. These values are indicated in bold. The allelotyping p-values were plotted in Figure 1B for the discovery cohort. The position of each SNP on the chromosome is presented on the x-axis. The y-axis gives the negative logarithm (base 1 O) of the p-value comparing the estimated allele in the case group to that of the control group. The minor allele frequency of the control group for each SNP designated by an X or other symbol on the gxaphs in Figure 1B can be determined by consulting Table 17. For example, the left-most X on the left graph is at position 102409525. By proceeding down the Table from top to bottom and across the graphs from left to right the allele frequency associated with each symbol shown can be determined.
[0263] To aid the interpretation, multiple lines have been added to the graph.
The broken horizontal lines are drawn at two common significance levels, 0.05 and 0.01.
The vertical broken lines are drawn every 20kb to assist in the interpretation of distances between SNPs. Two other lines are drawn to expose linear trends in the association of SNPs to the disease. The generally bottom-most curve is a nonlinear smoother through the data points on the graph using a local polynomial regression method (W.S. Cleveland, E. Grosse and W.M. Shyu (1992) Local regression models. Chapter 8 of Statistical Models in S eds J.M. Chambers and T.J. Hastie, Wadsworth &
BrookslCole.). The black line provides a local test for excess statistical significance to identify regions of association. This was created by use of a l Okb sliding window with lkb step sizes. Within each window, a chi-square goodness of fit test was applied to compare the proportion of SNPs that were significant at a test wise level of 0.01, to the proportion that would be expected by chance alone (0.05 for the methods used here). Resulting p-values that were less than 10-8 were truncated at that value.
[0264] Finally, the exons and introns of the genes in the covered region are plotted below each graph at the appropriate chromosomal positions. The gene boundary is indicated by the broken horizontal line. The exon positions are shown as thick, unbroken bars. An arrow is place at the 3' end of each gene to show the direction of transcription.
Example 6 ILIRLI Region Proximal SNPs [0265] It has been discovered that SNP rs1041973 in Interleukin 1 receptor-like 1 isoform 1 (ILIRLI) is associated with occurrence of osteoarthritis in subjects.
Interleukin 1 receptor-like 1 isoform 1 is a member of the interleukin 1 receptor family with no known ligand (orphan receptor).
ILIRLl exists in both a soluble and transmembrane form, suggesting that it may have ligand or lig~.nd scavenging activity. Studies of the similar gene in mouse suggested that this receptor can be induced by proinflammatory stimuli. This gene and four other interleukin 1 receptor family genes, including interleulcin 1 receptor, type I (IL1R1), interleukin 1 receptor, type II
(IL1R2), interleukin 1 receptor-like 2 (IL1RL2), and interleukin 18 receptor 1 (IL18R1), form a cytokine receptor gene cluster.
[0266] Ninety-one additional allelic variants proximal to rs 1041973 were identified and subsequently allelotyped in osteoarthritis case and control sample sets as described in Examples 1 and 2.
The polymorphic variants are set forth in Table 20. The chromosome positions provided in column four of Table 20 are based on Genome "Build 34" of NCBI's GenBank.

dhSNP Position Chromosome Allele in rs# ChromosomeSEQ ID Position variants NO: 4 rs884517 2 207 102527857 c/t rs14769842 6019 102533669 a/

dbSNP Position Chromosome Allele rs# Chromosomein Position Variants SEQ ID
NO: 4 rs951774 2 6414 102534064 a/c rs20417372 7341 102534991 a/

rs14200912 10984 102538634 a/

rs21106602 12351 102540001 c/

rs13623472 13335 102540985 a/

rs30739682 16584 102544234 -/t t /t t a rs40904732 16737 102544387 c/

rs15586222 23897 102551547 c/t rs15586212 24057 102551707 c/t rs15586202 25145 102552795 a/

rs15586192 25300 102552950 a/c rs950881 2 26262 102553912 a/c rs950880 2 26312 102553962 /t rs13623462 26589 102554239 c/t rs19681712 27302 102554952 a/

rs18132992 27358 102555008 a/t rs18132982 27451 102555101 c/

rs19681702 27552 102555202 c/t rs974389 2 30731 102558381 c/t rs971764 2 32085 102559735 a/

rs14200892 32139 102559789 a/

rs14200882 33184 102560834 a/

rs14201032 42382 102570032 /t rs14201022 42569 102570219 a/

rs19974672 44823 102572473 c/t rs19974662 45217 102572867 c/

rs13623502 45548 102573198 c/

rs23102202 45601 102573251 a/

rs13623492 45722 102573372 c/

rs37552782 45967 102573617 a/

rs37711802 47367 102575017 a/c rs37711792 47642 102575292 a/c rs985523 2 48126 102575776 c/t rs10419732 49218 102576868 a/c rs32143632 49274 102576924 -/a rs873022 2 49433 102577083 /t rs37711772 49610 102577260 a/c rs37321292 51282 102578932 a/

rs14201012 51466 102579116 a/

rs12905 2 53757 102581407 a/

rs37711752 53960 102581610 a/t rs38212042 54031 102581681 c/

rs21602032 54574 102582224 c/t rs19461312 55679 102583329 a/

rs10540962 56100 102583750 c/t rs22870382 56182 102583832 c/t rs19216222 59817 102587467 a/

rs18612462 60533 102588183 a/

rs18612452 60656 102588306 a/

rs37552762 72209 102599859 a/

rs22870372 72778 102600428 a/

rs14200992 74293 102601943 c/

dbSNP ChromosomePosition Chromosome Allele rs# in Position Variants SEQ ID
NO: 4 rs3771174 2 77335 102604985 a/

rs1420098 2 78029 102605679 a/

rs1362348 2 78374 102606024 c/

rs1882348 2 78421 102606071 a/t rs1558627 2 78434 102606084 c/t rs2058622 2 79174 102606824 c/t rs3836110 2 79397 102607047 -/

rs3771172 2 79562 102607212 a/

rs3771171 2 79700 102607350 a/

rs3771170 2 79730 102607380 a/t rs2160202 2 79904 102607554 c/t rs2058623 2 79920 102607570 a/

rs3771167 2 79938 102607588 c/t rs3771166 2 79972 102607622 c/t rs1974675 2 80125 102607775 c/t rs1465321 2 80368 102608018 a/

rs2041740 2 83484 102611134 c/t rs3771164 2 85536 102613186 a/t rs2270298 2 85829 102613479 c/t rs2270297 2 86425 102614075 a/

rs2041739 2 88083 102615733 a!

rs2080289 2 88770 102616420 c/t rs3821203 2 90622 102618272 a/

rs3771162 2 90924 102618574 alt rs3213733 2 91634 102619284 It rs3213732 2 92029 102619679 c/t rs1035130 2 95152 102622802 a/

rs3752659 2 95348 102622998 clt rs3755274 2 96145 102623795 c/t rs2241117 2 96793 102624443 a/

rs2241116 2 97015 102624665 /t rs881890 2 97064 102624714 c/t rs3771161 2 97711 102625361 /t rs3771160 2 97855 102625505 a/c rs3771159 2 98708 102626358 a/

rs1420104 2 not ma not ma ed c/t ed rs2041738 2 not ma not ma ed a/c ed Assay for Verifying and Allelotypin~ SNPs [0267] The methods used to verify and allelotype the 91 proximal SNPs of Table 20 are the same methods described in Examples 1 and 2 herein. The primers and probes used in these assays are provided in Table 21 and Table 22, respectively.

dbSNP Forward Reverse rs# PCR primer PCR primer rs884517ACGTTGGATGCATTTTCTGGTGTGACTCCCACGTTGGATGATGTTCGGTCACTTGTGAGC

rs1476984ACGTTGGATGTGAGAGAGTTGAAGAATGGGACGTTGGATGCCAAGAAGTGATTTCCTTCC

dbSNP Forward Reverse rs# PCR primer PCR primer rs951774ACGTTGGATGTCAGCCAGAGGTCTTTACTCACGTTGGATGTTAGAAGTCTCTTGGGTGGG

rs2041737ACGTTGGATGGAGATGGAGTTTCCCTCTTGACGTTGGATGAAACCAAGAGGTGGAGGTTG

rs1420091ACGTTGGATGCACCCCTATTATAAAACCCACACGTTGGATGACCAGAAATGGCATCTATGG

rs2110660ACGTTGGATGTCTCTCCGAGATGAGGAATCACGTTGGATGGTGATCTCCTCAGTACTCTG

rs1362347ACGTTGGATGTTCTTTGGTAATGAGGTAGGACGTTGGATGTGCTTGCCCTCTATTTATGG

rs3073968ACGTTGGATGGAATGATGAGGAAGGAAGGGACGTTGGATGTAAAGCCACATGTTCACCCG

rs4090473ACGTTGGATGTAGTGTGTTTCACTCTTCCCACGTTGGATGTCAAGCACCTCTGTTAACTC

rs1558622ACGTTGGATGATACTTCCTGGTTTTCTGGGACGTTGGATGGGCTCAAAGTCATCACCCAA

rs1558621ACGTTGGATGACAGTGGCGATGCCAACATTACGTTGGATGCCTGTAGTAGGACCCTACTG

rs1558620ACGTTGGATGTTGCAGGTGTCTGGTGATAGACGTTGGATGAGTTTGCCTTTCTTCATGGC

rs1558619ACGTTGGATGCCCTAATTAGGATTCCGCACACGTTGGATGCTCCATCACACTTTGACTGC

rs950881ACGTTGGATGCTTATCTCAGTCTGCCAGTGACGTTGGATGGGTGAGTGAATTAGTCCTGG

rs950880ACGTTGGATGTGCCAAAGACAATCAAATCCACGTTGGATGCACTCACCTCTGATTTCTAG

rs1362346ACGTTGGATGTTCCTCAGGTTCACCAAGAGACGTTGGATGTCCCGAACCTCATCTCATAC

rs1968171ACGTTGGATGAATGTTTCAGCCCAGCATGGACGTTGGATGATCTCCTGACCTCATGATCC

rs1813299ACGTTGGATGAATTCCAGCACTTTGGGAGGACGTTGGATGTTTCACCGTGTTAGCCAGGA

rs1813298ACGTTGGATGTTACTGCAAGCTCCACCTCCACGTTGGATGATTAACTGGGCGTGGTGGTG

rs1968170ACGTTGGATGAGCTTGCAGTAAGCCCAGATACGTTGGATGTGTTAGGGTAATTACAGTGC

rs974389ACGTTGGATGCTCTAGCCCAATATGTCTCCACGTTGGATGACTGGAGATGTGAACCCATC

rs971764ACGTTGGATGGAGATGATGGAGATTAAGAGGACGTTGGATGAGTTGTTTGACTTCGGACTG

rs1420089ACGTTGGATGAGACAGCACATATCAATGACACGTTGGATGTATTGTGCGGTTCGCTATAG

rs1420088ACGTTGGATGGGATGACTGTCAAAAACATCACGTTGGATGTAATTTTTCAGGAGCAAGGC

rs1420103ACGTTGGATGTCCATTGGAATATGACCTCCACGTTGGATGCCAGGCACATGAGCTATATC

rs1420102ACGTTGGATGGATTGGTCAGGAACTCAAACACGTTGGATGTGGGTTGCTTCTAGCTATTG

rs1997467ACGTTGGATGTGAATTTCAGTGAGTCAGGCACGTTGGATGTGAGGGGAAAAAAAACATCC

rs1997466ACGTTGGATGATAGGCACATACAGGATTTCACGTTGGATGCTCCCTTTTCAGATTAATCTC

rs1362350ACGTTGGATGGAGAACATTCTCTATACCAGACGTTGGATGTGCCTGAATAGTGAGAAGCC

rs2310220ACGTTGGATGGGTTGAAACCAGACTTGCTGACGTTGGATGCAGCCTAATCTCTGGTATAG

rs1362349ACGTTGGATGCAATACTCTGTGGTACTTATCACGTTGGATGTAAACAGTCTTATCCTTGGG

rs3755278ACGTTGGATGAGTGCTGAATAGGTTTGTTCACGTTGGATGGCCTAGTTTAAGAATGAATGC

rs3771180ACGTTGGATGGTCAACATCAAGAATTCTTAGACGTTGGATGCCTGAAATTTGATTTGTGGC

rs3771179ACGTTGGATGGTCTTCATAATTCATGATTGACGTTGGATGTCTTAAAATATAAGGGGAAG

rs985523ACGTTGGATGTCCTATGGAAGTTTTGGGTCACGTTGGATGCTGCGAAGTAGCATGATAAC

rs1041973ACGTTGGATGGGGACTTCTGACAATACAGGACGTTGGATGAATCGTGTGTTTGCCTCAGG

rs3214363ACGTTGGATGCAGGCAATCAACCACTGAAGACGTTGGATGCTGCAGTTGCTGATTCTGGT

rs873022ACGTTGGATGCCTAGTCCTTTCTGGAACAGACGTTGGATGATCCCTGCAACTGTAAATCC

rs3771177ACGTTGGATGAAGGTTAGAAGCCCCTTTTCACGTTGGATGGGCTGGAATTAAGAACAAAC

rs3732129ACGTTGGATGCTAATTCAAAGCCACATCTGACGTTGGATGTAAGTTAGCATTCAGATTGC

rs1420101ACGTTGGATGCAACATTTATGTACACCATAGACGTTGGATGTTAGTAATACTCATTGGATT

rs12905 ACGTTGGATGCTCCCAGCAAACAGGAACAGACGTTGGATGATCAAGACAATGGGAATGGC

rs3771175ACGTTGGATGAAAGAGCACAAAAGAACACGACGTTGGATGTTATGAACTCCCTCTGTGTC

rs3821204ACGTTGGATGCATGTTGTAAGCATGGTCCGACGTTGGATGACTTTACCACCCTCGCTAAC

rs2160203ACGTTGGATGACACAGACCCAAACCATACCACGTTGGATGTTCCCGTGTGTTCCATGTAC

rs1946131ACGTTGGATGGGGAACTCAGGGTTTAACACACGTTGGATGTACACTCATCACTCCTCAGG

rs1054096ACGTTGGATGATCAAGGTGCTATGTGAGGGACGTTGGATGAAAGCAGGAGTACACAAGGG

rs2287038ACGTTGGATGAATGTCCCTGGTTACCTATGACGTTGGATGACAAATAAGCTAGAAGGAGC

rs1921622ACGTTGGATGGCCACTTCTTAATTCTGTCCACGTTGGATGATTTCAGCTAGTGCCTATGG

rs1861246ACGTTGGATGCACAAGCTCTTCACCTCTTCACGTTGGATGTGGCTGAGGAGAAGTGTAAC

rs1861245ACGTTGGATGTGCTGCCTTCAATGTGTGACACGTTGGATGAGGAAAGGTCAGAGGACATG

rs3755276ACGTTGGATGCCAGCACTCACTAACATGTGACGTTGGATGAAACTCATATGGGCAGCCAC

rs2287037ACGTTGGATGCAGATTCAGCCAAAGCTTTCACGTTGGATGAAAAATCTGTGTGCCAGAAG

rs1420099ACGTTGGATGTTACACACTCTCCAGAGGTGACGTTGGATGAAAGCTTCTAGCTGCCTGAG

dbSNP Forward Reverse rs# PCR primer PCR primer rs3771174ACGTTGGATGACCCAGATTCTCTGGCTTTGACGTTGGATGTACCACAAGTGCCGAAAGAG

rs1420098ACGTTGGATGGGGACGTGAAGTACAAGATACGTTGGATGGGAGACCAAAAAAAGTTACC

rs1362348ACGTTGGATGCATGTCATAGGAAGAGTAGGACGTTGGATGTCAGCAACTCAAATATGCAG

rs1882348ACGTTGGATGCCTACTCTTCCTATGACATGACGTTGGATGCCCTAAAAGGAAATCCTATC

rs1558627ACGTTGGATGCCCTAAAAGGAAATCCTATCACGTTGGATGCCTACTCTTCCTATGACATG

rs2058622ACGTTGGATGCTGTGAAACCTTGGTAGCACACGTTGGATGTTTCTGATGCCTGGGAGTTC

rs3836110ACGTTGGATGACTCACAAATGGGGTAAAGGACGTTGGATGTGCCTTCATTCAATCAGGAG

rs3771172ACGTTGGATGCAGAAGCAAATGGCATTGGCACGTTGGATGCCATTGTTGCTTCCTAAGCC

rs3771171ACGTTGGATGAGGGTAGCAGATAGGAGATGACGTTGGATGAAGCTGCTTCTCTCCTCATC

rs3771170ACGTTGGATGCAAGGCCATTGTCAAAGCTGACGTTGGATGGTGTCCCAGAGTGGATATTG

rs2160202ACGTTGGATGAGCAGTATTTACTGCAGATGACGTTGGATGCCCACATCAAACTGCAAAGG

rs2058623ACGTTGGATGATTTACTGCAGATGTGTGTGACGTTGGATGTGTTCACTGATAGATCCCAC

rs3771167ACGTTGGATGCTAACTTAAGTGTGTAACCCACGTTGGATGCTAACGGGAAATTTTCAGGTG

rs3771166ACGTTGGATGGTGAACAGACTTTACACCTGACGTTGGATGCCTCAGTGGCATTTGATTAT

rs1974675ACGTTGGATGACTAAGAAGGAAGGGGATACACGTTGGATGGTACATTTCCCTCTACCTTC

rs1465321ACGTTGGATGTCACAGCTTTGGGTCAGTTGACGTTGGATGTCAACAACACACTGCACCTG

rs2041740ACGTTGGATGCATCCATGTCCCTACAAAAGACGTTGGATGAAAGCTCTTATACACCATGG

rs3771164ACGTTGGATGCCTGTGACATGTATGGAAATGACGTTGGATGTCAAATCCATAGGTACACTC

rs2270298ACGTTGGATGTGAAGTAGTGTTCTCTCTCACGTTGGATGAATATGAGCACTGTAGCTGC

rs2270297ACGTTGGATGTTTCCTGCCAAAAAGAAAGGACGTTGGATGGACCACACCACTAGTTCAAA

rs2041739ACGTTGGATGTAGACCCTGAAGTTTCCCACACGTTGGATGCACCTAGAGGTTCCTTTTGC

rs2080289ACGTTGGATGTGGAGAATGTCAACTGAGTCACGTTGGATGATACAAACAAGAGGCCATGG

rs3821203ACGTTGGATGTCAAAGACAAAGGGCAGGAGACGTTGGATGGGATCCAGAGAAAGGTAGTC

rs3771162ACGTTGGATGTGAGTGGAGTACAGTGAGACACGTTGGATGTGGCACTGCACTTTCTGAGA

rs3213733ACGTTGGATGTGAAAGCACCTTGTATCTGGACGTTGGATGCATCTTCCTCTGCCTTTTAG

rs3213732ACGTTGGATGGTCAGGTTAAAAGTGGCAACACGTTGGATGTGACACTGGATACACATTTC

rs1035130ACGTTGGATGTTAGGATCCGATCCATTTTCACGTTGGATGCTCTGCTTTGCTGAATGAAG

rs3752659ACGTTGGATGTGCATAATGCGTCCACCTAGACGTTGGATGGGCTGATGTGTATTTTGGGC

rs3755274ACGTTGGATGTATCAAAGGTGTGTGCACCCACGTTGGATGAGGGGTAGAAAACCACAGTG

rs2241117ACGTTGGATGTGGCTGGAAGATCATGATGCACGTTGGATGCCCCAAGTTGTTAGGAAGAG

rs2241116ACGTTGGATGAATGCAGGCAACATCACAGCACGTTGGATGAGTAGGCTCTGTTCGTTACC

rs881890ACGTTGGATGATGCCATTTGCCTTCTGGAGACGTTGGATGTCTCAGGGTAACGAACAGAG

rs3771161ACGTTGGATGCCATCAGGTGAGCACTGAAAACGTTGGATGTCATTGCCTCCTGAACTTGG

rs3771160ACGTTGGATGAGAAATGGCTGTGACTGGAGACGTTGGATGTATCCAGGGAGTTGATGGTG

rs3771159ACGTTGGATGCAGGTGATGGTCCAACAAAGACGTTGGATGTGCTGTGGTCCACTCACTTG

rs1420104ACGTTGGATGTATTCTGGAGGCTGAGGTGGACGTTGGATGTGGAGTGCAGTGGTGTGATC

rs2041738ACGTTGGATGTGGTGAAACCCCATCTCTACACGTTGGATGTTTCAAGCTATTCTCCTGCC

dbSNP Extend Term rs# Primer Mix rs884517 GGTGTGACTCCCAGACCAA ACT

rs1476984 ATGGGTAGTTAATGGTGGAAATTTACT

rs951774 CAAAGTAGTTGACTTGTCTTTCT ACT

rs2041737 CCAGGCTAGTGCAGTGGC ACT

rs1420091 CCCACATTATATTGTCATTACTTTACG

rs2110660 ATGAGGAATCAGAGCTGGGA ACT

rs1362347 GTAATGAGGTAGGAATAATATTG ACT

rs3073968 GGCAATTGTGTGTGTGTGTG CGT

rs4090473 CTTACTCCTATTCCAAAGTTCA ACT

rs1558622 ACTGCAAGGGAGAGCCCC I ACT

dbSNP Extend Term rs# Primer Mix rs1558621 AGTGTGTGTGTGTGCGTGC ACT

rs1558620 GTCTGGTGATAGTTGGGTGC ACG

rs1558619 GATTCCGCACATCCTATGCCT ACT

rs950881 GATGGTTTGTGCCTCTGGTC ACT

rs950880 ATTTAAGAATGCTTTCGTCATAAGACT

rs1362346 GAATATCTATGCCCACCAGAT ACG

rs1968171 GCCCAGCATGGTGGCTCA ACG

rs1813299 GTGGATCATGAGGTCAGGAG CGT

rs1813298 GCCTCAGCCTCCCGAGTA ACT

rs1968170 AGCCTGGGTGACAGAGCC ACT

rs974389 GTCTCCTGAATTTCAGAAGCA ACT

rs971764 GTCAAGGTAAAAACATTATTGTG ACG

rs1420089 GCACATATCAATGACAAGACTA ACT

rs1420088 CATGTTATGTAACTCTGAGTTC ACT

rs1420103 GAATATGACCTCCAGAAGGCAA ACT

rs1420102 GAACTCAAACAAATACTTGGACACACG

rs1997467 TTCAGTGACTCTCACAATAAGC ACG

rs1997466 AAGAAAAAGCTGGTTCAATGAG ACT

rs1362350 ACATTCTCTATACCAGAGATTAGGACT

rs2310220 CTGAACTTCAAAGTCAAGCTTTT ACG

rs1362349 CTGTGGTACTTATCATTAACATCAACT

rs3755278 ACTCGGAATTCTTTTACATTTGGTACT

rs3771180 CATCAAGAATTCTTAGTACATGATACT

rs3771179 TATGTTAGTAAATTTCTATGTTGGACT

rs985523 CATATAGCTTTCACAATGATCATGACG

rs1041973 ATACCAGAATCAGCAACT ACT

rs3214363 GAGCAGGGTGAAAGAAGATGGG ACT

rs873022 TTCTAGGAATACTATCAGGTTGA ACT

rs3771177 TTTTCACCTACTAGAGGCCC CGT

rs3732129 GCCACATCTGTTCTTTATTCTTT ACG

rs1420101 CCATCACAAAGCCTCTCATTA ACT

rs12905 AGACAGCAAACAACATCC ACG

rs3771175 CACAAAAGAACACGTTCAGTTT CGT

rs3821204 TAAGCATGGTCCGTTCTATAC ACT

rs2160203 CCACACACATTATCATTGTTA ACT

rs1946131 TTAACACTCTTTGGCTATTTGACAACT

rs1054096 TCCATCCAGCCTGCCCAC ACG

rs2287038 TACCTATGTGTTTGAATTATCTTCACT

rs1921622 GAAAGAGGACTTAAAAATTGATGAACT

rs1861246 CTTCACCTCTTCTTTTTCAGTC ACG

rs1861245 CTGGAATGGTTTTCTACTTCC ACG

rs3755276 GTGTGTATGCATGTGTTCGC ACT

rs2287037 ACAAAAGTGTGCCTATCTTATGAAACT

rs1420099 GGTGGGAGGTTGATAATTGAAA ACT

rs3771174 CTGACCATCATCTACCCAGG ACT

rs1420098 ACGTGAAGTACAAGATTCTTCA ACT

rs1362348 GAGTAGGAAAGAAAAGGATGTG ACT

rs1882348 TCCTATGACATGAAATACATTCT CGT

rs1558627 AAGCAGAGAGAGATAAACTTATT ACG

dbSNP Extend Term rs# Primer Mix rs2058622 AAACCTTGGTAGCACTTCTGT ACT

rs3836110 AACAAACACCGCCCCCCC CGT

rs3771172 GCATTGGCCATCTTTCTGATA ACG

rs3771171 GAGGTGTCCCAGAGTGGATA ACG

rs3771170 CAAAGCTGCTTCTCTCCTCA CGT

rs2160202 TATACACATATGTGTTCTAACTTAACT

rs2058623 ACTTAGGTGTGTAACCCTTTG ACG

rs3771167 CTTTGTAGTTTGATGTGGGATCTACT

rs3771166 ACTTTACACCTGAAAATTTCCC ACT

rs1974675 GAAGGGGATACAAAAGGGATA ACT

rs1465321 CAGTTGGCCTCAGTGTTAACCC ACG

rs2041740 GAACTCATGCTTTTTTATGGCTGACG

rs3771164 GACATGTATGGAAATGTGTGTG CGT

rs2270298 CTCTCTCTCTGCATGTGTGT ACT

rs2270297 AGCCAAGTAGAGGAGCACC ACT

rs2041739 CTCCTGAGTTCCTGTGAATAC ACT

rs2080289 TCTCAGGACTCCACTCAAATGTCACT

rs3821203 GGCAGGAGGCAATTTCGGT ACT

rs3771162 CAGTGAGACTCAGGAGTGC CGT

rs3213733 TGTATCTGGTTTTCTCTCACTCAACT

rs3213732 CAACATTCAAAAAATGGCACTCTTACG

rs1035130 TCCGATCCATTTTCTTCCCC ACT

rs3752659 CCTAGGGTATGGCCACTATAATTAACG

rs3755274 CACCCAACTATAAAGAAAGACCTCACG

rs2241117 ATCATGATGCTAAGTTGAAAATATACT

rs2241116 TCAAGCATTTTAAACATGTGAATTCGT

rs881890 TGCCTTCTGGAGTCCTGTAA ACT

rs3771161 GTGAGCACTGAAAAACTTTAAGAACT

rs3771160 GCCAGAAAGCTGTGATTTCCA ACT

rs3771159 CCAACAAAGATTTGAGCCCC ACT

rs1420104 CTGGGAGGTGGAGACTGCA ACT

rs2041738 AAAAATACAAAAATTAGCTGGGCI ACT

Genetic Anal.
[0268] Allelotyping results from the discovery cohort are shown for cases and controls in Table 23.
The allele frequency for the A2 allele is noted in the fifth and sixth columns for osteoarthritis case pools and control pools, respectively, where "AF" is allele frequency. The allele frequency for the A1 allele can be easily calculated by subtracting the A2 allele frequency from 1 (A1 AF
= 1-A2 AF). For example, the SNP rs951774 has the following case and control allele frequencies: case A1 (A) = 0.24;
case A2 (C) = 0.76; control A1 (A) = 0.20; and control A2 (C) = 0.80, where the nucleotide is provided in paranthesis. Some SNPs are labeled "untyped" because of failed assays.

dbSNP Position ChromosomeAllA2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 4 rs884517 207 102527857C/T

rs1476984 6019 102533669A/G 0.83 0.83 0.973 rs951774 6414 102534064A/C 0.76 0.80 0.099 rs2041737 7341 102534991A/G 0.38 0.32 0.146 rs1420091 10984 102538634A/G 0.33 0.35 0.388 rs2110660 12351 102540001C/G 0.41 0.40 0.753 rs1362347 13335 102540985A/G 0.83 0.83 0.895 /TGTG/T
rs3073968 16584 102544234GTGAG 0.48 0.48 0.878 rs4090473 16737 102544387C/G 0.42 0.43 0.633 rs1558622 23897 102551547C/T 0.40 0.39 0.879 rs1558621 24057 102551707C/T 0.32 0.31 0.795 rs1558620 25145 102552795A/G 0.37 0.37 0.998 rs1558619 25300 102552950A/C 0.46 0.47 0.556 rs950881 26262 102553912A/C 0.75 0.74 0.636 rs950880 26312 102553962G/T 0.45 0.48 0.285 rs1362346 26589 102554239C/T

rs1968171 27302 102554952A/G 0.43 0.43 0.891 rs1813299 27358 102555008A/T

rs1813298 27451 102555101C/G

rs1968170 27552 102555202C/T 0.65 0.65 0.941 rs974389 30731 102558381C/T 0.41 0.42 0.734 rs971764 32085 102559735A/G 0.45 0.44 0.738 rs1420089 32139 102559789A/G 0.16 0.19 0.099 rs1420088 33184 102560834A/G 0.41 0.40 0.869 rs1420103 42382 102570032G/T 0.68 0.68 0.952 rs 1420102 42569 102570219A/G 0.48 0.46 0.349 rs1997467 44823 102572473C/T

rs1997466 45217 102572867C/G 0.46 0.46 0.693 rs1362350 45548 102573198C/G 0.48 0.46 0.475 rs2310220 45601 102573251A/G 0.40 0.41 0.480 rs1362349 45722 102573372C/G 0.41 0.42 0.893 rs3755278 45967 102573617A/G 0.07 0.08 0.876 rs3771180 47367 102575017A/C 0.91 0.90 0.669 rs3771179 47642 102575292A/C 0.08 0.08 0.986 rs985523 48126 102575776C/T 0.17 0.13 0.064 rs1041973 49218 102576868A/C

rs3214363 49274 102576924-/A

rs873022 49433 102577083G/T 0.53 0.56 0.321 rs3771177 49610 102577260A/C 0.33 0.31 0.278 rs3732129 51282 102578932A/G 0.46 0.50 0.127 rs1420101 51466 102579116A/G 0.55 0.57 0.257 rs12905 53757 102581407A/G 0.30 0.27 0.262 rs3771175 53960 102581610A/T 0.84 0.82 0.174 rs3821204 54031 102581681C/G 0.26 0.23 0.222 rs2160203 54574 102582224C/T 0.21 0.26 0.033 rs1946131 55679 102583329A/G 0.73 0.74 0.710 rs1054096 56100 102583750C/T 0.69 0.65 0.137 rs2287038 56182 102583832C/T 0.98 0.95 0.207 rs1921622 59817 102587467A/G 0.40 0.43 0.218 rs1861246 60533 102588183A/G 0.22 0.18 0.068 rs1861245 60656 102588306A/G 0.35 0.37 0.377 rs3755276 72209 102599859A/G 0.51 0.48 0.355 rs2287037 72778 102600428A/G 0.49 0.53 0.195 rs1420099 74293 102601943C/G 0.58 0.56 0.416 rs3771174 77335 102604985A/G

rs1420098 78029 102605679A/G 0.33 0.32 0.532 rs1362348 78374 102606024C/G 0.02 0.03 0.590 dbSNP ~ PositionChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 4 rs1882348 78421 102606071A/T 0.36 0.35 0.596 rs1558627 78434 102606084C/T 0.62 0.65 0.219 rs2058622 79174 102606824C/T 0.57 0.59 0.528 rs3836110 79397 102607047-/G 0.72 0.73 0.856 rs3771172 79562 102607212A/G 0.28 0.25 0.261 rs3771171 79700 102607350A/G

rs3771170 79730 102607380A/T 0.24 0.23 0.533 rs2160202 79904 102607554C/T 0.55 0.62 0.061 rs2058623 79920 102607570A/G 0.67 0.68 0.631 rs3771167 79938 102607588C/T

rs3771166 79972 102607622C/T 0.55 0.53 0.624 rs1974675 80125 102607775C/T 0.57 0.55 0.470 rs1465321 80368 102608018A/G 0.27 0.26 0.614 rs2041740 83484 102611134C/T 0.26 0.25 0.622 rs3771164 85536 102613186A/T 0.76 0.73 0.197 rs2270298 85829 102613479C/T 0.23 0.21 0.329 rs2270297 86425 102614075A/G 0.60 0.60 0.900 rs2041739 88083 102615733A/G 0.43 0.40 0.235 rs2080289 88770 102616420C/T 0.56 0.59 0.322 rs3821203 90622 102618272A/G 0.58 0.62 0.194 rs3771162 90924 102618574A/T 0.30 0.28 0.260 rs3213733 91634 102619284G/T 0.76 0.73 0.287 rs3213732 92029 102619679C/T 0.44 0.42 0.507 rs1035130 95152 102622802A/G 0.58 0.61 0.234 rs3752659 95348 102622998C/T 0.80 0.80 0.957 rs3755274 96145 102623795C/T 0.26 0.25 0.549 rs2241117 96793 102624443A/G 0.71 0.75 0.077 rs2241116 97015 102624665G/T 0.16 0.15 0.469 rs881890 97064 102624714C/T

rs3771161 97711 102625361G/T 0.70 0.68 0.348 rs3771160 97855 102625505A/C

rs3771159 98708 102626358A/G 0.38 0.40 0.294 rs1420104 not ma not ma C/T
ed ed rs2041738 not ma not ma A/C
ed ed (0269] The ILIRLl proximal SNPs were also allelotyped in the replication cohorts using the methods described herein and the primers provided in Tables 21 and 22. The replication allelotyping results for replication cohort #1 and replication cohort #2 are provided in Tables 24 and 25, respectively.

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position AlleleCase Control Value SEQ ID AF AF
NO: 4 rs884517 207 102527857 C/T

rs14769846019 102533669 A/G 0.82 0.81 0.878 rs951774 6414 102534064 A/C 0.76 0.82 0.024 rs20417377341 102534991 A/G 0.36 0.32 0.382 rs142009110984 102538634 A/G 0.32 0.35 0.340 rs211066012351 102540001 C/G 0.39 0.39 0.951 rs136234713335 102540985 A/G 0.83 0.83 0.766 /TGTG/T
rs307396816584 102544234 GTGAG 0.47 0.48 0.822 rs409047316737 102544387 C/G 0.40 0.41 0.663 rs155862223897 102551547 C/T 0.38 0.38 0.943 rs155862124057 102551707 C/T 0.33 0.32 0.631 rs155862025145 102552795 A/G 0.34 0.34 0.957 rs155861925300 102552950 A/C 0.44 0.47 0.368 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position _AlleleCase Control Value SEQ ID NO: AF AF

rs950881 26262 102553912A/C 0.76 0.74 0.476 rs950880 26312 102553962G/T 0.42 0.47 0.199 rs136234626589 102554239C/T

rs196817127302 102554952A/G 0.43 0.44 0.641 rs181329927358 102555008A/T

rs181329827451 102555101C/G

rs196817027552 102555202C/T 0.64 0.65 0.797 rs974389 30731 102558381C/T 0.39 0.41 0.678 rs971764 32085 102559735A/G 0.47 0.46 0.710 rs142008932139 102559789AIG 0.16 0.21 0.075 rs142008833184 102560834A/G 0.41 0.40 0.869 rs142010342382 102570032G/T 0.69 0.72 0.268 rs142010242569 102570219A/G 0.50 0.47 0.329 rs199746744823 102572473C/T

rs199746645217 102572867C/G 0.49 0.47 0.675 rs136235045548 102573198C/G 0.51 0.47 0.308 rs231022045601 102573251A/G 0.40 0.44 0.282 rs136234945722 102573372C/G 0.42 0.43 0.730 rs375527845967 102573617A/G 0.08 0.08 0.902 rs377118047367 102575017A/C 0.93 0.92 0.591 rs377117947642 102575292A/C 0.08 0.08 0.936 rs985523 48126 102575776C/T 0.17 0.13 0.156 rs104197349218 102576868A/C

rs321436349274 102576924-/A

rs873022 49433 102577083G/T 0.51 0.56 0.138 rs377117749610 102577260A/C 0.36 0.32 0.125 rs373212951282 102578932A/G 0.43 0.50 0.048 rs142010151466 102579116A/G 0.50 0.55 0.132 rs12905 53757 102581407A/G 0.33 0.28 0.127 rs377117553960 102581610A/T 0.86 0.83 0.217 rs382120454031 102581681C/G 0.29 0.23 0.071 rs216020354574 102582224C/T 0.19 0.26 0.016 rs194613155679 102583329A/G 0.72 0.73 0.771 rs105409656100 102583750C/T 0.70 0.65 0.079 rs228703856182 102583832C/T 0.93 NA 0.975 rs192162259817 102587467AlG 0.37 0.41 0.260 rs186124660533 102588183A/G 0.22 0.15 0.031 rs186124560656 102588306A/G 0.34 0.39 0.149 rs375527672209 102599859A/G 0.53 0.46 0.072 rs228703772778 102600428A/G 0.45 0.51 0.069 rs142009974293 102601943C/G 0.59 0.55 0.312 rs377117477335 102604985A/G

rs142009878029 102605679A/G 0.35 0.32 0.328 rs136234878374 102606024C/G 0.02 NA 0.025 rs188234878421 102606071A/T 0.40 0.37 0.399 rs155862778434 102606084C/T 0.64 0.69 0.118 rs205862279174 102606824C/T 0.59 0.62 0.491 rs383611079397 102607047-/G 0.74 0.75 0.625 rs377117279562 102607212A/G 0.31 0.27 0.200 rs377117179700 102607350A/G

rs377117079730 102607380A/T 0.22 0.20 0.346 rs216020279904 102607554C/T 0.55 0.60 0.217 rs205862379920 102607570A/G 0.69 0.72 0.266 rs377116779938 102607588C/T

rs377116679972 102607622C/T 0.57 unt ed NA

rs197467580125 102607775C/T 0.58 0.54 0.297 rs146532180368 102608018A/G 0.25 0.23 0.471 rs204174083484 102611134C/T 0.25 0.22 0.450 rs377116485536 102613186A/T 0.77 0.72 0.073 rs227029885829 102613479C/T 0.25 0.22 0.324 rs227029786425 102614075A/G 0.63 0.64 0.589 rs204173988083 102615733A/G 0.44 0.40 0.157 rs208028988770 102616420C/T 0.53 0.58 0.114 rs382120390622 102618272A/G 0.55 0.61 0.104 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position AlleleCase Control Value SEQ ID AF AF
NO: 4 rs377116290924 102618574 A/T 0.34 0.29 0.261 rs321373391634 102619284 G/T 0.77 0.73 0.260 rs321373292029 102619679 C/T 0.48 0.41 0.026 rs103513095152 102622802 A/G 0.55 0.60 0.152 rs375265995348 102622998 C/T 0.81 0.80 0.760 rs375527496145 102623795 C/T 0.25 0.22 0.319 rs224111796793 102624443 A/G 0.72 0.80 0.024 rs224111697015 102624665 G/T 0.18 NA NA

rs881890 97064 102624714 C/T

rs377116197711 102625361 G/T 0.71 0.66 0.146 rs377116097855 102625505 A/C

rs377115998708 102626358 A/G 0.38 0.42 0.175 rs1420104not ma not ma C/T
ed ed rs2041738not ma not ma A/C
ed ed dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 4 rs884517 207 102527857C/T

rs14769846019 102533669A/G 0.84 0.85 0.759 rs951774 6414 102534064A/C 0.77 0.75 0.730 rs20417377341 102534991A/G 0.40 NA

rs142009110984 102538634A/G 0.34 0.35 0.819 rs211066012351 102540001C/G 0.43 0.42 0.665 rs136234713335 102540985A/G 0.82 0.83 0.576 /TGTG/T
rs307396816584 102544234GTGAG 0.49 0.49 0.997 rs409047316737 102544387C/G 0.44 0.45 0.732 rs155862223897 102551547C/T 0.42 0.42 0.976 rs155862124057 102551707C/T 0.31 0.31 0.926 rs155862025145 102552795A/G 0.42 0.42 0.867 rs155861925300 102552950A/C 0.48 0.48 0.930 rs950881 26262 102553912A/C 0.73 0.73 0.955 rs950880 26312 102553962G/T 0.48 0.49 0.919 rs136234626589 102554239C/T

rs196817127302 102554952A/G 0.43 0.42 0.717 rs181329927358 102555008A/T

rs181329827451 102555101C/G

rs196817027552 102555202C/T 0.67 0.66 0.830 rs974389 30731 102558381C/T 0.44 0.45 0.857 rs971764 32085 102559735A/G 0.43 0.42 0.845 rs142008932139 102559789A/G 0.15 0.16 0.809 rs142008833184 102560834A/G

rs142010342382 102570032G/T 0.68 0.63 0.178 rs142010242569 102570219A/G 0.45 0.44 0.722 rs199746744823 102572473C/T

rs199746645217 102572867C/G 0.44 0.43 0.805 rs136235045548 102573198ClG 0.45 0.46 0.890 rs231022045601 102573251A/G 0.38 0.37 0.661 rs136234945722 102573372C/G 0.41 0.40 0.762 rs375527845967 102573617A/G 0.07 0.07 0.984 rs377118047367 102575017A/C 0.88 0.87 0.812 rs377117947642 102575292A/C 0.07 0.07 0.868 rs985523 48126 102575776C/T 0.16 0.13 0.270 rs104197349218 102576868A/C

rs321436349274 102576924-/A

rs873022 49433 102577083G/T 0.57 0.56 0.868 rs377117749610 102577260A/C 0.29 0.29 0.988 rs373212951282 102578932A/G 0.51 0.52 0.795 rs142010151466 102579116A/G 0.60 0.61 0.864 rs12905 53757 102581407A/G 0.26 0.26 0.994 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 4 rs377117553960 102581610A/T 0.82 0.80 0.444 rs382120454031 102581681C/G 0.22 0.23 0.769 rs216020354574 102582224C/T 0.23 0.25 0.732 rs194613155679 102583329A/G 0.75 0.77 0.723 rs105409656100 102583750C/T 0.66 0.65 0.807 rs228703856182 102583832C/T 0.97 0.00 rs192162259817 102587467A/G 0.44 0.46 0.472 rs186124660533 102588183AIG 0.23 0.24 0.824 rs186124560656 102588306A/G 0.36 0.34 0.590 rs375527672209 102599859A/G 0.48 0.51 0.423 rs228703772778 102600428A/G 0.55 0.54 0.941 rs142009974293 102601943C/G 0.58 0.58 0.904 rs377117477335 102604985A/G

rs142009878029 102605679A/G 0.30 0.31 0.827 rs136234878374 102606024C/G 0.04 -0.01 rs188234878421 102606071A/T 0.31 0.31 0.968 rs155862778434 102606084C/T 0.60 0.59 0.839 rs205862279174 102606824C/T 0.56 0.55 0.961 rs383611079397 102607047-/G 0.70 0.69 0.643 rs377117279562 102607212A/G 0.24 0.22 0.675 rs377117179700 102607350A/G

rs377117079730 102607380A/T 0.26 0.27 0.700 rs216020279904 102607554C/T unt 0.64 NA
ed rs205862379920 102607570A/G 0.65 0.62 0.389 rs377116779938 102607588C/T

rs377116679972 102607622C/T 0.53 0.53 0.820 rs197467580125 102607775C/T 0.55 0.56 0.842 rs146532180368 102608018A/G 0.29 0.30 0.781 rs204174083484 102611134C/T 0.28 0.30 0.658 rs377116485536 102613186A/T 0.73 0.74 0.905 rs227029885829 102613479C/T 0.19 0.18 0.654 rs227029786425 102614075A/G 0.57 0.53 0.249 rs204173988083 102615733A/G 0.42 0.41 0.892 rs208028988770 102616420C/T 0.61 0.60 0.840 rs382120390622 102618272A/G 0.62 0.63 0.927 rs377116290924 102618574A/T 0.26 0.25 0.621 rs321373391634 102619284G/T 0.75 0.74 0.728 rs321373292029 102619679C/T 0.39 0.45 0.176 rs103513095152 102622802A/G 0.62 0.63 0.792 rs375265995348 102622998C/T 0.79 0.80 0.826 rs375527496145 102623795C/T 0.27 0.29 0.618 rs224111796793 102624443A/G 0.70 0.67 0.480 rs224111697015 102624665G/T 0.15 0.15 0.849 rs881890 97064 102624714C/T

rs377116197711 102625361G/T 0.68 0.70 0.681 rs377116097855 102625505A/C

rs377115998708 102626358A/G 0.37 0.37 0.970 rs1420104not ma not ma C/T
ed ed rs2041738not ma not ma A/C
ed ed [0270] Allelotyping results were considered particularly significant with a calculated p-value of less than or equal to 0.05 for allelotype results. These values are indicated in bold. The allelotyping p-values were plotted in Figure 1 C for the discovery cohort. The position of each SNP on the chromosome is presented on the x-axis. The y-axis gives the negative logarithm (base 10) of the p-value comparing the estimated allele in the case group to that of the control group. The minor allele frequency of the control group for each SNP designated by an X or other symbol on the graphs in Figure 1 C can be determined by consulting Table 23. For example, the left-most X on the left graph is at position 102527857. By proceeding down the Table from top to bottom and across the graphs from left to right the allele frequency associated with each symbol shown can be determined.
[0271] To aid the interpretation, multiple lines have been added to the graph.
The broken horizontal lines are drawn at two common significance levels, 0.05 and 0.01.
The vertical broken lines are drawn every 20kb to assist in the interpretation of distances between SNPs. Two other lines are drawn to expose linear trends in the association of SNPs to the disease. The generally bottom-most curve is a nonlinear smoother through the data points on the graph using a local polynomial regression method (W.S. Cleveland, E. Grosse and W.M. Shyu (1992) Local regression models. Chapter 8 of Statistical Models in S eds J.M. Chambers and T.J. Hastie, Wadsworth &
Brooks/Cole.). The black line provides a local test for excess statistical significance to identify regions of association. This was created by use of a l Okb sliding window with lkb step sizes. Within each window, a chi-square goodness of fit test was applied to compare the proportion of SNPs that were significant at a test wise level of 0.01, to the proportion that would be expected by chance alone (0.05 for the methods used here). Resulting p-values that were less than 10'8 were truncated at that value.
[0272] Finally, the exons and introns of the genes in the covered region are plotted below each graph at the appropriate chromosomal positions. The gene boundary is indicated by the broken horizontal line. The exon positions are shown as thick, unbroken bars. An arrow is place at the 3' end of each gene to show the direction of transcription.
Example 7 WASPIP Region Proximal SNPs (0273] It has been discovered that rs1465621 in the untranslated region (LJTR) of the WASPIP gene is associated with occurrence of osteoarthritis in subjects. This gene encodes a protein that plays a role in actin cytoskeleton organization. The encoded protein binds to a region of Wiskott-Aldrich syndrome protein that is frequently mutated in Wiskott-Aldrich syndrome, an X-linked recessive disorder.
Impairment of the interaction between these two proteins may contribute to the disease. Alternative transcript variants exist for this gene. Biological activity of WASPIP or a pathway member downstream of WASPIP (e.g., IL-2) can be modulated by addition of an antibody, a recombinant binding partner, a binding agent, or a recombinant WASPIP or downstream pathway member protein or functional fragment thereof.
[0274] Sixty-one additional allelic variants proximal to rs1465621 were identified and subsequently allelotyped in osteoarthritis case and control sample sets as described in Examples 1 and 2.
The polymorphic variants are set forth in Table 26_ The chromosome positions provided in column four of Table 26 are based on Genome "Build 34" of NCBI's GenBank.

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs18644552 209 175603909 C/T

rs19717632 5908 175609608 C/T

rs934269 2 7460 175611160 A/G

rs934270 2 7733 175611433 A/G

rs20333092 7855 175611555 A/G

rs20333102 7904 175611604 A/C

rs934271 2 8869 175612569 G/T

rs934272 2 9480 175613180 C/T

rs18971102 13820 175617520 C/T

rs20333112 15152 175618852 A/G

rs10100272 17713 175621413 A/G

rs10100282 17804 175621504 C/T

rs28845022 18220 175621920 C/T

rs14301772 19083 175622783 C/T

rs14301782 19123 175622823 C/G

rs30437792 19605 175623305 -/GTAAA

rs15497422 20247 175623947 G/T

rs30437812 20592 175624292 -/CCCCC

rs20333132 21907 175625607 C/T

rs7739 2 23273 175626973 C/T

rs11482 2 23299 175626999 A/C

rs30879072 23623 175627323 G/T

rs23588882 23669 175627369 A/T

rs10460362 23844 175627544 A/T

rs32050602 24190 175627890 A/G

rs15327 2 24486 175628186 C/T

rs14301792 24896 175628596 A/C

rs14301802 25118 175628818 C/G

rs21632362 30551 175634251 C/G

rs32173512 30844 175634544 -/GAGA

rs23038912 30900 175634600 A/G

rs38159692 30942 175634642 AlG

rs22886222 31699 175635399 A/G

rs22886232 32081 175635781 G/T

rs10443352 35078 175638778 A/G

rs22886242 36196 175639896 A/T

rs10605112 36541 175640241 A/C

rs13672182 38356 175642056 A/G

rs13672172 45578 175649278 A/G

rs14656212 49634 175653334 A/T

rs14656222 49774 175653474 G/T

rs21158722 51119 175654819 AlG

rs14656232 51181 175654881 A/G

rs14695212 51652 175655352 C/T

rs18644512 54467 175658167 C/G

rs14301832 55762 175659462 A/G

rs14301822 55999 175659699 A/G

rs14301812 57865 175661565 A/C

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs19916012 66613 175670313 A/G

rs23588902 68377 175672077 C/T

rs21158752 69754 175673454 C/T

rs14301852 72859 175676559 A/G

rs22174292 76512 175680212 A/G

rs30499092 76717 175680417 -/AT

rs14301842 77722 175681422 ClT

rs22783212 80998 175684698 A/G

rs21158742 82033 175685733 C/T

rs20333152 89658 175693358 C/T

rs20333142 89960 175693660 A/G

rs19916002 94155 175697855 A/G

rs18644532 95679 175699379 A/G

Assay for Verifying and Allelotypin~ SNPs (0275] The methods used to verify and allelotype the 61 proximal SNPs of Table 26 are the same methods described in Examples 1 and 2 herein. The primers and probes used in these assays are provided in Table 27 and Table 28, respectively.

dbSNP Forward Reverse rs# PCR primer PCR primer rs1864455ACGTTGGATGACAGGTGTGCAGTGAATGTCACGTTG GATGTCAGCAGTTGTCCCATCTTC

rs1971 ACGTTGGATGAATGATTTACTTGAGGCCGGACGTTG GATGTCTCAAACTCCTGACCTCTG

rs934269ACGTTGGATGAAGTCCCTAGGACTACAGGTACGTTG GATGTGGGCAACATAGCAAGACCC

rs934270ACGTTGGATGATGATCTGCCCTGTTCTTGCACGTTG GATGAGGTGCAATCTACTCACCAG

rs2033 ACGTTGGATGCCATAGCTTCCTCACACAACACGTTG GATGTTCTCCTTGCAGACAAGGTG

rs2033 ACGTTGGATGATGAGTCTCTGTGAGTTGAGACGTTG GATGTTGTGTGAGGAAGCTATGGC

rs934271ACGTTGGATGCCTGAAATGCCAAGAAGAATGACGTTG GATGATTCTTGCTACATAGTCAGG

rs934272ACGTTGGATGAGTCTTGCTTCTCTTCACACACGTTG GATGACTAAGAGGTATTTGGGTGC

rs1897110ACGTTGGATGTCAGCATCCCAAAGTGCTAGACGTTG GATGTAAAAATCGGCTGGGTGTGG

rs2033 ACGTTGGATGCGGGACTCTGTGTTAACAAGACGTTG GATGGAGTTACAAGATGCTGGAGC

rs1010 ACGTTGGATGGCCGTCTCTGTTGTGAGAAGACGTTGGATGAATTCCTCTCTGACTCTTTC

rs1010 ACGTTGGATGGTAACTTAAGGCCTCACAGCACGTTGGATGGACTGAAAGAGTCAGAGAGG

rs2884502ACGTTGGATGGAAATCCCCATGTCAGAATCACGTTG GATGTGAACAGTACAAAGGAAGGG

rs1430177ACGTTGGATGGCCAGACCCTGTCTCAAATAACGTTG GATGTGAGTAGCTAGGAGTATAGG

rs1430178ACGTTGGATGTATTTGAGACAGGGTCTGGCACGTTG GATGTGAGCCCTGGAATTCAAGAC

rs3043 ACGTTGGATGAGTTCCTCAACTACTGTTTGACGTTG GATGCCCACATGATTTAATGGAGC

rs1549742ACGTTGGATGTGAGACACTGTGCCTAGCTGACGTTG GATGGGTCCAGGTTTTGTGATGTC

rs3043781ACGTTGGATGATAATAAATAGTTAGAAGCCACGTTGGATGAGAAGCTAATTAAGCTCAAG

rs2033 ACGTTGGATGAAGCCGTGCACTCACAAATCACGTTG GATGACCACCTACAAAGCTTCTGG

rs77 ACGTTGGATGTGATGACACAGATAGCAAAATGTGACGTTGGATGTTCCCTCCTTATAGTCAAGGACC

rs11482 ACGTTGGATGAAATGTTGGCATGAAATTAATTTTACGTTGGATGTGTGTCTGTTTACATAGTGCATG

rs3087907ACGTTGGATGGAACACTGAGTTTTAATACTGACGTTGGATGAATCAGAGCTTACATGTGTG

rs2358888ACGTTGGATGAATCAGAGCTTACATGTGTGACGTTG GATGGAGGTGAATGTTAAAATACTG

rs1046036ACGTTGGATGCAAAGTTGCCATTCATCCAGACGTTGGATGAGGGTGTAGGTGTATTAATG

rs3205060ACGTTGGATGAAGCCAACACTTTGCCAAGCACGTTGGATGTCCTCTCTCCTCTACCATTC

dbSNP Forward Reverse rs# PCR primer PCR primer rs15327 ACGTTGGATGGGGTTGGTrTCTTGGTAGCAACGTTGGATGCCTAAACATfGTATCATGGTITCA

rs1430179ACGTTGGATGAGACTAGGAAGGCTTGGTAGACGTTGGATGGGTTCCCTTCTfCTfCCATG

rs1430180ACGTTGGATGCTfCAAAGTACCAAGGTCAGACGTTGGATGCAGGCTITCCATfTGTTTCC

rs2163236ACGTTGGATGTTGAGTAGCCTGAGTGACACACGTTGGATGTAGATGGCTCCAAAGGGTfC

rs3217351ACGTTGGATGGTAACGAAAGGCACAGAATGACGTTGGATGTAGCACTTCCAGCTTTTCTG

rs2303891ACGTTGGATGACCACAGACATCAGTGCTAGACGTTGGATGCAGTGTACTAATTCGTGACC

rs3815969ACGTTGGATGGAAGTGCTACAAAGGTCACGACGTTGGATGGCTGGATCCTAATCACTCTC

rs2288622ACGTTGGATGGGCCTGGAGCAAAAAAAGACACGTTGGATGCATCAGCTGTACACCAATGG

rs2288623ACGTTGGATGGAAATTATTTfAGGTCTTCAGACGTi'GGATGTATACATCACAGAAACATGC

rs1044335ACGTTGGATGCTACTCAGTGTCCTCATCTCACGTfGGATGTTfAAGTGGCACACGACACG

rs2288624ACGTrGGATGCATAGGCTGTAGAAGTTGGGACGTTGGATGT'TGTTGGTCCTTCTTGGGAG

rs1060511ACGTTGGATGTCCCTATGAAGAGAAATGCCACGTTGGATGCTGATGGTTCTTIT1'CCTTTC

rs1367218ACGTTGGATGTTGTGAGCCGCTTTTCAAACACGTTGGATGCATGCAAAACACTTTfTCAG

rs1367217ACGTTG GATGGAGCTGTAACTAAAAAGGGTGACGTTGGATGGTGTATATTGCCAAAGATGC

rs1465621ACGTrGGATGTTCTCCTCCCATTCTTCCTGACGTTGGATGG CGGGACTAGAAGTAGATTC

rs1465622ACGTTGGATGGGTCTTfGAGTGCTCCAAACACGTTGGATGAGAATGTCAGGTGGAAAGCA

rs2115872ACGTTGGATGTAGACCGCCCACTTfGAATGACGTrGGATGAAGACACTGCTGGACTTGTC

rs1465623ACGTTGGATGGGATCCAGCAGATTCTCCATACGTTGGATGAGTGGGCGGTCTAGAAAATG

rs1469521ACGTTGGATGTGGTCCTAGGAGACGTCTGAACGTTGGATGAGGACTGGGTGCCTGTGTTA

rs1864451ACGTfGGATGCTGTATGTGAAAACAAAAGCCACGTTGGATGTCTTTACTfGGTGTGTTGAC

rs1430183ACGT'fGGATGCATGTCATTCTGTAGTGTGGACGTTGGATGTCCTTGGGATCAAGAAAGTG

rs1430182ACGTfGGATGAATGTI'GCTAAAAGTAACCCACGTTGGATGATCTTfTTGGGGAAAAGAAG

rs1430181ACGTTGGATGAAGCTCCTAGCCAGTCTfAGACGTTGGATGTTATTTTGGCGGGGAGTAGG

rs1991601ACGTTGGATGATCCTCAACAGATCTGGTTCACGTTGGATGTCTGGTGATGGCTTGTGATC

rs2358890ACGTTGGATGTCAGAGTAGAGTTACTCCAGACGTfGGATGCATGATGCAGCTATTCTGTG

rs2115875ACGTTGGATGCAGACCCTTTITTCTAGATCACGTTGGATGACTATTfTTGAAGTAGTGTG

rs1430185ACGTfGGATGATCTGAGCCTAGACCTfAACACGTfGGATGGGGAATGAATACAACAGTGC

rs2217429ACGTTGGATGTGCACAAAATTAGCCACAGCACGTfGGATGAGTGACCGTTTCTGTGTGTT

rs3049909ACGTfGGATGCAAAAGCAGGAATGCCTTGGACGTfGGATGGGGTCACAACTGCTGTTITC

rs1430184ACGTt-GGATGAATTAGCAATGGCTCTCTCCACGTTGGATGCCTAAAAACACAGTTGCTCC

rs2278321ACGTTGGATGCAGACAGCAGGTAGATGAACACGTTGGATGTCTGGAAAAGAGAGACAGCC

rs2115874ACGTTGGATGCAGTGGACTfAAGAGAGGAGACGTTGGATGGGTTCAGGTACCTGAAAAGC

rs2033315ACGTTGGATGGTCAAGGTAGTTGAGAGTATTACGTTGGATGCAATGACAAAAAGCAATTTC

rs2033314ACGTTGGATGCATCTfTCTTAATGGTCTTGGACGTTGGATGATGCAGAGTCACATfCCATG

rs1991600ACGTrGGATGTTTCGTCATCAGTCAGAAGGACGTTGGATGCTGGTTCCT1'TTTTTGGGAG

rs1864453ACGT'fGGATGAGATAGGAATGACTGCCAAGACGTTGGATGAGGTGACTTCATCTCTTTCC

dbSNP Extend Term rs# Primer Mix rs1864455 TCCTTTTCTCTCAGTTCCCC ACT

rs1971763 AGCACTTTGGGAGGCCAAGG ACG

rs934269 GCACGCCACCACACTCGG ACG

rs934270 CCCTGTTCTTGCTCCTGCTfCTT ACT

rs2033309 ACAACACAAAGAAGGGTfGTTA ACG

rs2033310 GGGTGGGAAATCTGCTGAG ACT

rs934271 GCATAATTTTTCAGGGAGGCAG ACT

rs934272 TGCTTCTCTTCACACTTATAAG ACG

rs1897110 GCATCCCAAAGTGCTAGGATTACAI ACT

dbSNP Extend Term rs# Primer Mix rs203331 CTTCCAGGAGGTGCGATGAG ACT
'I

rs1010027 TCTGTTGTGAGAAGATGCGC ACT

rs1010028 ACAGCTGTTGGGCTCACAG ACT

rs2884502 TGCCTAGTTAATTTGCTTTCCT ACT

rs1430177 CCCTGTCTCAAATAAATTTTAAAAACT

rs1430178 GACAGGGTCTGGCTATGTTGTC ACT

rs3043779 ACTGTTTGTTGATGATTTGAATAAACT

rs1549742 GCCTAGCTGGGGCTTCAAGTTA CGT

rs3043781 TAGAAGCCAACCCCCCCC ACT

rs2033313 CCCTGTGAGGCCATAGACAA ACT

rs7739 CTGTTTACATAGTGCATG ACT

rs11482 CTTATAGTCAAGGACCGT CGT

rs3087907 CAATATAAAATAAGAGGTGAATGTACT

rs2358888 GCTTACATGTGTGTTTTTT CGT

rs1046036 CATTCATCCAGAATAGATTGTTTTCGT

rs3205060 TTTGCCAAGCTTGTTATA ACG

rs15327 GGTAGCATCTCCCAGTAA ACG

rs1430179 GAGGGGAAAAAAGTCAGGAAAA ACT

rs1430180 AAGTACCAAGGTCAGAAATTGATTACT

rs2163236 AGTCCAGGCTTCTTGCCTG ACT

rs3217351 AGGCACAGAATGAAAGAGAGA ACT

rs2303891 TAGAAGTTTACAGAAAAGCTGGAAACT

rs3815969 TTAGTACACTGACATATATACAG ACT

rs2288622 CTTACATCCACATTCCATTACC ACT

rs2288623 TTTTAGGTCTTCAGAAGAACAAAGACT

rs1044335 GAAATATTGGTCCCACTTTCC ACG

rs2288624 GACTCGCAGGTAAATAGAGCT CGT

rs1060511 CCCAAAAAAAGTGGAAAA CGT

rs1367218 CTTTTCAAACACGATGGAGCAC ACT

rs1367217 AACTAAAAAGGGTGATTTCACTATACT

rs1465621 CCATTCTTCCTGACATTCGCC CGT

rs1465622 CAAACATAAGGTTGACCCCC CGT

rs2115872 TTTGAATGGGACTCTTCC ACT

rs1465623 TCCATACATGAGAGCTGCTG ACG

rs1469521 TAGGAGACGTCTGACTCCAA ACT

rs1864451 GAAAACAAAAGCCTTTTCTGTC ACT

rs1430183 ATTCTGTAGTGTGGGCCCTA ACT

rs1430182 GTAACCCTTAAATACTATCATAC ACG

rs1430181 CTAGCCAGTCTTAGTGATGTT CGT

rs1991601 AGCTCGCCTCAGCCTACAA ACT

rs2358890 GTCCAGAACACCATAATCCC ACT

rs2115875 TTTTTTCTAGATCAGCACTGTTCAACT

rs1430185 CTAGACCTTAACTCCAATTTATA ACG

rs2217429 AGTCCTTGGTTTATGAACATTTG ACT

rs3049909 TTTATGTTATGCACATGCAGAC ACT

rs1430184 CATAAAACCAACTTATTAATCCC ACG

rs2278321 GCTCACAGGCTTTGTAACATC ACT

rs2115874 GGGGAGATCTGCCATCTCCTGG ACT

rs20333~ GGTAGTTGAGAGTATTGTGAGA I ACG

dbSNP Extend Term rs# Primer Mix rs2033314 GTCTTGGTTTAATATCACTCCT ACT

rs1991600 TAAAGGGGAAAAAAAAGCTCTAA ACT

rs1864453 CTGCCAAGTTGAATACTGAGTT ACT

Genetic Anal [0276] Allelotyping results from the discovery cohort are shown for cases and controls in Table 29.
The allele frequency for the A2 allele is noted in the fifth and sixth columns for osteoarthritis case pools and control pools, respectively, where "AF" is allele frequency. The allele frequency for the A 1 allele can be easily calculated by subtracting the A2 allele frequency from 1 (A1 AF
= 1-A2 AF). For example, the SNP rs1971763 has the following case and control allele frequencies: case A1 (C~ = 0.456;
case A2 (T) = 0.544; control A1 (C) = 0.444-; and control A2 (T) = 0.556, where the nucleotide is provided in paranthesis. Some SNPs are labeled "untyped" because of failed assays.

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 5 rs1864455 209 175603909C/T

rs1971763 5908 175609608C/T 0.544 0.556 0.630 rs934269 7460 175611160A/G

rs934270 7733 175611433A/G

rs2033309 7855 175611555A/G 0.158 0.172 0.502 rs2033310 7904 175611604A/C 0.428 0.423 0.845 rs934271 8869 175612569G/T

rs934272 9480 175613180C/T

rs1897110 13820 175617520C/T

rs2033311 15152 175618852A/G

rs1010027 17713 175621413A/G

rs1010028 17804 175621504C/T 0.448 0.449 0.965 rs2884502 18220 175621920C/T

rs1430177 19083 175622783C/T 0.051 0.309 0.0001 rs1430178 19123 175622823C/G

rs3043779 19605 175623305-/GTAAA

rs1549742 20247 175623947G/T

rs3043781 20592 175624292-ICCGCC

rs2033313 21907 175625607C/T

rs7739 23273 175626973C/T 0.057 0.042 0.371 rs11482 23299 175626999A/C 0.934 0.935 0.958 rs3087907 23623 175627323G/T 0.427 0.425 0.918 rs2358888 23669 175627369A/T 0.083 0.064 0.245 rs1046036 23844 175627544A/T

rs3205060 24190 175627890A/G 0.478 0.483 0.859 rs15327 24486 175628186C/T 0.901 0.917 0.336 rs1430179 24896 175628596A/C

rs1430180 25118 175628818C/G

rs2163236 30551 175634251C/G 0.956 0.955 0.994 rs3217351 30844 175634544-/GAGA 0.481 0.487 0.823 rs2303891 30900 175634600A/G 0.750 0.687 0.006 rs3815969 30942 175634642A/G 0.232 0.239 0.771 rs2288622 31699 175635399A/G 0.863 0.828 0.082 rs2288623 32081 175635781G/T 0.081 0.106 0.134 rs1044335 35078 175638778A/G 0.105 0.115 0.550 rs2288624 36196 175639896A/T 0.901 0.871 0.117 rs1060511 36541 175640241A/C 0.968 0.979 0.413 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 5 rs1367218 38356 175642056A/G 0.931 0.958 0.068 rs1367217 45578 175649278A/G 0.027 0.020 0.648 rs1465621 49634 175653334A/T

rs1465622 49774 175653474G/T 0.084 0.108 0.161 rs2115872 51119 175654819A/G 0.483 0.500 0.500 rs1465623 51181 175654881A/G

rs1469521 51652 175655352C/T 0.433 0.435 0.953 rs 186445154467 175658167C/G 0.316 0.315 0.970 rs1430183 55762 175659462A/G 0.972 0.970 0.930 rs1430182 55999 175659699A/G 0.711 0.691 0.366 rs1430181 57865 175661565A/C 0.939 0.943 0.836 rs1991601 66613 175670313A/G 0.754 0.713 0.062 rs2358890 68377 175672077C/T 0.404 0.443 0.109 rs2115875 69754 175673454C/T 0.633 0.620 0.613 rs 143018572859 175676559A/G 0.768 0.750 0.445 rs2217429 76512 175680212A/G 0.428 0.489 0.028 rs3049909 76717 175680417-/AT 0.161 0.200 0.064 rs1430184 77722 175681422C/T 0.025 unt ed NA

rs2278321 80998 175684698A/G

rs2115874 82033 175685733C/T 0.729 0.698 0.179 rs2033315 89658 175693358C/T 0.649 0.663 0.542 rs2033314 89960 175693660A/G 0.697 0.692 0.835 rs1991600 94155 175697855A/G 0.526 0.576 0.048 rs1864453 95679 175699379A/G 0.675 0.672 0.883 [0277] The WASPIP proximal SNPs were also allelotyped in the replication cohorts using the methods described herein and the primers provided in Tables 27 and 28. The replication allelotyping results for replication cohort #1 and replication cohort #2 are provided in Tables 30 and 31, respectively.

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in PositionAllele Case Control Value SEQ ID AF AF
NO: 5 rs1864455209 175603909C/T

rs19717635908 175609608C/T 0.472 0.509 0.276 rs934269 7460 175611160A/G

rs934270 7733 175611433A/G

rs20333097855 175611555A/G 0.179 0.186 0.784 rs20333107904 175611604A/C 0.428 0.405 0.493 rs934271 8869 175612569G/T

rs934272 9480 175613180C/T

rs189711013820 175617520C/T

rs203331115152 175618852A/G

rs101002717713 175621413A/G

rs101002817804 175621504C/T 0.447 0.465 0.579 rs288450218220 175621920C/T

rs143017719083 175622783C/T 0.051 0.098 0.138 rs143017819123 175622823C/G

rs304377919605 175623305/GTAAA

rs154974220247 175623947G/T

rs304378120592 175624292/CCCCC

rs203331321907 175625607C/T

rs7739 23273 175626973C/T 0.076 0.053 0.342 rs11482 23299 175626999A/C 0.919 0.919 0.996 rs308790723623 175627323G/T 0.422 0.390 0.348 rs235888823669 175627369A/T 0.104 0.074 0.204 rs104603623844 175627544A/T

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position ~111e1eCase Control Value SEQ ID AF AF
NO: 5 rs3205060 24190 175627890A/G 0.501 0.472 0.391 rs15327 24486 175628186C/T 0.883 0.904 0.370 rs1430179 24896 175628596A/C

rs1430180 25118 175628818C/G

rs2163236 30551 175634251C/G 0.976 unt ed 0.921 rs3217351 30844 175634544-/GAGA 0.514 0.480 0.329 rs2303891 30900 175634600A/G 0.780 0.699 0.009 rs3815969 30942 175634642A/G 0.183 0.213 0.426 rs2288622 31699 175635399A/G 0.856 0.818 0.201 rs2288623 32081 175635781G/T 0.083 0.112 0.216 rs1044335 35078 175638778A/G 0.113 0.115 0.959 rs2288624 36196 175639896A/T 0.908 0.872 0.215 rs1060511 36541 175640241A/C 0.971 unt ed 0.945 rs1367218 38356 175642056A/G 0.952 0.947 0.824 rs1367217 45578 175649278A/G 0.020 unt ed NA

rs1465621 49634 175653334A/T

rs1465622 49774 175653474G/T 0.077 0.118 0.108 rs2115872 51119 175654819A/G 0.493 0.499 0.861 rs1465623 51181 175654881A/G

rs1469521 51652 175655352C/T 0.453 0.427 0.436 rs1864451 54467 175658167C/G 0.302 0.321 0.556 rs1430183 55762 175659462A/G 0.959 0.962 0.903 rs1430182 55999 175659699A/G 0.727 0.678 0.114 rs 143018157865 175661565A/C 0.942 0.940 0.943 rs1991601 66613 175670313A/G 0.773 0.722 0.081 rs2358890 68377 175672077C/T 0.389 0.443 0.111 rs2115875 69754 175673454C/T 0.639 0.601 0.267 rs1430185 72859 175676559A/G 0.790 0.774 0.586 rs22'1742976512 175680212A/G 0.412 0.504 0.029 rs3049909 76717 175680417-/AT 0.144 0.193 0.079 rs1430184 77722 175681422C/T

rs2278321 80998 175684698A/G

rs2115874 82033 175685733C/T 0.744 0.703 0.169 rs2033315 89658 175693358C/T 0.675 0.695 0.533 rs2033314 89960 175693660A/G 0.726 0.703 0.529 rs1991600 94155 175697855A/G 0.467 0.566 0.005 rs1864453 95679 175699379A/G 0.702 0.680 0.468 dbSNP Position Chromosome~1/A2 F A2 F A2 F p-rs# in positionAllele Case Control Value SEQ D AF AF
NO:

rs1864455209 175603909C/T

rs19717635908 175609608C/T 0.635 0.629 0.879 rs934269 7460 175611160A/G

rs934270 7733 175611433A/G

rs20333097855 175611555A/G 0.131 0.149 0.576 rs20333107904 175611604A/C 0.428 0.452 0.548 rs934271 8869 175612569G/T

rs934272 9480 175613180C/T

rs189711013820 175617520C/T

rs203331115152 175618852A/G

rs101002717713 175621413A/G

rs101002817804 175621504C/T 0.449 0.424 0.503 rs288450218220 175621920C/T

rs143017719083 175622783C/T unt ed 0.642 NA

rs143017819123 175622823C/G

rs304377919605 175623305-/GTAAA

rs154974220247 175623947G/T

rs304378120592 175624292-ICCCCC

rs203331321907 175625607C/T

dbSNP positionChromosomeAl/A2 F A2 F A2 F p-rs# in position Allele Case Control Value SEQ D AF AF
NO:

rs7739 23273 175626973C/T 0.032 0.023 0.700 rs 11482 23299 175626999A/C 0.953 0.960 0.743 rs308790723623 175627323G/T 0.435 0.479 0.295 rs235888823669 175627369A/T 0.055 0.048 0.731 rs104603623844 175627544A/T

rs320506024190 175627890A/G 0.449 0.500 0.197 rs15327 24486 175628186C/T 0.923 0.937 0.552 rs143017924896 175628596A/C

rs143018025118 175628818C/G

rs216323630551 175634251C/G 0.923 unt ed rs321735130844 175634544-/GAGA 0.439 0.496 0.125 rs230389130900 175634600A/G 0.712 0.667 0.208 rs381596930942 175634642A/G 0.294 0.281 0.705 rs228862231699 175635399A/G 0.872 0.843 0.309 rs228862332081 175635781G/T 0.078 0.096 0.444 rs104433535078 175638778A/G 0.094 0.117 0.366 rs228862436196 175639896A/T 0.894 0.869 0.356 rs106051136541 175640241A/C

rs136721838356 175642056A/G 0.903 0.976 0.001 rs136721745578 175649278A/G 0.035 0.021 0.504 rs146562149634 175653334A/T

rs146562249774 175653474G/T 0.092 0.093 0.959 rs211587251119 175654819A/G 0.471 0.502 0.397 rs146562351181 175654881A/G

rs146952151652 175655352C/T 0.408 0.447 0.282 rs186445154467 175658167C/G 0.334 0.306 0.420 rs143018355762 175659462A/G

rs143018255999 175659699A/G 0.691 0.711 0.547 rs143018157865 175661565A/C 0.936 0.946 0.651 rs199160166613 175670313A/G 0.730 0.700 0.372 rs235889068377 175672077C/T 0.423 0.444 0.566 rs211587569754 175673454C/T 0.625 0.650 0.510 rs143018572859 175676559A/G 0.740 0.714 0.462 rs221742976512 175680212A/G 0.447 0.464 0.644 rs304990976717 175680417-/AT 0.184 0.212 0.386 rs143018477722 175681422C/T

rs227832180998 175684698A/G

rs211587482033 175685733C/T 0.709 0.691 0.605 rs203331589658 175693358C/T 0.616 0.614 0.962 rs203331489960 175693660A/G 0.660 0.674 0.679 rs199160094155 175697855A/G 0.602 0.590 0.749 rs186445395679 175699379A/G 0.641 0.659 0.631 [0278] Allelotyping results were considered particularly significant with a calculated p-value of less than or equal to 0.05 for allelotype results. These values are indicated in bold. The allelotyping p-values were plotted in Figure 1D for the discovery cohort. The position of each SNP on the chromosome is presented on the x-axis. The y-axis gives the negative logarithm (base 10) of the p-value comparing the estimated allele in the case group to that of the control group. The minor allele frequency of the control group for each SNP designated by an X or other symbol on the graphs in Figure 1D can be determined by consulting Table 29. For example, the left-m~st X on the left graph is at position 175603909. By proceeding down the Table from top to bottom and across the graphs from left to right the allele frequency associated with each symbol shown can be determined.

[0279] To aid the interpretation, multiple lines have been added to the graph.
The broken horizontal lines are drawn at two common significance levels, 0.05 and 0.01.
The vertical broken lines are drawn every 20kb to assist in the interpretation of distances between SNP
s. Two other lines are drawn to expose linear trends in the association of SNPs to the disease. The generally bottom-most curve is a nonlinear smoother through the data points on the graph using a local polynomial regression method (W.S. Cleveland, E. Grosse and W.M. Shyu (1992) Local regression models. Chapter 8 of Statistical Models in S eds J.M. Chambers and T.J. Hastie, Wadsworth &
Brooks/Cole.). The black line provides a local test for excess statistical significance to identify regions of association. This was created by use of a lOkb sliding window with lkb step sizes. Within each window, a chi-square goodness of fit test was applied to compare the proportion of SNPs that were significant at a test wise level of 0.01, to the proportion that would be expected by chance alone (0.05 for the methods used here). Resulting p-values that were less than 10-$ were truncated at that value.
[0280] Finally, the exons and introns of the genes in the covered region are plotted below each graph at the appropriate chromosomal positions. The gene boundary is indicated by the broken horizontal line. The exon positions are shown as thick, unbroken bars. An arrow is place at the 3' end of each gene to show the direction of transcription.
Example 8 ADAMTS2 Region Proximal SNPs [0281] It has been discovered that SNP rs398829 in ADAMTS2 is associated with occurrence of osteoarthritis in subjects. This gene encodes a disintegrin and metalloproteinase with thrombospondin motifs-2 (ADAMTS2), which is a member of the ADAMTS protein family. Members of the family share several distinct protein modules, including a propeptide region, a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS) motif. ADAMTS~ is involved in collagens 1, 2 and 5 N-terminal processing, (type II collagen is the major form in cartilage). Mutations in this gene cause Ehlers-Danlos syndrome type VIIC, a recessively inherited connective-tissue disorder that causes loose joints and fragile skin. Mild loss of function may exacerbate physical j oint damage leading to a predisposition to OA and incorrectly processed collagen can act dominantly to inhibit self assembly of fibrils. Alternative splicing of the gene generates 2 transcript variants. The short transcript encodes a protein, which has no significant procollagen N-peptidase activity.
[0282] Two hundred-nine additional allelic variants proximal to rs398829 were identified and subsequently allelotyped in osteoarthritis case and control sample sets as des cribed in Examples 1 and 2.
The polymorphic variants are set forth in Table 32. The chromosome positi ons provided in column four of Table 32 are based on Genome "Build 34" of NCBI's GenBank.

dhSNP Chromo-Position Chromosome Allele in SEQ

rs# some ID NO: 6 Position Variants rs22782215 210 178695460 c/t dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs16503585 3608 178698858 c/

rs16438185 3609 178698859 c/

rs37339165 4318 178699568 clt rs16249335 5593 178700843 a/

rs16248575 5629 178700879 c/t rs16248325 5639 178700889 a/

rs16248295 5640 178700890 c/t rs21611715 8943 178704193 a/c rs15304995 17968 178713218 a/

rs888764 5 19887 178715137 a/

rs873987 5 21034 178716284 a/

rs40786995 21085 178716335 c/t rs870311 5 21596 178716846 a/

rs16438175 23379 178718629 a/c rs16438165 23432 178718682 a/c rs16503555 24007 178719257 a/c rs888763 5 26121 178721371 a/

rs18622125 26273 178721523 alt rs11105145 26755 178722005 a/t rs37976005 27411 178722661 c/t rs37976025 27710 178722960 /t rs37976035 27842 178723092 c/t rs37768195 28379 178723629 c/t rs252076 5 29603 178724853 c/t rs252075 5 31232 178726482 c/

rs252074 5 31504 178726754 a/

rs252068 5 32583 178727833 c/

rs252069 5 32794 178728044 a/

rs194040 5 32840 178728090 c/t rs252070 5 33044 178728294 c/t rs37976065 33150 178728400 a/c rs171667 5 33218 178728468 a/

rs187539 5 33513 178728763 clt rs38368345 33959 178729209 /tatcaaactaccatga as rs252071 5 34486 178729736 a/

rs252072 5 36289 178731539 c/t rs252073 5 36570 178731820 c/t rs379589 5 38247 178733497 a/t rs20524725 38477 178733727 a/c rs20524715 38518 178733768 c/t rs20524705 38529 178733779 c/t rs20524695 38667 178733917 a/

rs37976085 39781 178735031 c/t rs37976095 39856 178735106 c/t rs38226015 39927 178735177 c/t rs153131 5 40506 178735756 a/

rs751546 5 41869 178737119 c/

rs22799795 42452 178737702 c/t rs252060 5 44788 178740038 c/t rs37976105 46059 178741309 a/c dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs1940395 46846 178742096 al rs1687735 47712 178742962 a/t rs2520615 48796 178744046 c/t rs1875375- 49441 178744691 cl rs2520625 49602 178744852 a/t rs24312555 49723 178744973 a/c rs37976125 50050 178745300 c/t rs37976135 50171 178745421 c/t rs6141145 50477 178745727 c/t rs2520635 50818 178746068 c/t rs2520(i45 50833 178746083 c/t rs2520655 50881 178746131 a/

rs4505025 50882 178746132 a/

rs4392525 51386 178746636 clt rs2520665 51534 178746784 c/t rs4579575 52317 178747567 a/

rs37976145 52368 178747618 c/t rs4235525 52970 178748220 a/

rs3988295 53023 178748273 a/

rs4166465 53356 178748606 a/

rs1874505 53882 178749132 /t rs3378075 54553 178749803 c/t rs3378065 55475 178750725 a/c rs13964385 55530 178750780 a/

rs13964375 55691 178750941 c/t rs24118115 55848 178751098 a/c rs28988135 55879 178751129 c/

rs1892565 56316 178751566 a/

rs1730725 56911 178752161 a/c rs3378055 57320 178752570 a/

rs1914155 57391 178752641 c/t rs1800455 57437 178752687 clt rs1892555 57478 178752728 c/

rs6527665 57500 178752750 c/t rs4667505 59111 178754361 /t rs4424065 59333 178754583 a/

rs6624075 59715 178754965 a/

rs5929715 59804 178755054 a/

rs4571875 59851 178755101 a/

rs4594905 59929 178755179 c/t rs4596685 60052 178755302 c/t rs4626465 60240 178755490 c/t rs4582725 60359 178755609 /t rs4634555 60381 178755631 a/

rs6758805 60456 178755706 c/t rs8106175 60724 178755974 c/

rs4641565 60875 178756125 c/t rs4580835 60968 178756218 a/

rs4673335 60978 178756228 c/

rs4653815 60998 178756248 c/t rs4663635 61557 178756807 c/t rs24570995 62091 178757341 c/t dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs4639015 62645 178757895 c/t rs4656215 62943 178758193 a/c rs4637245 63131 178758381 a/t rs4652425 63145 178758395 /t rs4674195 63406 178758656 a/

rs4561355 63427 178758677 c/

rs4645365 63554 178758804 c/t rs4618985 63661 178758911 a/

rs3895585 64093 178759343 al rs4667525 64153 178759403 c/t rs4556555 64409 178759659 c/

rs4634355 64544 178759794 c/t rs21749715 65257 178760507 c/t rs19799795 65626 178760876 a/

rs4118045 65739 178760989 a/

rs16238855 66392 178761642 c/t rs16438115 66720 178761970 c/t rs4344305 69177 178764427 a/t rs1875385 69336 178764586 /t rs2520675 69636 178764886 a/

rs4593195 69823 178765073 a/

rs4672895 69928 178765178 c/t rs4626445 70547 178765797 c/t rs4587525 70633 178765883 c/t rs7083205 71805 178767055 a/c rs4579545 72181 178767431 c/

rs24118105 72200 178767450 c/t rs30846875 72474 178767724 -/at rs69638 5 72567 178767817 c/

rs4554525 72973 178768223 a/

rs4648505 73468 178768718 a/

rs4314725 73889 178769139 a/

rs24118095 75730 178770980 c/t rs24570945 75970 178771220 a/

rs24570955 76114 178771364 a/

rs22617405 76342 178771592 c/t rs11091805 76449 178771699 a/

rs11091795 76465 178771715 c/t rs11091785 76791 178772041 a/c rs4569095 78042 178773292 a/

rs4691245 80758 178776008 a/

rs4680395 80778 178776028 c/t rs4670175 81356 178776606 a/c rs4692905 81576 178776826 a/

rs4690905 81689 178776939 c/t rs4695685 81759 178777009 /t rs4683865 81950 178777200 c/

rs4693495 82562 178777812 a/c rs4690995 83591 178778841 c/t rs4568685 83700 178778950 a/

rs4653895 83821 178779071 c/

rs4638925 83842 178779092 c/

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs4685485 83923 178779173 /t rs6546125 83929 178779179 a/c rs4685425 84021 178779271 c/

rs4692625 84175 178779425 c/t rs7083235 84417 178779667 a/

rs4690895 84747 178779997 c/

rs4693965 85746 178780996 c/

rs4687235 86129 178781379 c/t rs4676045 86335 178781585 a/

rs3388745 87315 178782565 c/

rs3388755 87648 178782898 a/

rs13858035 87764 178783014 a/c rs13858045 87770 178783020 c/

rs3388765 88221 178783471 c/t rs1898035 90474 178785724 a/c rs4522155 91148 178786398 /t rs6411705 91150 178786400 It rs5843985 91160 178786410 /t rs3853305 91733 178786983 c/t rs4295385 91772 178787022 a/c rs3712295 91785 178787035 c/t rs4608745 93140 178788390 a/t rs6461215 93148 178788398 a/t rs4682625 96080 178791330 a/

rs4678635 96157 178791407 c/

rs1914345 96313 178791563 a/c rs20547825 96759 178792009 c/t rs4684995 97026 178792276 a/c rs1802875 97320 178792570 c/

rs3388775 97732 178792982 a/t rs6506655 98713 178793963 c/

rs1934195 99707 178794957 a/c rs1802885 99959 178795209 cl rs1868345 100009 178795259 a/

rs1892665 100020 178795270 c/

rs1892675 100065 178795315 a/c rs1709375 100086 178795336 c/

rs4632635 101270 178796520 c/

rs4632625 101276 178796526 /t rs4604545 101371 178796621 c/t rs4604555 101376 178796626 c/

rs4605055 101439 178796689 c/t rs9313165 101820 178797070 c/t rs4634315 102392 178797642 c/

rs4615425 102602 178797852 a/

rs4635575 102604 178797854 a/c rs1914535 102896 178798146 c/t rs22712125 189104 178884354 c/t rs4620095 189134 178884384 c/t rs22712115 189205 178884455 a/

rs3964745 Not ma Not ma ed a/c ed rs4289015 Not mappedNot mapped ~ a/t dbSNP Chromo-Position Chromosome Allele in SEQ

rs# some ID NO: Position Variants rs452300 5 Not ma Not ma ed /t ed rs670256 5 Not ma Not ma ed /t ed Assay for Verif~n~ and AllelotYpin~ SNPs [0283] The methods used to verify and allelotype the 209 proximal SIvTPs of Table 32 are the same methods described in Examples 1 and 2 herein. The primers and probes used in these assays are provided in Table 33 and Table 34, respectively.

dbSNP Forward Reverse rs# PCR primer PCR primer rs2278221ACGTTGGATGTCTCATGGGCCACCACAAACACGTTGGATGTATGCTCCTGTCACCGGCAT

rs1650358ACGTTGGATGTGGATGGCTCCATGTTCTTGACGTTGGATGAAGTGCTGGGATTACAGGTG

rs1643818ACGTTGGATGCTGGGATTACAGGTGTGAACACGTTGGATGTGGATGGCTCCATGTTCTTG

rs3733916ACGTTGGATGCCGAGCAGGCTGTAGTGTTGACGTTGGATGCTTTGTACCACCTGGAACAG

rs1624933ACGTTGGATGAGGCTGGTCTCAAACTCCTGACGTTGGATGTAACAAAAAGTTGGCCGTGC

rs1624857ACGTTGGATGTGAGGTCAGGAGTTTGAGACACGTTGGATGGCCACCAAGCCAGACTAAGT

rs1624832ACGTTGGATGTGAGGTCAGGAGTTTGAGACACGTTGGATGGCCACCAAGCCAGACTAAGT

rs1624829ACGTTGGATGTGAGGTCAGGAGTTTGAGACACGTTGGATGGCCACCAAGCCAGACTAAGT

rs2161171ACGTTGGATGCCCGTCACCACTTTATTTCCACGTTGGATGAGAGTGGATCCAGTCTGCAG

rs1530499ACGTTGGATGACTCCAAGATTTCCCATTTCACGTTGGATGTTCTGTGTTCCACCCTATGG

rs888764ACGTTGGATGTAGTTGAATGTTGTATTGGCACGTTGGATGACCGTGATAAACACAGAATG

rs873987ACGTTGGATGGCTGTTAATCATGTGTCGGGACGTTGGATGATTTGGCCACATCACCAGAC

rs4078699ACGTTGGATGGTACCGTGGATTCTTTTAGGACGTTGGATGGT-ATTGGAAAAGAGCAGAGAC

rs870311ACGTTGGATGTCAGGGCTCCAGTGTTGAAGACGTTGGATGAAAAGGAGGAGTGCCCTGTG

rs1643817ACGTTGGATGATGGGAAACTCCTGGTCCTGACGTTGGATGAAAATGCAAGCCGCCACCTG

rs1643816ACGTTGGATGTTTTCTCCCCTTTCTAGCCCACGTTGGATGTTGGCATGAGAGATGGACAG

rs1650355ACGTTGGATGTCAACAGCAACAAAACCAAAACGTTGGATGTTAAATAGGTCAGAGGGTTG

rs888763ACGTTGGATGAAGAGGAAGAGACATACCAGACGTTGGATGAACAACATGGACTCAGGCTG

rs1862212ACGTTGGATGGGCCACATTTTAAAACAAGGGACGTTGGATGTCCCCTGAGGTTCCTATAAG

rs1110514ACGTTGGATGTGCCCACGTTCCATGTTCAGACGTTGGATGA-f'CACTGTAGCCCCTTCCTG

rs3797600ACGTTGGATGCCTTCCTGTCACCTCCTTTGACGTTGGATGG GAAGTGACTGCTGAGCTG

rs3797602ACGTTGGATGAGAAACAGGGACTGGCTGTGTACGTTGGATGAGCAGGCTCCGGGAAGTATG

rs3797603ACGTTGGATGCACCCATCCATCATGATGTCACGTTGGATGTGCTACCTCAAAACAGTGGG

rs3776819ACGTTGGATGCAAGCACCATTCCATTGCACACGTTGGATGAAATGAGGATTGCAGTCCCC

rs252076ACGTTGGATGACTTCTGACTTCAGGTGATCACGTTGGATGTATAGGAACGAAAGAAAGCC

rs252075ACGTTGGATGTGGGAGCATTTGCAGGCATGACGTTGGATGAAGCCTCAGATGGTTCGGAG

rs252074ACGTTGGATGTTGCGATGGCCTCCTGGCTACGTTGGATGAAGTTGAGGGCTCCGGAGCA

rs252068ACGTTGGATGGGGTAGGAAGGGTTTAAGCACGTTGGATGG CAGCCCCTCAATTCTTTAG

rs252069ACGTTGGATGTGCCCATTTCCTGTTATTCCACGTTGGATGT-T'TGGACTTGCCGTGCAACT

rs194040ACGTTGGATGTGCCCATTTCCTGTTATTCCACGTTGGATGT-fTGGACTTGCCGTGCAACT

rs252070ACGTTGGATGCTCAAGGACATTGTCCCTGGACGTTGGATGG GAGAAGCAGCTCTCCTTTC

rs3797606ACGTTGGATGGTTTCCCCAAACAAGAGAGCACGTTGGATGG GAAATGTTCAAAGCCGCAG

rs171667ACGTTGGATGGGGAAACACATTGTAATGCGACGTTGGATGCCTTCCTCATTGTCTATTCC

rs187539ACGTTGGATGAGCCACCCCAACCTTCAGGAACGTTGGATG'1-TGCTCCTGGACATGGTTTT

rs3836834ACGTTGGATGAAGAAACGTGACTCTTGCTCACGTTGGATGTAGTAATTCTGATCCTGGCC

rs252071ACGTTGGATGGCTTCAACCTGAAACAACCCACGTTGGATGGGGATATTCCCACTCTGAG

rs252072ACGTTGGATGTTGTTTCCCCAAAGGCGACGACGTTGGATGTGTGTTTTCCAGAGCTGGAG

12~

dbSNP Forward Reverse rs# PCR primer PCR primer rs252073ACGTTGGATGGGGAAAGGCCGAGAAAAGTCACGTTGGATGACAAGCTCAGCAGAGTTCCA

rs379589ACGTTGGATGAAACACGGGAGTACTGAGCAACGTTGGATGTTGTTAGCTGTCTGTCCGTC

rs2052472ACGTTGGATGAACCAGCTCAAGGATCACCCACGTTGGATGAAAGGAGACGGTCAGCTGTC

rs2052471ACGTTGGATGACAGCTGACCGTCTCCTTTGACGTTGGATGCCCGTCCTGGACAAGCTTTT

rs2052470ACGTTGGATGACAGCTGACCGTCTCCTTTGACGTTGGATGCCCGTCCTGGACAAGCTTTT

rs2052469ACGTTGGATGAGGGAAAGATATCGCACGCGACGTTGGATGAGTGAACAACTGCTCGCCTC

rs3797608ACGTTGGATGTGCTTTGCCTTGGCTTCTGCACGTTGGATGTGCACTAAGGGAGTGAGTGG

rs3797609ACGTTGGATGTGCAGAAGCCAAGGCAAAGCACGTTGGATGACAGCATTTGGAGTCCCCTG

rs3822601ACGTTGGATGAGGTCAGTGAGGCCTGAGATACGTTGGATGTGTCTGGCCTGAAGATCGAG

rs153131ACGTTGGATGTAATCACGTGTCCTGATCCCACGTTGGATGAGCTGTCCTCAGT-CATGTTC

rs751546ACGTTGGATGTCCTGCTCTGCCGTTCTACAACGTTGGATGATCAGCTCAAAGGACCGGTG

rs2279979ACGTTGGATGTATTGCTACCAGGAACACGTAACGTTGGATGAAAAAGGGGCCACTTCAGGG

rs252060ACGTTGGATGTGGCCAGAGCCCGTGTTTCACGTTGGATGCGGCCAATCCCATCTCTATG

rs3797610ACGTTGGATGAAAAGCTTCTCCCTTGGGTGACGTTGGATGCAAGTAGGGCAGAAACTCAG

rs194039ACGTTGGATGAAAGTGCTGGGATTACAGGCACGTTGGATGTGCTGGGAGAAGACATTCAC

rs168773ACGTTGGATGTGGTGCACTGGAGATATCACACGTTGGATGGATCCCTATCCTA.CCTCTTC

rs252061ACGTTGGATGTGTCACACTCCTCTTGTAAGACGTTGGATGCTGTCCTTCCATGCTTTTGC

rs187537ACGTTGGATGCGAGGATGTCATGCTAAGTGACGTTGGATGGTACCTCGCATAA.GTGGATC

rs252062ACGTTGGATGAAGCACATTCATGTGGCTGGACGTTGGATGCTGAAACTCAATG GGCACAG

rs2431255ACGTTGGATGGGTGAAGACGGTGACTTATGACGTTGGATGCTGGTGTCCTTGAAGAACTG

rs3797612ACGTTGGATGAGTGAGGACGCAGGGCATTCACGTTGGATGAGCGTGGGCGAGGGAGATAA

rs3797613ACGTTGGATGATCAGAGGCAGAGACCCCCCACGTTGGATGGGGTGTCCTGCAGAGGCGG

rs614114ACGTTGGATGGGTTGGAGGATGTCTAGAACACGTTGGATGGGCTGGATCACTAGGGTTTG

rs252063ACGTTGGATGTTGGAATTACAGTCCGATGGACGTTGGATGCTGAGAGACTGAAAAGCACA

rs252064ACGTTGGATGCTGAGAGACTGAAAAGCACAACGTTGGATGTTGGAATTACAGTCCGATGG

rs252065ACGTTGGATGAAAACTAAGGCTCAGAGGACACGTTGGATGTGGGCTTGGAATT-ACAGTCC

rs450502ACGTTGGATGATGAGAAAACCAAGGCTCAGACGTTGGATGCTGGGCTTGGAATTACAGTC

rs439252ACGTTGGATGATCTCCTGACCTCGTGATCCACGTTGGATGTCATAATAACGGGCGGGTGC

rs252066ACGTTGGATGTTTCCTCTTGACCGGTCTTGACGTTGGATGTAAAACGAATTCTGCCGATG

rs457957ACGTTGGATGTTCACGTGCATTAGAGCGAGACGTTGGATGAATTCCCTCCCCAATTCCTC

rs3797614ACGTTGGATGACTGCGAGCTTTAAGGAGGGACGTTGGATGCCAAACAGAAGCCCCTTTTC

rs423552ACGTTGGATGGCAGGACCTCGATGTTGTAGACGTTGGATGATCCTAGAGGAGCACGCCAAC

rs398829ACGTTGGATGTAGTCATCGTCCGCAGCATGACGTTGGATGAAGACGGTGTCCTCTCCTTG

rs416646ACGTTGGATGGCTGGGTCTCTCACAGTCTCACGTTGGATGAGACAGGCACCTCTGTGACTT

rs187450ACGTTGGATGAGAAGGCAGGGACGATATCCACGTTGGATGACCAAGATGAACCCCTCTGT

rs337807ACGTTGGATGTCACCCAGTGCTGACAGCAGACGTTGGATGATGCTGGGATGCCATGGGTC

rs337806ACGTTGGATGAATTAAGAGATGGGGCCACCACGTTGGATGGCCCTGTGTGTTTTGTCTCC

rs1396438ACGTTGGATGTACCTTCTGGTGCCAGAATGACGTTGGATGCCTGGAGACAAAACACACAG

rs1396437ACGTTGGATGTAAAAACTCTGCCTGCTCGGACGTTGGATGTCCAGACATTCCCCGTAGGA

rs2411811ACGTTGGATGGAGGGATGCTCTAGAACATAACGTTGGATGCTGAATTTCACC'T-GAAATGG

rs2898813ACGTTGGATGTCCTCACCCACTTTGCCTTTACGTTGGATGATCGTGATAATTTTGGGGTG

rs189256ACGTTGGATGCTCCCTATAGCAAGGCTCTAACGTTGGATGTTAACCCAGGCCATGAAGAG

rs173072ACGTTGGATGAGCTGGAGATCTCTTTGCTCACGTTGGATGCTAAAACAGGATCGCTCTGG

rs337805ACGTTGGATGGAAACAAACCAAGGAGCAGGACGTTGGATGATGTGGACAACGTTGGACTC

rs191415ACGTTGGATGAATTACATGACTCGGACAAGACGTTGGATGTGCTGGTGAAGTACAGAAGG

rs180045ACGTTGGATGGTCCCAGGTTTTCTGTTCTCACGTTGGATGTGTACTTCACCACCACTGAG

rs189255ACGTTGGATGAGGTTGCAGACTCAGTCCCAACGTTGGATGGGGTGATTTGCGGGAATGAG

rs652766ACGTTGGATGGGGTGATTTGCGGGAATGAGACGTTGGATGACCATCCCACGA.TGCTCCC

rs466750ACGTTGGATGTATCTCCTTAAATGCCTTGGACGTTGGATGTGACCAGGAGGAGTTAAAAC

rs442406ACGTTGGATGTGACAAGGTCACGTGTTCTGACGTTGGATGCCAGACAAGTCTGATACAGC

rs662407ACGTTGGATGCCACAGTCACCATTACTGAGACGTTGGATGCTTGAGCCATGAGTGGAATG

rs592971ACGTTGGATGGGAAGCATTTCTTTGACTGCACGTTGGATGATTCCATCTCATCGCTCAAG

dbSNP Forward Reverse rs# PCR primer PCR primer rs457187ACGTTGGATGTGTGAGATGAGGAGTATCTGACGTTGGATGGCAGTCAAAGAAATGCTTCC

rs459490ACGTTGGATGACAGATACTCCTCATCTCACACGTTGGATGGGGAGTTTTGCTGTTATAGC

rs459668ACGTTGGATGGCTTCATTTACTGAGGTCTTCACGTTGGATGTGAATGTTCAACGACTACAC

rs462646ACGTTGGATGCAATTATTCGACGGAGATTAACGTTGGATGCTCCTCCAAATGAATCAAGAA

rs458272ACGTTGGATGATGCCTCCTCATTGTCATTCACGTTGGATGCCCAACAAAGTGATTCCAAC

rs463455ACGTTGGATGATGCCTCCTCATTGTCATTCACGTTGGATGCCCAACAAAGTGATTCCAAC

rs675880ACGTTGGATGCAGCTCCATTGATCTGTTTCACGTTGGATGAAGAATGACAATGAGGAGGC

rs810617ACGTTGGATGTGATCTCAGCTTACCACAGCACGTTGGATGATGCCTGTAATCCCAGCTAC

rs464156ACGTTGGATGCAGATCCAAGAATATGTGGGACGTTGGATGTTCTAGAAAGGAGCCAAATC

rs458083ACGTTGGATGTGTTGTTTCTTCCCCTCCTGACGTTGGATGTGGCTCCTTTCTAGAATCCC

rs467333ACGTTGGATGCTTGTTATTTCTTCCCCTCCACGTTGGATGTTGGCTCCTTTCTAGAATCC

rs465381ACGTTGGATGACTTGCCCATCTGTTTCCAGACGTTGGATGACAAGCCTCTAAGGATAGGG

rs466363ACGTTGGATGAAGTGACCCTGAGGTGATGGACGTTGGATGTGAAGACAGTTCACCCCGTG

rs2457099ACGTTGGATGTCTCCTTACACTGCCAGCGTACGTTGGATGCACTGTATTGCTACTTGAGC

rs463901ACGTTGGATGAGAGTGCCAAGTGCAAAAGGACGTTGGATGTGTCTTGCGTCTGTGTATCC

rs465621ACGTTGGATGGGAAGTCATGGAAGTGCTAGACGTTGGATGAAAGAGCCCTAGGCTTGGAA

rs463724ACGTTGGATGAGTGTGCCTGTCTGCCCTCAACGTTGGATGAAGGGCAGATGGCACACTTG

rs465242ACGTTGGATGAGTGTGCCTGTCTGCCCTCAACGTTGGATGAAGGGCAGATGGCACACTTG

rs467419ACGTTGGATGAGTCCCCAAAACGTAAGTCCACGTTGGATGAGTCTAATTCCCTGAGCCTC

rs456135ACGTTGGATGAGTCTAATTCCCTGAGCCTCACGTTGGATGACGTAAGTCCTAATGACCGC

rs464536ACGTTGGATGTGCTCCAGGCTTTGGTCCTCACGTTGGATGAATTAGACTAAGGCCATGATG

rs461898ACGTTGGATGGGGAATACACAGCCACAGAGACGTTGGATGAGGTCAACGGGAACAAGGTC

rs389558ACGTTGGATGGCAGTCCTGACAGTTCTCTAACGTTGGATGTTTTTCTCCCTGAAGCATGG

rs466752ACGTTGGATGGGCCTTCTCTCCTTTAGTGCACGTTGGATGAGTCCTGACAGTTCTCTAAA

rs455655ACGTTGGATGCTATTTGCACCCCATATGGCACGTTGGATGAACACACAGCATCAGGTTCC

rs463435ACGTTGGATGTTCAGCCATAGCTGGATTTGACGTTGGATGCTCTGCTGGGAAAATGTGAC

rs2174971ACGTTGGATGAACACAACTTCCCCTTCGTCACGTTGGATGTGAATCCTTGGAGGTGAGTG

rs1979979ACGTTGGATGTGGCTGTCAGCACCCCACTTACGTTGGATGCCCAAAGGAAGGGAGAATTC

rs411804ACGTTGGATGCAGATGACAGGCGGAAAATCACGTTGGATGAGGCTTCCAGATGATGTCCA

rs1623885ACGTTGGATGAATCAGCTAGGAAGAGCCTGACGTTGGATGTTCCTGACCCCTCTAGGTCAG

rs1643811ACGTTGGATGCAGGGCCCTGGTACTTTCAGACGTTGGATGCATGGTGGTGATTGCACCTG

rs434430ACGTTGGATGTCCAGGAGTTCACTGTAGAGACGTTGGATGCACATGCATACATTCATCAC

rs187538ACGTTGGATGACATGGGGCTTGGCAAAATGACGTTGGATGCACCTGCTCAGAAGTAGCAT

rs252067ACGTTGGATGAGAATTGCTGTGGTGTGAGGACGTTGGATGTTTTTCTTGGGAGCTGTCGC

rs459319ACGTTGGATGCCATCTCTCTGACCTAGACAACGTTGGATGGCTCCAAGGAAAATTGGGAG

rs467289ACGTTGGATGGGCCCTCTTGGCTTGTCTTTACGTTGGATGAGGCAGTGTGCCCTCTCATC

rs462644ACGTTGGATGATGATGTGGGTGAGCCCTTGACGTTGGATGTAACACTCAGCACGCACCAG

rs458752ACGTTGGATGCACCCACATCATGTGCGCTTACGTTGGATGCCCTTCTCTACCCAGCACTT

rs708320ACGTTGGATGAAACCAGCCTGGCTAACATGACGTTGGATGACAGGTGCCTGCTATCATAC

rs457954ACGTTGGATGAACCAGACCTTGACTGATGGACGTTGGATGCCTCATACAAGTAGCCAAGG

rs2411810ACGTTGGATGGCTTAACCAGACCTTGACTGACGTTGGATGAGTGTAAGGATATCCACGGC

rs3084687ACGTTGGATGATCCCTTGAGCCAGAGATTCACGTTGGATGATGTCCTGTGCACACACAAG

rs69638ACGTTGGATGTGCTCATTGCTGTCCTCATCACGTTGGATGAGAAGAAAGGTGTGCAGTGG

rs455452ACGTTGGATGAGTGATGATGAGCCTGCTGGACGTTGGATGTCAGGTTCCCTCTCTGTGTC

rs464850ACGTTGGATGTCTCTCTGTGCTCCAGACCAACGTTGGATGTGGGCTGAGATTTCTGTGGG

rs431472ACGTTGGATGAACCAGTGTGGGTGTGAAGCACGTTGGATGAGAGACTGCATCAGGCAGGA

rs2411809ACGTTGGATGAGCGCATAAGTGACCACCAGACGTTGGATGGCACTCACAGGGCATTGATG

rs2457094ACGTTGGATGTTACTGTCACCTTGGGTCTCACGTTGGATGGGAAGTCTGTATAGACGCAG

rs2457095ACGTTGGATGTTATCAAGGCCTGCGCAGTGACGTTGGATGACTCCTGACCTCAGGCAATC

rs2261740ACGTTGGATGATCGTGCCACTGCACTCCAGACGTTGGATGTCATCTTTTGGTAGCCCCCC

rs1109180ACGTTGGATGCCAGGCCTGTATTGCACATCACGTTGGATGAGAATGCGTGTGCATGTGGG

rs1109179ACGTTGGATGTGTAATGGTATGCAGACCCCACGTTGGATGGAGTGCCGTATTTGTCCTTC

dbSNP Forward Reverse rs# PCR primer PCR primer rs1109178ACGTTGGATGGCAAACAACAACAGCAACAGACGTTGGATGAAGTGTGGATTTGTGCAGAC

rs456909ACGTTGGATGTAGCTGCTTCATCTGTAAAGACGTTGGATGGGCACTTTACCGATCTACTC

rs469124ACGTTGGATGACTTGGACACACATAGGCTGACGTTGGATGTGAAATGCTCAGGGTGTGTG

rs468039ACGTTGGATGTGAAATGCTCAGGGTGTGTGACGTTGGATGAGGACTTGGACACACATAGG

rs467017ACGTTGGATGGTCTAGCTGCCACTAAACAGACGTTGGATGATGTGCCAAGAGGCTTTGAG

rs469290ACGTTGGATGTGCCCTTTGTGTGCTCAGAGACGTTGGATGTCCCTCTGTGCTGTGTTTGG

rs469090ACGTTGGATGACTTGTCTTCAGGTGCTTGGACGTTGGATGGATGGTTAGTCTCCTGGTTC

rs469568ACGTTGGATGAGCACCTCTGGCTTTCATTGACGTTGGATGATTCACCAGGAAATCCCAAC

rs468386ACGTTGGATGTAATCCCAGCCCTTTGGAAGACGTTGGATGTATGGAGACAGGGTTTTACC

rs469349ACGTTGGATGTTAGAGACAGAGTCTCACTCACGTTGGATGTTGATCCCAGGAGTTCAAGG

rs469099ACGTTGGATGTTGGAGCTGCTCTAGTTCTCACGTTGGATGTGAAAACCGGGACTCAGCTC

rs456868ACGTTGGATGACAGAGCAGGGAGCTGCGGTACGTTGGATGATTCACCCCCAGCTACTGTG

rs465389ACGTTGGATGAGGCTTTGTAGACAGCTCCCACGTTGGATGTGCCAGTGCTCTGAGTATGC

rs463892ACGTTGGATGAGGCTTTGTAGACAGCTCCCACGTTGGATGTGCCAGTGCTCTGAGTATGC

rs468548ACGTTGGATGACTGGAAGGGAACATGCAAGACGTTGGATGCCTGGATGCCCTTTATAGAC

rs654612ACGTTGGATGACTGGAAGGGAACATGCAAGACGTTGGATGTGGATGCCCTTTCTAGACAC

rs468542ACGTTGGATGGCCTCCATTTTCCTTCTCACACGTTGGATGTGTCTAGAAAGGGCATCCAG

rs469262ACGTTGGATGTTCTGAGCTGAACGAAGCAGACGTTGGATGGGTCAGGGATCCTTTGATGC

rs708323ACGTTGGATGCACATACTATACAGGTCACCACGTTGGATGGAGGGAGAAGATGTTGTGAA

rs469089ACGTTGGATGTTTGGAAGTACCACCTCAGCACGTTGGATGAATGGAAGGAAGGATCAGCC

rs469396ACGTTGGATGAGTGACTCCAATGAGGGAACACGTTGGATGTCTCACACCACTGATCCTTC

rs468723ACGTTGGATGTGTGGATCTTGCTGTTTGGGACGTTGGATGTATTGGCATCGCGTATCAGG

rs467604ACGTTGGATGACTCCTGCCATTAAACTCTCACGTTGGATGCTTGGCTTAACTTACAAGGG

rs338874ACGTTGGATGCCCCACCACAGCCACTGGGACGTTGGATGAAGGGCCTTGCCCCACCCAA

rs338875ACGTTGGATGTGCTGTCTTGCTCGCGTGTGACGTTGGATGACACTGGATATGTCAGGGTC

rs1385803ACGTTGGATGTCACCACCATTCCAGAAGTGACGTTGGATGACCTTCCTTATTGCTGTGGC

rs1385804ACGTTGGATGTCACCACCATTCCAGAAGTGACGTTGGATGACCTTCCTTATTGCTGTGGC

rs338876ACGTTGGATGTTAGGGCTGGGTGGAGGAAGACGTTGGATGTCCAACTCCCAGTGACAGAG

rs189803ACGTTGGATGCCTCCAGTTTCTCTCTTCTGACGTTGGATGATCCTGGATTAGCCAGATGG

rs452215ACGTTGGATGTAGCTCTATTCTTCCACCCCACGTTGGATGAGCGAGACTCCGTCTCAAAA

rs641170ACGTTGGATGATAGCTCTATTCTTCCACCCACGTTGGATGAGCGAGACTCCGTCTCAAAA

rs584398ACGTTGGATGTTCCTGTGAGCTATAGAAACACGTTGGATGCGAGACTCCGTCTCAAAAAAA

rs385330ACGTTGGATGTTGCCCCAACTATTGTCCTGACGTTGGATGGGTTTCCCAGACAGTGTTTG

rs429538ACGTTGGATGTATTATCTGCAGACACCTGGACGTTGGATGATCTCATTCCCACCCTCTTC

rs371229ACGTTGGATGTATTATCTGCAGACACCTGGACGTTGGATGATCTCATTCCCACCCTCTTC

rs460874ACGTTGGATGGTCCTGCGGCTAAAAATTCCACGTTGGATGGGGCAGGTCAACTAGAAAAC

rs646121ACGTTGGATGGGGCAGGTCAACTAGAAAACACGTTGGATGGTCCTGCGGCTAAAAATTCC

rs468262ACGTTGGATGGCCAGGTTTCGAAAGTTAGGACGTTGGATGTGGGTTGGTCATGCGGTAAC

rs467863ACGTTGGATGTTTCGAAACCTGGCTGATGGACGTTGGATGTGCCACTGTCAGAAGACAAG

rs191434ACGTTGGATGCCAGCTGAAACACTAGACAGACGTTGGATGAGCTGAAGAGGTCTTTCTCC

rs2054782ACGTTGGATGAAAAAAGCAGGCCTCAGACCACGTTGGATGTCTGACTCTCATCTGCAGAC

rs468499ACGTTGGATGCTCCAGGAGGGACACTACGTACGTTGGATGTGGCCAGCTTCTCCTCGATG

rs180287ACGTTGGATGTTGTCTGCAGAATTACCTATACGTTGGATGGAAAAAGAAAAAAAAATCAG

rs338877ACGTTGGATGCGTGGATGGAAATTTACATTACGTTGGATGTTCTTTGGATCAATGTTGCC

rs650665ACGTTGGATGCCCATCTTACTCTATGATCTCACGTTGGATGAAAGTGCTGGGATTATAGGC

rs193419ACGTTGGATGGCAAATCCAAAGACACAGGGACGTTGGATGATGTTTTCATCACCCCAGTG

rs180288ACGTTGGATGTGTGACCTGGTAGCTTAGAGACGTTGGATGTTGTAGGAGGTCAGAAGAGG

rs186834ACGTTGGATGTAAGCTACCAGGTCACACACACGTTGGATGAGTTGATAGGAGAGTCAGGC

rs189266ACGTTGGATGTAAGCTACCAGGTCACACACACGTTGGATGAGTTGATAGGAGAGTCAGGC

rs189267ACGTTGGATGCCTCATTGTGCCCTGTTGTGACGTTGGATGCTCTGCCTGACTCTCCTATC

rs170937ACGTTGGATGCCTATCAACTGTTGATGGCGACGTTGGATGTTCCTCATTGTGCCCTGTTG

rs463263ACGTTGGATGTACTGGACCCCTTTGCACAGACGTTGGATGTGCCCATGCTCATGTGTTGG

dbSNP Forward Reverse rs# PCR primer PCR primer rs463262ACGTTGGATGTGCCCATGCTCATGTGTTGGACGTTGGATGACCCCTTTGCACAGATGCTG

rs460454ACGTTGGATGAAGAAGGACCGTGTCAGAGAACGTTGGATGACATGAGCATGGGCAGGTAC

rs460455ACGTTGGATGACATGAGCATGGGCAGGTACACGTTGGATGAAGAAGGACCGTGTCAGAGA

rs460505ACGTTGGATGACCGTGGACAGCGTCTCTGAACGTTGGATGTGCTCTGAGGGCAGAACAAG

rs931316ACGTTGGATGATGCACACACCCATGGTCAGACGTTGGATGCGGTTCACTCCAGCATTTCC

rs463431ACGTTGGATGTCACCACAGCCCATGGGGAACGTTGGATGTTTGAAACTCACAATGTGGG

rs461542ACGTTGGATGTGATGAAGGCCAAGAATGCTACGTTGGATGTGTGTCCAGAACGTCAGGTG

rs463557ACGTTGGATGTGATGAAGGCCAAGAATGCTACGTTGGATGTGTGTCCAGAACGTCAGGTG

rs191453ACGTTGGATGCATCCAACAGCTCTGTCTGCACGTTGGATGACCCATCTGTAGCGCATCAG

rs2271212ACGTTGGATGAGCTTCCCCGGAGGCAACGAACGTTGGATGTGCAGGTCTCGGCCAAAGAC

rs462009ACGTTGGATGCAGGCTCCTCCTCGTTGCCACGTTGGATGTTGGTGTCCCACGTGGTGT

rs2271211ACGTTGGATGTCGTACCCCTGCTCTGGACGACGTTGGATGACTGACGCCCAGGGCCGCTT

rs396474ACGTTGGATGTGGGAGTTGGAGATGATGAGACGTTGGATGTTCCTCAGATCCCAGTCAAG

rs428901ACGTTGGATGTCAGTGACAGAGCGAGACTCACGTTGGATGGGGCTCGATAATGTAGCCAT

rs452300ACGTTGGATGAGCACAAGCTGAAGAGGTCTACGTTGGATGAGGAGAGAAGTGCACAGATC

rs670256ACGTTGGATGTAGCTCTATTCTTCCACCCCACGTTGGATGAGCGAGACTCCGTCTCAAAA

dbSNP Extend Term rs# Primer Mix rs2278221 CAAACGCTGAGGAGAAGCC ACT

rs1650358 AAGAGACAAAAGGCCGGGC ACT

rs1643818 TACAGGTGTGAACCACCGC ACT

rs3733916 AGGCTGTAGTGTTGACAGAC ACG

rs1624933 GTCTCAAACTCCTGACCTCA ACT

rs1624857 AGACCAGCCTGGCCAACAT ACT

rs1624832 GGCCAACATGGTGAAACCC ACG

rs1624829 TGGCCAACATGGTGAAACCCT ACT

rs2161171 TGGAATAAGAGCCCTGCAGTGG ACT

rs1530499 CCCCTGCCCCAGCCACAGGAA ACT

rs888764 ATGTTGTATTGGCTATATTTGTCAACG

rs873987 AAAACCTAAAAGAATCCACGGTAACG

rs4078699 GACACATGATTAACAGCAAACAATACT

rs870311 AAGGGCGTGACGGCCCC ACT

rs1643817 GAAAGGGGAGAAAAGATTATCCCCGT

rs1643816 AGGACCAGGAGTTTCCCATTTT ACT

rs1650355 GAATCAATGAAGAAGAGAGCTT ACT

rs888763 GGTCAGGAGGCAGAGGGA ACT

rs1862212 GGGGTGAAAGGGAGCAGGG CGT

rs1110514 CAGGCCCCAGGTGAGGAA CGT

rs3797600 CTTTGTTGGTTAACCAAACCC ACG

rs3797602 GCTGACAGCTCCGGACATG ACT

rs3797603 TGTCATTCTCCTTGTGAACCCTCACT

rs3776819 CCATTCCATTGCACCTGCATG ACT

rs252076 CAAAGTGCTGGGATTGCAGG ACG

rs252075 GAGCATTTGCAGGCATGCCCTCTACT

rs252074 CTGGGTGGCTGCTGGGC ACG

rs252068 GGAAGGGTTTAAGCAAGGAG ACT

rs252069 TGAGCACCTACTATGGGCTAG ~ ACT

dbSNP Extend Term rs# Primer Mix rs194040 ATTCCATATCTTCAAAGTGATTCAACG

rs252070 CCTGGGCTTCCCCTCCC ACG

rs3797606 AGCCCTTGGCCTCTCTCC ACT

rs171667 CGCCTTTTGCTTATGCAAAGA ACG

rs187539 AACCTTCAGGAAAGTTCCCAT ACT

rs3836834 TCAAAATATCAAACTACCATGAAAACG

rs252071 ACCCTGAGACACAGGGACT ACT

rs252072 GCTGGGTCACACTCGCGGA ACG

rs252073 GCCGAGAAAAGTCAGGGATTCT ACT

rs379589 CGGGAGTACTGAGCACCCAGG CGT

rs2052472 CCCCACTGTGACTATCTCCAC ACT

rs2052471 GTCTCCTTTGGCTGCCAAG ACT

rs2052470 TGCCAAGGCCCTGTCCTC ACT

rs2052469 CGCGGGGAAGTACTCGGC ACT

rs3797608 GTCCTCCTGTTCTGAGGCCC ACT

rs3797609 GGCAGAGCGGATGGCCTG ACG

rs3822601 GTGAGGCCTGAGATGAGAACC ACG

rs153131 TCCCCATACTCCTGTGCTC ACG

rs751546 CCGTTCTACAGCGGTTAAGA ACT

rs2279979 GGCCACCAGACAGATGTAAG ACT

rs252060 CGTGTTTCGGCAGAGGTGA ACT

rs3797610 CTTCTCCCTTGGGTGATGTGTT ACT

rs194039 CCACCGTGCCGGGACATTTTTTTTACT

rs168773 ACTGGAGATATCACGGGAGC CGT

rs252061 CCAGCTGGTCACAGGGCTCCC ACG

rs187537 TCATGCTAAGTGAAATAAGCCA ACT

rs252062 GCCACCACCGTCCACAGA CGT

rs2431255 CTGTATATTTCACCGCAATTAAAAACT

rs3797612 GGCATTCATCGTCAGGGCAA ACG

rs3797613 CCGCCGCCGGTCTCCCA ACG

rs614114 GAACGTTCTCTCACTTTTGCC ACT

rs252063 CTCCCGTCCTCTGAGCCTT ACT

rs252064 GAAAACTAAGGCTCAGAGGAC ACT

rs252065 TGGAAAAGGCGAGGCCTGGAGT ACG

rs450502 GGAAAAGGCGAGGCCTGGAGTT ACT

rs439252 GCCTCCCAAAGTGCTGGGATTA ACG

rs252066 TAGCCCTCTGGAGCCCAG ACG

rs457957 GGGCCCCTCCTTAAAGCTC ACT

rs3797614 TGGCCCTCGCTCTAATGCA ACG

rs423552 CTCGATGTTGTAGTCATCGTC ACG

rs398829 TGGCGTGCTCCTCTAGGA ACG

rs416646 CTCAGCAGGTCTGATCCATC ACT

rs187450 GGGCAGACTCCCCAGGAT ACT

rs337807 GCAGGCCACTCGGTGGAC ACT

rs337806 CCACCCCAGGGGTAGCCC ACT

rs1396438 GGCAGGCAGGTGGCCTG ACT

rs1396437 CGGCAGAAGCAGCCTCAAGA ACG

rs2411811 ACATAATTTCCAAATTTCACCCC CGT

rs2898813 GGTCCTGGGTGGAGGGAT ACT

dbSNP Extend Term rs# Primer Mix rs189256 AGCAAGGCTCTATTTGGGGA ACT

rs173072 CTTTGCTCACATCGTGGCCAAA ACT

rs337805 GGAGCAGGAAAATTACATGACT ACG

rs191415 GAGTCCAACGTTGTCCACAT ACT

rs180045 ACTTGTTTCTACAATTCTCATTC ACG

rs189255 GACTCAGTCCCAGGTTTTCT ACT

rs652766 AGAAAACCTGGGACTGAGTCT ACT

rs466750 TCCTTAAATGCCTTGGTTGGCAATACT

rs442406 TTCTGGCTGTTGGGTTTGAAC ACT

rs662407 AAACATCTGAAATTAAAAGCACC ACT

rs592971 AGCATTTCTTTGACTGCTCTTTCAACT

rs457187 GGAGTATCTGTTCCTTGTGG ACT

rs459490 TTGAACATAGGAATAACCCGC ACT

rs459668 GTCTTCTTTTGTGTTTTTGGAGA ACG

rs462646 ATTATTCGACGGAGATTATTTGACACT

rs458272 ATTATTTTTCTGTCTGGTGTGG ACT

rs463455 CCTCCTCATTGTCATTCTTTTTC ACT

rs675880 CTTTCATGACATTGACACAACTACACT

rs810617 CCACAGCCTCCGCCTCCC ACT

rs464156 GGGTTTCCAGGTTAAAATGGC ACT

rs458083 CTCCTGCTCTGCCTATCCTT ACT

rs467333 ATTTCTTCCCCTCCTGCTCT ACT

rs465381 GCCTCCCACAGTTCCCTTGTT ACT

rs466363 GTGATGGCTCTGCACCAGA ACG

rs2457099 AGCGTGTGCCAGCTCTCC ACT

rs463901 GACACAATTCAGAGCGACTTAC ACT

rs465621 AAGTGCTAGAAGAAAATGTAGC ACT

rs463724 CCTTGCGCCATCCCCTAG CGT

rs465242 TGTGCCCATCCCCCCCTT ACT

rs467419 AACGTAAGTCCTAATGACCGCCC ACG

rs456135 CCCTCTCCTCTTCTGGGCA ACT

rs464536 GCTTTGGTCCTCCTGAGCC ACG

rs461898 CACAGAGCGACTCTCTCTTGGTT ACT

rs389558 CTGACAGTTCTCTAAACTCCCA ACG

rs466752 TTCCTTTTTCTCCCTGAAGCA ACG

rs455655 CACCCCATATGGCTCATGGG ACT

rs463435 GGGAAGGAGGTACTTAGCAG ACG

rs2174971 GTGCCACTCTCCAGCGGCC ACG

rs1979979 TTGCCGGCCCCCACCTC ACG

rs411804 GAAAATCCCTGTCACCAGTC ACG

rs1623885 CTTGGCTGCAGCACCCCA ACT

rs1643811 GCCCTGGTACTTTCAGCTCCCT ACG

rs434430 GTGTGCATGTGTGTGCCTG CGT

rs187538 TAAACGGGCCAAAAACGCCTAT ACT

rs252067 GCGCCTACGGATGTCAGG ACT

rs459319 CATGTTGAACAGAGAGAAACGGTCACG

rs467289 TCACTGAGAAATATTTTGCTCCC ACT

rs462644 GGTGAGCCCTTGGCTGTG ACG

rs458752 TAAAGCGCTCTTACAAATCAACA ACT

dbSNP Extend Term rs# Primer Mix rs708320 TGGTGAAATCCTGTCTCTACTAAACGT

rs457954 CACCGTTTCTTATAATGCAGCC ACT

rs2411810 GGGGACGTTACTTCTTTTCAC ACG

rs3084687 ATTTATATATGTGTGTGTACACATACT

rs69638 CCCATTGGCTGTCCTGGAA ACT

rs455452 CCTCAACCCCAGATGCCCTC ACG

rs464850 ACTCCTGCCTGAGTGTCTC ACT

rs431472 GTGAAGCGGAAGGAGACTC ACG

rs2411809 CTGCACACCCTCTGCACAG ACG

rs2457094 TGGCTGGCACCACTGCACTGC ACT

rs2457095 TGGCTCATGCTTCTAATCCCA ACT

rs2261740 CTGCACTCCAGCCTGGGC ACT

rs1109180 ACATCAGTGACAGTGTAATGGTA ACG

rs1109179 TATGCAGACCCCCTCCCC ACT

rs1109178 AACAACAGCAACAGAAATGAAG ACT

rs456909 CGATTCCCACGCGTGTCTG ACG

rs469124 CCTGGCTCCATTGGTGTGAA ACT

rs468039 CCTTCACACCAATGGAGCCAG ACT

rs467017 CTGCCACTAAACAGATGAGAA ACT

rs469290 ATTTCTGGGCCCAAAGTCCA ACT

rs469090 CCAATTGTTCCAGCCACTCCC ACT

rs469568 TGATATTGCTTGCTTGGGTCTTAGACT

rs468386 GGTCAAGAATTCAAGAGCAGC ACT

rs469349 GTGCAGTGGCACGATCCTA ACT

rs469099 GCAGGTGGAACCGCAGAC ACT

rs456868 GGAGCTGCGGTGACTCCC ACT

rs465389 CCCTGGCACTCGCAGACC ACT

rs463892 AGCTCCCCCCGCACCAC ACT

rs468548 AAGGGAACATGCAAGCAAAGACTCACT

rs654612 TGCAAGCAAAGACTCGAATGA ACT

rs468542 TCACTCACTTGATTCCTGCCATC ACT

rs469262 CACTGTGGGATTTCCAGCAGA ACT

rs708323 TATACAGGTCACCCATTTAAAGT ACT

rs469089 CCTCGGCCTTCCCCAGCT ACT

rs469396 AATGAGGGAACCTGCAGTTTAAGAACT

rs468723 CAGACCCCATGCCTTGCC ACT

rs467604 GAGTTTCCTCCTCTTTCACAA ACT

rs338874 CACAGCCACTGGGGAGTAG ACT

rs338875 TTGCTCGCGTGTGCCAGCAAAT ACG

rs1385803 AAGTGGAATTCTCATGGCAGAT ACT

rs1385804 CATTCCAGAAGTGGAATTCTCATGACT

rs338876 AGGAAGGTGCTCCGGCCT ACG

rs189803 TGCTTCCCCCTTCCCCCT CGT

rs452215 TCTATTCTTCCACCCCCATCTTT ACT

rs641170 CTATTCTTCCACCCCCATCT ACT

rs584398 CTCTTATATAGCTCTATTCTTCC CGT

rs385330 AGGTGTCTGCAGATAATACATT ACG

rs429538 CCTGGGGCACAGGACAATA ACT

rs371229 I GACAATAGTTGGGGCAAGAC ACT

dbSNP Extend Term rs# Primer Mix rs460874 ACAAAACTATCCTTCAAAAATACACGT

rs646121 GTTTTTGTTTCTCTGAAAGTGTCTCGT

rs468262 CACCCAACTACTTGCTCCC ACG

rs467863 GCTGATGGGAGGCCAATGT ACT

rs191434 GTCCAGAGATCCTGCTCACT CGT

rs2054782 CCCCCTCCATCACCTCCC ACG

rs468499 GTGAGCCAGCAATTCTCCTA ACT

rs180287 CAATGATCAGAACTCAGAGGTTTTACT

rs338877 AGAGATAAATTTCCAGTGTGAG CGT

rs650665 AGACATCCCGGCCGGGC ACT

rs193419 CCAAAGACACAGGGAGTAGATTA ACT

rs180288 GAGAATATTCTTGTGGGCTTAAT ACT

rs186834 CCAGGTCACACACACACTC ACG

rs189266 CACACACTCCCTCTCACTGT ACT

rs189267 TTCTGTGCATCTTTGACGCCATC CGT

rs170937 GATGGCGTCAAAGATGCACA ACT

rs463263 CCCCTTTGCACAGATGCTG ACT

rs463262 GGGGAGCAGCCAGTTCCTA ACT

rs460454 AGAGGCTGGGGACAGAGAA ACT

rs460455 GGTACCCACCAGTCTCCTTCT ACT

rs460505 CAGCGTCTCTGACACGGTC ACG

rs931316 GGTCAGAGCAGACACATCCACAT ACG

rs463431 CCCATGGGGAGCACCAAG ACT

rs461542 TGGGAGCTCCCGGGATATTGCC ACG

rs463557 GCTCCCGGGATATTGCCCA ACT

rs191453 CTGGGCTGGGGCCCTGC ACT

rs2271212 CGAGGAGGAGCCTGGCAG ACG

rs462009 CTCCTCGTTGCCTCCGGG ACT

rs2271211 GACGTAGCTGCCGACACCA ACG

rs396474 CTGGTGGCCCATCTATCCTGG ACT

rs428901 GAGCGAGACTCCGTCTCAA CGT

rs452300 CTGAAGAGGTCTTTCTCCTTCC CGT

rs670256 TTCTTCCACCCCCATCTTTG ACT

Genetic Anal, [0284] Allelotyping results from the discovery cohort are shown for cases and controls in Table 35.
The allele frequency for the A2 allele is noted in the fifth and sixth columns for osteoarthritis case pools and control pools, respectively, where "AF" is allele frequency. The allele frequency for the A1 allele can be easily calculated by subtracting the A2 allele frequency from 1 (Al AF
= 1-A2 AF). For example, the SNP rs2278221 has the following case and control allele frequencies: case A1 (C) = 0.36;
case A2 (T) = 0.64; control A1 (C) = 0.37; and control A2 (T) = 0.63, where the nucleotide is provided in paranthesis. Some SNPs are labeled "untyped" because of failed assays.

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 6 rs2278221 210 178695460C/T 0.64 0.63 0.770 rs1650358 3608 178698858C/G

rs1643818 3609 178698859C/G

rs3733916 4318 178699568C/T

rs1624933 5593 178700843A/G 0.69 0.71 0.255 rs1624857 5629 178700879C/T 0.79 0.81 0.574 rs1624832 5639 178700889A/G 0.41 0.44 0.203 rs1624829 5640 178700890C/T 0.89 0.93 0.044 rs2161171 8943 178704193A/C

rs1530499 17968 178713218A/G 0.39 0.39 0.861 rs888764 19887 178715137A/G

rs873987 21034 178716284AlG

rs4078699 21085 178716335C/T 0.56 0.54 0.374 rs870311 21596 178716846A/G 0.51 0.50 0.590 rs1643817 23379 178718629A/C 0.27 NA NA

rs1643816 23432 178718682A/C

rs1650355 24007 178719257A/C

rs888763 26121 178721371A/G 0.40 0.42 0.390 rs1862212 26273 178721523A/T 0.55 0.54 0.753 rs1110514 26755 178722005A/T 0.29 0.28 0.572 rs3797600 27411 178722661C/T 0.56 0.57 0.738 rs3797602 27710 178722960GlT 0.65 0.64 0.564 rs3797603 27842 178723092C/T

rs3776819 28379 178723629C/T 0.46 0.46 0.850 rs252076 29603 178724853C/T 0.46 0.48 0.519 rs252075 31232 178726482C/G 0.35 0.36 0.859 rs252074 31504 178726754A/G 0.35 0.34 0.816 rs252068 32583 178727833C/G 0.47 0.48 0.656 rs252069 32794 178728044A/G 0.28 0.27 0.626 rs194040 32840 178728090C/T 0.31 0.32 0.665 rs252070 33044 178728294C/T 0.58 0.57 0.573 rs3797606 33150 178728400A/C 0.88 0.88 0.684 rs171667 33218 178728468A/G 0.48 0.51 0.166 rs187539 33513 178728763C/T 0.33 0.34 0.652 /TATCA
rs3836834 33959 178729209AACTAC
CATGAA
A

rs252071 34486 178729736A/G 0.30 0.31 0.666 rs252072 36289 178731539C/T 0.49 0.50 0.677 rs252073 36570 178731820C/T

rs379589 38247 178733497A/T 0.59 0.63 0.096 rs2052472 38477 178733727A/C 0.05 0.06 0.508 rs2052471 38518 178733768C/T 0.89 0.88 0.459 rs2052470 38529 178733779C/T 0.83 0.80 0.125 rs2052469 38667 178733917A/G 0.83 0.80 0.172 rs3797608 39781 178735031C/T 0.06 0.07 0.578 rs3797609 39856 178735106C/T 0.05 0.05 0.812 rs3822601 39927 178735177C/T 0.08 0.08 0.802 rs153131 40506 178735756A/G 0.76 0.77 0.944 rs751546 41869 178737119C/G 0.93 0.92 0.585 rs2279979 42452 178737702C/T 0.93 0.92 0.436 rs252060 44788 178740038C/T 0.81 0.82 0.760 rs3797610 46059 178741309A/C 0.17 0.17 0.858 rs194039 46846 178742096A/G 0.41 0.47 0.035 rs168773 47712 178742962A/T 0.35 0.38 0.266 rs252061 48796 178744046C/T 0.21 0.19 0.508 rs187537 49441 178744691C/G

rs252062 49602 178744852A/T 0.95 0.95 0.960 rs2431255 49723 178744973A/C 0.24 0.19 0.034 rs3797612 50050 178745300C/T 0.38 0.43 0.036 dbSNP Position .ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID NO: AF AF

rs379761350171 178745421C/T 0.21 0.21 0.941 rs614114 50477 178745727C/T 0.50 0.53 0.387 rs252063 50818 178746068C/T 0.57 0.55 0.313 rs252064 50833 178746083C/T 0.52 0.52 0.806 rs252065 50881 178746131A/G 0.22 0.22 0.857 rs450502 50882 178746132A/G

rs439252 51386 178746636C/T

rs252066 51534 178746784C/T 0.19 0.18 0.618 rs457957 52317 178747567A/G 0.67 0.70 0.172 rs379761452368 178747618C/T

rs423552 52970 178748220A/G 0.90 0.92 0.215 rs398829 53023 178748273A/G

rs416646 53356 178748606A/G 0.56 0.57 0.650 rs187450 53882 178749132G/T

rs337807 54553 178749803C/T 0.55 0.59 0.208 rs337806 55475 178750725A/C 0.11 0.10 0.925 rs139643855530 178750780A/G 0.56 0.54 0.494 rs139643755691 178750941C/T

rs241181155848 178751098A/C

rs289881355879 178751129C/G

rs189256 56316 178751566A/G 0.19 0.19 0.988 rs173072 56911 178752161A/C

rs337805 57320 178752570A/G 0.25 0.24 0.657 rs191415 57391 178752641C/T

rs180045 57437 178752687C/T 0.51 0.47 0.211 rs189255 57478 178752728C/G 0.15 0.12 0.273 rs652766 57500 178752750C/T 0.57 0.61 0.213 rs466750 59111 178754361G/T 0.35 0.33 0.493 rs442406 59333 178754583A/G 0.57 0.59 0.420 rs662407 59715 178754965A/G 0.31 0.27 0.102 rs592971 59804 178755054A/G

rs457187 59851 178755101A/G 0.23 0.24 0.842 rs459490 59929 178755179C/T 0.21 0.20 0.604 rs459668 60052 178755302C/T 0.20 0.19 0.648 rs462646 60240 178755490C/T 0.43 0.43 0.905 rs458272 60359 178755609G/T 0.22 0.20 0.523 rs463455 60381 178755631AIG 0.25 0.24 0.644 rs675880 60456 178755706C/T 0.63 0.65 0.591 rs810617 60724 178755974C/G

rs464156 60875 178756125C/T 0.34 0.34 0.892 rs458083 60968 178756218A/G 0.80 0.82 0.499 rs467333 60978 178756228C/G 0.11 0.12 0.369 rs465381 60998 178756248C/T

rs466363 61557 178756807C/T 0.31 0.34 0.358 rs245709962091 178757341C/T 0.44 0.44 0.956 rs463901 62645 178757895C/T 0.43 0.45 0.395 rs465621 62943 178758193A/C 0.62 0.63 0.534 rs463724 63131 178758381A/T 0.09 0.08 0.523 rs465242 63145 178758395G/T

rs467419 63406 178758656A/G 0.65 0.66 0.647 rs456135 63427 178758677C/G 0.79 0.80 0.686 rs464536 63554 178758804C/T 0.36 0.34 0.296 rs461898 63661 178758911A/G 0.30 0.32 0.411 rs389558 64093 178759343A/G 0.24 0.26 0.325 rs466752 64153 178759403C/T 0.35 0.37 0.446 rs455655 64409 178759659C/G 0.87 0.89 0.536 rs463435 64544 178759794C/T 0.68 0.66 0.428 rs217497165257 178760507C/T 0.52 0.51 0.695 rs197997965626 178760876A/G 0.07 0.06 0.692 rs411804 65739 178760989A/G 0.78 0.78 0.976 rs162388566392 178761642C/T 0.82 0.80 0.492 rs164381166720 178761970C/T 0.24 0.24 0.924 rs434430 69177 178764427A/T

rs187538 ~ -69336 L 178764586I-.-G~ I f 13~

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 6 rs252067 69636 178764886 A/G 0.21 0.23 0.606 rs459319 69823 178765073 A/G 0.19 0.20 0.640 rs467289 69928 178765178 C/T 0.26 0.26 0.988 rs462644 70547 178765797 C/T 0.59 0.58 0.914 rs458752 70633 178765883 C/T 0.18 0.20 0.513 rs708320 71805 178767055 A/C

rs457954 72181 178767431 C/G 0.71 0.73 0.327 rs2411810 72200 178767450 C/T 0.28 0.26 0.252 rs3084687 72474 178767724 -lAT 0.13 0.12 0.884 rs69638 72567 178767817 C/G 0.54 0.52 0.449 rs455452 72973 178768223 A/G 0.59 0.60 0.733 rs464850 73468 178768718 A/G 0.11 0.09 0.249 rs431472 73889 178769139 A/G 0.33 0.34 0.713 rs2411809 75730 178770980 C/T

rs2457094 75970 178771220 A/G 0.71 0.73 0.383 rs2457095 76114 178771364 A/G 0.74 0.76 0.551 rs2261740 76342 178771592 C/T 0.35 0.36 0.702 rs1109180 76449 178771699 A/G

rs1109179 76465 178771715 C/T

rs1109178 76791 178772041 A/C 0.46 0.45 0.820 rs456909 78042 178773292 A/G 0.55 0.53 0.444 rs469124 80758 178776008 A/G

rs468039 80778 178776028 C/T

rs467017 81356 178776606 A/C 0.33 0.32 0.665 rs469290 81576 178776826 A/G 0.57 0.57 0.871 rs469090 81689 178776939 C/T 0.82 0.83 0.387 rs469568 81759 178777009 G/T 0.38 0.38 0.888 rs468386 81950 178777200 C/G

rs469349 82562 178777812 A/C

rs469099 83591 178778841 C/T 0.66 0.63 0.264 rs456868 83700 178778950 A/G

rs465389 83821 178779071 C/G

rs463892 83842 178779092 C/G

rs468548 83923 178779173 G/T

rs654612 83929 178779179 A/C

rs468542 84021 178779271 C/G

rs469262 84175 178779425 C/T 0.45 0.47 0.405 rs708323 84417 178779667 A/G 0.73 0.69 0.138 rs469089 84747 178779997 C/G

rs469396 85746 178780996 C/G 0.38 0.37 0.817 rs468723 86129 178781379 C/T 0.37 0.38 0.754 rs467604 86335 178781585 A/G 0.34 0.32 0.504 rs338874 87315 178782565 C/G 0.43 0.44 0.879 rs338875 87648 178782898 A/G 0.48 0.50 0.289 rs1385803 87764 178783014 A/C

rs1385804 87770 178783020 C/G

rs338876 88221 178783471 C/T 0.39 0.39 0.889 rs189803 90474 178785724 A/C

rs452215 91148 178786398 G/T

rs641170 91150 178786400 G/T

rs584398 91160 178786410 G/T

rs385330 91733 178786983 C/T

rs429538 91772 178787022 A/C

rs371229 91785 178787035 C/T

rs460874 93140 178788390 A/T 0.74 0.71 0.351 rs646121 93148 178788398 A/T 0.93 0.94 0.687 rs468262 96080 178791330 A/G

rs467863 96157 178791407 C/G

rs191434 96313 178791563 A/C

rs2054782 96759 178792009 C/T 0.44 0.42 0.353 rs468499 97026 178792276 A/C

rs180287 97320 178792570 C/G

rs338877 97732 178792982 A/T 0.04 0.04 0.863 rs650665 98713 178793963 C/G

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 6 rs193419 99707 178794957~A/C

rs180288 99959 178795209C/G

rs186834 100009 178795259A/G

rs189266 100020 178795270C/G

rs189267 100065 1787 95315A/C

rs170937 100086 178795336C/G

rs463263 101270 178796520C/G

rs463262 101276 1787 96526G/T

rs460454 101371 178796621C/T

rs460455 101376 178796626C/G

rs460505 101439 178796689C/T

rs931316 101820 178797070C/T

rs463431 102392 1787 97642ClG

rs461542 102602 178797852A/G

rs463557 102604 178797854A/C

rs191453 102896 178798146C/T 0.11 0.14 0.123 rs2271212189104 178884354C/T 0.65 0.57 0.003 rs462009 189134 1788 84384C/T

rs2271211189205 1788 84455A/G

rs396474 Not ma Not ma A/C
ed ed rs428901 Not ma Not ma A/T 0.64 0.72 0.015 ed ed rs452300 Not ma Not ma G/T
ed ed rs670256 Not ma Not ma G/T
ed ed [0285] The ADAMTS2 proximal SNPs were also allelotyped in the replication cohorts using the methods described herein and the primers provided in Tables 33 and 34. The replication allelotyping results for replication cohort #1 and replication cohort #2 are provided in Tables 36 and 37, respectively.

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position AlleleCase Control Value SEQ ID AF AF
NO: 6 rs2278221210 178695460 C/T 0.64 0.62 0.624 rs16503583608 1786 98858C/G

rs16438183609 1786 98859C/G

rs37339164318 178699568 C/T

rs16249335593 178700843 A/G 0.65 0.69 0.322 rs16248575629 178700879 C/T 0.81 unt ed NA

rs16248325639 178700889 A/G 0.38 0.42 0.265 rs16248295640 178700890 C/T 0.87 unt ed NA

rs21611718943 1787 04193A/C

rs 153049917968 178713218 A/G 0.39 0.40 0.765 rs888764 19887 178715137 A/G

rs873987 21034 178716284 A/G

rs407869921085 178716335 C/T 0.55 0.54 0.733 rs870311 21596 178716846 A/G 0.50 0.50 0.828 rs164381723379 178718629 A/C 0.27 unt ed rs164381623432 178718682 A/C

rs165035524007 178719257 A/C

rs888763 26121 178721371 A/G 0.40 0.40 0.816 rs186221226273 178721523 A/T 0.55 0.55 0.936 rs111051426755 178722005 A/T 0.29 0.29 0.997 rs379760027411 178722661 C/T 0.57 0.58 0.604 rs379760227710 178722960 G/T 0.64 0.63 0.879 rs379760327842 178723092 C/T

rs377681928379 178723629 C/T 0.47 0.46 0.889 rs252076 29603 178724853 C/T 0.46 0.49 0.410 rs252075 31232 178726482 C/G 0.35 0.37 0.572 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 6 rs252074 31504 178726754 A/G 0.35 0.35 0.914 rs252068 32583 178727833 C/G 0.48 0.48 0.853 rs252069 32794 178728044 A/G 0.29 0.28 0.765 rs194040 32840 178728090 C/T 0.31 0.33 0.450 rs252070 33044 178728294 C/T 0.57 0.58 0.609 rs3797606 33150 178728400 A/C 0.87 0.91 0.119 rs171667 33218 178728468 A/G 0.45 0.50 0.125 rs187539 33513 178728763 C/T 0.33 0.34 0.709 /TATCA
rs3836834 33959 178729209 AACTAC
CATGAA
A

rs252071 34486 178729736 A/G 0.30 0.32 0.566 rs252072 36289 178731539 C/T 0.48 0.51 0.400 rs252073 36570 178731820 C/T

rs379589 38247 178733497 A/T 0.59 0.65 0.035 rs2052472 38477 178733727 A/C 0.04 0.06 0.493 rs2052471 38518 178733768 C/T 0.87 0.88 0.697 rs2052470 38529 178733779 C/T 0.84 0.78 0.036 rs2052469 38667 178733917 A/G 0.84 0.79 0.086 rs3797608 39781 178735031 C/T 0.06 0.07 0.530 rs3797609 39856 178735106 C/T 0.04 0.05 0.841 rs3822601 39927 178735177 C/T 0.08 0.08 0.904 rs153131 40506 178735756 A/G 0.77 0.77 0.964 rs751546 41869 178737119 C/G 0.94 0.92 0.265 rs2279979 42452 178737702 C/T 0.94 0.92 0.238 rs252060 44788 178740038 C/T 0.82 0.80 0.553 rs3797610 46059 178741309 A/C 0.16 0.18 0.459 rs194039 46846 178742096 A/G 0.43 0.45 0.589 rs168773 47712 178742962 A/T 0.34 0.35 0.845 rs252061 48796 178744046 C/T 0.23 0.22 0.884 rs187537 49441 178744691 C/G

rs252062 49602 178744852 A/T 0.98 0.96 0.310 rs2431255 49723 178744973 A/C 0.24 0.19 0.108 rs3797612 50050 178745300 C/T 0.42 0.46 0.254 rs3797613 50171 178745421 C/T 0.19 0.21 0.576 rs614114 50477 178745727 C/T 0.52 0.54 0.717 rs252063 50818 178746068 C/T 0.55 0.57 0.537 rs252064 50833 178746083 C/T 0.52 0.50 0.609 rs252065 50881 178746131 A/G 0.21 0.25 0.234 rs450502 50882 178746132 A/G

rs439252 51386 178746636 C/T

rs252066 51534 178746784 C/T 0.20 0.20 0.883 rs457957 52317 178747567 A/G 0.66 0.71 0.162 rs3797614 52368 178747618 C/T

rs423552 52970 178748220 A/G 0.90 0.92 0.380 rs398829 53023 178748273 A/G

rs416646 53356 178748606 A/G 0.58 0.59 0.915 rs187450 53882 178749132 G/T

rs337807 54553 178749803 C/T 0.60 NA NA

rs337806 55475 178750725 A/C 0.10 0.10 0.997 rs1396438 55530 178750780 A/G 0.52 0.57 0.188 rs1396437 55691 178750941 C/T

rs2411811 55848 178751098 A/C

rs2898813 55879 178751129 CIG

rs189256 56316 178751566 A/G 0.21 0.20 0.852 rs173072 56911 178752161 A/C

rs337805 57320 178752570 A/G 0.24 0.24 0.950 rs191415 57391 178752641 C/T

rs180045 57437 178752687 C/T 0.47 0.46 0.918 rs189255 57478 178752728 C/G 0.14 0.13 0.764 rs652766 57500 178752750 C/T 0.59 0.61 0.570 rs466750 59111 178754361 G/T 0.38 0.37 0.606 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 6 rs442406 59333 178754583A/G 0.56 0.57 0.882 rs662407 59715 178754965A!G 0.32 0.27 0.134 rs592971 59804 178755054A/G

rs457187 59851 178755101A/G 0.23 0.25 0.451 rs459490 59929 178755179C/T 0.22 0.21 0.671 rs459668 60052 178755302C/T 0.20 0.19 0.712 rs462646 60240 178755490C/T 0.42 0.44 0.439 rs458272 60359 178755609G/T 0.21 0.21 0.755 rs463455 60381 178755631A/G 0.25 0.25 0.783 rs675880 60456 178755706C/T 0.62 0.63 0.741 rs810617 60724 178755974C/G

rs464156 60875 178756125C/T 0.32 0.34 0.541 rs458083 60968 178756218A/G 0.80 0.82 0.499 rs467333 60978 178756228C/G 0.10 0.13 0.243 rs465381 60998 178756248C/T

rs466363 61557 178756807C/T 0.31 0.34 0.494 rs245709962091 178757341C/T 0.45 0.45 0.997 rs463901 62645 178757895C/T 0.46 0.46 0.852 rs465621 62943 178758193A/C 0.64 0.63 0.853 rs463724 63131 178758381A/T 0.09 0.08 0.737 rs465242 63145 178758395G/T

rs467419 63406 178758656A/G 0.64 0.65 0.694 rs456135 63427 178758677C/G 0.79 0.76 0.339 rs464536 63554 178758804C/T 0.36 0.34 0.553 rs461898 63661 178758911A/G 0.31 0.33 0.727 rs389558 64093 178759343A/G 0.27 0.28 0.762 rs466752 64153 178759403C/T 0.34 0.38 0.223 rs455655 64409 178759659C/G 0.87 unt ed NA

rs463435 64544 178759794C/T 0.65 0.65 0.973 rs217497165257 178760507C/T 0.49 0.51 0.476 rs197997965626 178760876A/G 0.08 0.07 0.579 rs411804 65739 178760989A/G 0.77 0.79 0.420 rs162388566392 178761642C/T 0.81 0.78 0.451 rs164381166720 178761970C/T 0.26 0.25 0.715 rs434430 69177 178764427A/T

rs187538 69336 178764586G/T

rs252067 69636 178764886A/G 0.22 0.22 0.978 rs459319 69823 178765073A/G 0.19 0.22 0.245 rs467289 69928 178765178C/T 0.26 0.29 0.377 rs462644 70547 178765797C/T 0.58 0.56 0.637 rs458752 70633 178765883C/T 0.18 0.23 0.129 rs708320 71805 178767055A/C

rs457954 72181 178767431C/G 0.69 0.73 0.143 rs241181072200 178767450C/T 0.28 0.23 0.083 rs308468772474 178767724-/AT 0.12 0.13 0.767 rs69638 72567 178767817C/G 0.53 0.49 0.157 rs455452 72973 178768223A/G 0.58 0.61 0.313 rs464850 73468 178768718A/G 0.13 0.10 0.171 rs431472 73889 178769139A/G 0.32 0.39 0.048 rs241180975730 178770980C/T

rs245709475970 178771220A/G 0.70 0.75 0.157 rs245709576114 178771364A/G 0.74 0.75 0.707 rs226174076342 178771592C/T 0.34 unt ed NA

rs110918076449 178771699A/G

rs110917976465 178771715C/T

rs110917876791 178772041A/C 0.47 0.48 0.715 rs456909 78042 178773292A/G 0.56 0.54 0.537 rs469124 80758 178776008A/G

rs468039 80778 178776028C/T

rs467017 81356 178776606A/C 0.33 0.31 0.480 rs469290 81576 178776826A/G 0.63 0.66 0.427 rs469090 81689 178776939C/T 0.80 0.83 0.300 rs469568 81759 178777009G/T 0.39 0.43 0.234 rs468386 81950 178777200C/G

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 6 rs469349 82562 178777812A/C

rs469099 83591 178778841C/T 0.66 0.60 0.066 rs456868 83700 178778950A/G

rs465389 83821 178779071C/G

rs463892 83842 178779092C/G

rs468548 83923 178779173G/T

rs654612 83929 178779179A/C

rs468542 84021 178779271C/G

rs469262 84175 178779425C/T 0.46 0.50 0.232 rs708323 84417 178779667A/G 0.72 0.66 0.071 rs469089 84747 178779997C/G

rs469396 85746 178780996C/G 0.37 0.35 0.522 rs468723 86129 178781379C/T 0.39 0.41 0.495 rs467604 86335 178781585A/G 0.33 0.30 0.303 rs338874 87315 178782565C/G 0.44 0.46 0.628 rs338875 87648 178782898A/G 0.49 0.54 0.106 rs138580387764 178783014A/C

rs138580487770 178783020C/G

rs338876 88221 178783471C/T 0.38 0.36 0.609 rs1898p3 90474 178785724A/C

rs452215 91148 178786398G/T

rs641170 91150 178786400G/T

rs584398 91160 178786410G/T

rs385330 91733 178786983C/T

rs429538 91772 178787022A/C

rs371229 91785 178787035C/T

rs460874 93140 178788390A/T 0.74 0.69 0.118 rs646121 93148 178788398A/T 0.93 0.95 0.477 rs468262 96080 178791330A/G

rs467863 96157 178791407C/G

rs191434 96313 178791563A/C

rs205478296759 178792009C/T 0.45 0.42 0.514 rs468499 97026 178792276A/C

rs180287 97320 178792570C/G

rs338877 97732 178792982A/T 0.04 0.04 0.781 rs650665 98713 178793963C/G

rs193419 99707 178794957A/C

rs180288 99959 178795209C/G

rs186834 100009 178795259A/G

rs189266 100020 178795270C/G

rs189267 100065 178795315A/C

rs170937 100086 178795336C/G

rs463263 101270 178796520C/G

rs463262 101276 178796526G/T

rs460454 101371 178796621C/T

rs460455 101376 178796626C/G

rs460505 101439 178796689C/T

rs931316 101820 178797070C/T

rs463431 102392 178797642C/G

rs461542 102602 178797852A/G

rs463557 102604 178797854A/C

rs191453 102896 178798146C/T 0.15 0.19 0.139 rs2271212189104 178884354C/T 0.64 0.58 0.072 rs462009 189134 178884384C/T

rs2271211189205 178884455A/G

rs396474 Not ma Not ma A/C
ed ed rs428901 Not ma Not ma AIT 0.66 unt ed NA
ed ed rs452300 Not ma Not ma G/T
ed ed rs670256 Not ma Not ma G/T
ed ed dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in PositionAllele Case Control Value SEQ ID AF AF
NO: 6 rs2278221210 178695460C/T 0.64 0.64 0.837 rs16503583608 178698858C/G

rs16438183609 178698859C/G

rs37339164318 178699568CIT

rs16249335593 178700843A/G 0.73 0.75 0.447 rs16248575629 178700879C/T 0.78 0.81 0.289 rs16248325639 178700889A/G 0.44 0.47 0.423 rs16248295640 178700890C/T 0.90 0.93 0.294 rs21611718943 178704193A/C

rs153049917968 178713218A/G 0.39 0.36 0.499 rs888764 19887 178715137A/G

rs873987 21034 178716284A/G

rs407869921085 178716335C/T 0.57 0.54 0.316 rs870311 21596 178716846A/G 0.52 0.50 0.579 rs164381723379 178718629A/C

rs164381623432 178718682A/C

rs165035524007 178719257A/C

rs888763 26121 178721371A/G 0.40 0.44 0.264 rs186221226273 178721523A/T 0.56 0.53 0.529 rs1 'I 26755 178722005A/T 0.30 0.27 0.381 rs379760027411 178722661C/T 0.55 0.54 0.840 rs379760227710 178722960G/T 0.68 0.65 0.534 rs379760327842 178723092C/T

rs377681928379 178723629C/T 0.45 0.47 0.662 rs252076 29603 178724853C/T 0.46 0.46 0.986 rs252075 31232 178726482C/G 0.36 0.34 0.666 rs252074 31504 178726754A/G 0.35 0.33 0.604 rs252068 32583 178727833C/G 0.47 0.48 0.648 rs252069 32794 178728044A/G 0.27 0.26 0.640 rs194040 32840 178728090C/T 0.31 0.30 0.734 rs252070 33044 178728294C/T 0.61 0.55 0.157 rs379760633150 178728400A/C 0.91 0.83 0.005 rs171667 33218 178728468A/G 0.51 0.52 0.674 rs187539 33513 178728763C/T 0.32 0.33 0.836 /TATCA
rs383683433959 178729209AACTAC
CATGAA
A

rs252071 34486 178729736A/G 0.30 0.30 0.942 rs252072 36289 178731539C/T 0.50 0.49 0.684 rs252073 36570 178731820C/T

rs379589 38247 178733497A/T 0.60 0.61 0.981 rs205247238477 178733727A/C 0.06 0.06 0.856 rs205247138518 178733768C/T 0.91 0.86 0.079 rs205247038529 178733779C/T 0.82 0.83 0.828 rs205246938667 178733917A/G 0.82 0.82 0.983 rs379760839781 178735031C/T 0.06 0.06 0.969 rs379760939856 178735106C/T 0.05 0.05 0.879 rs382260139927 178735177C/T 0.07 0.08 0.838 rs'15313140506 178735756A/G 0.76 0.76 0.981 rs751546 41869 178737119C/G 0.91 0.92 0.526 rs227997942452 178737702C/T 0.92 0.92 0.906 rs252060 44788 178740038C/T 0.81 0.85 0.157 rs379761046059 178741309A/C 0.18 0.16 0.593 rs'19403946846 178742096A/G 0.39 0.49 0.005 rs'16877347712 178742962A/T 0.37 0.43 0.098 rs252061 48796 178744046C/T 0.19 0.15 0.164 rs'18753749441 178744691C/G

rs252062 49602 178744852A/T 0.93 0.95 0.290 rs243125549723 178744973A/C 0.23 0.19 0.201 rs379761250050 178745300C/T 0.32 0.38 0.102 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ I~ AF AF
NO: 6 rs379761350171 178745421C/T 0.23 NA

rs614114 50477 178745727CIT 0.48 0.51 0.423 rs252063 50818 178746068C/T 0.60 0.51 0.011 rs252064 50833 178746083C/T 0.51 0.56 0.265 rs252065 50881 178746131A/G 0.22 0.18 0.175 rs450502 50882 178746132AIG

rs439252 51386 178746636C/T

rs252066 51534 178746784C/T 0.18 0.16 0.451 rs457957 52317 178747567A/G 0.67 0.68 0.728 rs379761452368 178747618C/T

rs423552 52970 178748220A/G 0.89 0.91 0.398 rs398829 53023 178748273A/G

rs416646 53356 178748606AIG 0.54 0.55 0.643 rs187450 53882 178749132G/T

rs337807 54553 178749803C/T 0.49 0.59 0.009 rs337806 55475 178750725A/C 0.11 0.10 0.889 rs139643855530 178750780A/G 0.61 0.50 0.007 rs139643755691 178750941CIT

rs241181155848 178751098A/C

rs289881355879 178751129C/G

rs189256 56316 178751566A/G 0.17 0.17 0.923 rs173072 56911 178752161A/C

rs337805 57320 178752570AIG 0.27 0.25 0.582 rs191415 57391 178752641C/T

rs180045 57437 178752687C/T 0.56 0.48 0.115 rs189255 57478 178752728C/G 0.16 0.12 0.168 rs652766 57500 178752750CIT 0.55 0.61 0.231 rs466750 59111 178754361G/T 0.31 0.28 0.473 rs442406 59333 178754583A/G 0.58 0.63 0.209 rs662407 59715 178754965A/G 0.30 0.28 0.449 rs592971 59804 178755054A/G

rs457187 59851 178755101A/G 0.23 0.21 0.402 rs459490 59929 178755179C/T 0.20 0.19 0.708 rs459668 60052 178755302C/T 0.21 0.20 0.821 rs462646 60240 178755490C/T 0.44 0.41 0.460 rs458272 60359 178755609G/T 0.22 0.20 0.524 rs463455 60381 178755631A/G 0.23 0.22 0.629 rs675880 60456 178755706C/T 0.65 0.67 0.564 rs810617 60724 178755974C/G

rs464156 60875 178756125C/T 0.37 0.34 0.439 rs458083 60968 178756218A/G

rs467333 60978 178756228C/G 0.11 0.11 0.902 rs465381 60998 178756248C/T

rs466363 61557 178756807C/T 0.32 0.34 0.547 rs245709962091 178757341C/T 0.43 0.43 0.974 rs463901 62645 178757895C/T 0.39 0.43 0.342 rs465621 62943 178758193A/C 0.59 0.64 0.195 rs463724 63131 178758381A/T 0.09 0.07 0.539 rs465242 63145 178758395G/T

rs467419 63406 178758656A/G 0.66 0.67 0.752 rs456135 63427 178758677C/G 0.79 0.85 0.029 rs464536 63554 178758804C/T 0.36 0.32 0.332 rs461898 63661 178758911A/G 0.28 0.31 0.423 rs389558 64093 178759343A/G 0.20 0.23 0.311 rs466752 64153 178759403C/T 0.36 0.35 0.781 rs455655 64409 178759659C/G NA 0.72 NA

rs463435 64544 178759794C/T 0.72 0.68 0.230 rs217497165257 178760507C/T 0.56 0.51 0.142 rs197997965626 178760876A/G 0.05 0.05 0.993 rs411804 65739 178760989A/G 0.80 0.77 0.343 rs162388566392 178761642C/T 0.84 0.84 0.819 rs164381166720 178761970C/T 0.22 0.23 0.847 rs434430 69177 178764427A/T

rs187538 69336 178764586G/T

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in PositionAllele Case Control Value SEQ ID AF AF
NO: 6 rs252067 69636 178764886_ 0.21 0.24 0.369 A/G

rs459319 69823 178765073A/G 0.18 0.15 0.353 rs467289 69928 178765178C/T 0.27 0.22 0.179 rs462644 70547 178765797C/T 0.60 0.61 0.609 rs458752 70633 178765883C/T 0.18 0.15 0.271 rs708320 71805 178767055A/C

rs457954 72181 178767431C/G 0.72 0.72 0.882 rs241181072200 178767450C/T 0.29 0.30 0.630 rs308468772474 178767724-/AT 0.13 0.11 0.509 rs6 9638 72567 178767817ClG 0.54 0.57 0.440 rs455452 72973 178768223A/G 0.60 0.58 0.499 rs464850 73468 178768718A/G 0.10 0.09 0.839 rs431472 73889 178769139A/G 0.35 0.27 0.025 rs241180975730 178770980C/T

rs245709475970 178771220A/G 0.71 0.70 0.792 rs245709576114 178771364A/G 0.75 0.76 0.602 rs226174076342 178771592C/T 0.36 0.36 0.924 rs11 0918076449 178771699A/G

rs110917976465 178771715C/T

rs110917876791 178772041A/C 0.45 0.42 0.420 rs456909 78042 178773292A/G 0.53 0.51 0.598 rs469124 80758 178776008A/G

rs468039 80778 178776028C/T

rs467017 81356 178776606A/C 0.34 0.35 0.762 rs469290 81576 178776826A/G 0.49 0.44 0.223 rs469090 81689 178776939C/T 0.83 0.84 0.883 rs469568 81759 178777009G/T 0.36 0.30 0.115 rs468386 81950 178777200C/G

rs469349 82562 178777812A/C

rs469099 83591 178778841C/T 0.65 0.67 0.560 rs456868 83700 178778950A/G

rs465389 83821 178779071C/G

rs463892 83842 178779092C/G

rs468548 83923 178779173G/T

rs654612 83929 178779179A/C

rs468542 84021 178779271C/G

rs469262 84175 178779425C/T 0.45 0.43 0.762 rs708323 84417 178779667A/G 0.74 0.74 0.899 rs469089 84747 178779997C/G

rs469396 85746 178780996C/G 0.39 0.42 0.569 rs468723 86129 178781379C/T 0.36 0.34 0.573 rs467604 86335 178781585A/G 0.35 0.36 0.763 rs338874 87315 178782565C/G 0.42 0.40 0.564 rs338875 87648 178782898A/G 0.46 0.45 0.701 rs138580387764 178783014A/C

rs138580487770 178783020C/G

rs338876 88221 178783471C/T 0.41 0.44 0.580 rs189803 90474 178785724A/C

rs452215 91148 178786398G/T

rs641170 91150 178786400G/T

rs584398 91160 178786410G/T

rs385330 91733 178786983C/T

rs429538 91772 178787022A/C

rs371229 91785 178787035C/T

rs460874 93140 178788390A/T 0.73 0.75 0.550 rs646121 93148 178788398A/T 0.93 0.92 0.697 rs468262 96080 178791330A/G

rs467863 96157 178791407C/G

rs191434 96313 178791563A/C

rs205478296759 178792009C/T 0.43 0.40 0.473 rs468499 97026 178792276A/C

rs180287 97320 178792570C/G

rs338877 97732 178792982A/T 0.04 0.04 0.928 rs6 5066598713 178793963C/G

dbSNP Position ChromosomeAl/A2 ~ F F A2 F p-rs# in Pos Allele A2 Control Value SEQ ID itio Case AF
NO: 6 n AF

rs 19341999707 _ A/C
_ rs 18028899959 178795209C/G

rs186834 100009 178795259A/G

rs189266 100020 178795270C/G

rs 189267100065 178795315A/C

rs170937 100086 178795336C/G

rs463263 101270 178796520C/G

rs463262 101276 178796526G/T

rs460454 101371 178796621C/T

rs460455 101376 178796626C/G

rs460505 101439 178796689C/T

rs 931316101820 178797070C/T

rs463431 102392 178797642C/G

rs461542 102602 178797852A/G

rs463557 102604 178797854A/C

rs 191453102896 178798146C/T 0.06 0.06 0.929 rs2271212189104 178884354C/T 0.66 0.56 0.012 rs462009 189134 178884384C/T

rs2271211189205 178884455A/G

rs396474 Not ma Not ma A/C
ed ed rs428901 Not ma Not ma A/T 0.61 0.72 0.002 ed ed rs452300 Not ma Not ma G/T
ed ed rs670256 Not ma Not ma G/T
ed ed [0286] Allelotyping results were considered particularly significant with a calculated p-value of less than or equal to 0.05 for allelotype results. These values are indicated in bold. The allelotyping p-values were plotted in Figure lE for the discovery cohort. The position of each SNP on the chromosome is presented on the x-axis. The y-axis gives the negative logarithm (base 10) of the p-value comparing the estimated allele in the case group to that of the control group. The minor allele frequency of the control group for each SNP designated by an X or other symbol on the graphs in Figure lE can be determined by consulting Table 35. For example, the left-most ~ on the left graph is at position 17 8695460. By proceeding down the Table from top to bottom and across the graphs from left to right the allele frequency associated with each symbol shown can be determined.
[0287] To aid the interpretation, multiple lines have been added to the graph.
The broken horizontal lines are drawn at two common significance levels, 0.05 and 0.01.
The vertical broken lines are drawn every 20kb to assist in the interpretation of distances between SNPs. Two other lines are drawn to expose linear trends in the association of SNPs to the disease. The generally bottom-most curve is a nonlinear smoother through the data points on the graph using a local polynomial regression method (W.S. Cleveland, E. Grosse and W.M. Shyu (1992) Local regression models. Chapter 8 of Statistical Models in S eds J.M. Chambers and T.J. Hastie, Wadsworth &
Brooks/Cole.). The black line provides a local test for excess statistical significance to identify regions of association. This was created by use of a lOkb sliding window with lkb step sizes. Within each window, a chi-square goodness of fit test was applied to compare the proportion of SNPs that were significant at a test wise level of 0.01, to the proportion that would be expected by chance alone (0.05 for the methods used here). Resulting p-values that were less than 10-$ were truncated at that value.

[0288] Finally, the exons and introns of the genes in the covered region are plotted below each graph at the appropriate chromosomal positions. The gene boundary is indicated by the broken horizontal line. The exon positions are shown as thick, unbroken bars. An arrow is place at the 3' end of each gene to show the direction of transcription.
Example 9 BVES Proximal SNPs [0289] It was discovered that rs 1018810, an intronic SNP in the BYES gene, is associated with occurrence of osteoarthritis in subjects. BYES was identified as a blood vessel epicardial substance.
Sequence analysis predicted 3 transmembrane helices with an extracellular C
terminus. Northern blot analysis revealed that expression of an approximately 5.5-kb BYES transcript is restricted to skeletal muscle and adult and fetal heart. BYES is highly expressed in osteoarthritic cartilage according to EST
database analysis, and may play a role in chondrocyte and/or bone cell development. BYES biological activity may be modulated by addition of an antibody, a recombinant binding partner, a binding agent, or a recombinant BVES protein or functional fragment thereof.
[0290] One hundred fifty-four additional allelic variants proximal to rs 1018810 were identified and subsequently allelotyped in osteoarthritis case and control sample sets as described in Examples 1 and 2. The polymorphic variants are set forth in Table 38. The chromosome positions provided in column four of Table 38 are based on Genome "Build 34" of NCBI's GenBank.

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs24000806 241 105557091 A/G

rs69302096 801 105557651 A/G

rs221628 6 899 105557749 A/G

rs221629 6 2091 105558941 C/G

rs221630 6 2290 105559140 C/T

rs221631 6 2440 105559290 A/G

rs11492846 4959 105561809 G/T

rs221633 6 7914 105564764 C/G

rs423366 6 7969 105564819 A/G

rs436460 6 7972 105564822 C/T

rs22110106 10831 105567681 C/T

rs379908 6 12399 105569249 C/T

rs11492856 13841 105570691 C/T

rs73411946 14461 105571311 C/T

rs715153 6 14680 105571530 C/T

rs221634 6 16808 105573658 A/T

rs77573076 18231 105575081 C/T

rs221fi356 18394 105575244 C/T

rs41454186 18505 105575355 G/T

rs221636 6 18684 105575534 A/T

rs31859586 19257 105576107 C/T

rs49466546 20263 105577113 A/T

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs2216376 20656 105577506 A/C

rs2216386 21499 105578349 A/G

rs2216396 21563 105578413 AIC

rs6435456 21612 105578462 C/G

rs2216406 21834 105578684 C/T

rs39576966 22406 105579256 A/T

rs39955546 22408 105579258 A/T

rs74535026 22685 105579535 A/T

rs11904716 23303 105580153 C/T

rs2216416 23306 105580156 C/G

rs2216426 25139 105581989 A/G

rs11904726 25211 105582061 C/T

rs11904736 25364 105582214 A/G

rs1864046 25381 105582231 A/C

rs2216436 25414 105582264 A/T

rs2216446 25835 105582685 C/T

rs12034756 26214 105583064 A/G

rs2216456 27224 105584074 A/G

rs1702776 27526 105584376 A/G

rs2216466 27934 105584784 C/T

rs2216476 28550 105585400 C/T

rs2216486 29015 105585865 A/G

rs2216496 29879 105586729 G/T

rs2216506 29979 105586829 A/G

rs11492876 30030 105586880 A/G

rs2216516 30585 105587435 C/T

rs77625916 31753 105588603 C/G

rs77485556 31934 105588784 C/T

rs58788336 33227 105590077 -/T

rs58788346 33228 105590078 -/T

rs2216526 35172 105592022 C/T

rs2216536 36901 105593751 A/G

rs2216546 36921 105593771 A/G

rs2216556 36932 105593782 A/G

rs2216566 37061 105593911 C/T

rs2216576 37570 105594420 C/T

rs2216586 38745 105595595 G/T

rs1100656 38970 105595820 A/T

rs2216596 39725 105596575 C/T

rs2216606 40070 105596920 A/C

rs77428216 40460 105597310 C/G

rs2216626 41470 105598320 A/G

rs77484266 41562 105598412 A/G

rs69114946 41956 105598806 A/G

rs69398466 42047 105598897 A/T

rs3684716 42280 105599130 A/G

rs4301906 42358 105599208 A/G

rs4551146 42629 105599479 C/G

rs4059566 43075 105599925 C/T

rs58788356 43387 105600237 -/A

rs14738146 43393 105600243 G/T

rs4232726 43438 105600288 C/T

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO: 7 rs4138066 441 15 105600965 A/G

rs49466556 44537 105601387 A/G

rs69156326 45642 105602492 A/G

rs20957236 46629 105603479 A/G

rs74500786 47496 105604346 A/G

rs74530716 47515 105604365 A/C

rs90188906 48329 105605179 A/G

rs74509446 48862 105605712 C/G

rs77486576 48908 105605758 A/G

rs10131376 49038 105605888 C/T

rs58788366 49080 105605930 -/T

rs19814806 50204 105607054 A/T

rs19814796 50404 105607254 A/G

rs30351876 50426 105607276 -/TTA

rs74539936 50531 105607381 C/T

rs20011196 50 840 105607690 C/T

rs20011186 50964 105607814 C/T

rs20011176 50971 105607821 C/T

rs69404336 51 378 105608228 C/T

rs13187466 52610 105609460 A/C

rs7630996 53906 105610756 A/T

rs58788376 53951 105610801 -/C

rs9647316 54111 105610961 A/C

rs9647306 54149 105610999 G/T

rs69218696 555f>3 105612413 C/G

rs39450296 55999 105612849 C/T

rs49457156 58415 105615265 C/G

rs77752526 58 961 105615811 C/G

rs77420986 60447 105617297 C/T

rs37572896 61 377 105618227 A/G

rs69054586 61 528 105618378 A/G

rs37572906 61606 105618456 C/G

rs22752896 62 1 40 105618990 A/G

rs49457166 62461 105619311 C/T

rs69226386 63 826 105620676 C/T

rs77395726 64950 105621800 G/T

rs69011876 65 076 105621926 G/T

rs49466566 66 1 21 105622971 C/T

rs13380206 66406 105623256 C/T

rs77714726 67 051 105623901 A/C

rs69262606 68 860 105625710 C/T

rs69266276 69 014 105625864 C/T

rs49466576 70 796 105627646 C/T

rs65712186 72325 105629175 G/T

rs74499446 73414 105630264 A/C

rs9521756 75258 105632108 C/G

rs18902286 76 347 105633197 A/G

rs19332376 76 839 105633689 A/C

rs13380196 77 358 105634208 A/G

rs74531276 77 822 105634672 A/G

rs73815516 77 946 105634796 G/T

rs6571219I - ~ _ $0002 ~ 105636852 dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs65712206 80024 1 05636874 A/G

rs21850176 80285 1 05637135 A/G

rs15917206 80397 1 05637247 C/G

rs69250466 82075 1 05638925 C/T

rs69404236 82153 1 05639003 A/G

rs11902746 83981 1 05640831 A/G

rs11902766 84184 1 05641034 A/G

rs15917196 85089 1 05641939 C/T

rs19332366 85288 1 05642138 A/G

rs69052026 85330 1 05642180 C/T

rs12091506 85581 1 05642431 A/T

rs11902776 85642 1 05642492 A/G

rs69262786 86433 1 05643283 A/G

rs11902786 86904 1 05643754 A/G

rs46264636 88391 1 05645241 A/G

rs69246206 89042 105645892 C/T

rs11902806 90828 1 05647678 G/T

rs45575526 92676 1 05649526 C/T

rs69327116 92881 1 05649731 C/T

rs16861406 94227 1 05651077 G/T

rs11902816 94585 1 05651435 A/G

rs23081626 94616 105651466 -/ATAA

rs11902826 94712 1 05651562 C/G

rs17659076 94738 1 Q5651588 A/G

rs58788386 95253 105652103 -/G

rs11902836 95522 1 05652372 A/G

rs11902846 95869 1 05652719 G/T

rs11902856 97856 1 05654706 C/T

Assay for Verifying and Allelotypin~ SNPs [0291] The methods used to verify and allelotype the 154 proximal SNPs of Table 38 are the same methods described in Examples 1 and 2 herein. The primers and probes used in these assays are provided in Table 39 and Table 40, respectively.

dbSNP Forward Reverse rs# PCR primer PCR primer rs2400080ACGTTGGATGGTGCCCAGCAAGTGATGATAACGTTGGATGACAGAGCAAGACTCCATCTC

rs6930209ACGTTGGATGGCTCTGTGGTGCATATTTACACGTTGGATGGGTTCTCTCACTTAACTGTG

rs221628ACGTTGGATGAGTGAGAGAACCAAATGTTGACGTTGGATGCCAGTTTTGGCTTCATTTGC

rs221629ACGTTGGATGTCTGTCCATTTCTCCCTCTGACGTTGGATGGCTGATTCTTGGCAAAAGGC

rs221630ACGTTGGATGTCCTTCTCATTGCTGTGTAGACGTTGGATGTCATGTGCAAGAGCCAAAAG

rs221631ACGTTGGATGCACTGGCCCTCTATAAATGCACGTTGGATGCCAGCCCCCTGCATTATTAT

rs1149284ACGTTGGATGGATGAGAAATTAACTAGACACACGTTGGATGGTCCATTTGGTTTTCATTTG

rs221633ACGTTGGATGCTTAACAATTTGTCTTGGAGACGTTGGATGAGCCACATATACCAAAAAAC

rs423366ACGTTGGATGAGCCACATATACCAAAAAACACGTTGGATGGAGATCTTTGCATGTCAATAC

rs436460ACGTTGGATGAGCCACATATACCAAAAAACACGTTGGATGGAGATCT't-f'GCATGTCAATAC

dbSNP Forward Reverse rs# PCR primer PCR primer rs2211010ACGTTGGATGTTTTTTGAGACAGAGTCTCGACGTTGGATGTTTGCAGTGAGCTGAGATTG

rs379908ACGTTGGATGTGAGTGGGCAAAATGGTTCCACGTTGGATGCTCTCCTGCAGACACATCAA

rs1149285ACGTTGGATGCCAAATACATTTATGACTCCACGTTGGATGGAGAGAGATTCCATCTCAAA

rs7341194ACGTTGGATGCTGTAGAAACCAGCTAAACTGACGTTGGATGCTGACTAGACTCTGACTTTC

rs715153ACGTTGGATGTT'f-f'GTTGAATATTCGCTGCACGTTGGATGCTTCCATATAGAAAGGATTCC

rs221634ACGTTGGATGTGCCCATAACATCTAGAGCCACGTTGGATGTTGGTCCTGTTAGGTTTCGG

rs7757307ACGTTGGATGTGCTTAAGTTGAACAGTGCCACGTTGGATGGCAAAGTCTCCAAACATTTCC

rs221635ACGTTGGATGGGCAGCACAGACAGTAAATGACGTTGGATGTGCAGGTATTCATGCTAGGC

rs4145418ACGTTGGATGTGCATTGCCAGTCTCTTAGCACGTTGGATGGGCCTTCTAGTGAAGACTAG

rs221636 rs3185958ACGTTGGATGGACACAGATCATACAACCACACGTTGGATGAGCATCAAACTCTGTCTTAC

rs4946654ACGTTGGATGATGTAGTCAGAAGAGTGGTCACGTTGGATGGGTACTGATAAAATTTGCCC

rs221637ACGTTGGATGCAATCGTAGCTTACTGTGGGACGTTGGATGCTGTAGTCCAGCTACTCAAG

rs221638ACGTTGGATGCACACCTGGCTGAAAATCTTAACGTTGGATGTGGTTATTTCTAGGCGATGG

rs221639ACGTTGGATGCCCGCATGTGTATGTATCTCACGTTGGATGCCCATCGCCTAGAAATAACC

rs643545ACGTTGGATGAAAATCACCCGCATGTGTATACGTTGGATGCGCCTAGAAATAACCATTAGC

rs221640ACGTTGGATGTAATCCCAGCACTTTGGGAGACGTTGGATGTTTCACCATGTTAGCCAGGC

rs3957696ACGTTGGATGAACCAGTATGTTGCCCTTTCACGTTGGATGCCAGGCAGTCCAAATTAATTC

rs3995554ACGTTGGATGAACCAGTATGTTGCCCTTTCACGTTGGATGCCAGGCAGTCCAAATTAATTC

rs7453502ACGTTGGATGCTCCAAGGTTGGAGTTTGTGACGTTGGATGT'rfCTGAGCTCCTCAGCATC

rs1190471ACGTTGGATGATATGTGGCCCGATGATCTCACGTTGGATGCCTCCCAAAGTGCTAGGATT

rs221641ACGTTGGATGCCTCCCAAAGTGCTAGGATTACGTTGGATGATATGTGGCCCGATGATCTC

rs221642ACGTTGGATGTCTTCCACCATGATTGTGAGACGTTGGATGAGACATACCTGAGACTGGAC

rs1190472ACGTTGGATGTGTCCAGTCTCAGGTATGTCACGTTGGATGGCCCAGCTAAGGTTTTGTAG

rs1190473ACGTTGGATGTTGATCACACCACTGCACTCACGTTGGATGCCCCAATGAAGAAGTCTTGC

rs186404ACGTTGGATGTTGATCACACCACTGCACTCACGTTGGATGCCCCAATGAAGAAGTCTTGC

rs221643ACGTTGGATGCCCCAATGAAGAAGTCTTGCACGTTGGATGGAGACACAGTGAGACTGTCA

rs221644ACGTTGGATGGTGTCTTTCCTAGCTAGCTCACGTTGGATGTTACAGATGGGTTCAGGGAG

rs1203475ACGTTGGATGTAATCCCAGCTACTTGGGAGACGTTGGATGACAATCTCGGCTCACTGCAA

rs221645ACGTTGGATGTGTTTTTCATCTGCCCAATGACGTTGGATGGCTGCTGTTAAGGACCACAT

rs170277ACGTTGGATGACAAGGAAGTTCTGAACCTCACGTTGGATGTTTTGGATCAAGAGGTGACC

rs221646ACGTTGGATGAATTGGCTCTTCTCTCTGCCACGTTGGATGTTACAGCAGAAATGGCTGGA

rs221647ACGTTGGATGTTCCCAGCTCCTTTCCTTAGACGTTGGATGTTCCTAAGAAAATGCCCCTC

rs221648ACGTTGGATGATCATGCCACTGCACTCCAGACGTTGGATGTTAGGTCTCCAGGACGACAG

rs221649ACGTTGGATGGACAGGATGAAGAAGAAGGCACGTTGGATGTCTTGCTATTCGCCAAGGAC

rs221650ACGTTGGATGTAATATCCAGGATCCAGCTGACGTTGGATGTTGAACCCCTGAACTCAAGC

rs1149287ACGTTGGATGATGGAGGTCTCACCATGTTCACGTTGGATGTAGCACTTTGGGAGGCCAAG

rs221651ACGTTGGATGGGAGGATCACTTGAATCCAGACGTTGGATGAGACAGGTTCTTGCTCTGTT

rs7762591ACGTTGGATGATCTCTGCTCAC'rGCAGCTTACGTTGGATGAAATTAGCCAGGTGTGGTGG

rs7748555ACGTTGGATGTTGGGATTACAGGTGTGAGCACGTTGGATGCCCACTGCTTCACTTGACTA

rs5878833ACGTTGGATGACACTGTCTACACTGCCTTCACGTTGGATGACCTGACTTCAAAGGTCCTG

rs5878834ACGTTGGATGACACTGTCTACACTGCCTTCACGTTGGATGACCTGACTTCAAAGGTCCTG

rs221652ACGTTGGATGTACTTTCTACTCAGGGAAGGACGTTGGATGAGTTTACACGCGCATAAGAC

rs221653ACGTTGGATGGTTTCACTGTGTTAGCCAGGACGTTGGATGTAATCCCAGCACTCTGGGAG

rs221654ACGTTGGATGGAGATCAAGACCATCCTGGCACGTTGGATGAGTAGCTGGGACTACAGGCA

rs221655ACGTTGGATGGTCAGGAGATCAAGACCATCACGTTGGATGCCGCGCCCAGCTAATTTTTT

rs221656ACGTTGGATGAGATGGAGTTTCACTCTGTCACGTTGGATGAATCCAGGAGGTGGAGTTTG

rs221657ACGTTGGATGAGAACTCTTCCATCCTTGAC~1CGTTGGATGTTCTGCTTTAGTGCATCCAG

rs221658ACGTTGGATGCCAGCTGAGTTCAGCATTTGACGTTGGATGACACCCATATCTTCGCTACC

rs110065ACGTTGGATGTGACATGCTCATAGCCCTTGACGTTGGATGAGATCAGCTGTCATTCACTG

rs221659ACGTTGGATGCGAAACACAACCTCTACTTCACGTTGGATGCAGGTAAGGAAATTAAGGCAC

rs221660ACGTTGGATGAATATGATGGAAACCAGGGCACGTTGGATGTCTTAGCTCTCTTGAGTGTG

dbSNP Forward Reverse rs# PCR primer PCR primer rs7742821ACGTTGGATGAGCTCTTGGGAAGTTCTCACACGTTGGATGCCCAACTCTCTCACCTATAC

rs221662ACGTTGGATGGACAATGGGTTAAATGTTGGGACGTTGGATGAAGTGCTTTGAGTTTCTGAG

rs7748426ACGTTGGATGATTCACCCTCACCACATCTGACGTTGGATGCCACCCCTCTCTGTTTTCTT

rs6911494ACGTTGGATGTCAATGGTACAGAAGGCCAGACGTTGGATGAACCCCTCGCTTGGAATTAG

rs6939846ACGTTGGATGTCCTCAAAGCTGGGCTTTCTACGTTGGATGAGACAAAAGGATCACCTGCC

rs368471ACGTTGGATGCCCCTAATACATCCAAAACCACGTTGGATGACCAGGCAAACCTGTAGAAG

rs430190ACGTTGGATGTCTCTGGAAGATAGTTGGGCACGTTGGATGACTTCTACAGG'tTtGCCTGG

rs455114ACGTTGGATGCCCAGAAAATTGATTCTTAGACGTTGGATGACAGAAGTCTTTTCCTGATC

rs405956ACGTTGGATGAAACTCCAAGTCAAGGACCCACGTTGGATGAAAGGTGTCCACTGTTTCGC

rs5878835ACGTTGGATGCTGTCTTCCAGAGTCTTGAGACGTTGGATGTACATCCACTATGTACCCAC

rs1473814ACGTTGGATGGTTAAAGAACCACAGAAGGCACGTTGGATGTACATCCACTATGTACCCAC

rs423272ACGTTGGATGCACAGAAGGCCTTAAAAACCACGTTGGATGTCACGTTGCATTCCTGTATC

rs413806ACGTTGGATGCTGACAGATTTCACATCGTGACGTTGGATGGTTCCAGAGGATGAACAAAC

rs4946655ACGTTGGATGCTAAAGAGTAGCTTTGGCTTGACGTTGGATGTTTTGTACGCTTTGCCTGAG

rs6915632ACGTTGGATGGTCGTGATCTTGACTCACTGACGTTGGATGGCCTGTAATCCCAGTTACTC

rs2095723ACGTTGGATGTGTGCTCTCTCATGCCAGTAACGTTGGATGCTGTATAAAATACCTTCAGG

rs7450078ACGTTGGATGGCCATCACCTCCAGATAATTACGTTGGATGAAGGCAGGAGGATCTCTTGA

rs7453071ACGTTGGATGAATCCCAGCACT'(-fGGGAGGACGTTGGATGTATGTTGCCCAGGCTCGTCT

rs1018810ACGTTGGATGTGCTGCTCCCATTTCTCATGACGTTGGATGAAGGAGTAGAGACCTTGCTG

rs7450944ACGTTGGATGATTCAGCCACTACACCTCAGACGTTGGATGGTTGTTCTACAGGACAAACC

rs7748657ACGTTGGATGAGAGAGAGATGGAAAGGGAGACGTTGGATGTCGAATCACGATCTGAACAG

rs1013137ACGTTGGATGATTACAAGCAGTGTCACTCCACGTTGGATGGGGTTAATGAATAGGTGGAAC

rs5878836ACGTTGGATGTTTGGTATGGAGTGACACTGACGTTGGAT~CCAATGATAATCTCCAGTGTC

rs1981480ACGTTGGATGCGACTGTCTTCCTTCTGCAGACGTTGGATGTGCTGCACTTCCCTACTCTT

rs1981479ACGTTGGATGTGAGTAGCTAGAACTACAGGACGTTGGATGATCACTGCAGCCTTAAACTC

rs3035187ACGTTGGATGTGAGTAGCTAGAACTACAGGACGTTGGATGATCACTGCAGCCTTAAACTC

rs7453993ACGTTGGATGTGACAAAGTGAGACCAACTCACGTTGGATGTGGGAGATCACCTTTCATAC

rs2001119ACGTTGGATGGCTTCTTTAGGTCTTCATTTCACGTTGGATGTGAGTTTGTGTTAAAAGCTC

rs2001118ACGTTGGATGGGTCCAGCCAAAAAACAACCACGTTGGATGAGGCTGGAATTTACAAGGCC

rs2001117ACGTTGGATGGTCCAGCCAAAAAACAACCCACGTTGGATGAGGCTGGAATTTACAAGGCC

rs6940433ACGTTGGATGTTGTGAGCTACCTCATTCACACGTTGGATGCAACATCTGGGTTATTTGTG

rs1318746ACGTTGGATGTAAGCTGGTGCTTATTTCAGACGTTGGATGGGTGGCCAATAAACATAAGC

rs763099ACGTTGGATGGAGGCAAGTTGTGAAAGACCACGTTGGATGGGCCCTTGAAGTTTTCTCAG

rs5878837ACGTTGGATGTCACCAGCCGTATTCATCAGACGTTGGATGTGAAAGACCTTCTGCCCATC

rs964731ACGTTGGATGGGAAATCATACCCCCTTTCCACGTTGGATGTGAGGGATACTTGAGCTCTG

rs964730ACGTTGGATGCACTCTGGCAAAGGGATTTAACGTTGGATGGTAGGAAAGCAGAAAGGTAC

rs6921869ACGTTGGATGTAGTAGAGACAGGGTTTCACACGTTGGATGTACTTGGGAGGCTAAGATGG

rs3945029ACGTTGGATGCTCTTCCTGTAAATCTTGCCACGTTGGATGAGAGAAAGGCTGAACACATG

rs4945715ACGTTGGATGCTCAAGGGACAGTCATTGAGACGTTGGATGGTCAGGGTGCTCATGAATTG

rs7775252ACGTTGGATGGACTAGGGATTGGATTTTGGACGTTGGA'f-GTTTCTTCATCCAGCTATGGC

rs7742098ACGTTGGATGGAAGAAAACCAGAAAACTGGCACGTTGGAT-GAAGAACTTCGTTCTTTCCCC

rs3757289ACGTTGGATGGCGATTTTATTTTGTAGTACAGACGTTGGATGAATACTTGTGCCTCAAGAAG

rs6905458ACGTTGGATGAGGAATATCAGCCT'ITT'GGGACGTTGGATGGCTCTTCTAACAGAAGTGACC

rs3757290ACGTTGGATGTAACAATGCCAGCACAACAGACGTTGGAT'GTGCTCCAGAGTTAAT1-t'GTC

rs2275289ACGTTGGATGTTGAAAAGGAACTCAGTGGCACGTTGGAT'GGTCCAGTTAGTCTTCTGAAC

rs4945716ACGTTGGATGTAGAGCCTCACTGTGTTACCACGTTGGATGAATTCTGGCACTTTGGGAGG

rs6922638ACGTTGGATGGCTTAGTGTCTGTGCTTTTGACGTTGGA'I-GCCTGCTGTTTCATTTTGAGG

rs7739572ACGTTGGATGGTTTTAAGAGACATTGGGTGACGTTGGAT-GTCTATTTGGACCATGCATTC

rs6901187ACGTTGGATGTCAGCACAGACCCTTAAATGACGTTGGAT-GGGCTTTTTTTCTCACCCACC

rs4946656ACGTTGGATGTGGCCCAGACGATATAAAGGACGTTGGATGATTAAGCTCCCCACTTAGGC

rs1338020ACGTTGGATGTCTGTGGTCAACAACAGTCCACGTTGGATGCATCTCAGGCAGGATATAGC

r rs7771472ACGTTGGATGTTACCTGAAGGTGAATCTAG~ ACGTTGGAT-GGTACAAACCTTTTGGAAAAC;
l dbSNP Forward Reverse rs# PCR primer PCR primer rs6926260ACGTTGGATGTACCACAGTGCTGGGATTACACGTTGGATGCGTAGAGTAGTGCATTGTGC

rs6926627ACGTTGGATGAGGTGTGCACCCATTATCCAACGTTGGATGGGATACTATACCCATTTACTC

rs4946657ACGTTGGATGCCAGGTAGAATTATTATGGGACGTTGGATGCCACCATTAAATCACTGTATC

rs6571218ACGTTGGATGCGCACGACACCTTATTAAAGACGTTGGATGTTCGACAATAGGTAACTGGC

rs7449944ACGTTGGATGAACTTTGTCGGCCCTGGCGGACGTTGGATGCCAGCGAGGAGGGACAGAG

rs952175ACGTTGGATGATGCTCTGCCAGCCTTTTTTACGTTGGATGTCAAAACAGCTGGTAGGGAC

rs1890228ACGTTGGATGTTAAGGCATTCCCATATCCTACGTTGGATGCCCAGATGTATGAATAGTAGC

rs1933237ACGTTGGATGGGGTTCAAGCAATTCCTGTCACGTTGGATGCAAAAATTAGCCCGGTGTGG

rs1338019ACGTTGGATGTATGTGTGTCACAAAGGGAGACGTTGGATGCCTGCAGAATCTACAACATG

rs7453127ACGTTGGATGCATCACCTCAGATAGTTACCACGTTGGATGGTGACTCCAGTTAGCTATAC

rs7381551ACGTTGGATGAGTTTGTACCCTTTGACCACACGTTGGATGGTTGA,ACTCACAGAAACAGAG

rs6571219ACGTTGGATGGACAGTACTGAAAGTCTTCGACGTTGGATGCTTCT'fCCTATCTGATTTGG

rs6571220ACGTTGGATGTCCTATCTGATTTGGAAGGCACGTTGGATGAACAAGACGAGAGTGTCTTG

rs2185017ACGTTGGATGATGTGGGAAGATCACTTGAGACGTTGGATGAGCCCGCTAATTGTCATAT

rs1591720ACGTTGGATGTTGGAATTACAGGTGTGAGCACGTTGGATGACAAGCCCACAGCTAACATC

rs6925046ACGTTGGATGGCTTGCTTTTTGAGACAGGGACGTTGGATGTAGAGGCTGTAGTGAGCTGT

rs6940423ACGTTGGATGGTGCTGGGATTACAGATGTGACGTTGGATGCCCTGTCTCAAAAAGCAAGC

rs1190274ACGTTGGATGCATTTAGTCTCTGAGGACAACACGTTGGATGCCTTT-CTAACCACTAAATACC

rs1190276ACGTTGGATGCTGTAATCCCAGCACTTTGGACGTTGGATGTAGTAGAGACTGGCTTTCAC

rs1591719ACGTTGGATGCTCACACATTCCCCTGAAAGACGTTGGATGCTGTCAGAAACTGCTCTGTC

rs1933236ACGTTGGATGCCAAGTCATTTGAAACCTTCACGTTGGATGTAAGCTCAGAAAATGGCATC

rs6905202ACGTTGGATGGTATTACAGTGTGAATCAGGACGTTGGATGCCCATTCAACATCAATTTTC

rs1209150ACGTTGGATGTCCTCCAGAAACTTTTGACCACGTTGGATGGGCCTTTATTACTTGCTACC

rs1190277ACGTTGGATGATCATGTGCTAAGCACCACGACGTTGGATGCCCTCCAGGTCAAAAGTTTC

rs6926278ACGTTGGATGTAGAACTCCCAGGCTCAAGAACGTTGGATGTATTAGCTGGGTGTAGTGGC

rs1190278ACGTTGGATGAGATACTGAGAAGGGTAGTCACGTTGGATGGTGCTACTGAATACTAGATC

rs4626463ACGTTGGATGAGAAATTGCCAACCAGCCTCACGTTGGATGGGTCCAGAAGCAAGACAAAG

rs6924620ACGTTGGATGAGAACAATGCCTGGCACATGACGTTGGATGTGACAGAGTGAGACTCTGTC

rs1190280ACGTTGGATGTAGAAAGTGCCATCCAATGCACGTTGGATGACAAACTAGGCAGACAGTAC

rs4557552ACGTTGGATGCGTCCTTTACATAACCCCAGACGTTGGATGCATTTTCTCGGTGACCTAGG

rs6932711ACGTTGGATGATCACCTGCTCAAGGTCATCACGTTGGATGGATGGTGCATTTGCATGCAG

rs1686140ACGTTGGATGAGAAAGAACCCTAGTTGGAGACGTTGGATGGAACATAGTCTGCATGTGATC

rs1190281ACGTTGGATGCACTTTTTTGCTACAACCTCACGTTGGATGATC'f-CTTGCATTTATTCTAC

rs2308162ACGTTGGATGCACTTnTTGCTACAACCTCCACGTTGGATGGCAT'CAAGTAACTGCACATT

rs1190282ACGTTGGATGTATGTGGACAGTAGCAACCCACGTTGGATGAGAC-TCAGGAGTTGCTTCTC

rs1765907ACGTTGGATGCTTTCTTGAGAAGCAACTCCACGTTGGATGGGGAGAATGAAATTCCACTT

rs5878838ACGTTGGATGCCCTGTCATTCAAGGCATAGACGTTGGATGTTGC'TCAGCATCGCTACATC

rs1190283ACGTTGGATGCCCACTGACCTACAATATATACGTTGGATGGACAGATTGAAGATGGCTAG

rs1190284ACGTTGGATGATCTTTCAAAACTGCCAGACACGTTGGATGGCCAGTGGATTTCAGTTGTT

rs1190285ACGTTGGATGACTTGAGTCACAGACATAGCI ACGTTGGATGGGCTCTTGATTATTTTCTGC

dbSNP Extend T erm rs# Primer Mix rs2400080 TCCTTTACTTTACCTITITfTCCACG

rs6930209 GATTTTTATGCAAATATCAGATGAACT

rs221628 AAGAATAGACATATTTGTAGATCAACT

rs221629 TCTCCCTCTGGCCCAACTG ACT

rs221630 GACAGGTGATGGCTTGGGA ACG
I I

dbSNP Extend Term rs# Primer Mix rs221631 TGTCAAAATGGAAAGATGATTAATACT

rs1149284 CTAGACACATTGTCTGCTAGT ACT

rs221633 AACAATTTGTCTTGGAGATCTTTACT

rs423366 ACCAAAAAACATTTTGCAGATAGACG

rs436460 ATATACCAAAAAACATTTTGCAGAACG

rs2211010 GAGACAGAGTCTCGCTCTGT ACG

rs379908 TGGATAACACAGTGCATACCA ACG

rs1149285 ATTTATGAAGCACAAAGAACAACACT

rs7341194 ACTGGAAAAATTTTTTTCCTTTGTACT

rs715153 GCCCTCTAGTGGGCTTAATG ACT

rs221634 GCCAGGATGACCCCAAAATA CGT

rs7757307 CCCATAATTCTTTAAACTAAATACACT

rs221635 ACAGTAAATGAAGGACATTGGC ACG

rs4145418 TAGCCCTGTAAGCTGATC CGT

rs221636 rs3185958 CCACATCTTAAAGAGGCTGTT ACT

rs4946654 GCCTATTGAAGAAATCATTTTAGACGT

rs221637 ACTTGAGCGATCCTCCCAC CGT

rs221638 CCTGGCTGAAAATCTTAAAAAAAACT

rs221639 GTGTGTGTGTGTGTGTAACCA ACT

rs643545 CACCCGCATGTGTATGTATCT ACT

rs221640 TCGTCTGAAGTCAGGAGTTC ACT

rs3957696 TCTCTCTCTCTCTCTCTCAC CGT

rs3995554 TCTCTCTCTCTCTCTCACAC CGT

rs7453502 GAGTTTGTGTTTTAAAGAACTTTTCGT

rs1190471 AAGAGTGATAAATGACCAGGC ACT

rs221641 GAGATGTGAGCCACTGCGC ACT

rs221642 CCAACCATGTGGAACTGTGA ACT

rs1190472 TTATCAACAGCATGAAAACGGA ACG

rs1190473 CTGCACTCCAGCCCGGGA ACT

rs186404 GGAGACACAGTGAGACTGTC CGT

rs221643 AATGAAGAAGTCTTGCATTTCTTCGT

rs221644 CTAGCTCCAAGCCAGGTTAT ACT

rs1203475 GCAGGAGAATCGCTTGAACC ACG

rs221645 CAGACCTCAAAGTGGTCAAGA ACT

rs170277 GACCCTTGCTAGCACTCAGA ACG

rs221646 CAGGCAAACAGGTCCAGAG ACG

rs221647 AGCTCCTTTCCTTAGGTTATC ACT

rs221648 GGCAACGGAGTGAGACCC ACG

rs221649 AAGAAGAAGGCTGGGAGAAC ACT

rs221650 GGCACAGTGGCTCACACTT ACT

rs1149287 TCCCAGGCTGGTCTTGAAC ACG

rs221651 AGCTGCAATGAGCTGTGATCG ACG

rs7762591 CTTCCGTCTCCTGAGTTCCA ACT

rs7748555 CAGGTGTGAGCCACCATGC ACG

rs5878833 GCCTTCTGGCCA~ ACG

rs5878834 GCCTTCTGGCCATTTTTTTTTT ACG

rs221652 TACTCAGGGAAGGATGTTACA ACG

rs221653 I TGTGTTAGCCAGGATGGTCT ACG

dbSNP Extend Term rs# Primer Mix rs221654 AAGACCATCCTGGCTAACAC ACT

rs221655 GCTAACACGGTGAAACCCC ACT

rs221656 CAGGCTGGAGTGTAGTGGC ACT

rs221657 CACTTCCTCCCTCCGACTC ACG

rs221658 TCAGCATTTGTGGGCTGCC ACT

rs110065 CTCCTTGCTGGTTGTGGCA CGT

rs221659 ATGAATTCTATCTGTGCGACC ACG

rs221660 GGAAACCAGGGCTTTTTTTTTTACT

rs7742821 ATTTCCATTTGTGTTGAGTCCTACT

rs221662 GAAATAAAAAGGAATCACACCCACT

rs7748426 CACATCTGTACTATTATTTCTACTACT

rs6911494 AGGCCAGGCTAACTGGGG ACG

rs6939846 GTGGCCATGACAGTTGCAG CGT

rs368471 TTATATTTCAAGGGAATGCTCTTACT

rs430190 GCCTCTGGGCAAATTTCTGA ACG

rs455114 TTTTTACAGTTGGGAGGCAGA ACT

rs405956 AAGACTGGGACAGCAGCGA ACT

rs5878835 GAACCACAGAAGGCCTTAAAAACGT

rs1473814 GAACCACAGAAGGCCTTAAAAACGT

rs423272 GTGGGTACATAGTGGATGTAT ACT

rs413806 ACAGATTTCACATCGTGGTACTCACG

rs4946655 GTAGCTTTGGCTTGTGCACC ACT

rs6915632 CTTGACTCACTGCAACCTCA ACT

rs2095723 TCTGTCCTCACACAGCATTTT ACG

rs7450078 CGCTATGTTGCCCAGGCTC ACT

rs7453071 CCAAGGCAGGAGGATCTCT ACT

rs1018810 CTGCTTTTATACATGCCACAC ACT

rs7450944 GGGCTCCCTTTCCATCTCT ACT

rs7748657 GTAGTGGCTGAATGCGATGT ACT

rs1013137 CACTCCATACCAAATTAAATATACACG

rs5878836 GTGACACTGCTTGTAATTCTG CGT

rs1981480 TACAATGGCAGTGACCCAGA CGT

rs1981479 CTACAGGCCTGCACCACGA ACG

rs3035187 ATGCCTGGCATTTTTTTTTT1T1-1'CGT

rs7453993 GTGAGACCAACTCCCATCC ACG

rs2001119 CTTACAAAAGCTTCTGTGCCATACT

rs2001118 CAGCCAAAAAACAACCCTAAAAACT

rs2001117 AAAAACAACCCTAAAAAGGAAGAACT

rs6940433 TGCCAAGAGGCACATTTTCC ACT

rs1318746 AGGCTACTAAGTATATTTGATTTTACT

rs763099 AAAGACCTTCTGCCCATCCA CGT

rs5878837 CGTATTCATCAGCAACAGCC ACT

rs964731 ATACCCCCTTTCCTTCAGTAT ACT

rs964730 TGAGGGATACTTGAGCTCTGT ACT

rs6921869 GTCTCGAGCTCCTGGCCT ACT

rs3945029 ATTAGCAGCCTCCTCCACTA ACT

rs4945715 CTTCTCTTTCCTCCTTTTCATCACT

rs7775252 TTGAGAATTATTCCCGGTAATTAACT

rs7742098 I CCAGAAAACTGGCTTTGCCTTI ACT

dbSNP Extend Term rs# Primer Mix rs3757289 AAAAATTCCACAGAGATGATGG ACT

rs6905458 CCTCTCAGAAGTGTGCCAG ACG

rs3757290 GACTGACTCTCTCCCCAAAA ACT

rs2275289 AGGAACTCAGTGGCATGTAC ACG

rs4945716 CTCACTGTGTTACCCAGGCT ACT

rs6922638 GTGCTTTTGTTTCTTCTCATACTACT

rs7739572 AGACATTGGGTGTTTCTCTTTT ACT

rs6901187 CTGACACATAGCTGCCAGAG ACT

rs4946656 CTGTTGAAGAGCAAAGTTAACA ACG

rs1338020 GCAAGACATTCTGAATAGTGC ACT

rs7771472 GAAGGTGAATCTAGGGAATGAA CGT

rs6926260 GTAAGCCACTGTGTCCAGC ACG

rs6926627 AAGGCAGAGCAGGGTCCC ACT

rs4946657 GTTTCATGTTGTATCTCTCTGT ACT

rs6571218 CCTTATTAAAGAGAGAGAGAGA ACT

rs7449944 GGCGGCAGCTGCTTGTTC ACT

rs952175 CTGGGCGCACTGCAACCT ACT

rs1890228 CCATATCCTGGGCTATGTGT ACG

rs1933237 CTTAGCCTCCAGAGTAGCTG ACT

rs1338019 GTCACAAAGGGAGAACTCAAA ACG

rs7453127 CTACTCTCTTAGCAAATTCAGTTACT

rs7381551 TTCCCACCCTTCAGCCCC ACT

rs6571219 CGCTGGGGCAGAAAAAGAAA ACG

rs6571220 TTCTTTTTCTGCCCCAGCGA ACT

rs2185017 CAACACAGTGAGCAGTGAGA ACG

rs1591720 GTGTGAGCCACCATGCCCA ACT

rs6925046 GACAGGGTCTTGCTCTGTC ACT

rs6940423 GGATTACAGATGTGAGCCAC ACG

rs1190274 GGACAACACTTTTAAAGGTACT ACT

rs1190276 CCAGCACTTTGGGAGGCC ACT

rs1591719 TTGAATCTCTTTTTAGAGTATGGACT

rs1933236 ATTTCCTGATTCACACTGTAATAACG

rs6905202 GAAATTITfCACGTTTTGAAGGTACG

rs1209150 TGACCTGGAGGGAGAAAAAG CGT

rs1190277 GCTAAGCACCACGGAGATAC ACT

rs6926278 CTCCCACCTCAGCCTCCC ACG

rs1190278 GGGTAGTCGGTAAAGGGGA ACG

rs4626463 AGGGACTTTCCACACTAACC ACT

rs6924620 TAAATATTCATTGCATAGAAGGAAACT

rs1190280 ATGCTGCATGTATATTTATGGC ACT

rs4557552 ACCCCAGTACTTCCTCTCC ACG

rs6932711 GTCATCACTCCCGCAGTTCA ACG

rs1686140 CCCTTCCTTTGGAAAACTGG ACT

rs1190281 TTTAAATGTGCAGTTACTTGATGACG

rs2308162 CCTCCAGTGAAAGCAATTATTT CGT

rs1190282 GCTGAGAATACTTGCTGGCT ACT

rs1765907 TGAGAAGCAACTCCTGAGTC ACG

rs5878838 TGCCAATTAGCACTGAAP,AAAGACT

rs1190283 I CTACAAAATTCGTTACTACATACACT

dbSNP Extend Term rs# Primer Mix rs1190284 CAGACGTGGCAGCAGAGTAA ACT

rs1190285 GTCACAGACATAGCCATTTAGAI ACT
I

Genetic Analysis [0292] Allelotyping results from the discovery cohort are shown for cases and controls in Table 41.
The allele frequency for the A2 allele is noted in the fifth and sixth columns for osteoarthritis case pools and control pools, respectively, where "AF" is allele frequency. The allele frequency for the A1 allele can be easily calculated by subtracting the A2 allele frequency from 1 (A1 AF
= 1-A2 AF). For example, the SNP rs1474555 has the following case and control allele frequencies: case Al (C) = 0.64;
case A2 (T) = 0.36; control A1 (C) = 0.70; and control A2 (T) = 0.30, where the nucleotide is provided in paranthesis. Some SNPs are labeled "untyped" because of failed assays.

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position AlleleCase Control Value SEQ ID AF AF
NO: 7 rs2400080241 105557091A/G

rs6930209801 105557651A/G

rs221628899 105557749A/G 0.716 0.755 0.216 rs2216292091 105558941C/G 0.775 0.801 0.338 rs2216302290 105559140C/T 0.066 0.049 0.465 rs2216312440 105559290A/G 0.147 0.137 0.686 rs11492844959 105561809G/T

rs2216337914 105564764C/G 0.094 0.091 0.911 rs4233667969 105564819A/G 0.392 0.418 0.448 rs4364607972 105564822C/T 0.186 0.175 0.720 rs221101010831 105567681C/T

rs37990812399 105569249C/T 0.773 0.809 0.242 rs114928513841 105570691C/T

rs734119414461 105571311C/T

rs71515314680 105571530C/T

rs22163416808 105573658A/T 0.330 0.314 0.630 rs775730718231 105575081C/T

rs22163518394 105575244C/T

rs414541818505 105575355G/T 0.380 0.377 0.929 rs22163618684 105575534A/T 0.807 0.829 0.458 rs318595819257 105576107C/T

rs494665420263 105577113A/T

rs22163720656 105577506A/C 0.879 0.901 0.409 rs22163821499 105578349A/G 0.089 0.072 0.427 rs22163921563 105578413A/C 0.934 0.951 0.537 rs64354521612 105578462C/G 0.824 0.842 0.486 rs22164021834 105578684C/T

rs395769622406 105579256A/T

rs399555422408 105579258A/T

rs745350222685 105579535A/T

rs119047123303 105580153C/T

rs22164123306 105580156C/G 0.070 0.053 0.415 rs22164225139 105581989A/G 0.868 0.869 0.987 rs119047225211 105582061C/T 0.227 0.191 0.244 rs119047325364 105582214A/G 0.722 0.742 0.521 rs18640425381 105582231A/C

rs22164325414 105582264A/T 0.550 0.766 -0.0001 rs22164425835 10_5582685C/T 0.695_ 0.774 0.007 rs1203475~ 26214 ~ 105583064A/G
~

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in PositionAllele Case Control Value SEQ ID AF AF
NO: 7 rs22164527224 105584074A/G 0.066 0.048 0.344 rs17027727526 105584376A/G 0.840 0.882 0.137 rs22164627934 105584784C/T 0.866 0.897 0.244 rs22164728550 105585400C/T 0.844 0.884 0.102 rs22164829015 105585865A/G 0.865 0.891 0.341 rs22164929879 105586729G/T 0.102 0.081 0.359 rs22165029979 105586829A/G 0.856 0.887 0.192 rs114928730030 105586880A/G

rs22165130585 105587435C/T 0.177 un ed NA

rs776259131753 105588603C/G

rs774855531934 105588784C/T 0.670 0.712 0.199 rs587883333227 105590077-/T 0.140 0.113 0.338 rs587883433228 105590078-/T 0.142 0.114 0.309 rs22165235172 105592022C/T 0.172 0.120 0.064 rs22165336901 105593751A/G

rs22165436921 105593771A/G

rs22165536932 105593782A/G

rs22165637061 105593911C/T

rs22165737570 105594420C/T 0.924 0.953 0.218 rs22165838745 105595595G/T 0.043 0.028 0.421 rs11006538970 105595820A/T 0.834 0.894 0.031 rs22165939725 105596575C/T 0.048 0.027 0.347 rs22166040070 105596920A/C 0.841 0.878 0.133 rs774282140460 105597310C/G

rs22166241470 105598320A/G 0.778 0.879 0.0001 rs774842641562 105598412A/G

rs691149441956 105598806A/G 0.043 0.032 0.652 rs693984642047 105598897A/T

rs36847142280 105599130A/G 0.150 0.104 0.074 rs43019042358 105599208A/G 0.053 0.033 0.386 rs45511442629 105599479C/G 0.059 0.027 0.100 rs40595643075 105599925C/T 0.132 0.089 0.063 rs587883543387 105600237-/A

rs147381443393 105600243G/T 0.126 unt ed NA

rs42327243438 105600288C/T 0.023 unt ed NA

rs41380644115 105600965A/G 0.837 0.895 0.037 rs494665544537 105601387A/G 0.062 0.033 0.128 rs691563245642 105602492A/G

rs209572346629 105603479A/G

rs745007847496 105604346A/G 0.261 0.163 0.001 rs745307147515 105604365A/C

rs101881048329 105605179A/G

rs745094448862 105605712C/G

rs774865748908 105605758A/G 0.972 unt ed NA

rs101313749038 105605888C/T 0.699 0.785 0,006 rs587883649080 105605930-/T

rs198148050204 105607054A/T 0.880 0.946 0.012 rs 198147950404 105607254A/G 0.052 0.035 0.453 rs303518750426 105607276-/TTA 0.033 unt ed NA

rs745399350531 105607381C/T 0.170 0.135 0.222 rs200111950840 105607690C/T 0.176 0.122 0.033 rs200111850964 105607814C/T 0.793 0.883 0.001 rs200111750971 105607821C/T 0.575 0.650 0.035 rs694043351378 105608228C/T

rs131874652610 105609460A/C 0.140 0.089 0.171 rs76309953906 105610756A/T 0.865 0.922 0.029 rs587883753951 105610801-/C 0.423 0.463 0.215 rs96473154111 105610961A/C 0.865 0.926 0.089 rs96473054149 105610999G/T 0.903 0.951 0.022 rs692186955563 105612413C/G

rs394502955999 105612849C/T 0.972 0.976 0.820 rs494571558415 105615265C/G 0.057 0.021 0.048 rs777525258961 105615811C/G 0.027 unt ed NA

rs774209860447 105617297C/T

dbSNP Position ChromosomeAl/A2 ~ F A2 F A2 F p-rs# in Position AlleleCase C Value SEQ ID AF ont NO: 7 ro I AF

rs375728961377 105618227A/G _ _ _ rs690545861528 105618378A/G 0.045 0.023 0.345 rs375729061606 105618456C/G

rs227528962140 105618990A/G

rs494571662461 105619311C/T

rs692263863826 105620676C/T 0.086 0.054 0.120 rs773957264950 105621800G/T 0.920 0.931 0.613 rs690118765076 105621926G/T 0.054 0.026 0.122 rs494665666121 105622971C/T

rs133802066406 105623256C/T 0.109 0.077 0.145 rs777147267051 105623901A/C 0.035 unt ed NA

rs692626068860 105625710C/T 0.921 0.952 0.196 rs692662769014 105625864C/T

rs494665770796 105627646C/T 0.224 0.136 0.001 rs657121872325 105629175G/T 0.589 0.677 0.011 rs744994473414 105630264A/C

rs952175 75258 105632108C/G 0.650 0.730 0.007 rs189022876347 105633197A/G 0.046 0.028 0.426 rs193323776839 105633689A/C 0.925 0.953 0.175 rs133801977358 105634208A/G 0.888 0.930 0.101 rs745312777822 105634672A/G 0.415 0.534 0.002 rs738155177946 105634796G/T 0.026 unt ed NA

rs657121980002 105636852A/G 0.837 0.903 0.017 rs657122080024 105636874A/G 0.464 unt ed NA

rs218501780285 105637135A/G 0.066 0.036 0.196 rs159172080397 105637247C/G 0.027 unt ed NA

rs692504682075 105638925C/T

rs694042382153 105639003A/G 0.024 0.029 0.840 rs119027483981 105640831A/G 0.067 0.041 0.183 rs119027684184 105641034A/G

rs159171985089 105641939C/T

rs193323685288 105642138A/G 0.892 0.942 0.046 rs690520285330 105642180C/T 0.888 0.909 0.435 rs120915085581 105642431A/T 0.862 22 .023 0.9 0 rs119027785642 105642492A/G 0.158 _ _ _ _ 0.118 0.098 rs692627886433 105643283p~G __ . _ rs119027886904 105643754A/G 0.211 0.147 0.030 rs462646388391 105645241A/G 0.067 0.050 0.383 rs692462089042 105645892C/T

rs119028090828 105647678G/T 0.890 0.948 0.008 rs455755292676 105649526C/T 0.033 0.025 0.736 rs693271192881 105649731C/T

rs168614094227 105651077G/T

rs119028194585 105651435A/G 0.914 0.950 0.140 rs230816294616 105651466-/ATAA0.127 0.072 0.035 rs119028294712 105651562C/G 0.879 0.937 0.009 rs176590794738 105651588A/G 0.095 0.058 0.143 rs587883895253 105652103-/G

rs119028395522 105652372A/G 0.054 0.032 0.245 rs119028495869 105652719G/T 0.858 0.921 0.005 rs119028597856 105654706C/T 0.908 0.957 0.017 rs6931398 A/G

[0293] Allelotyping results were considered particularly significant with a calculated p-value of less than or equal to 0.05 for allelotype results. These values axe indicated in bold. The allelotyping p-values were plotted in Figure 1F for the discovery cohort. The position of each SNP on the chromosome is presented on the x-axis. The y-axis gives the negative logarithm (base 10) of the p-value comparing the estimated allele in the case group to that of the control group. The minor allele frequency of the control group for each SNP designated by an X or other symbol on the graphs in Figure 1F can be determined by consulting Table 41. For example, the left-most X on the left graph is at position 105557091. By proceeding down the Table from top to bottom and across the graphs from left to right the allele frequency associated with each symbol shown can be determined.
[0294] To aid the interpretation, multiple lines have been added to the graph.
The broken horizontal lines are drawn at two common significance levels, 0.05 and 0.01.
The vertical broken lines are drawn every 20kb to assist in the interpretation of distances between SNPs. Two other lines are drawn to expose linear trends in the association of SNPs to the disease. The generally bottom-most curve is a nonlinear smoother through the data points on the graph using a local polynomial regression method (W.S. Cleveland, E. Grosse and W.M. Shyu (1992) Local regression models. Chapter 8 of Statistical Models in S eds J.M. Chambers and T.J. Hastie, Wadsworth &
Brooks/Cole.). The black line provides a local test for excess statistical significance to identify regions of association. This was created by use of a l Okb sliding window with lkb step sizes. Within each window, a chi-square goodness of fit test was applied to compare the proportion of SNPs that were significant at a test wise level of 0.01, to the proportion that would be expected by chance alone (0.05 for the methods used here). Resulting p-values that were less than 10-8 were truncated at that value.
[0295] Finally, the exons and introns of the genes in the covered region are plotted below each graph at the appropriate chromosomal positions. The gene boundary is indicated by the broken horizontal line. The exon positions are shown as thick, unbroken bars. An arrow is place at the 3' end of each gene to show the direction of transcription.
Example 10 TM7SF3 Region Proximal SNPs [0296] It has been discovered that SNP rs1484086 in TM7SF3 is associated with occurrence of osteoarthritis in subjects. TM7SF3 is an orphan receptor and is a member of the superfamily of 7-transmembrane domain proteins, one of the largest superfamilies of cell surface proteins. Members of this family include receptors for a variety of ligands, such as peptides, hormones, and ions, and for external sensory stimuli, such as odorants and light. Many 7-transmembrane molecules are able to recruit small G proteins, suggesting that they can transduce external signals to the cytoplasm.
[0297] Thirty-seven additional allelic variants proximal to rs1484086 were identified and subsequently allelotyped in osteoarthritis case and control sample sets as described in Examples 1 and 2.
The polymorphic variants are set forth in Table 42. The chromosome positions provided in column four of Table 42 are based on Genome "Build 34" of NCBI's GenBank.

dbSNP ChromosomePositionChromosome Allele rs# in Position Variants SEQ ID
NO:

rs105870112 230 27004780 a/c rs11613 12 231 27004781 c/

rs900743 12 5330 27009880 /t rs212909112 6334 27010884 a/c rs15556 12 11372 27015922 c/t rs105372412 11456 27016006 /t rs9699 12 11501 27016051 a/

rs4856 12 13393 27017943 c/t rs378231412 16666 27021216 a/

rs208773612 17596 27022146 c/t rs206837212 19710 27024260 al rs206837112 19800 27024350 a/

rs118452912 20297 27024847 a/

rs210125612 20967 27025517 /t rs155225712 32514 27037064 c/t rs156558512 33159 27037709 a/

rs408080012 37600 27042150 a/

rs138865812 41259 27045809 a/

rs378231612 41329 27045879 c/t rs148408612 50060 27054610 c/t rs148408712 53292 27057842 c/t rs229154912 53393 27057943 a/

rs156558412 56417 27060967 c/t rs307116612 56435 27060985 -/tt rs190765212 58847 27063397 a/t rs375911912 59595 27064145 c/t rs375912012 59661 27064211 /t rs378231712 60355 27064905 c/t rs382516612 60407 27064957 a/c rs187219112 62357 27066907 a/

rs8628 12 68230 27072780 /t rs187219312 68516 27073066 a/

rs104283312 69055 27073605 c/t rs2476 12 72603 27077153 c/

rs197620612 73928 27078478 a/

rs138865912 85897 27090447 c/t rs118452812 91554 27096104 a/

Assay for Verifyin$ and Allelotypin_~ SNPs [0298] The methods used to verify and allelotype the 37 proximal SNPs of Table 42 are the same methods described in Examples 1 and 2 herein. The primers and probes used in these assays are provided in Table 43 and Table 44, respectively.

dbSNP Forward Reverse rs# PCR primer PCR primer rs1058701ACGTTGGATGCTTCTCTCCAGTCCATGTTGACGTTGGATGGTAACAAGTCCGAAGGATTC

rs11613 ACGTTGGATGTCCAAGTGCCTTCTCTCCAGACGTTGGATGTCCTTGATGCATCTCGACAC

rs900743 ACGTTGGATGAACAGATCCGGAACTf~fTTTACGTTGGATGGGCTCATAGAACCCTTTnT

rs2129091ACGTTGGATGTTAAAATTGGTATGGTCTCCACGTTGGATGGTTTTGCACTAAGAAGAGAC

rs15556 ACGTTGGATGTGTAGGGACAAAGTTATATGGAAACGTTGGATGTGTCTTTACAGTCTTCACTGGCA

rs1053724ACGTTGGATGCCATATAACTTTGTCCCTACACGTTGGATGAAAATACAGTGCAGGTGACC

rs9699 ACGTTGGATGTTTCAGTGTTACTGAAGTTAATTACGTTGGATGCAACATAGAAAATATAAAACAATTT

rs4856 ACGTTGGATGTTGTAAACCAAAAGGTAATTTCTCAACGTTGGATGGATGACCAAAAGGTTGGTGG

rs3782314ACGTTGGATGAATGCTGCACAACTTAGGCCACGTTGGATGAGCAGTCAGCCTATTCTTGC

rs2087736ACGTTGGATGCAGTGAGACTCTGTCTCTACACGTTGGATGTACATCAGCCTCCCAAGTAG

rs2068372ACGTTGGATGCTAGAGAGGGTTGCTCTATGACGTTGGATGCCAGCTTCAGCTTTCTGTAG

rs2068371ACGTTGGATGATTGACAAGCCAAGCCTGTCACGTTGGATGATAGAGCAACCCTCTCTAGG

rs1184529ACGTTGGATGTTCCTTTCCTGGTGGTTTGCACGTTGGATGGGTGTCAGTCTTGTAATCAG

rs2101256ACGTTGGATGCTGGGTTTTTTTGGTGTGTTGACGTTGGATGCTTGTACTGTATCTCAATTTC

rs1552257ACGTTGGATGCAATACCTTAGCTCACCTACACGTTGGATGCATTAGGGAAAATCTGGATC

rs1565585ACGTTGGATGGCTAGAATATACCACAGGTGACGTTGGATGTCACTGAAAATGGATCAGCC

rs4080800ACGTTGGATGGGGTTCAAGCAATTCTCCTGACGTTGGATGAAAATTAGCCAGGTGTGGTG

rs1388658ACGTTGGATGGAAAAGAGAGAGGATGGGTGACGTTGGATGCAGGAGCTTAAGAACCACTG

rs3782316ACGTTGGATGGTCTTGCTGTAATGTCATTAGACGTTGGATGCTTCTCTTTTTTAACTAGATC

rs1484086ACGTTGGATGTGTCACTCTTCGGAAGTCTCACGTTGGATGCATGTACAGGGCATTCACAG

rs1484087ACGTTGGATGGCATGGAATTTTTACACCCCACGTTGGATGTTCCCTCTCAAACTCTGTAG

rs2291549ACGTTGGATGACTAAAGCGCCTCTTTGCTGACGTTGGATGCATTAAGCCGCTAGTTCCAC

rs1565584ACGTTGGATGGAAAAGGCAAGTTATGATGCACGTTGGATGAGTATCCATTCCTCTGAGTC

rs3071166ACGTTGGATGGAAAAGGCAAGTTATGATGCACGTTGGATGAGTATCCATTCCTCTGAGTC

rs1907652ACGTTGGATGCCATATTTCCAGTACCTAGCACGTTGGATGGGTTGATAAATATGTGCCAG

rs3759119ACGTTGGATGCTAAACTGTTCTTAGTGCCGACGTTGGATGGGGAATTTCAAAGAGTGTGG

rs3759120ACGTTGGATGCGGCACTAAGAACAGTTTAGAACGTTGGATGGGTTTTTATGACTGTAGCAAC

rs3782317ACGTTGGATGGGAAGCTCTTGAAGCTGTAGACGTTGGATGGCCATTGAGAAATCCTGAGC

rs3825166ACGTTGGATGACCAGACTCTCAACTTAGCCACGTTGGATGTGGCAGGTGGGTTATTCTTG

rs1872191ACGTTGGATGTTTATGCCGAAGCCCTGTCTACGTTGGATGTAAAGCAAGGGAGGAAAGGG

rs8628 ACGTTGGATGCAAGCCTTACCAACAATTACAGAAACGTTGGATGGCTTATCAAGAGTGAAAATAGAAGA

rs1872193ACGTTGGATGAATGCCACCTCTAAGAGGCAACGTTGGATGCTCAAGCCAAAGGAGAAGAC

rs1042833ACGTTGGATGTCATCCAACCCTTGGATCTCACGTTGGATGATACAGCCCCAGGAAATAGC

rs2476 ACGTTGGATGAGGAGCAGGTGACGTTAATGACGTTGGATGATTGACTAGCCACCAGGAAG

rs1976206ACGTTGGATGAGCTGGGATTGGATTACAGGACGTTGGATGATGGAGAAACCCCGTCTCTA

rs1388659ACGTTGGATGACCTCAGCCTTCCACATTTGACGTTGGATGAGCAGGAGGAAACTTTTGGG

rs1184528ACGTTGGATGTGAGAATCGCTTGAACCCAGACGTTGGATGTTTGAATCAGAGTCTCCCTC

dbSNP Extend Term rs# Primer Mix rs1058701 CCAGTCCATGTTGAGGTGC ACT

rs11613 CCAGTCCATGTTGAGGTG ACT

rs900743 ATCCGGAACTTTTTTTTTGAAATTACT

rs2129091 ATTTAATTTGAAAAGTGCTTACCCACT

rs15556 GTTTGTTATTTTCTATAC ACG

rs1053724 CATCAAGTTTCAGTGTTA CGT

rs9699 TACAGAATAAGCAGTAAA ACG

rs4856 CAAGTATTTGGAAATAAG ~ ACT

dbSNP Extend Term rs# Primer Mix rs3782314 ACAAATATATGAGAACTCCTCTTTACT

rs2087736 ACTCTGTCTCTACTAAAAATAAAAACT

rs2068372 TGGCTTCATGGCACCACTG ACT

rs2068371 AGCCAAGCCTGTCACTGGCCCT ACT

rs1184529 TCCTGGTGGTTTGCCACTTA ACT

rs2101256 GTTTTTTTGGTGTGTTGATATGTAACT

rs1552257 AGCTCACCTACGAAAATGAATAAACG

rs1565585 TGTCAGACTGCACTACAT ACT

rs4080800 ATTCTCCTGTCTCAGCCTCC ACG

rs1388658 GAGAGGATGGGTGAAATAAGG ACT

rs3782316 TGTAATGTCATTAGGAAGAAACAACG

rs1484086 CTCTTCGGAAGTCTCTTTCTCA ACT

rs1484087 TTTACACCCCCAAATCTAGAG ACT

rs2291549 CCTCTTTGCTGCCCAGTGG ACT

rs1565584 TGATGCAATAAGTATATATAGTACACT

rs3071166 TAGTACGTGGCTTTTTTTTTTTTTCGT

rs1907652 TCCAGTACCTAGCACCTAAC CGT

rs3759119 TTAGTGCCGGGATGAATAACT ACT

rs3759120 AAATTGCAACTGTGAGTATTAAAGACT

rs3782317 AGAATAACCCACCTGCCAAAT ACT

rs3825166 ACTTAGCCTACATTTGAAAAGGGACT

rs1872191 CTCAGTCCGCTCCCCACTT ACG

rs8628 TTAAACACTATGACACAT ACG

rs1872193 AGAGGCAGGACACTAGCC ACG

rs1042833 CCCTTGGATCTCTTTGAG ACG

rs2476 GTGACGTTAATGGGACAGCT ACT

rs1976206 TACAGGCGCCCACCACCA ACG

rs1388659 CCACATTTGGTAAGTTTTGACATACT

rs1184528 ~ AGAGGTTGCAGAGAGCCAAGATCACT
I

Genetic Anal, [0299] Allelotyping results from the discovery cohort are shown for cases and controls in Table 45.
The allele frequency for the A2 allele is noted in the fifth and sixth columns for osteoarthritis case pools and control pools, respectively, where "AF" is allele frequency. The allele frequency for the A1 allele can be easily calculated by subtracting the A2 allele frequency from 1 (A1 AF
= 1-A7, AF). For example, the SNP rs900743 has the following case and control allele frequencies: case A1 (G) = 0.92;
case A2 (T) = 0.08; control A1 (G) = 0.90; and control A2 (T) = 0.10, where the nucleotide is provided in paranthesis. Some SNPs are labeled "untyped" because of failed assays.

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-in SEQ

rs# ID NO: 8 Position Allele Case C__ont_rolValue AF AF

rs1058701 230 27004780 A/C

rs11613 231 27004781 C/G

rs900743 5330 27009880 G/T 0.08 0.10 0.381 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in SEQ Position AlleleCase Control Value ID NO: 8 AF AF

rs2129091 6334 27010884 A/C 0.19 0.20 0.646 rs15556 11372 27015922 C/T 0.74 0.74 0.923 rs1053724 11456 27016006 G/T 0.14 0.15 0.592 rs9699 11501 27016051 A/G 0.67 0.68 0.595 rs4856 13393 27017943 C/T 0.10 0.09 0.474 rs3782314 16666 27021216 A/G 0.20 0.22 0.278 rs2087736 17596 27022146 C/T

rs2068372 19710 27024260 A/G 0.11 0.10 0.634 rs2068371 19800 27024350 A/G

rs1184529 20297 27024847 A/G

rs2101256 20967 27025517 G/T

rs1552257 32514 27037064 C/T 0.67 0.67 0.969 rs1565585 33159 27037709 A/G 0.69 0.65 0.064 rs4080800 37600 27042150 A/G

rs1388658 41259 27045809 A/G 0.35 0.38 0.362 rs3782316 41329 27045879 C/T 0.47 0.46 0.740 rs1484086 50060 27054610 C/T

rs1484087 53292 27057842 C/T 0.35 0.38 0.127 rs2291549 53393 27057943 A/G

rs1565584 56417 27060967 C/T 0.66 0.69 0.327 rs3071166 56435 27060985 -/TT 0.52 0.47 0.042 rs1907652 58847 27063397 A/T 0.64 0.64 0.984 rs3759119 59595 27064145 C/T 0.08 0.05 0.042 rs3759120 59661 27064211 G/T 0.15 0.14 0.861 rs3782317 60355 27064905 C/T 0.08 0.07 0.780 rs3825166 60407 27064957 A/C 0.83 0.84 0.660 rs1872191 62357 27066907 A/G 0.04 0.05 0.555 rs8628 68230 27072780 G/T 0.59 0.61 0.411 rs1872193 68516 27073066 A/G 0.92 0.91 0.669 rs1042833 69055 27073605 C/T 0.85 0.86 0.605 rs2476 72603 27077153 C/G 0.81 0.82 0.392 rs1976206 73928 27078478 A/G 0.16 0.15 0.781 rs1388659 85897 27090447 C/T 0.49 0.50 0.692 rs1184528 91554 27096104 AlG 0.20 0.17 0.228 [0300] The TM7SF3 proximal SNPs were also allelotyped in the replication cohorts using the methods described herein and the primers provided in Tables 43 and 44. The replication allelotyping results for replication cohort #1 and replication cohort #2 are provided in Tables 46 and 47, respectively.

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in SEQ Position Allele Case Control Value ID NO: 8 AF AF

rs1058701230 27004780 A/C

rs11613 231 27004781 C/G

rs900743 5330 27009880 G/T 0.07 0.11 0.258 rs21290916334 27010884 A/C 0.18 0.20 0.450 rs15556 11372 27015922 C/T 0.73 0.74 0.858 rs105372411456 27016006 G/T 0.15 0.15 0.969 rs9699 11501 27016051 A/G 0.65 0.68 0.290 rs4856 13393 27017943 C/T 0.11 0.10 0.735 rs378231416666 27021216 A/G 0.18 0.22 0.171 rs208773617596 27022146 C/T

rs206837219710 27024260 A/G 0.11 0.11 0.867 rs206837119800 27024350 A/G

rs118452920297 27024847 A/G

rs210125620967 27025517 G/T

rs155225732514 27037064 C/T 0.70 0.66 0.239 rs156558533159 27037709 A/G 0.67 0.65 0.599 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in SEQ Position Allele Case Control Value ID NO: AF AF

rs4080800 37600 27042150 A/G

rs1388658 41259 27045809 A/G 0.36 NA NA

rs3782316 41329 27045879 C/T 0.45 0.49 0.230 rs1484086 50060 27054610 C/T

rs1484087 53292 27057842 C/T 0.32 0.40 0.023 rs2291549 53393 27057943 A/G

rs1565584 56417 27060967 C/T 0.61 0.65 0.297 rs3071166 56435 27060985 -/TT 0.55 0.45 0.003 rs1907652 58847 27063397 A/T 0.62 NA 0.638 rs3759119 59595 27064145 C/T 0.09 0.04 0.025 rs3759120 59661 27064211 G/T 0.16 0.15 0.651 rs3782317 60355 27064905 C/T 0.07 0.07 0.986 rs3825166 60407 27064957 A/C 0.84 0.84 0.945 rs1872191 62357 27066907 A/G 0.04 0.06 0.562 rs8628 68230 27072780 G/T 0.58 0.64 0.060 rs1872193 68516 27073066 A/G 0.92 0.91 0.957 rs1042833 69055 27073605 C/T 0.85 0.86 0.746 rs2476 72603 27077153 C/G 0.81 0.84 0.397 rs1976206 73928 27078478 A/G 0.17 0.16 0.788 rs1388659 85897 27090447 C/T 0.47 0.50 0.283 rs1184528 91554 27096104 A/G 0.21 0.16 0.170 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in SEQ Position AlleleCase ~ Value ID NO: AF Control rs1058701230 27004780 A/C

rs11613 231 27004781 C/G

rs900743 5330 27009880 G/T 0.10 0.09 0.763 rs21290916334 27010884 A/C 0.21 0.20 0.896 rs15556 11372 27015922 C/T 0.75 0.75 0.974 rs105372411456 27016006 G/T 0.12 0.15 0.373 rs9699 11501 27016051 A/G 0.69 0.67 0.615 rs4856 13393 27017943 C/T 0.10 0.08 0.413 rs378231416666 27021216 A/G 0.22 0.22 0.944 rs208773617596 27022146 C/T

rs206837219710 27024260 A/G 0.11 0.10 0.561 rs206837119800 27024350 A/G

rs118452920297 27024847 A/G

rs210125620967 27025517 G/T

rs 155225732514 27037064 C/T 0.63 0.68 0.247 rs156558533159 27037709 A/G 0.73 0.66 0.029 rs408080037600 27042150 A/G

rs138865841259 27045809 A/G 0.33 0.38 0.217 rs378231641329 27045879 C/T 0.51 0.42 0.036 rs148408650060 27054610 C/T

rs148408753292 27057842 C/T 0.38 0.36 0.575 rs229154953393 27057943 A/G

rs156558456417 27060967 C/T 0.73 0.74 0.635 rs307116656435 27060985 -/TT 0.48 0.49 0.727 rs190765258847 27063397 A/T 0.66 -0.02 rs375911959595 27064145 CIT 0.06 0.05 0.669 rs375912059661 27064211 G/T 0.13 0.14 0.881 rs378231760355 27064905 C/T 0.08 0.07 0.655 rs382516660407 27064957 A/C 0.82 0.84 0.546 rs187219162357 27066907 A/G 0.04 0.04 0.894 rs8628 68230 27072780 G/T 0.61 0.56 0.234 rs187219368516 27073066 A/G 0.93 0.91 0.528 rs104283369055 27073605 C/T 0.85 0.86 0.682 rs2476 72603 27077153 C/G 0.80 0.81 0.829 rs197620673928 27078478 A/G 0.14 0.14 0.834 rs138865985897 27090447 C/T 0.51 0.48 0.499 rs118452891554 27096104 A/G 0.18 0.18 0.993 [0301] Allelotyping results were considered particularly significant with a calculated p-value of less than or equal to 0.05 for allelotype results. These values are indicated in bold. The allelotyping p-values were plotted in Figure 1G for the discovery cohort. The position of each SNP on the chromosome is presented on the x-axis. The y-axis provides the negative logarithm (base 10) of the p-value comparing the estimated allele in the case group to that of the control group. The minor allele frequency of the control group for each SNP designated by an X or other symbol on the graphs in Figure 1 G can be determined by consulting Table 45. For example, the left-most X on the left graph is at position 27004780. By proceeding down the Table from top to bottom and across the graphs from left to right the allele frequency associated with each symbol shown can be determined.
[0302] To aid the interpretation, multiple lines have been added to the graph.
The broken horizontal lines are drawn at two common significance levels, 0.05 and 0.01.
The vertical broken lines are drawn every 20kb to assist in the interpretation of distances between SNPs. Two other lines are drawn to expose linear trends in the association of SNPs to the disease. The generally bottom-most curve is a nonlinear smoother through the data points on the graph using a local polynomial regression method (W.S. Cleveland, E. Grosse and W.M. Shyu (1992) Local regression models. Chapter 8 of Statistical Models in S eds J.M. Chambers and T.J. Hastie, Wadsworth &
Brooks/Cole.). The black line provides a local test for excess statistical significance to identify regions of association. This was created by use of a lOkb sliding window with lkb step sizes. Within each window, a chi-square goodness of fit test was applied to compare the proportion of SNPs that were significant at a test wise level of 0.01, to the proportion that would be expected by chance alone (0.05 for the methods used here). Resulting p-values that were less than 10-$ were truncated at that value.
[0303] The exons and introns of the genes in the covered region are plotted below each graph at the appropriate chromosomal positions. The gene boundary is indicated by the broken horizontal line. The exon positions are shown as thick, unbroken bars. An arrow is place at the 3' end of each gene to show the direction of transcription.
Exam In a 11 LOXLI Region Proximal SNPs [0304] It has been discovered that rs8818 in the untranslated region (UTR) of the lysyl oxidase-like 1 (LO~~LI) gene is associated with occurrence of osteoarthritis in subjects.
LOXLl is a Lysyl oxidase-like protein that catalyzes the cross-linking of collagen via lysine residues.
Deficiency of the related protein, lysyl oxidase, causes a form of Ehlers-Danlos syndrome. LOXLI likely is a secreted protein and its biological activity may be modulated by addition of an antibody, a recombinant binding partner, a binding agent, or a recombinant LOXLI protein or functional fragment thereof.
[0305] Fifty-eight additional allelic variants proximal to rs912428 were identified and subsequently allelotyped in osteoarthritis case and control sample sets as described in Examples 1 and 2. The polymorphic variants are set forth in Table 48. The chromosome positions provided in column four of Table 48 are based on Genome "Build 34" of NCBI's GenBank.

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs104866115 213 71935363 G/T

rs382594215 249 71935399 C/T

rs155043615 1824 71936974 C/T

rs155043815 2057 71937207 C/T

rs155043915 2306 71937456 A/T

rs216524115 2869 71938019 C/T

rs155043315 3976 71939126 A/C

rs305631415 4288 71939438 -/TC

rs241520415 4290 71939440 A/C

rs199231415 4434 71939584 C/G

rs144010115 5298 71940448 A/G

rs228941415 5467 71940617 A/G

rs241520515 8486 71943636 C/G

rs289980715 8487 71943637 A/T

rs893815 15 8831 71943981 C/G

rs305634215 9036 71944186 -/AG

rs407728415 9058 71944208 A/G

rs893816 15 9131 71944281 C/T

rs893817 15 9732 71944882 A/G

rs893818 15 9862 71945012 A/G

rs893819 15 10191 71945341 A/G

rs893820 15 10270 71945420 C/T

rs230471915 16167 71951317 C/T

rs100150715 17620 71952770 G/T

rs153016715 17751 71952901 C/T

rs153016815 17764 71952914 C/T

rs153016915 17787 71952937 C/T

rs230472015 19401 71954551 C/T

rs230472115 21021 71956171 A/C

rs893821 15 21902 71957052 C/T

rs750460 15 22173 71957323 C/T

rs230472215 22416 71957566 C/T

rs144010215 22653 71957803 A/G

rs8898 15 24945 71960095 ClG

rs3522 15 25011 71960161 C/T

rs241520615 28563 71963713 C/T

rs198452615 48574 71983724 C/G

rs198452515 48710 71983860 C/T

rs303165315 48880 71984030 -/TTG

rs241518715 50194 71985344 C/T

rs2507 15 56343 71991493 A/G

rs228941115 56455 71991605 C/T

rs320207715 56729 71991879 C/T

rs228941215 56759 71991909 A/G

rs228941315 56895 71992045 A/G

rs106108215 57036 71992186 ClG

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs227760015 57702 71992852 C/G

rs73485415 62515 71997665 C/T

rs241518815 62629 71997779 C/G

rs321469515 63501 71998651 -/C

rs381619715 63547 71998697 C/T

rs381619815 64876 72000026 C/G

rs230471515 65073 72000223 C/G

rs230127215 67149 72002299 C/T

rs230127315 67549 72002699 C/T

rs378456315 71660 72006810 A/C

rs378456115 71 72007056 C/T

rs37845601 15 _ 72007061 A/C
~ __ ~
71911 ~

Assay for Verifying and Allelotypin_g SNPs [0306] The methods used to verify and allelotype the 58 proximal SNPs of Table 48 are the same methods described in Examples 1 and 2 herein. The primers and probes used in these assays are provided in Table 49 and Table 50, respectively.

dbSNP Forward Reverse rs# PCR primer PCR primer rs1048661ACGTTGGATGTTGCTGGGAGACGGAGGTGACGTTGGATGATTCGGCTfTGGCCAGGTGC

rs3825942ACGTfGGATGTAGGTGCTGGCGAAGGCCGAAACGTTGGATGACCTCCGTCTCCCAGCAAC

rs1130133ACGTTGGATGACCAAGTCAGGGAGACCGCGACGTTGGATGAGCGGAACGGCGCGCAGCA

rs1550436ACGTTGGATGGCCAAAAAAACTCAGTAACGACGTTGGATGGTTCATTACAGATAGTITfGC

rs1550437ACGTTGGATGTTGGGCCTTCCCAAGAGGAGACGTTGGATGAGAGCCCCAGCTGTGGACA

rs1550438ACGTTGGATGAGTCAGCCCTTGTCACAGTAACGTTGGATGCATGAGGACACAGTGGAAAG

rs1550439ACGTTGGATGATTCTCTGCTCCCCATTGAGACGTTGGATGTATACTCTGAGGCACTGGAG

rs2165241ACGT1'GGATGTAGAAGACCCACTGACTTGGACGTfGGATGGGGCAGAGAAAACTGAGCTC

rs1550433ACGTTGGATGATAGCAGGAGTGGTCACATCACGTTGGATGTAGCAAATCCTTGAAGAGAG

rs3056314ACGTTGGATGTCTCTCCTGGCCTCTGATTGACGTfGGATGCCTGACGTGTGTCCTCTATC

rs2415204ACGTTGGATGGTTCTCTCCTGGCCTCTGATACGTfGGATGCCTGACGTGTGTCCTCTATC

rs1992314ACGTTGGATGTTTGTCCTAAAGGCCCTGAGACGTTGGATGAGATAAACCCCTGCAGTCTG

rs1440101ACGTTGGATGAAAAGTCAGCAAGTGAGCTCACGTTGGATGTTAATTCCCAGGTCCTAGCC

rs2289414ACGTTGGATGTTGCTTATCTfGTACACCTCACGTfGGATGCTCACCCTGTCACAACCAGT

rs2415205ACGTTGGATGTGATGCTfCAGTTACTCCAGACGTTGGATGTGTGGGCAGCGTAAGTTTTG

rs2899807ACGTTGGATGTGATGCTTCAGTTACTCCAGACGTTGGATGTGTGGGCAGCGTAAGTTTTG

rs893815ACGTTGGATG CACCCTTTTACAGCACTCACACGTTGGATGATCCCTTCTGTGAGTCAAGC

rs3056342ACGTTGGATGTAAGGATCAGTAGGCAGGTCACGTTGGATGATAGCTGGGAATTCCAGGAC

rs4077284ACGTfGGATGTAAGGATCAGTAGGCAGGTCACGTTGGATGATAGCTGGGAATfCCAGGAC

rs893816ACGTTGGATGATfGCCCACAGAATCAAGCCACG1TGGATGTTCTGGAAGGCTAGGTAAGG

rs893817ACGTTGGATGAAACAGGTGAGGTGTGGACGACGTfGGATGAGAAATCTGTTCCCTCCTGC

rs893818ACGTTGGATGTTTTAGGAGCTGTTCAGTTCACGTTGGATGTGGGAGAATTTCCTGACTGC

rs893819ACGTTGGATGCTGTCACACTGACTCTt'GGGACGTTGGATGATGGTCTT'fGTCCTCCGGTT

rs893820ACG'TTGGATGAGAGTCAGTGTGACAGGTTCACGTfGGATGTTCTATATCCTGGCTCTGCC

rs2304719ACGTTGGATGTTTCATCAGTGAGCCTTGCCACGTTGGATGCCTfGTATAGTGAGGTACAG

rs1001507I ACGT1'GGATGAGAATCCTGCAAAACTGGAGACGTTGGATGTGCAGCATGTGAACTGGCAC

dbSNP Forward Reverse rs# PCR primer PCR primer rs1530167ACGTTGGATGAAACATCCTCCTTCCCTCTGACGTTGGATGGCCTAGAACCTAGACCCTTA

rs1530168ACGTTGGATGCAAAACATCCTCCTTCCCTCACGTTGGATGGACCCTTATGGTTfCCCATG

rs1530169ACGTTGGATGTGTGCTGAGCTGAACAGAAGACGTTGGATGGGAATCTGTCTATGTCTGGG

rs2304720ACGTTGGATGATGCTGGGTTCTGGTGTCACACGTTGGATGATAGGCTGTGCTGCAGGGAC

rs2304721ACGTTGGATGCTCAAGTGATGCCTCAGATGACGTTGGATGCTGAAAGAAGCTI'CAGCCTC

rs893821ACGTTGGATGTGGATTAACTAGGGTAGGGCACGTTGGATGGAAAGTTGCATCCCTGCATC

rs750460ACGTTGGATGATGTTTCCCTAGAGCTAGAGACGTTGGATGCTCAGCTCCTCATTACTGCA

rs2304722ACGTTGGATGTrACCACCTTCTCTGGTGAGACGTTGGATGGAGGAAGAAGAGAAACAGGG

rs1440102ACGTTGGATGAGTAAGAGTTrGCCCACCACACGTTGGATGTGACCTAAAGTGCAGGTATC

rs8818 ACGTTGGATGAATCTCTCCCCTTCCAAAGCACGTTGGATGTCCCTGTGGTTTTCATCCAC

rs3522 ACGTTGGATGAACAACACTGTAGAGAAAAGTGAAACGTTGGATGACGTGGATGAAAACCACAGG

rs2415206ACGTrGGATGCACCTTGAGGTGAAACAGACACGTTGGATGTTACTTAGTAGACCCCGAGG

rs1984526ACGTTGGATGATCCTTTGTTCTTGAAACAGACGTTGGATGGGATI'ACAAACGTGAGCCAC

rs1984525ACGTTGGATGCAGCTGGGATTACAGGTATGACGTTGGATGACCAACATGGTGAAACCCTG

rs3031653ACGTTGGATGATAAACGTrAAGCTCAGTTGACGTTGGATGP~AAAAAAAAGTGAAAGTCG

rs2415187ACGTTGGATGTTCTATGAGTTACTTGACACACGTTGGATGGTGTCTTTATCTGACTAGTG

rs2507 ACGTTGGATGGCTGCTCCCAAAGATT'TCTGACGTTGGATGTAAGAAGCACAGAACGCAGG

rs2289411ACGTTGGATGCTGTGGCGAAGTTACCTGGGACGTTGGATGTGCTCCTTCCCATGCCCAAT

rs3202077ACGTTGGATGACAGTGGTTCTCTGGACAAGACGTTGGATGTCTCCTCCTGGAATCACACC

rs2289412ACGTTGGATGGGACAAAGCCTTGTCCAGAGACGTTGGATGATGAATGGAGGCTGCAGGAG

rs2289413ACGTTGGATGTTGGCTGACTTTCCAGAGCCACGTTGGATGTGCAGATGAACACCTCCTCC

rs1061082ACGTTGGATGGGCCCTGCTATGCAGAGAGACGTTGGATGAGGTCGCCCTTCACCTTCAG

rs2277600ACGTTGGATGTAGTGAGGTCCAGGAAGTAGACGTTGGATGCCTGCTACCAGTTCAATGTC

rs734854ACGTTGGATGATAACTCCAAAGGCCATGTGACGTTGGATGCAGACCACAGAGATGAAAAG

rs2415188ACGTTGGATGAAAGTTGACAAAGCCCTTTCACGTTGGATGAGGAAACTGTCTGTCCTTGG

rs3214695ACGTTGGATGACACTTGCCCAAGTTCACTCACGTTGGATGTACATCTGCAGGTGAGAGCA

rs3816197ACGTTGGATGGTGAACTTGGGCAAGTGTACACGTTGGATGAGATfGAGAGCCCTGAGAAG

rs3816198ACGTTGGATGTAGGGTCATGGGGCTTfGGACGTTGGATGGGCTGATAAGAGCCGAGGAC

rs2304715ACGTTGGATGGTGAGTGGCCGCCTGGCACACGTTGGATGTCCTCGGAGGCAGAGATTCG

rs2301272ACGTfGGATGATGATACCCAAGGAGTGTGCACGTrGGATGTCAGCAACTTCCCATCACTC

rs2301273ACGTTGGATGACCTACCGCTGACTTACGGACGTTGGATGACGGATGAATGGATCAAAG

rs3784563ACGTTGGATGAATGTGGTCTGCAGATATGCACGTTGGATGAAACTTACTATCCACCTGCG

rs3784561ACGTT'GGATGATGACCACAATTTATGCTGCACGTTGGATGTGCAAAGATGATTCTGCAGC

rs3784561ACGTTGGATGCAGTAAGGCTGGATTCTAGGACGTTGGATGGCTGCCTGGTGTTAATGGTT

rs3784560I ACGTTGGATGGCTGGATTCTAGGATCAGAGACGTTGGATGACATTCTCAGATAGCGCTGC

dbSNP Extend Term rs# Primer Mix rs1048661 GGAGACGGAGGTGCGGGCC CGT

rs3825942 GAGACCGAGGAGGCGGAG ACG

rs1130133 GGCCGGTACACGCTGCC ACG

rs1550436 AAAAAACTCAGTAACGGAGATAA ACT

rs1550437 TTCACCCCCTGAAAAGCCAGA ACT

rs1550438 GTAGCCCTGTCTGCTAACAGCAT ACT

rs1550439 CTCCCCATTGAGGTTGCTG CGT

rs2165241 CCAGGCATGCCTCTGCCA ACT

rs1550433 GGTCACATCGAGGGAGCC ACT

rs3056314 TGGCCTCTGATTGGCCATG ACT

dbSNP Extend Term rs# Primer Mix rs2415204 CTCCTGGCCTCTGATTGGCCA ACT

rs1992314 AAGGCCCTGAGGAGCTACA ACT

rs1440101 CTCGTCACCACATCTGTAACA ACG

rs2289414 TTTATTCACTCATfCATTTGGTC ACT

rs2415205 CTCAGGCCCTGCACAGTGA ACT

rs2899807 CTCAGGCCCTGCACAGTG CGT

rs893815 ACAGCACTCACCTGTCCAC ACT

rs3056342 CACACCCCAACCTTTTTTACCCC ACT

rs4077284 GGCAGGTCTCTGGCAGCA ACG

rs893816 CAGAGTGGCAGCTAAAGCC ACT

rs893817 GGTGTGGACGAGCAATGGGAA ACT

rs893818 AGCCCTCTCACAACCCCTACAGA ACG

rs893819 CACCCTGTCCTCCTGCTCAA ACG

rs893820 ACAGGTTCCTCCTACTGTGC ACG

rs2304719 CAGGAGGGGAGGGGAGCAAG ACG

rs1001507 GGCCCTCTGAGATCATTTCAA ACT

rs1530167 CTGTTCAGCTCAGCACACC ACT

rs1530168 CAGTTAAATCCTGCCCTTCTGTTCACT

rs1530169 TGAACAGAAGGGCAGGATTTAAC ACG

rs2304720 TGTGCCCCAACCCCCCC ACG

rs2304721 TCAGATGCTGCCTCTGCTC ACT

rs893821 GCCAGCTTTATTTGCAGAACATCTACT

rs750460 CAGAGAGGTTGGATCCTGCC ACG

rs2304722 CTCTGGTGAGCAGTTGAGG ACG

rs1440102 GCAGGCAAGGCCACCTGA ACT

rs8818 AGCCCCCAACCCACAGGCA ACT

rs3522 TATAAAATGGGGTCTGGC ACT

rs2415206 GAAACAGACCCCCACCCC ACG

rs1984526 AGCATAAAGGTGAAAGATGGGCC ACT

rs1984525 GGATTACAGGTATGCACCACCA ACG

rs3031653 AAGCTCAGTTGTGGCTCCAAACAAACT

rs2415187 TCTTTTTAAAAAACTACACCAGGTACG

rs2507 TGACTCATCTGCCAGCTC ACG

rs2289411 GGGATCCTGGCTGGCCC ACT

rs3202077 CTGGACAAGGCTTTGTCCAT ACG

rs2289412 GCCTTGTCCAGAGAACCACT ACT

rs2289413 CAAGCCTGGCACCAAGCC ACG

rs1061082 CTATGCAGAGAGCTGCGGC ACT

rs2277600 GGAAGTAGGCGCTTTGGGTG ACT

rs734854 ACTCCAAAGGCCATGTGTCTTAACACG

rs2415188 GGGGTGCTGTTAGGGCAGCC ACT

rs3214695 CGCTfGGCAGCTGTCGTG ACT

rs3816197 CTTGGGCAAGTGTACCTTACG ACG

rs3816198 CCCCAGAGCCAGCCAGC ACT

rs2304715 CCGCCTGGCACGGCGGA ACT

rs2301272 TGTGCTAGGACAAGATCCTAGCT ACT

rs2301273 GCTGACTTACGGTAAAGCGG ACT

rs3784563 TGACCACAATT1'ATGCTGCCA ACT

rs3784561 GCAGGTGGATAGTAAGTTTCCA I ACT

dbSNP Extend Term rs# Primer Mix rs3784561 GCTGGATTCTAGGATCAGAGACAACT

rs3784560 CTAGGATCAGAGACAGGTAG ACT

Genetic Analysis [0307] Allelotyping results from the discovery cohort are shown for cases and controls in Table 51.
The allele frequency for the A2 allele is noted in the fifth and sixth columns for osteoarthritis case pools and control pools, respectively, where "AF" is allele frequency. The allele frequency for the A1 allele can be easily calculated by subtracting the A2 allele frequency from 1 (A1 AF
= 1-A2 AF). For example, the SNP rs1048661 has the following case and control allele frequencies: case A1 (G) = 0.725;
case A2 (T) = 0.275; control A1 (G) = 0.767; and control A2 (T) = 0.233, where the nucleotide is provided in paranthesis. Some SNPs are labeled "untyped" because of failed assays.

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in SEQ Position Allele Case Control Value ID NO: 10 AF AF

rs1048661213 71935363 G/T 0.275 0.233 0.077 rs3825942249 71935399 C/T 0.107 0.148 0.056 rs15504361824 71936974 C/T 0.401 0.420 0.470 rs15504382057 71937207 C/T

rs15504392306 71937456 A/T

rs21652412869 71938019 C/T 0.427 0.430 0.883 rs15504333976 71939126 A/C

rs30563144288 71939438 -/TC

rs24152044290 71939440 A/C 0.176 0.177 0.982 rs19923144434 71939584 C/G 0.599 0.601 0.938 rs14401015298 71940448 A/G

rs22894145467 71940617 A/G

rs24152058486 71943636 C/G

rs28998078487 71943637 A/T 0.951 0.956 0.863 rs893815 8831 71943981 C/G

rs30563429036 71944186 -/AG 0.290 0.292 0.927 rs40772849058 71944208 A/G 0.358 0.358 0.985 rs893816 9131 71944281 C/T 0.517 0.515 0.928 rs893817 9732 71944882 A/G 0.162 0.158 0.819 rs893818 9862 71945012 A/G 0.311 0.313 0.920 rs893819 10191 71945341 A/G 0.637 0.642 0.866 rs893820 10270 71945420 C/T 0.901 0.910 0.605 rs230471916167 71951317 C/T 0.320 0.299 0.387 rs100150717620 71952770 G/T 0.910 0.916 0.709 rs153016717751 71952901 C/T

rs153016817764 71952914 ClT

rs153016917787 71952937 C/T 0.209 0.203 0.779 rs230472019401 71954551 C/T 0.942 0.947 0.724 rs230472121021 71956171 A/C 0.798 0.814 0.519 rs893821 21902 71957052 C/T 0.113 0.116 0.879 rs750460 22173 71957323 C/T 0.473 0.438 0.176 rs230472222416 71957566 CIT 0.744 0.747 0.926 rs144010222653 71957803 A/G

rs8818 24945 71960095 C/G

rs3522 25011 71960161 C/T 0.424 0.441 0.472 rs241520628563 71963713 C/T 0.376 0.366 0.731 rs198452648574 71983724 ClG 0.593 unt ed NA

rs198452548710 71983860 C/T

rs303165348880 71984030 -/TTG

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in SEQ Position Allele Case Control Value ID NO: 10 AF AF

rs241518750194 71985344 C/T

rs2507 56343 71991493 A/G 0.655 0.653 0.924 rs228941156455 71991605 C/T

rs320207756729 71991879 C/T

rs228941256759 71991909 A/G 0.971 0.968 0.855 rs228941356895 71992045 A/G 0.972 0.972 0.997 rs106108257036 71992186 C/G

rs227760057702 71992852 C/G

rs734854 62515 71997665 C/T 0.381 0.379 0.915 rs241518862629 71997779 ClG 0.532 0.538 0.832 rs321469563501 71998651 -!C 0.308 0.300 0.751 rs381619763547 71998697 C/T 0.327 0.311 0.512 rs381619864876 72000026 ClG 0.598 0.584 0.575 rs230471565073 72000223 ClG 0.660 0.643 0.534 rs230127267149 72002299 C/T 0.974 0.972 0.853 rs230127367549 72002699 C/T 0.952 0.966 0.409 rs378456371660 72006810 A/C 0.495 0.508 0.590 rs378456171906 72007056 C/T 0.470 0.466 0.872 rs378456071911 72007061 A/C

[0308] The LOXLI proximal SNPs were also allelotyped in the replication cohorts using the methods described herein and the primers provided in Tables 49 and 50. The replication allelotyping results for replication cohort # 1 and replication cohort #2 are provided in Tables 52 and 53, respectively.

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in SEQ PositionAllele Case Control Value II? NO: AF AF

rs1048661213 , 71935363G/T 0.250 0.252 0.953 rs3825942249 71935399C/T 0.126 0.141 0.539 rs15504361824 71936974C/T 0.397 0.405 0.845 rs15504382057 71937207C/T

rs15504392306 71937456A/T

rs21652412869 71938019C/T 0.429 0.425 0.894 rs15504333976 71939126A/C

rs30563144288 71939438-/TC

rs24152044290 71939440A/C 0.162 unt ed 0.176 rs19923144434 71939584C/G 0.583 0.594 0.756 rs14401015298 71940448A/G

rs22894145467 71940617A/G

rs24152058486 71943636C/G

rs28998078487 71943637A/T 0.939 unt ed NA

rs893815 8831 71943981C/G

rs30563429036 71944186-/AG 0.317 0.311 0.846 rs40772849058 71944208A/G 0.372 0.365 0.881 rs893816 9131 71944281C/T 0.510 0.518 0.793 rs893817 9732 71944882A/G 0.178 0.170 0.784 rs893818 9862 71945012A/G 0.327 0.320 0.818 rs893819 10191 71945341A/G 0.610 unt ed NA

rs893820 10270 71945420C/T 0.874 0.903 0.218 rs230471916167 71951317C/T 0.309 0.289 0.537 rs100150717620 71952770G/T 0.908 0.924 0.525 rs153016717751 71952901C/T

rs153016817764 71952914C/T

rs153016917787 71952937C/T 0.237 0.202 0.249 rs230472019401 71954551C/T 0.935 0.944 0.661 rs230472121021 71956171A/C 0.759 0.823 0.091 rs893821 21902 71957052C/T 0.114 0.122 0.778 dbSNP Position~.inChromosomeAl/A2 F A2 F A2 F p-rs# SEQ Position Allele Case Control Value ID NO: 10 AF AF

rs750460 22173 71957323 C/T 0.469 0.440 0.433 rs230472222416 71957566 C/T 0.729 0.746 0.572 rs144010222653 71957803 A/G

rs8818 24945 71960095 C/G

rs3522 25011 71960161 C/T 0.416 0.440 0.454 rs241520628563 71963713 C/T 0.362 unt ed NA

rs198452648574 71983724 C/G 0.593 unt ed rs198452548710 71983860 C/T

rs303165348880 71984030 -/TTG

rs241518750194 71985344 C/T

rs2507 56343 71991493 A/G 0.676 0.653 0.471 rs228941156455 71991605 C/T

rs320207756729 71991879 C/T

rs228941256759 71991909 A/G 0.964 0.954 0.626 rs228941356895 71992045 A/G 0.963 0.959 0.833 rs106108257036 71992186 ClG

rs227760057702 71992852 C/G

rs734854 62515 71997665 C/T 0.403 0.383 0.531 rs241518862629 71997779 C/G 0.555 0.564 0.809 rs321469563501 71998651 -/C 0.289 0.300 0.721 rs381619763547 71998697 C/T 0.304 0.308 0.904 rs381619864876 72000026 ClG 0.601 0.598 0.922 rs230471565073 72000223 C/G 0.649 0.678 0.457 rs230127267149 72002299 C/T 0.966 0.959 0.752 rs230127367549 72002699 C/T 0.935 0.946 0.649 rs378456371660 72006810 A/C 0.502 0.516 0.685 rs378456171906 72007056 C/T 0.438 0.471 0.319 rs378456071911 72007061 A/C

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in SEQ Position AlleleCase Control Value ID NO: 10 AF AF

rs1048661213 71935363 G/T 0.307 0.203 0.007 rs3825942249 71935399 C/T 0.084 0.159 0.031 rs15504361824 71936974 C/T 0.406 0.445 0.274 rs15504382057 71937207 C/T

rs15504392306 71937456 A/T

rs21652412869 71938019 C/T 0.423 0.439 0.669 rs15504333976 71939126 A/C

rs30563144288 71939438 -/TC

rs24152044290 71939440 A/C 0.200 unt ed rs19923144434 71939584 C/G 0.618 0.612 0.854 rs14401015298 71940448 A/G

rs22894145467 71940617 A/G

rs24152058486 71943636 C/G

rs28998078487 71943637 A/T 0.965 0.956 0.737 rs893815 8831 71943981 C/G

rs30563429036 71944186 -/AG 0.257 0.264 0.833 rs40772849058 71944208 A/G 0.341 0.345 0.905 rs893816 9131 71944281 C/T 0.526 0.509 0.655 rs893817 9732 71944882 A/G 0.142 0.139 0.895 rs893818 9862 71945012 A/G 0.290 0.302 0.712 rs893819 10191 71945341 A/G 0.671 0.642 0.431 rs893820 10270 71945420 C/T 0.934 0.922 0.681 rs230471916167 71951317 C/T 0.334 0.316 0.613 rs100150717620 71952770 G/T 0.911 0.903 0.741 rs153016717751 71952901 C/T

rs153016817764 71952914 C/T

rs153016917787 71952937 C/T 0.173 0.203 0.360 rs230472019401 71954551 C/T 0.951 0.952 0.952 rs230472121021 71956171 A/C 0.848 0.799 0.150 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in SEQ Position AlleleCase Control Value ID NO: 10 AF AF

rs89382121902 71957052 C/T 0.112 0.106 0.829 rs75046022173 71957323 C/T 0.478 0.435 0.242 rs230472222416 71957566 C/T 0.764 0.748 0.626 rs144010222653 71957803 A/G

rs8818 24945 71960095 C/G

rs3522 25011 71960161 C/T 0.435 0.444 0.814 rs241520628563 71963713 C/T 0.394 0.366 0.419 rs198452648574 71983724 C/G

rs198452548710 71983860 C/T

rs303165348880 71984030 -/TTG

rs241518750194 71985344 C/T

rs2507 56343 71991493 A/G 0.630 0.653 0.509 rs228941156455 71991605 C/T

rs320207756729 71991879 C/T

rs228941256759 71991909 A/G 0.979 unt ed rs228941356895 71992045 A/G

rs106108257036 71992186 C/G

rs227760057702 71992852 C/G

rs73485462515 71997665 C/T 0.354 0.372 0.611 rs241518862629 71997779 C/G 0.502 0.497 0.897 rs321469563501 71998651 -/C 0.331 0.300 0.367 rs381619763547 71998697 C/T 0.357 0.317 0.259 rs381619864876 72000026 C/G 0.594 0.562 0.416 rs230471565073 72000223 C/G 0.674 0.587 0.020 rs230127267149 72002299 C/T

rs230127367549 72002699 C/T 0.973 unt ed rs378456371660 72006810 A/C 0.485 0.496 0.777 rs378456171906 72007056 C/T 0.511 0.459 0.174 rs378456071911 72007061 A/C

[0309] Allelotyping results were considered particularly significant with a calculated p-value of less than or equal to 0.05 for allelotype results. These values are indicated in bold. The allelotyping p-values were plotted in Figure 1H for the discovery cohort. The position of each SNP on the chromosome is presented on the x-axis. The y-axis gives the negative logarithm (base 10) of the p-value comparing the estimated allele in the case group to that of the control group. The minor allele frequency of the control group for each SNP designated by an X or other symbol on the graphs in Figure lE can be determined by consulting Table 51. For example, the left-most X on the left graph is at position 71935363. By proceeding down the Table from top to bottom and across the graphs from left to right the allele frequency associated with each symbol shown can be determined.
[0310] To aid the interpretation, multiple lines have been added to the graph.
The broken horizontal lines are drawn at two common significance levels, 0.05 and 0.01.
The vertical broken lines are drawn every 20kb to assist in the interpretation of distances between SNPs. Two other lines are drawn to expose linear trends in the association of SNPs to the disease. The generally bottom-most curve is a nonlinear smoothcr through the data points on the graph using a local polynomial regression method (W.S. Cleveland, E. Grosse and W.M. Shyu (1992) Local regression models. Chapter 8 of Statistical Models in S eds J-M. Chambers and T.J. Hastie, Wadsworth &
Brooks/Cole.). The black line provides a local test for excess statistical significance to identify regions of association. This was created by use of a l Okb sliding window with lkb step sizes. Within each window, a chi-square goodness of fit test was applied to compare the proportion of SNPs that were significant at a test wise level of 0.01, to the proportion that would be expected by chance alone (0.05 for the methods used here). Resulting p-values that were less than 10-$ were truncated at that value.
[0311] Finally, the exons and introns of the genes in the covered region are plotted below each graph at the appropriate chromosomal positions. The gene boundary is indicated by the broken horizontal line. The exon positions are shown as thick, unbroken bars. An arrow is place at the 3' end of each gene to show the direction of transcription.
Example 12 CASPR4 Region Proximal SNPs [0312] It has been discovered that rs1395486 in the cell recognition protein CASPR4 gene is associated with occurrence of osteoarthritis in subjects. This gene product belongs to the neurexin family, members of which function in the nervous system as cell adhesion molecules and receptors.
Like other neurexin proteins, CASPR4 contains epidermal growth factor repeats and laminin G domains.
In addition, it includes an FS/8 type C domain, discoidin/neuropilin- and fibrinogen-like domains, and thrombospondin N-terminal-like domains. Alternative splicing of this gene results in 2 transcript variants encoding different isoforms. CASPR4 biological activity can be modulated by addition of an antibody, a recombinant binding partner, a binding agent, or a recombinant CASPR4 protein or functional fragment thereof.
[0313] Fifty-six additional allelic variants proximal to rs1395486 were identified and subsequently allelotyped in osteoarthritis case and control sample sets as described in Examples 1 and 2. The polymorphic variants are set forth in Table 54. The chromosome positions provided in column four of Table 54 are based on Genome "Build 34" of NCBI's GenBank.

dbSNP Chromo- Position ChromosomeAllele rs# some in SEQ Position Variants ID NO:

rs189675316 205 76177855 C/T

rs397445116 866 76178516 C/T

rs182077016 4212 76181862 C/T

rs142875316 5934 76183584 C/T

rs722229 16 11486 76189136 C/T

rs385175416 16969 76194619 A/G

rs234043016 22509 76200159 A/G

rs234043116 22796 76200446 AIG

rs115941516 28097 76205747 C/T

rs150683616 28626 76206276 C/T

rs150683716 28853 76206503 C/T

rs150683816 28873 76206523 C/T

rs966668 16 30155 76207805 A/G

rs191124516 30827 76208477 C/T

rs150683916 31956 76209606 C/T

rs150684016 32404 76210054 ~C~

dbSNP Chromo- Position ChromosomeAllele rs# some in SEQ Position Variants ID NO:

rs187627516 32944 76210594 A/G

rs191124216 35205 76212855 A/G

rs191124316 35227 76212877 C/T

rs981231 16 35781 76213431 C/T

rs150682916 41052 76218702 C/T

rs150683316 45051 76222701 A/G

rs139548616 46039 76223689 C/T

rs150683216 47276 76224926 A/G

rs150683016 47678 76225328 CIT

rs968537 16 47716 76225366 A/G

rs150681616 51014 76228664 A/G

rs150682816 54408 76232058 A/G

rs150682716 54596 76232246 C/T

rs154296916 56853 76234503 CIG

rs139548416 61851 76239501 A/G

rs187627416 62016 76239666 A/G

rs187627316 62461 76240111 C/T

rs150682216 68257 76245907 C/G

rs150682016 69793 76247443 C/T

rs150681916 73976 76251626 A/C

rs150681816 73999 76251649 A/T

rs150681716 74053 76251703 A/G

rs139548816 75315 76252965 A/G

rs222153416 75729 76253379 G/T

rs191124416 76466 76254116 A/G

rs213562416 77216 76254866 C/T

rs213562316 77217 76254867 G/T

rs150683516 79239 76256889 C/G

rs150683416 80825 76258475 A/G

rs199565316 81060 76258710 C/G

rs199565216 81097 76258747 A/C

rs139548716 81426 76259076 G/T

rs394708316 84787 76262437 C/T

rs150682516 84896 76262546 A/T

rs150682416 85165 76262815 C/G

rs156711816 86502 76264152 C/G

rs103968316 86753 76264403 CIT

rs287977716 86941 76264591 C/T

rs187627216 88787 76266437 C/T

rs303587816 95598 76273248 -/AGAGC

Assa ~~for-Verifyin~ and Allelotypin~ SNPs [0314] The methods used to verify and allelotype the 56 proximal SNPs of Table 54 are the same methods described in Examples 1 and 2 herein. The primers and probes used in these assays are provided in Table 55 and Table 56, respectively.

dbSNP Fo rward Reverse rs# PCR primer PCR primer rs1896753ACGTTGGATGTTTGAAGAGAGGGACTAGAGACGTTGGATGGAAAATGAACTGGAATGGGG

rs3974451ACGTTGGATGTTGCATAAGGTGTGAGGAAGACGTTGGATGAATGGTGTTGGGA.AAACTGG

rs1820770ACGTTGGATGCTTGGAACCAACCCAAATGCACGTTGGATGGGCTGCATAGTAT-fCCACAG

rs1428753ACGTTGGATGCAATAGCTATCTCCTACTTGACGTTGGATGGATGCTTTGTATTGACAACC

rs722229ACGTTGGATGGAAGGAGGCTCACTATTTCCACGTTGGATGGGCTAGGGTAGCAAACATCA

rs3851754ACGTTGGATGAGGTTTGGAGAATGCCAACTACGTTGGATGAGATTGAATCAGA-fGGACTG

rs2340430ACGTTGGATGATGGCCTTCCAAAGATGTTCACGTTGGATGCATCTACAATCCCAATATGCC

rs2340431ACGTTGGATGTTTGTGCAACCTCTGCAAGCACGTTGGATGAGATGTCAGCAGGATGCATG

rs1159415ACGTTGGATGGCTTTCCAATGATTTGGGAGACGTTGGATGCTGGGTCTTCCTAATGTGTT

rs1506836ACGTTGGATGCCTGGGCACAGATTCATTTCACGTTGGATGCTGCAGCGACCTTTCATTCA

rs1506837ACGTTGGATGCTGACATTGAGCTAGTCTTTCACGTTGGATGGTAGTTGGTGAATTTGGTGG

rs1506838ACGTTGGATGGTAGTTGGTGAATTTGGTGGACGTTGGATGGACATTGAGCTAGTCTTTCC

rs966668ACGTTGGATGCACTTCATAGTGTGAAAAGTCACGTTGGATGCCAGTAAATGCAAGATTTTCC

rs1911245ACGTTGGATGAACAACTAGGCAATTCGGTGACGTTGGATGCCATCAGAAGTAAACCGTTTC

rs1506839ACGTTGGATGCCAAATTTTGCTTTGTTAGACACGTTGGATGTGCACAATTCAAGTGAAGTC

rs1506840ACGTTGGATGGGAAGAATGACCTTGTGTGGACGTTGGATGAGCTGTGAGTGAGGATGATG

rs1876275ACGTTGGATGAACTGTTCTCTGCCCTTTGGACGTTGGATGTTCACGGACATAAGGGAAGG

rs1911242ACGTTGGATGGTTCCCTAAGTACTTTAGAAACGTTGGATGCTCTGCAAAGCAATAAGCTAC

rs1911243ACGTTGGATGCTTATAATTCAGTTCCCTAAGACGTTGGATGGCAATAAGCTACCAAAATAG

rs981231ACGTTGGATGATGCTAACCTGTCTAAATCCACGTTGGATGTAGTGCTCTGGACTAGAAAG

rs1506829ACGTTGGATGTGGAAAGTTGCAATTCCCTGACGTTGGATGCCATCTTAAAACCATGCGAG

rs1506833ACGTTGGATGGTTTTATCTGGTTCCTTACAGACGTTGGATGGCTGTATACGTACTTTAAAC

rs1395486ACGTTGGATGCTCATTTATTTCATGTTCACACGTTGGATGTGCTGGAATAATGATTGTTG

rs1506832ACGTTGGATGGGTAATGGTCATAAGAATGCCACGTTGGATGGAGCTCAATTAGCATCTCTC

rs1506830ACGTTGGATGCAACAGTAAAGGCATGAAAGACGTTGGATGCATTGGACTATCAAAAAGTG

rs968537ACGTTGGATGATTATTTGGTGGGAAGAGGGACGTTGGATGAAATGTTACGTAGGCCAAAC

rs1506816ACGTTGGATGTACATATGACCACTGTTTCCACGTTGGATGCTAAGCAGGGAAGTAGTAAG

rs1506828ACGTTGGATGGAGCTTTTTCCATTAGACCCACGTTGGATGGTTGAAAATCAGACAAGGGC

rs1506827ACGTTGGATGAATGCGCTATATCTGATGACACGTTGGATGAACCCATTTCTTAGCCAGAG

rs1542969ACGTTGGATGCAGATTACAGCCAAGTTTGCACGTTGGATGGGTTTGAATTCCCAAGACAG

rs1395484ACGTTGGATGCAAGCTCACATAACACAGGCACGTTGGATGAAGAGATGCCGCGATTTTGG

rs1876274ACGTTGGATGGGTATCTGATCATCTGCCTGACGTTGGATGGGGATTGATTGACAAGGAG

rs1876273ACGTTGGATGTGGAAGAAACATAGCTCCTGACGTTGGATGAAAATCCCTCCAGTGTTTGC

rs1506822ACGTTGGATGTTCTCCAGATCTGCAAACAGACGTTGGATGGTAATGAGAGAAGTAGAGGC

rs1506820ACGTTGGATGTTCTATATATGTGTGTGTGCACGTTGGATGTTAGGGTTCTCTAGAAAGAC

rs1506819ACGTTGGATGTGAGGGAATTGTGTCTGCAGACGTTGGATGGCCAGAGAGGCTAGAAATTG

rs1506818ACGTTGGATGAGGGCTGCTTAGCATTTCACACGTTGGATGAGATCAGAGAGCAATGGTCC

rs1506817ACGTTGGATGCCTCTTTCTCGTGCTTTCTCACGTTGGATGCTCAGATCCTTGG CCAATTC

rs1395488ACGTTGGATGGACACTTGAATGCATCACCGACGTTGGATGGGTGACTTCTGTGACATTGC

rs2221534ACGTTGGATGTAATGCAGGTCTCAAGTGCCACGTTGGATGCAAATCAGACTGAGTCGCTG

rs1911244ACGTTGGATGACCTGTATTCCTGTTCCAGGACGTTGGATGCAACATTCTACTTCCTGGGC

rs2135624ACGTTGGATGGTACGCCCTACTCTCATATCACGTTGGATGAGCTCTTAATTCCATGGCAG

rs2135623ACGTTGGATGGTACGCCCTACTCTCATATCACGTTGGATGAGCTCTTAATTCCATGGCAG

rs1506835ACGTTGGATGAATT-AGCTGGACATGGTGGCACGTTGGATGTCAAGTGAACCTCCAACCTC

rs1506834ACGTTGGATGACATTTTCCCAGCACTGTCCACGTTGGATGCTCACTCCTACTCTGAGTAC

rs1995653ACGTTGGATGCCAGCCTTCTGTTACTCTTGACGTTGGATGCTGTCCTCATGGTGTTTCCA

rs1995652ACGTTGGATGCGTGTTACAACCTGTAATGCACGTTGGATGACATAAATATGGCCCCTGTC

rs1395487ACGTTGGATGAAAAGCTTTAGGTGCCACAGACGTTGGATGGCTTGTGTTACTT-f'AGCTAC

rs3947083ACGTTGGATGAAGGTGGGCTCTTTATAGTGACGTTGGATGGAGGTGTGATGGT-fATGTTTC

rs1506825ACGTTGGATGCCTGCATATGATGTTCTGTGACGTTGGATGTAGCAGCTTTCGGTGTATAG

dbSNP Forward Reverse rs# PCR primer PCR primer rs1506824ACGTTGGATGAGCAATGGATTCAAATGCTCACGTTGGATGCACTGGTCGATGAAAAATAC

rs1567118ACGTTGGATGTCGGCCAATCTGTCCAAATGACGTTGGATGAATTGTCCCCGTTTCCACAG

rs1039683ACGTTGGATGTGATGTGTGGAGGCATGTTGACGTTGGATGACAGGCAACAACTGCCAAAG

rs2879777ACGTTGGATGCTAATCATGTGCGATGAGGGACGTTGGATGAAGAAGAGATGGGCCATAGT

rs1876272ACGTTGGATGTTCTTTGTCTGGAGTGGGAGACGTTGGATGGGTTCCAACACTAGCAGTTC

rs3035878ACGTTGGATGTTCTACAAGGAGCTGTGTAGACGTTGGATGCTGACTGGTAAATTCACGAC

dbSNP Extend Term rs# Primer Mix rs1896753 GGAATT1-AATTTGGTGCCTCTTCAACT

rs3974451 TTCAGT-TTCAGCTTTCTGCATA ACG

rs1820770 GAACCAACCCAAATGCCCATCA ACT

rs1428753 TAACATT-f'ACTGATAGAATAAAGCACT

rs722229 TTCCCTGCAGAAAATGAGACA ACT

rs3851754 AACTCACACACACACACAGAA ACT

rs2340430 CGTTG GGACCTATAGGTATG ACT

rs2340431 CTCTGCAAGCTGGAAAGGAC ACT

rs1159415 TATGTTTAGGAACATTTTCCTAACACT

rs1506836 GTCTCACAGCTTGAAGATGC ACG

rs1506837 CATTGAGCTAGTCTTTCCTCTGT ACG

rs1506838 GTTGGTGAATTTGGTGGAGAATCTACT

rs966668 TCATAGT-GTGAAAAGTCTAAAAAAACT

rs1911245 TTCCTCTTTTTCAGACAAAATTG ACG

rs1506839 AATTTTGCTTTGTTAGACCTTAGGACG

rs1506840 GCTGGTGTCCTGTGAAATTG ACG

rs1876275 TCTTGGTTCAGGTATCACCTA ACG

rs1911242 TAGAAAAATTTGCCTTTTGAGAAAACG

rs1911243 TAATTCA.GTTCCCTAAGTACTTTAACT

rs981231 CCTGTCTAAATCCATTTGATTAAAACT

rs1506829 GATCTAAATAGCTACTGGGAAA ACT

rs1506833 TCTGGT'>-CCTTACAGAAACACTTAACG

rs1395486 TTTCATGTTCACAAAAAATCTTCTACG

rs1506832 GGTCATAAGAATGCCATTATTCT ACG

rs1506830 AATAATATGTTTGGCCTACGTAA ACG

rs968537 AGGGAGGTAAGAGTCAACAGTAA ACT

rs1506816 ATATGACCACTGTTTCCTCATTT ACT

rs1506828 CCATTAGACCCCTTAGCATAT ACG

rs1506827 TGACAA'1-AGAAACTAAGACAAATAACT

rs1542969 GCCAAGTTTGCATCTTTCATGT ACT

rs1395484 AACACAGGCACAGCTGTGAT ACT

rs1876274 CTAATTCACAAATATTCCCTTACTACT

rs1876273 TAGCTCCTGGCCCTACCAT ACT

rs1506822 CTGCAAACAGGATCACTGCT ACT

rs1506820 ATATACAGAACACACACACACA ACG

rs1506819 TCTGCAGGAGCACGGACC CGT

rs1506818 GGCCAAGGATCTGAGGGAA CGT

dbSNP Extend Term rs# Primer Mix rs1506817 TGCTTTCTCTAGGGCTGCTT ACT

rs1395488 TGAATGCATCACCGGAGGAT ACT

rs2221534 CTCAAGTGCCTATCTATCATG CGT

rs1911244 TTCCAGGTTAGAATTCCAGAGAT ACG

rs2135624 CTCTCATATCAATTCTCCCTGTT ACG

rs2135623 CTCTCATATCAATTCTCCCTGT ACT

rs1506835 GACATGGTGGCAAATTCCTGTA ACT

rs1506834 ACTGTCCCA'1-TCACTGTCATAAACT

rs1995653 TTCTGTTACTC-TTGATCAGAATGCACT

rs1995652 TAATGCTTTTA~'GAACTTAGTTGTACT

rs1395487 CTTTAGGTGCCACAGAAGATA CGT

rs3947083 GGGCTCTTTA'rAGTGTATTTTCCTACG

rs1506825 ATACTGTGAGAAAGATGAAGGT CGT

rs1506824 CAAATGCTCAAATATCAATATGTGACT

rs1567118 TGTCCAAATGGCAATGTTGGT ACT

rs1039683 GGAGGCATGTT-GGAACTTACAGACACT

rs2879777 GAGGGGTGGTCACACAGC ACT

rs1876272 CTGGAGTGGGAGACAGGGT ACG

rs3035878 TGTGTAGCTAAATGTTGAGCAGAGACT
~

Genetic Anal, skis [0315] Allelotyping results from the discovery cohort are shown for cases and controls in Table 57.
The allele frequency for the A2 allele is noted in the fifth and sixth columns for osteoarthritis case pools and control pools, respectively, where "AF" is allele frequency. The allele frequency for the A1 allele can be easily calculated by subtracting the A2 allele frequency from 1 (A1 AF
= 1-A2 AF). For example, the SNP rs1896753 has the following case arid control allele frequencies: case A1 (A) = 0.79;
case A2 (T) = 0.21; control A1 (A) = 0.81; and control A2 (T) = 0.19, where the nucleotide is provided in paranthesis. Some SNPs are labeled "untyped" because of failed assays.

dbSNP Position ChromosomeA.1JA2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 11 rs1896753 205 76177855 C/T

rs3974451 866 76178516 C/T

rs1820770 4212 76181862 C/T

rs1428753 5934 76183584 C/T 0.486 0.467 0.459 rs722229 11486 76189136 C/T

rs3851754 16969 76194619 A/G 0.287 0.300 0.569 rs2340430 22509 76200159 A/G 0.488 0.523 0.155 rs2340431 22796 76200446 A/G 0.030 0.028 0.844 rs1159415 28097 76205747 C/T 0.480 0.477 0.919 rs1506836 28626 76206276 C/T 0.401 0.404 0.891 rs1506837 28853 76206503 C/T 0.394 0.396 0.933 rs1506838 28873 76206523 C/T 0.334 0.343 0.727 rs966668 30155 76207805 A/G

rs1911245 30827 76208477 C/T 0.836 0.824 0.631 rs1506839 31956 76209606 C/T 0.434 0.436 0.936 rs1506840 32404 76210054 C/T 0.382 0.381 0.993 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 11 rs1876275 32944 76210594 A/G 0.463 0.461 0.918 rs1911242 35205 76212855 A/G 0.419 0.410 0.703 rs1911243 35227 76212877 C/T

rs981231 35781 76213431 C/T 0.451 0.430 0.510 rs1506829 41052 76218702 C/T 0.393 0.379 0.576 rs1506833 45051 76222701 A/G 0.509 0.530 0.378 rs1395486 46039 76223689 C/T

rs1506832 47276 76224926 A/G 0.518 0.516 0.949 rs1506830 47678 76225328 C/T 0.036 0.031 0.710 rs968537 47716 76225366 A/G 0.243 0.275 0.175 rs1506816 51014 76228664 A/G 0.392 0.369 0.348 rs1506828 54408 76232058 A/G 0.418 0.413 0.816 rs1506827 54596 76232246 C/T 0.432 0.449 0.477 rs1542969 56853 76234503 C/G

rs1395484 61851 76239501 A/G 0.417 0.441 0.349 rs1876274 62016 76239666 A/G 0.381 0.369 0.629 rs1876273 62461 76240111 C/T 0.382 0.364 0.445 rs150(i82268257 76245907 C/G 0.355 0.351 0.855 rs1506820 69793 76247443 C/T 0.326 0.256 0.054 rs1506819 73976 76251626 A/C 0.446 0.424 0.358 rs1506818 73999 76251649 A/T 0.126 0.145 0.465 rs1506817 74053 76251703 A/G 0.186 0.199 0.570 rs1395488 75315 76252965 A/G 0.489 0.499 0.689 rs2221534 75729 76253379 G/T 0.450 0.431 0.455 rs1911244 76466 76254116 A/G 0.493 0.491 0.960 rs2135624 77216 76254866 C/T

rs2135623 77217 76254867 G/T 0.034 0.032 0.899 rs1506835 79239 76256889 C/G 0.549 0.538 0.666 rs1506834 80825 76258475 A/G 0.390 0.392 0.958 rs1995653 81060 76258710 C/G 0.396 0.402 0.783 rs1995652 81097 76258747 A/C 0.436 0.435 0.979 rs1395487 81426 76259076 G/T 0.505 0.504 0.975 rs3947083 84787 76262437 C/T 0.373 0.366 0.773 rs1506825 84896 76262546 A/T 0.412 0.398 0.569 rs1506824 85165 76262815 C/G 0.444 0.414 0.242 rs1567118 86502 76264152 C/G 0.032 0.024 0.557 rs1039683 86753 76264403 C/T 0.382 0.373 0.707 rs2879777 86941 76264591 C/T 0.269 0.279 0.676 rs1876272 88787 76266437 C/T

rs3035878 95598 76273248 -/AGAGC0.978 unt ed NA

[0316] The CASPR4 proximal SNPs were also allelotyped in the replication cohorts using the methods described herein and the primers provided in Tables 55 and 56. The replication allelotyping results for replication cohort #1 and replication cohort #2 are provided in Tables 58 and 59, respectively.

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in SEQ Position AlleleCase Control Value ID NO: AF AF

rs1896753205 76177855 C/T

rs3974451866 76178516 C/T

rs18207704212 76181862 C/T

rs14287535934 76183584 C/T 0.463 0.474 0.756 rs722229 11486 76189136 C/T

rs385175416969 76194619 A/G 0.283 0.309 0.375 rs234043022509 76200159 A/G 0.494 0.519 0.477 rs234043122796 76200446 A/G 0.035 0.028 0.748 rs115941528097 ~ 76205747 C/T 0.436 0.472 __ ~ ~ ~ ~ ~ 0.287 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in SEQ PositionAllele Case Control Value ID NO: AF AF

rs150683628626 76206276C/T 0.392 0.401 0.786 rs150683728853 76206503C/T 0.388 0.399 0.727 rs150683828873 76206523C/T 0.318 0.327 0.778 rs966668 30155 76207805A/G

rs191124530827 76208477C/T 0.825 0.821 0.896 rs150683931956 76209606C/T 0.450 0.441 0.817 rs150684032404 76210054C/T 0.379 0.383 0.926 rs187627532944 76210594A/G 0.469 0.470 0.986 rs191124235205 76212855A/G 0.437 0.415 0.514 rs191124335227 76212877C/T

rs981231 35781 76213431C/T 0.449 0.414 0.415 rs150682941052 76218702C/T 0.398 0.394 0.894 rs150683345051 76222701A/G 0.515 0.544 0.393 rs139548646039 76223689C/T

rs150683247276 76224926A/G 0.526 0.511 0.720 rs150683047678 76225328C/T 0.053 0.039 0.488 rs968537 47716 76225366A/G 0.241 0.298 0.045 rs150681651014 76228664A/G 0.379 0.370 0.771 rs150682854408 76232058A/G 0.416 0.429 0.706 rs150682754596 76232246C/T 0.428 0.435 0.836 rs154296956853 76234503C/G

rs139548461851 76239501A/G 0.418 0.459 0.208 rs187627462016 76239666A/G 0.384 0.382 0.942 rs 187627362461 76240111C/T 0.393 0.360 0.271 rs150682268257 76245907C/G 0.353 0.368 0.637 rs150682069793 76247443C/T 0.288 unt ed NA

rs150681973976 76251626A/C 0.453 0.424 0.378 rs150681873999 76251649AIT 0.149 NA 0.126 rs150681774053 76251703A/G 0.195 0.212 0.573 rs139548875315 76252965A/G 0.490 0.490 1.000 rs222153475729 76253379G/T 0.446 0.433 0.711 rs191124476466 76254116A/G 0.495 0.480 0.646 rs213562477216 76254866C/T

rs213562377217 76254867G/T 0.027 0.030 0.896 rs150683579239 76256889C/G 0.563 0.556 0.848 rs150683480825 76258475A/G 0.377 0.388 0.722 rs199565381060 76258710C/G 0.381 0.395 0.675 rs199565281097 76258747A/C 0.435 0.423 0.750 rs139548781426 76259076G/T 0.505 0.500 0.874 rs394708384787 76262437C/T 0.367 0.370 0.929 rs150682584896 76262546A/T 0.406 0.397 0.798 rs150682485165 76262815C/G 0.446 0.413 0.361 rs156711886502 76264152C/G 0.029 0.023 0.776 rs103968386753 76264403C/T 0.376 0.365 0.729 rs287977786941 76264591C/T 0.265 0.278 0.669 rs187627288787 76266437C/T

0.972 untyped rs303587895598 76273248/AGAGC NA

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in SEQ Position AlleleCase Control Value ID NO: AF AF

rs1896753205 76177855 C/T

rs3974451866 76178516 C/T

rs18207704212 76181862 C/T

rs14287535934 76183584 C/T 0.515 0.457 0.124 rs72222911486 76189136 C/T

rs385175416969 76194619 A/G 0.292 0.286 0.868 rs234043022509 76200159 A/G 0.480 0.531 0.169 rs234043122796 76200446 A/G 0.024 0.027 0.900 rs115941528097 76205747 CIT 0.535 0.485 0.252 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in SEQ PositionAlleleCase Co, ntrolValue ID NO: 11 AF AF

rs150683628626 76206276C/T 0.412 0.410 _ 0.947 rs150683728853 76206503C/T 0.402 0.391 0.768 rs150683828873 76206523C/T 0.355 0.368 0.734 rs96666830155 76207805A/G

rs191124530827 76208477C/T 0.849 0.828 0.569 rs150683931956 76209606C/T 0.414 0.428 0.746 rs150684032404 76210054C/T 0.384 0.379 0.905 rs187627532944 76210594A/G 0.456 0.447 0.805 rs191124235205 76212855A/G 0.397 0.402 0.892 rs191124335227 76212877C/T

rs98123135781 76213431C/T 0.454 0.455 0.971 rs150682941052 76218702C/T 0.386 0.356 0.424 rs150683345051 76222701A/G 0.500 0.509 0.811 rs139548646039 76223689C/T

rs150683247276 76224926A/G 0.508 0.524 0.689 rs150683047678 76225328C/T

rs96853747716 76225366A/G 0.246 0.237 0.806 rs150681651014 76228664A/G 0.408 0.367 0.284 rs150682854408 76232058A/G 0.421 0.387 0.358 rs150682754596 76232246C/T 0.436 0.471 0.346 rs154296956853 76234503C/G

rs139548461851 76239501A/G 0.416 0.413 0.938 rs187627462016 76239666A/G 0.376 0.350 0.447 rs187627362461 76240111C/T 0.367 0.370 0.924 rs150682268257 76245907C/G 0.358 0.325 0.355 rs150682069793 76247443C/T 0.373 0.256 0.007 rs150681973976 76251626A/C 0.438 0.424 0.703 rs150681873999 76251649A/T 0.139 -0.013 rs150681774053 76251703A/G 0.174 0.178 0.897 rs139548875315 76252965A/G 0.487 0.512 0.505 rs222153475729 76253379G/T 0.455 0.429 0.463 rs191124476466 76254116A/G 0.489 0.509 0.581 rs213562477216 76254866C/T

rs213562377217 76254867G/T 0.042 0.035 0.748 rs150683579239 76256889C/G 0.531 0.510 0.562 rs150683480825 76258475A/G 0.407 0.397 0.787 rs199565381060 76258710C/G 0.414 0.413 0.984 rs199565281097 76258747A/C 0.437 0.455 0.629 rs139548781426 76259076G/T 0.506 0.512 0.869 rs394708384787 76262437C/T 0.379 0.359 0.559 rs150682584896 76262546A/T 0.419 0.399 0.579 rs150682485165 76262815C/G 0.442 0.414 0.471 rs156711886502 76264152C/G 0.036 0.025 0.574 rs103968386753 76264403C/T 0.389 0.385 0.910 rs287977786941 76264591C/T 0.275 0.280 0.883 rs187627288787 76266437C/T

rs303587895598 76273248- untyped 0.980 /AGAG NA
C

[0317] Allelotyping results were considered particularly significant with a calculated p-value of less than or equal to 0.05 for allelotype results. These values are indicated ire bold. The allelotyping p-values were plotted in Figure lI for the discovery cohort. The position of each SNP on the chromosome is presented on the x-axis. The y-axis gives the negative logarithm (base 10]
of the p-value comparing the estimated allele in the case group to that of the control group. The minor allele frequency of the control group for each SNP designated by an X or other symbol on the grapras in Figure lI can be determined by consulting Table 57. For example, the left-most X on the left graph is at position 76177855. By proceeding down the Table from top to bottom and across the graphs from left to right the allele frequency associated with each symbol shown can be determined.
[0318] To aid the interpretation, multiple lines have been added to the graph.
The broken horizontal lines are drawn at two common significance levels, 0.05 and 0.01.
The vertical broken lines are drawn every 20kb to assist in the interpretation of distances between SNPs. Two other lines are drawn to expose linear trends in the association of SNPs to the disease. The generally bottom-most curve is a nonlinear smoother through the data points on the graph using a local polynomial regression method (W.S. Cleveland, E. Grosse and W.M. Shyu (1992) Local regression models. Chapte=r 8 of Statistical Models in S eds J.M. Chambers and T.J. Hastie, Wadsworth &
Brooks/Cole.). Th a black line provides a local test for excess statistical significance to identify regions of association. This was created by use of a lOkb sliding window with lkb step sizes. Within each window, a chi-square goodness of fit test was applied to compare the proportion of SNPs that were significant at a rtest wise level of 0.01, to the proportion that would be expected by chance alone (0.05 for the methods used here). Resulting p-values that were less than 10-8 were truncated at that value.
[0319] Finally, the exons and introns of the genes in the covered region are plotted below each graph at the appropriate chromosomal positions. The gene boundary is indicated by the broken horizontal line. The exon positions are shown as thick, unbroken bars. An arrow is place at -the 3' end of each gene to show the direction of transcription.
Example 13 APOL3 Region Proximal SNPs [0320] It has been discovered that SNP rs132659 inAPOL3 is associated with occurrence of osteoarthritis in subjects. APOL3 belongs to the high density lipoprotein family that plays a central role in cholesterol transport. The cholesterol content of membranes is important in cellular proce sses such as modulating gene transcription and signal transduction both in the adult brain and during neurodevelopment. It has been shown that the APOL1-APOL4 gene cluster on chromosome 22 exists only in primates (humans and African green monkeys) and not in dogs, pigs, or rodents, suggesting that this gene cluster has arisen recently in evolution (Monajemi et. al., Genofnies 79: 539-546, 2002). Six transcript variants encoding three different isoforms have been identified.
[0321] Expression of this gene is upregulated by tumor necrosis factor-alpha in endothe lial cells lining the normal and atherosclerotic iliac artery and aorta (Horrevoets et.
al., Blood 93: 3418-3431, 1999). APOL3 is genetically linked to OA and may play a role in the pathophysiology of OA brought about by inflammation. APOL3 is likely inhibited by a small molecule inhibitor or by specific antibodies. APOL3 activity may be increased in a subject by administeringAPOL3 recombinant protein or a functional fragment thereof.
[0322] Two hundred-nineteen additional allelic variants proximal to rs132659 were identified and subsequently allelotyped in osteoarthritis case and control sample sets as described in Examples 1 and 2.

The polymorphic variants are set forth in Table 60. The chromosome positions provided in column four of Table 60 are based on Genome "Build 34" of NCBI's GenBank.

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs388881822 201 34781551 c/t rs201060522 425 34781775 a/

rs743919 22 1095 34782445 /t rs100813422 2201 34783551 a/c rs132607 22 7879 34789229 a/

rs147602922 8395 34789745 c/t rs147603022 8461 34789811 c/t rs241338022 9503 34790853 c/t rs205160922 10304 34791654 /t rs241338122 10695 34792045 c/t rs189460422 16300 34797650 a/

rs189460522 16444 34797794 /t rs132609 22 17591 34798941 c/t rs132610 22 17988 34799338 -/a rs132611 22 19116 34800466 -/t rs132612 22 19358 34800708 c/t rs100879022 20300 34801650 a/

rs23085 22 20669 34802019 a/t rs105161 22 20891 34802241 a/

rs132613 22 21451 34802801 c/t rs132614 22 21978 34803328 c/t rs132615 22 22785 34804135 c/

rs132617 22 24248 34805598 c/t rs386572422 24770 34806120 c/t rs201965722 24844 34806194 a/

rs386572522 25066 34806416 /t rs201936422 25096 34806446 c/t rs200838322 25309 34806659 a/

rs398600222 25344 34806694 a/c rs388894222 25529 34806879 a/t rs388894322 25537 34806887 a/

rs388894422 25554 34806904 a/c rs132618 22 27963 34809313 a/t rs132619 22 28134 34809484 /t rs382734622 28356 34809706 a/

rs132620 22 29648 34810998 -/a rs132621 22 29986 34811336 a/

rs80575 22 30217 34811567 /t rs80578 22 30267 34811617 a/

rs80577 22 30315 34811665 a/

rs80578 22 30585 34811935 c/t rs80579 22 30724 34812074 a/c rs80580 22 30897 34812247 c/t rs132622 22 30931 34812281 c/t rs132623 22 31080 34812430 /t rs 13262422 31246 34812596 c/t rs132625 22 31373 34812723 a/t dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs13262622 31463 34812813 a/

rs13262722 31467 34812817 a/

rs180767222 32188 34813538 /t rs13262822 32288 34813638 c/t rs13262922 32520 34813870 a/t rs13263022 32594 34813944 a/c rs13263122 32657 34814007 a/c rs13263222 32677 34814027 a/

rs13263322 32764 34814114 c/t rs13263422 32784 34814134 al rs13263522 32830 34814180 c/t rs13263622 32872 34814222 c/t rs12960322 33121 34814471 a/c rs13263722 33348 34814698 /t rs378851822 33952 34815302 c/

rs13263822 34184 34815534 c/

rs13263922 34361 34815711 a/t rs13264022 35026 34816376 a/

rs13264122 35192 34816542 a/

rs13264222 35600 34816950 a/t rs13264322 36033 34817383 c/t rs13264422 36289 34817639 c/t rs13264522 38869 34820219 a/

rs201732922 39629 34820979 a/t rs73919822 40530 34821880 c/t rs13264722 41621 34822971 c/t rs209746522 42379 34823729 c/t rs210591522 42802 34824152 c/t rs13264822 42865 34824215 t/c rs13264922 43644 34824994 a/

rs 13265022 45051 34826401 c/t rs13265122 45828 34827178 a/c rs13265222 45829 34827179 a/t rs80584 22 46257 34827607 c/t rs13265322 47286 34828636 a/c rs91633422 47427 34828777 c/t rs 13265422 47963 34829313 c/t rs 13265522 48013 34829363 c/t rs13265622 48229 34829579 c/t rs383468422 48282 34829632 -/a rs13265722 48376 34829726 -/

rs91633522 48404 34829754 a/

rs93265922 49900 34831250 c/t rs13266022 52699 34834049 It rs13266122 52897 34834247 a/

rs13266222 53414 34834764 a/

rs13266322 53487 34834837 alt rs13266422 54112 34835462 /t rs13266722 55492 34836842 a/

rs 13267022 59766 34841116 c/t rs13267122 60307 34841657 a/

rs13267222 60701 34842051 alg ~

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs13267322 60952 34842302 al rs13267422 61401 34842751 c/t rs13267522 62379 34843729 c/t rs80585 22 62870 34844220 c/t rs80586 22 62879 34844229 a/

rs13267622 63499 34844849 a/t rs13267722 64284 34845634 -/a rs13267822 64408 34845758 a/

rs13268022 64760 34846110 a/

rs13268122 65230 34846580 a/

rs13268322 66127 34847477 a/

rs226959422 66634 34847984 c/t rs13268422 66686 34848036 a/

rs13268522 66694 34848044 c/

rs13268622 67113 34848463 a/

rs13268722 67257 34848607 a/

rs13268822 67403 34848753 a/

rs13268922 67609 34848959 a/

rs13269022 68418 34849768 -/a rs13269122 68610 34849960 c/

rs13269222 69629 34850979 c/t rs13269322 70024 34851374 a/

rs13269422 70848 34852198 a/

rs13269522 71428 34852778 c/

rs196626622 71553 34852903 c/t rs196626722 71633 34852983 a/

rs10680822 71768 34853118 a/c rs13269622 71769 34853119 a/

rs223982922 73039 34854389 a/

rs228515422 73325 34854675 a/

rs223983022 73412 34854762 a/c rs223983122 73547 34854897 c/t rs386572222 73769 34855119 a/t rs386572322 73806 34855156 a/

rs398599622 74467 34855817 c/t rs398599722 74472 34855822 c/t rs398599822 74473 34855823 a/

rs398599922 74482 34855832 c/t rs398600022 74494 34855844 a/c rs241338222 74592 34855942 a/

rs241338322 74670 34856020 /t rs241338422 74672 34856022 !t rs241338522 74714 34856064 /t rs241338622 74723 34856073 a/t rs189460622 74749 34856099 a/

rs91633622 74861 34856211 c/

rs91633722 74892 34856242 c/t rs91633822 74893 34856243 c/t rs13269722 75176 34856526 a/

rs12781 22 75705 34857055 a/

rs105398322 75989 34857339 a/

rs 1053982I 32 ~ 76027 ~ 34857377 ~ a/g -dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs222716722 77949 34859299 a/

rs222716822 77974 34859324 c/t rs13270022 78167 34859517 c/t rs307536422 78310 34859660 -/ct rs222716922 78415 34859765 c/t rs209746622 78575 34859925 c/t rs209746722 78590 34859940 c/t rs241338722 78709 34860059 c/t rs13270122 78875 34860225 c/t rs13270222 79864 34861214 c/t rs13270322 81316 34862666 c/t rs226959522 81320 34862670 a/

rs226959622 81409 34862759 c/t rs13270422 81737 34863087 c/t rs200746822 81843 34863193 a/

rs13270522 82102 34863452 clt rs200770622 82833 34864183 c/t rs 13270622 83461 34864811 c/t rs13270722 83624 34864974 c/t rs13270822 83660 34865010 c/

rs13270922 83701 34865051 a/t rs13271022 83708 34865058 al rs13271122 83782 34865132 c/t rs13271222 85707 34867057 a/

rs13271322 85717 34867067 a/

rs13271422 86486 34867836 c/t rs13271622 86833 34868183 a/

rs13271722 87115 34868465 c/t rs13271822 87234 34868584 a/

rs13271922 87479 34868829 /t rs13272022 87561 34868911 a/

rs13272122 87604 34868954 a/

rs13272222 87674 34869024 c/t rs13272322 87958 34869308 a/

rs13272422 87992 34869342 -/

rs13272522 88019 34869369 a/

rs13272622 88074 34869424 c/

rs13272722 88079 34869429 c/

rs13272822 88115 34869465 a/

rs13272922 88118 34869468 c/

rs13273022 88120 34869470 a/

rs13273122 88135 34869485 -/ctcat rs13273222 88142 34869492 /t rs13273322 88143 34869493 /t rs14057522 88149 34869499 aca/t rs13273422 88340 34869690 a/

rs13273522 88344 34869694 /t rs80587 22 88512 34869862 c/

rs13273622 88521 34869871 c/t rs13273722 88650 34870000 c/

rs13273822 88827 34870177 c/t rs180767322 89230 34870580 a/

1~~

dbSNP Chromo-Position Chromosome Allele rs# some in SEQ Position Variants ID NO:

rs201470022 89236 34870586 a/

rs132739 22 90754 34872104 /a rs181202322 90984 34872334 a/

rs181202422 91110 34872460 a/

rs200559022 92026 34873376 c/t rs132740 22 92954 34874304 c/t rs398600122 93375 34874725 -ltt c rs241339022 93794 34875144 c/t rs132743 22 94937 34876287 c/

rs132744 22 95068 34876418 c/t rs241339122 96188 34877538 a/

rs132749 22 97092 34878442 clt rs132750 22 98812 34880162 c/t rs132741 22 not ma not ma ed a/c ed rs241338822 not ma not ma ed a/t ed rs2413389~ 22 not mappednot mapped c/~
~ ~ ~

Assay for Verifying and AllelotXping SNPs [0323] The methods used to verify and allelotype the 219 proximal SNPs of Table 60 are the same methods described in Examples 1 and 2 herein. The primers and probes used in these assays are provided in Table 61 and Table 62, respectively.

dbSNP Forward Reverse rs# PCR primer PCR primer rs3888818ACGTTGGATGTGAGGTCAGGAGTTTGAGACACGTTGGATGCCATGCCCAGCTAATTTTCG

rs2010605ACGTTGGATGTGTGCTTTTTATGTCTTAGGACGTTGGATGGACTTTTAGAAGAAAAGTAC

rs743919ACGTTGGATGTTCTTCACCAAGCCCTCTTCACGTTGGATGCCCAACACACACAAAGATGG

rs1008134ACGTTGGATGACATATCCGGGCATCTTTTCACGTTGGATGCATCCACAGGATGCAATATC

rs132607ACGTTGGATGTAGTTTGCAGGTCACAAGGGACGTTGGATGGGAAGGAAGACCCAAACAGC

rs1476029ACGTTGGATGTGGGTGACAGAGATCCTTACACGTTGGATGAAACTCAGGGAAACGGACTC

rs1476030ACGTTGGATGATCCTAGCACTGGGATTTGGACGTTGGATGCGTTTCCCTGAGTTTCACTG

rs2413380ACGTTGGATGATGATACTGAGTCCAGGAGGACGTTGGATGAAAGGCTACTTCTTGCTCAC

rs2051609ACGTTGGATGTAATCCCAGCACTTTGGGAGACGTTGGATGACAGACGGGGTTTCATCATG

rs2413381ACGTTGGATGAGGGCTGCAGTAGAAAAGCGACGTTGGATGACGATGCGTGTGCCGACAG

rs1894604ACGTTGGATGAAGTGCTGCTGCAAAAAGAGACGTTGGATGTTCTCCACTTCCATTCTGTG

rs1894605ACGTTGGATGTGATGAGAGATGCAGATCGCACGTTGGATGTATTCAGAATTCAGCCTGCG

rs132609ACGTTGGATGGCATTTGAAAGGTCCGTATCACGTTGGATGCCCAAATCTGTCTTTTAGCC

rs132610ACGTTGGATGTTCTACAAGAGCTAGGGACCACGTTGGATGGATCTATTGCTGCTTAGGCC

rs132611ACGTTGGATGGCCTTCTTTACTCTGTCCTCACGTTGGATGGGTTTTCTTTCAGGTCCTCC

rs132612ACGTTGGATGAAAAATCTTCCCGCTACCTCACGTTGGATGTTCTGTGAGCTTTCTCTCTG

rs1008790ACGTTGGATGGTGAGGTCCCTTTTATGATGACGTTGGATGATAACAGCCCCTGACAGATG

rs23085ACGTTGGATGAAACCGTGCCAGCTGAGGATACGTTGGATGGTCGGCAAGGAAGAGGAATC

rs105161ACGTTGGATGAAGGAGCGGGAAATCTTTTGACGTTGGATGGTAGGAGGCTGAAATGCTAG

rs132613ACGTTGGATGATGTAAAACCAATGGCCTCCACGTTGGATGAAGCTTCAGATTGTTCACCC

rs132614ACGTTGGATGCAAGAGCCCTGCTTTGTGAGACGTTGGATGTCCTGCACCAGCAGAGATGA

rs132615ACGTTGGATGAAATCTGGAGGCTTGGTGACACGTTGGATGTGAGCATTCACATGGGACAG

rs132617ACGTTGGATGGAGAAGAAGAGTGTGTGTGCACGTTGGATGACAGCCACCTGAATTTGTGC

~rs3865724~ ACGTTGGATGTTCCTGGATAATTCCCATTCACGTTGGATGGCTGGATCACTGAAGAAGTA

1~9 dbSNP Forward Reverse rs# PCR primer PCR primer rs2019657ACGTTGGATGACGCCAGAACATTGTGTTTCACGTTGGATGGTGCCAGAAACATTCAAAGC

rs3865725ACGTTGGATGAATATAGAACTGCTGGGCGCACGTTGGATGTGACTTAGGAGAGGTTCTGG

rs2019364ACGTTGGATGTGACTTAGGAGAGGTTCTGGACGTTGGATGAATATAGAACTGCTGGGCGC

rs2008383ACGTTGGATGTGATTCTAGGAGCAGGACTGACGTTGGATGACATGGGTGACCCTATCAAG

rs3986002ACGTTGGATGCTTCTGTCCTTCTCTGTGTCACGTTGGATGCAGGCAGAGGATTTGTTTGG

rs3888942ACGTTGGATGCTGGGCTTTTGTGCTAAGAGACGTTGGATGGGGCCAATTTGCCCCATAAA

rs3888943ACGTTGGATGCTGGGCTTTTGTGCTAAGAGACGTTGGATGTTGGGCCAATTTGCCCCATA

rs3888944ACGTTGGATGATACAGCCCTTGCCACTATGACGTTGGATGTTGAAGACATGGAAGCAGGG

rs132618ACGTTGGATGAATCCGTGCCATCAGGCAAGACGTTGGATGCCTGCAATCGTTCTCTCTGC

rs132619ACGTTGGATGTCATCAGCAGAAGCTGAAGCACGTTGGATGGGTGTGATGTCACGCATAAC

rs3827346ACGTTGGATGAAGAGGTCCACAGAGGCTGACGTTGGATGAAAACAAGACCAGCAAGGGA

rs132620ACGTTGGATGTCACATTAGATCAGGAAGCCACGTTGGATGTTAGGCCAGTTTAGCAGAAA

rs132621ACGTTGGATGCTTCAAATCTGCAACTGGTGACGTTGGATGGATAGCTTAAGGACTCAGAG

rs80575ACGTTGGATGGCTGCACATGAACTCTCAAGACGTTGGATGTGACATGTGACAGTGAGACC

rs80576ACGTTGGATGTGAAGCTGTCACCTGCTAAGACGTTGGATGAACTCTCAAGCCACTTGACG

rs80577ACGTTGGATGAGTCCATAAGAGGTTCCATGACGTTGGATGAACTAATGCCTTAGCAGGTG

rs80578ACGTTGGATGACTGTTTCCCTGACAGCATGACGTTGGATGTGTAGAACAGAAGAGGGTCC

rs80579ACGTTGGATGTGGGAGTAGGGTGAGAAGAGACGTTGGATGACTCACTGGTCCTCTGCAAG

rs80580ACGTTGGATGTTCAATCAGATGGGCGTGTGACGTTGGATGGATGGCATCATGCTACTTGG

rs132622ACGTTGGATGTATGTCTTGGAGACTGGGACACGTTGGATGACCTGCTGTTCATTCTCAGG

rs132623ACGTTGGATGAGCTCTGTCCAACTCCATTCACGTTGGATGCTGAGGAACTGCACAAACAC

rs132624ACGTTGGATGTGCTGGGATTACAGGCATGAACGTTGGATGTCAAAGAAAGTCCTGCTGGG

rs132625ACGTTGGATGTTTCACGCCATTCTCCTGCCACGTTGGATGCGATGAAACCCCGTCTGTAC

rs132626ACGTTGGATGTGGAGTGCAGTGGCATGATCACGTTGGATGGCAGGAGAATGGCGTGAAAC

rs132627ACGTTGGATGAGGAGAATGGCGTGAAACCGACGTTGGATGAGACAGAGTCTTGCTTGTCC

rs1807672ACGTTGGATGGTGTGCTACAGCCTAAATGGACGTTGGATGAATACCCCATGTGACAGCTG

rs132628ACGTTGGATGTATAGACTGAGTTGTGTGCCACGTTGGATGTCCTTAAAGGCTCAATCTCC

rs132629ACGTTGGATGCTCTCTCCCTGTCTCTCTTTACGTTGGATGTGTGTCCTCACATGGCCTTC

rs132630ACGTTGGATGTTCCAAGGTGAAGGTGCCAGACGTTGGATGAAGGCCATGTGAGGACACAG

rs132631ACGTTGGATGGGTGGCTCCAACAACTGATGACGTTGGATGATCAACCCTGCTGGCACCTT

rs132632ACGTTGGATGCTTGGAATTTTTGCCTCCAGACGTTGGATGTCAGGATGCCTTAGTAAAAC

rs132633ACGTTGGATGAGAAGAGTGATTCACCAGGGACGTTGGATGGGAAAGCTCACTTTCTGGTG

rs132634ACGTTGGATGAAGTGCCATGGTGCTTTGTGACGTTGGATGGAAAGCATGGTGGAAAGCTC

rs132635ACGTTGGATGAATAGGCACATGGCAGAAGGACGTTGGATGCACCAGAAAGTGAGCTTTCC

rs132636ACGTTGGATGAAGCGTTTGACAATAGGCACACGTTGGATGAAAGTGAGCTTTCCACCATG

rs129603ACGTTGGATGGTGTCATATTGACACAGATTGACGTTGGATGAGGGTGTATATATATATACCC

rs132637ACGTTGGATGGCATCTTAGTACACAGCAGGACGTTGGATGTTCCCAAATCCCTGCAAACC

rs3788518ACGTTGGATGAATCCTTCAGAAGGGCTTGGACGTTGGATGGCCGCGTTATTAAACCACAG

rs132638ACGTTGGATGCATCCTTTCAGTGAAGGAGGACGTTGGATGTTGCCAAGGCAACTCAGTGA

rs132639ACGTTGGATGACACCTGGGCAAACAAAAGCACGTTGGATGAAGTTCCCCATAGTTGGCAG

rs132640ACGTTGGATGTAAGAAGCTCCAGGTGACACACGTTGGATGAAAAGAGTGACTCAGCGTCC

rs132641ACGTTGGATGAGGGTCAGCTGGGAGCAGAACGTTGGATGAGGGCTGAGAGAGGAGGTTG

rs132642ACGTTGGATGAAGAAGCAAGCCTACCTGAGACGTTGGATGAAACGAACCCTTCCAGTCAG

rs132643ACGTTGGATGATCACAGACACCCAGTACACACGTTGGATGACGTTCTGACAATGACCTGG

rs132644ACGTTGGATGGCATAGAGTGCAAGACACAGACGTTGGATGGGGCTCCACTCCCTTAAATA

rs132645ACGTTGGATGTGAAGGCAAACAGTACAAGAACGTTGGATGAAGTTAACCAAGTGTTTAC

rs2017329ACGTTGGATGCCTTCCCAATTAAAAGCAGCACGTTGGATGGGGCAACAAGAGTGAAATTC

rs739198ACGTTGGATGAAACTTTGGTCTCCACAACCACGTTGGATGTGAGTTTGTCTAAAGACCGG

rs132647ACGTTGGATGCCTCACTACAGAAACCATGGACGTTGGATGAACTCAACTGGTTCAACCAC

rs2097465ACGTTGGATGGAATTGACCAAACTGCAGGCACGTTGGATGAGGGTTGAAGCTGGATACTG

rs2105915ACGTTGGATGAACCCAGGAGTTCAGGACAAACGTTGGATGGGGAACTACAAGTGCATCAC

rs132648ACGTTGGATGGTGGCTCAGGGCTGTAATTCACGTTGGATGTGTCCTGAACTCCTGGGTTC

dbSNP Forward Reverse rs# PCR primer PCR primer rs132649ACGTTGGATGGTCCTCCCCAGTCTTATTACACGTTGGATGATTCAGAGGTTAGCTGGCTC

rs132650ACGTTGGATGAAAGTGCTGGGATTACAGGCACGTTGGATGCTAAATCTCCTGCCATAGGG

rs132651ACGTTGGATGAGGTCAGGTGTTGACCTTCCACGTTGGATGAGCAGGGTAGGGCATCCTAA

rs132652ACGTTGGATGAGCAGGGTAGGGCATCCTAACACGTTGGATGAGGTCAGGTGTTGACCTTCC

rs80584 ACGTTGGATGCATGGAGTCCTGTGATCTACACGTTGGATGAAACTGAGGCCATGGGAGAT

rs132653ACGTTGGATGCAGCCGTGCATCTGCATAATACGTTGGATGCACTTTCCCTTTTGGGTTCC

rs916334ACGTTGGATGAAACAGGATGCTTCCCAGCCACGTTGGATGCTGCTCTTGGATCAGCAGGA

rs132654ACGTTGGATGTAAGGAAGTGTCCAGAAGCCACGTTGGATGAAATGATCCTCCTGCCTCAG

rs132655ACGTTGGATGACTTTTCCAGGTGAAGGTAGACGTTGGATGTTGTCGAACGCCATACCTGT

rs132656ACGTTGGATGTCACTAGAAGCAAGGAACCCACGTTGGATGCCCAGGTTGACTGAACAAAG

rs3834684ACGTTGGATGAGCCCTTGTTCACTAGAAGCACGTTGGATGGGTGGATGTGGGAGTAAAAG

rs132657ACGTTGGATGGGCTGACTGACAATTACCTGACGTTGGATGAGGGCTCTGAGCTTTTCAAG

rs916335ACGTTGGATGGATGACGAGAAAAAGGTGGGACGTTGGATGATTTGAAGGATGCAGTCTTG

rs932659ACGTTGGATGGGCCCATAGTGGGTCATAACACGTTGGATGGTGGGGTGAGTGCCCAAAAG

rs132660ACGTTGGATGTACATGTGGTTGTACCCTCCACGTTGGATGCTGGCATGGTTTTACCCATC

rs132661ACGTTGGATGCTTCGCAGAAATCATTCCGCACGTTGGATGCCAAAATGCAAGCTCAAGGC

rs132662ACGTTGGATGCATCTCTTAAATGGGCCAGGACGTTGGATGTTGAAAGCCACAGCCTCATG

rs132663ACGTTGGATGCCACTAAACGGATTGAGATCACGTTGGATGTGGCTTTCAACCAGCAACTC

rs132664ACGTTGGATGATCATGCCACTGCAATCCAGACGTTGGATGGCATATGTGACTGCTTCCTC

rs132667ACGTTGGATGCTGGAGAAATCAAATAGAGAGACGTTGGATGTGTACAGCTTTTGACAGTTG

rs132670ACGTTGGATGTAAGGTCGGGAGTTCAAGACACGTTGGATGACGCCCGGCTGATTTTGTAT

rs132671ACGTTGGATGGTGAGCCATACCATCACATCACGTTGGATGCTGTAGTAAAGGTCTGGTCG

rs132672ACGTTGGATGCTCCCCAATAAGCTCAACACACGTTGGATGCTGTTAGGGCAATGAAAGGC

rs132673ACGTTGGATGTGAGTAGTTGGTGTGAGTGGACGTTGGATGCAATGGATGAAGCTGATCCC

rs132674ACGTTGGATGAACTGTAGTCCCAGCTACTCACGTTGGATGTAGCTCTATCACTCATGCTG

rs132675ACGTTGGATGGTAGAGCAGATGTGCAATGGACGTTGGATGTCCTAACCATCTGCCTTGTG

rs80585 ACGTTGGATGCTGTTGTTCCAACACTTCACACGTTGGATGGGTCTGCTACTAGAATTCAG

rs80586 ACGTTGGATGGTAAGTGTAAGAAGGTCTGCACGTTGGATGCAAGGCATAATATTCTGACC

rs132676ACGTTGGATGCAAACATTCTGCAGAAAGCGACGTTGGATGAAGCGTGTTGCTGAGAAATG

rs132677ACGTTGGATGCTCTGTTACAAAATGAAGGGACGTTGGATGGCTATCTAGGCTAAAAATCCC

rs132678ACGTTGGATGAAGGCACTGAAAATGCCTAGACGTTGGATGGGAATCCAGATGCTTACATG

rs132680ACGTTGGATGGCCTTAGCTATCATGTTCTCACGTTGGATGGCGTGTTTAAGGCAATTCTC

rs132681ACGTTGGATGTACTGAAGCCTGAGACTAGCACGTTGGATGCTAGCAGAAACTAACCGAGC

rs132683ACGTTGGATGTTACCCTATGGTAATGGCAGACGTTGGATGACTGATTAGTACAGGAAGGG

rs2269594ACGTTGGATGTGGCATGGCTAAAAGGACAGACGTTGGATGGATTGTTCTGATGCCCAGTG

rs132684ACGTTGGATGCCTTTTAGCCATGCCATTCGACGTTGGATGTCAGTGTAAAACGTGCCACC

rs132685ACGTTGGATGTCAGTGTAAAACGTGCCACCACGTTGGATGCCTTTTAGCCATGCCATTCG

rs132686ACGTTGGATGCAGAATATCCACGTCAGGTGACGTTGGATGGACAGCTTAGGACTATGTGC

rs132687ACGTTGGATGCAACTGTAAGCAGCCCATTGACGTTGGATGCTGACGGTGCAAATGGATAC

rs132688ACGTTGGATGAGTACTACAGGACGTGCTTGACGTTGGATGGGTCGCCTCATATATGGTAG

rs132689ACGTTGGATGTACTGGGACAGTCTGCTTTCACGTTGGATGACTTTACAGTGCTGGAGCAG

rs132690ACGTTGGATGTGTTTTGCTTTGCGCTCTCCACGTTGGATGTCTGCAACCAACTCTTTGGG

rs132691ACGTTGGATGGTCAAAGCCAGGCATTTGTCACGTTGGATGCTGTCATCTTGTGGAAAGGG

rs132692ACGTTGGATGGAATCTAAGCCAGCTGTTGGACGTTGGATGGGAGCATCATGTGGATTCCT

rs132693ACGTTGGATGGCCAGAAGAAAAGAGTGTGGACGTTGGATGATTCTGCATGTGGAACGTCC

rs132694ACGTTGGATGATAGAGACTGAGAGCTGCAGACGTTGGATGCAGAACAAAGCAGGAAGCTC

rs132695ACGTTGGATGGCCTCTCTCTATGACTACACACGTTGGATGTTCACAGCAGGGAACTCTTC

rs1966266ACGTTGGATGTGATTGTACAAGGCAGACCCACGTTGGATGTGTAAGCACCTGCATTCAGC

rs1966267ACGTTGGATGTAACTCACAGACCATGAGGGACGTTGGATGGGAGGAAAGCACAGCAGAAT

rs106808ACGTTGGATGAACAAGGCAGATCCTTCCCGACGTTGGATGATGGTTCCTGAAGAGCAGTG

rs132696ACGTTGGATGATGGTTCCTGAAGAGCAGTGACGTTGGATGAACAAGGCAGATCCTTCCCG

rs2239829ACGTTGGATGTGTCTTTGTCGTTCGGATGGACGTTGGATGAAAGAGCGAAACTCCGTCTC

dbSNP Forward Reverse rs# PCR primer PCR primer rs2285154ACGTTGGATGTGAACTCAAATGATCCGCCCACGTTGGATGAAGAACCCTTTTCGACTGGG

rs2239830ACGTTGGATGAAACCCTAATGGGAAGCCTCACGTTGGATGTGTGGTAGCAAGCAGTTGAC

rs2239831ACGTTGGATGAGAACAGTCACTGACCCAAGACGTTGGATGGCTCCACACACTTTGATTCC

rs3865722ACGTTGGATGCCACTGTACTGCTAGTATTGACGTTGGATGACCTGCTCTAGTTTTCATCC

rs3865723ACGTTGGATGCCTGCATTTGATGCAATTCCACGTTGGATGGTTTCTGTTTCTGTTGCTTGC

rs3985996ACGTTGGATGACATGGGTGACCCTATCAAGACGTTGGATGTGATTCTAGGAGCAGGACTG

rs3985997ACGTTGGATGCAAGAATTTCTCCCGGCATCACGTTGGATGTGATTCTAGGAGCAGGACTG

rs3985998ACGTTGGATGTGATTCTAGGAGCAGGACTGACGTTGGATGCAAGAATTTCTCCCGGCATC

rs3985999ACGTTGGATGTGATTCTAGGAGCAGGACTGACGTTGGATGCAAGAATTTCTCCCGGCATC

rs3986000ACGTTGGATGCAGGCAGAGGATTTGTTTGGACGTTGGATGCTTCTGTCCTTCTCTGTGTC

rs2413382ACGTTGGATGAAACAAATCCTCTGCCTGGGACGTTGGATGAAAAGCCCAGAGCCTTCATG

rs2413383ACGTTGGATGCTGGGCTTTTGTGCTAAGAGACGTTGGATGGGGCCAAGTTGACCCATAAA

rs2413384ACGTTGGATGCTGGGCTTTTGTGCTAAGAGACGTTGGATGGGGCCAAGTTGACCCATAAA

rs2413385ACGTTGGATGAATGGTCTTCGCTGATACACACGTTGGATGATGGAAGCCGGTGTTTGATG

rs2413386ACGTTGGATGTTTTATGGGTCAACTTGGCCACGTTGGATGTTCCAAAATGGTCTTCGCTG

rs1894606ACGTTGGATGTTTTATGGGTCAACTTGGCCACGTTGGATGAGACTCCTGCAAAAGCTTCC

rs916336ACGTTGGATGGGATGAGGGTATTTGCTGTCACGTTGGATGGGCCTGTATGTAGGTTGAAG

rs916337ACGTTGGATGAGATCAGAAGGGCCTGTATGACGTTGGATGATTTGCTGTCTGGCTGTCTC

rs916338ACGTTGGATGATTTGCTGTCTGGCTGTCTCACGTTGGATGAGATCAGAAGGGCCTGTATG

rs132697ACGTTGGATGCATGAGGAAGAGAAGTCAGGACGTTGGATGACACTGACTGATGACTGAGC

ACGTTGGATGGAGCCAGAAAATTAACTGAAAA
rs12781ACGTTGGATGTTACACACAGGGCACTCAGCGC

rs1053983ACGTTGGATGCCATCATCAAGAAGCCACTGACGTTGGATGTGTCTTACCAGCATCCACTC

rs1053982ACGTTGGATGGGAGAGTGGATGCTGGTAAGACGTTGGATGCGGTTGAATGTCCTTCCAAG

rs2227167ACGTTGGATGCTCCTGAGTGTATGGACATCACGTTGGATGGGCATTAAGGGACATTCTGC

rs2227168ACGTTGGATGCCAATTGGAGGCATTAAGGGACGTTGGATGCTCCTGAGTGTATGGACATC

rs132700ACGTTGGATGAATGTGGTGTCTGGCTCCACACGTTGGATGCTCAGCCCTGCTGTAAATGG

rs3075364ACGTTGGATGGAACAGCAGTTTAGGGAGTGACGTTGGATGCGAAGCCTTTCTATGGACTC

rs2227169ACGTTGGATGAGGTAAGTAAGCTGCCTTTCACGTTGGATGTTCAGAGCTTCATAGAGAGC

rs2097466ACGTTGGATGCTGGGATTACAAGCATGAGCACGTTGGATGCTGCATAAATCACAGAGCTG

rs2097467ACGTTGGATGATCTCCTGACCTTGTGATCCACGTTGGATGATTCTTTTCAAGGCCGGGCG

rs2413387ACGTTGGATGAAGTAGCTGGGACTACAGGCACGTTGGATGTAACACGGTGAAACCCCGTC

rs132701ACGTTGGATGGTGGCATATCTATGTTGTACACGTTGGATGGCGAGACTCCATCTCAAAAA

rs132702ACGTTGGATGGAAGCTCACCCAGTTAAGGAACGTTGGATGCCCCTGTAACAACAATCCTG

rs132703ACGTTGGATGCTTGACCTGATCAATGTGTGACGTTGGATGTTTGTGCAGTTCCTCAGAAG

rs2269595ACGTTGGATGAGAAGTTCAGGAAAAGGGCCACGTTGGATGCAGCAGGACTTTCTTTGGGA

rs2269596ACGTTGGATGAGGTGCTCAGTTAGCGTTACACGTTGGATGTCCCAAAGAAAGTCCTGCTG

rs132704ACGTTGGATGATATTCTTCCTGCACTGCTGACGTTGGATGATCTCCCCGGGCTAGTTTTC

rs2007468ACGTTGGATGAGGTTACCTGGGCAATTCAGACGTTGGATGGAAAATCCTGCTGACTAGCG

rs132705ACGTTGGATGTTTTGATGGAGGCACCAGTGACGTTGGATGTCTCCAAATACGGTCACTGG

rs2007706ACGTTGGATGCCCAGGAATTTACATAAGGGACGTTGGATGTTGAACATAGCAAGAGTGAG

rs132706ACGTTGGATGAAGGATCAGTGCTGAGGGTCACGTTGGATGATTCCTCCTGCTGGTCATGG

rs132707ACGTTGGATGAATCCTTAGGAAGGGCTGGGACGTTGGATGAGCTGGCCCCGTTAGTAAAC

rs132708ACGTTGGATGTCTTGTTTCAGAGGGAGAGCACGTTGGATGTCTCAGCCAATCCCAGAATC

rs132709ACGTTGGATGTGAGTCCTGTCCAAGATGAGACGTTGGATGAGCCCTTCCTAAGGATTCTG

rs132710ACGTTGGATGTGAGTCCTGTCCAAGATGAGACGTTGGATGCCTAAGGATTCTGGGATTGG

rs132711ACGTTGGATGTCATCTTGGACAGGACTCAGACGTTGGATGTTGCCATGGCAACCAAGTCA

rs132712ACGTTGGATGGTCTTCAAGGCTGAGTGAGCACGTTGGATGACTCCACGTGGCCTCTCTTG

rs132713ACGTTGGATGAAGGCTGAGTGAGCCCCAACACGTTGGATGACTCCACGTGGCCTCTCTT

rs132714ACGTTGGATGACACGGTGAAACCCCTTCTCACGTTGGATGAGTAGCTGGGACTACAGGTG

rs132716ACGTTGGATGTGGATTTGCAATGAGGAGTCACGTTGGATGTCAATGACTGTGCTCTACTC

rs132717ACGTTGGATGAATGTGGGCAGTTTTACGTGACGTTGGATGGATGGACCTTAGGGTGTTTC

dbSNP Forward Reverse rs# PCR primer PCR primer rs132718ACGTTGGATGTCAGAGGGTATCAACATCTCACGTTGGATGTGGGCATCTTCATATACTGC

rs132719ACGTTGGATGATACCCTCAGTTGTACCCAGACGTTGGATGCTGAACAAAGGAGAAGGAGG

rs132720ACGTTGGATGATACTGGGTACAACTGAGGGACGTTGGATGCCTCTCCACCTTTTCCTAAC

rs132721ACGTTGGATGCAGCTACAAAGTTGCTAATGGACGTTGGATGTCTTATTTGTACCCTCCCTC

rs132722ACGTTGGATGACAATGGTAATGCTTGGAGCACGTTGGATGGGGAGGGTACAAATAAGATG

rs132723ACGTTGGATGACACAGATGTCTGTCTTCTGACGTTGGATGATACTCCCCTGGTGAATGCT

rs132724ACGTTGGATGCCCCATGCAACAAGGGTAAAACGTTGGATGTGTCCCTTACAGCAAGAAGC

rs132725ACGTTGGATGCCCCATGCAACAAGGGTAAAACGTTGGATGTGTCCCTTACAGCAAGAAGC

rs132726ACGTTGGATGGGGTCACACAGTGAACAAAGACGTTGGATGTTCTTGCTGTAAGGGACAGG

rs132727ACGTTGGATGGGGTCACACAGTGAACAAAGACGTTGGATGTTCTTGCTGTAAGGGACAGG

rs132728ACGTTGGATGAGTTCTACTGGCTCATGGTGACGTTGGATGTTCGCCTTCTTCCTGCTTTG

rs132729ACGTTGGATGAGTTCTACTGGCTCATGGTGACGTTGGATGTTCGCCTTCTTCCTGCTTTG

rs132730ACGTTGGATGTTCGCCTTCTTCCTGCTTTGACGTTGGATGAGTTCTACTGGCTCATGGTG

rs132731ACGTTGGATGTTTGTTCACTGTGTGACCCCACGTTGGATGTCCTGGTCCTCCCAGTTCTA

rs132732ACGTTGGATGGCCAAGGCAACCATCTCAACACGTTGGATGTGCAGCTCATCACAAGCGTC

rs132733ACGTTGGATGGCAACCATCTCAACACCATGACGTTGGATGTGCAGCTCATCACAAGCGTC

rs140575ACGTTGGATGTGCAGCTCATCACAAGCGTCACGTTGGATGCCATCTCAACACCATGAGCC

rs132734ACGTTGGATGGGATACTGACTGTTAGCCTCACGTTGGATGCGGAATTGACCAACTGGTAG

rs132735ACGTTGGATGGGATACTGACTGTTAGCCTCACGTTGGATGCGGAATTGACCAACTGGTAG

rs80587ACGTTGGATGTCTGAGCCAAGCTCACCAGAACGTTGGATGTTTTCCTGCCCAAGGAGGAG

rs132736ACGTTGGATGTTTTCCTGCCCAAGGAGGAGACGTTGGATGAAGCTCACCAGATGCAGACG

rs132737ACGTTGGATGTCTAGGCAGCAATGAGCTAGACGTTGGATGTGCTCCTCCTGAGAAATCAC

rs132738ACGTTGGATGTGAAGCCTGTAATCCCAGTGACGTTGGATGCATAGAGACAGCATCTCCTG

rs1807673ACGTTGGATGTTGCAGTGAGCAGAGATTGCACGTTGGATGGTGAAATCTGAGTCGTGGTC

rs2014700ACGTTGGATGTTGCAGTGAGCAGAGATTGCACGTTGGATGGTGAAATCTGAGTCGTGGTC

rs132739ACGTTGGATGGGAATCAAAGAAGGTGGAGGACGTTGGATGTGGTTGTGGCCAGACCATAA

rs1812023ACGTTGGATGAGCAGGAGGGAGGGAGCAATACGTTGGATGGACCTCCCTCCATCTCCTTA

rs1812024ACGTTGGATGTGTCAGAGGAAGATCCCTTGACGTTGGATGCCTCATAGAGCTATTGCGAG

rs2005590ACGTTGGATGGGAGGCAATGCCTGATTTTGACGTTGGATGTGCTTCCACCACCTGGAAAA

rs132740ACGTTGGATGTTCATTCTTCTTGTGCACAGACGTTGGATGCTTGACTGGTACCTAACAATG

rs3986001ACGTTGGATGTTTTCTGACTTGGCATCACCACGTTGGATGCACAAAGTATTCCACCTTCC

rs2413390ACGTTGGATGATAAATTCGTGGCTGAGCTCACGTTGGATGATCTTGTGGCATAAGGAGTC

rs132743ACGTTGGATGACAGGGAGAAAGTGAGGAAGACGTTGGATGCATCCTGTTTCCCCTAAAGG

rs132744ACGTTGGATGGGGTCTGTTTCAGGAGCATGACGTTGGATGTCTATGGCTGATGGCCACAG

rs2413391ACGTTGGATGGGGCAAAAGCAGAAATACTGACGTTGGATGCCCTCAAACCCTGTTTTCTG

rs132749ACGTTGGATGCCATGCACTCTCTAGTACTCACGTTGGATGTGTGGCCTTGGGGAAATGAT

rs132750ACGTTGGATGTCCTGTGCCTGTGGAAACTCACGTTGGATGGGTTCTCCAGGTGGCAAAAG

rs132741ACGTTGGATGCTACAATTTATCCGCACTAGACGTTGGATGGCCAAGTCAGAAAAATGAGAG

rs2413388ACGTTGGATGTACAGAATTCAGACCAACCCACGTTGGATGGCCCTGAGATTTGATTTTCC

rs2413389ACGTTGGATGGCTAGAATCTCATAACAGACGACGTTGGATGGCGTCCTACTATGATTTGTC

dbSNP Extend Term rs# Primer Mix rs3888818 TGAGACCAGCCTAGCCAAC ACT

rs2010605 TGGTCCCAAGATATTCTATAGA ACT

rs743919 CTCACCTAAGGACTGCCTCT ACT

rs1008134 CCGGGCATCTTTTCTTCCATC ACT

rs132607 GCAGGCAGGACAGCATGTG ACT

rs1476029 CTTAGAGGCTATATTAAGACCA ACG
I

dbSNP Extend Term rs# Primer Mix rs1476030 TTTGGCAATACTGGCCTATTC ACT

rs2413380 TCCAGGAGGGAAGACAACC ACT

rs2051609 CGCTTGAGGTCAGGACCAG CGT

rs2413381 GCGTGTTGCCAACAGCCTC ACT

rs1894604 AAATGGGAGGGAATGTTGGC ACG

rs1894605 TGCAGATCGCAACTGAGCG ACT

rs132609 GTTTCTCAGAGGATCAGGGA ACT

rs132610 GGTGTGAGATTTGGAGACTTT ACG

rs132611 CTCTGTCCTCTAGCCCCC ACT

rs132612 ATCTTCCCGCTACCTCAAGAGT ACT

rs1008790 CATAATCACAAGTCCTATGATTA ACT

rs23085 AGGATGACCATGGCAAGGAA CGT

rs105161 GGCCCTGGCAGGAAACAG ACG

rs132613 CCAATGGCCTCCACTGGC ACT

rs132614 CGGCCACAGCGCTGCCC ACG

rs132615 GCTTTCAGAACAACGGTAGAA ACT

rs132617 AAGAGTGTGTGTGCAGTAGCAAG ACG

rs3865724 TCACTTAAGCTTTGAATGTTTCTGACT

rs2019657 GCCAGAACATTGTGTTTCATTTGTACG

rs3865725 GGCAAGAGATACAGAATGCACA CGT

rs2019364 GTATCTCTTGCCCCTGCTC ACG

rs2008383 GAAGGACAGAAGGCTGATGC ACG

rs3986002 TCCTTCTCTGTGTCACTCCT CGT

rs3888942 ACATGGAAGCAGGGGTTTGA CGT

rs3888943 AGCAGGGGTTTGATGAAATCT ACT

rs3888944 CATCCTCCACATTGGGCCAA ACT

rs132618 AATCTCAGCTGGAAGTGG CGT

rs132619 TGCAACCAGCATTGACCG CGT

rs3827346 GAGGCTGCACCATCTCCAA ACG

rs132620 GGAAGCCTTTATTCAGGATTGT ACT

rs132621 TCAAATCTGCAACTGGTGTCAGAAACT

rs80575 GAACTCTCAAGCCACTTGAC ACT

rs80576 GCTAAGGCATTAGTTTGGCTGG ACG

rs80577 TGAAATTGCACATGGCATTGG ACG

rs80578 ATGCCTGGGAACTGGGGC ACT

rs80579 GGGAGGCACTGAGGGCATGAAA ACT

rs80580 CTGAGAATGAACAGCAGGTCA ACT

rs132622 ATAGTAGTTCAATCAGATGGGC ACT

rs132623 ATTCCAGCCTCTCTGTGTTCTG ACT

rs132624 ACAGGCATGAGCCGCTGC ACT

rs132625 GGCCACCGCATCCGGCTA CGT

rs132626 AGTGGCATGATCTCGGCCCAC ACG

rs132627 GAGGCGGAGGTTGCGGTG ACT

rs1807672 CATTGAGAATAAGGTGGTTCGA ACT

rs132628 CCTCCAAATTCATATACTGAGACCACG

rs132629 TCTCTCTCTCTCACACAC CGT

rs132630 CTGCTCCTGGCTTACAGAG ACT

rs132631 TCACAGTTCTGGAGGCAAAAA ACT

rs132632 I TGGAATTTTTGCCTCCAGAACTGTACT

dbSNP Extend Term rs# Primer Mix rs132633 AGTGATTCACCAGGGAAGTGCCA ACG

rs132634 GGTGCTTTGTGGAGGAACC ACT

rs132635 ATTTCCCGTACATGGGGAGAAA ACT

rs132636 TGACAATAGGCACATGGCAG ACT

rs129603 GCTGCCATCCTAAACACATCTA ACT

rs132637 ACACAGCAGGATTACTGCCCAGA ACT

rs3788518 TGGGAGGCTCAAGGAAGAAACTCTACT

rs132638 GGAAAAAATAAAAGCAAAATACCCACT

rs132639 AAAGCAAACAGGCCTTCAGAA CGT

rs132640 GGTGACACAGAGAAGACGTGGC ACT

rs132641 GGGAGGTCAGAGGTCGGG ACT

rs132642 GTCACTGAGAGACTTTCC CGT

rs132643 GACACCCAGTACACACTGGCT ACT

rs132644 TTTGGAATGAGGAGTCATTTACA ACT

rs132645 CTCAACAGTAAGCAAGATTTAAA ACT

rs2017329 TGATGTTCAGATTTTCCTTTTTTTCGT

rs739198 TGGTCTCCACAACCTCTTATC ACT

rs132647 AAACCATGGAAGTCTCTAGAGTCAACT

rs2097465 CAAACTGCAGGCTTGCCCAG ACT

rs2105915 CAAGCCTGGGCAGCATAGCAC ACT

rs132648 AATTCCCGTGCTAATGCACG ACT

rs132649 CAGTCTTATTACTTTTGTACGAGGACT

rs132650 CATGAGCCACCGTGCCAG ACT

rs132651 CCTCAGGGTTTTTCACCTGCCT ACT

rs132652 AGGGCATCCTAACCCCCTA CGT

rs80584 ATCTACCTGCTCAACTTCCTGA ACG

rs132653 AATAACCAGACACGTTCTCCAG ACT

rs916334 GTCCAGCAGCACCCTTGGT ACG

rs132654 CGACAAGAGCAGGTCTGGAAC ACT

rs132655 CAGAAGAACCCACATAAGGAA ACT

rs132656 TCTTTGTCTTTTACTCCCACATCCACT

rs3834684 CACTAGAAGCAAGGAACCCCC ACT

rs132657 TACCTGACAATCACCCCCC CGT

rs916335 TCAGGTAATTGTCAGTCAGCC ACT

rs132659 AGAACTCCCCAAATCGTCCT ACG

rs132660 CCCCAGAGTGGGCTTTTCT ACT

rs132661 CCGCTCTCCCTCTGAGAGT ACT

rs132662 TGATCTGAGTTTACAGGTGAG ACT

rs132663 TGAGATCTGTCTCAGACGCA CGT

rs132664 CTGGGCTAGAGAGGGAGAC ACT

rs132667 CTTTAACTTTTGCTCACAAGAGT ACT

rs132670 AGACCAGCCTGATCAACATG ACT

rs132671 ACATCAATAGGCCTAAAAATCGTTACT

rs132672 GAAACTTGAAATTCCTTGAGAAATACT

rs132673 GTGTGAGTGGGAAGCCTCC ACG

rs132674 GGAGTTGGAGGCTGTAGTAA ACT

rs132675 AGATGTGCAATGGAATTTGGCAA ACT

rs80585 AGGCATAATATTCTGACCATTAAGACG

rs80586 I GGTCTGCTACTAGAATTCAGAAACG

dbSNP Extend Term rs# Primer Mix rs132676 ATCCCTTAATATTGCATAGGAC CGT

rs132677 GGGTTGAAGTACTATGCTAGT CGT

rs132678 AGGTTAGTTCATGTAACTCCAT ACT

rs132680 TTTTATTTTAGCTTGAGCTTTTCAACG

rs132681 CTAGCTCTAAATCACATTCTGC ACG

rs132683 CAGGCCCATACCCAAAATATGCT ACT

rs2269594 TGGCTAAAAGGACAGATAGAG ACT

rs132684 GACACTAAGAGCGGTGAGAC ACT

rs132685 CGTGCCACCCAACTGGAGA ACT

rs132686 TGTGCATCTTATGGTGTACCA ACG

rs132687 TCGTTACCCCCATTCTATCC ACT

rs132688 ACAGGACGTGCTTGAAAGAG ACG

rs132689 TGGCGATGGCCTCTGCTC ACT

rs132690 GCTCTCCTTGCTTCAAAAAAAAA CGT

rs132691 TGACCTATCCTGCTTCAGGT ACT

rs132692 CGAAGTGTGTTAGCTCATGAC ACT

rs132693 GAGTGTGGACACCAGGTCA ACT

rs132694 CACCTTAGGAATGGCAGCTTC ACG

rs132695 TATGACTACACATGCTGGCAAAC ACT

rs1966266 GCAGACCCCTAACTCTAATTTG ACG

rs1966267 CACTGAGTTATGAGTACTCAAC ACT

rs106808 GATCCTTCCCGAGGACACC ACT

rs132696 CAGGCTGCCTGGAAGGAGA ACT

rs2239829 GATGGCTGGATTCATAACAGGTAAACT

rs2285154 AGTGCTGGGATTACAGGCAT ACT

rs2239830 CAGTCACCTGAATTTGTGCTTATTACT

rs2239831 GTCACTGACCCAAGCTATCCTC ACG

rs3865722 CAATTGCAAGCAACAGAAACAGAACGT

rs3865723 TCCACTGTACTGCTAGTATTG ACG

rs3985996 AGAATTTCTCCCGGCATCAG ACG

rs3985997 TCTCCCGGCATCAGCCTTC ACG

rs3985998 GGGAGGAGTGACACAGAGAAGGA ACG

rs3985999 GGGGTACTGGGAGGAGTGACAC ACT

rs3986000 GCAGGACTGGGGTACTGG ACT

rs2413382 CAGGGGAACTCAGGCCACA ACT

rs2413383 AGCCATTGAAGACATGGAAGCC ACT

rs2413384 ATTGAAGACATGGAAGCCGG ACT

rs2413385 GGCCAGCTCTTCCTCCAC CGT

rs2413386 CTTGGCCCAATGTGGAGGA CGT

rs1894606 CCTAGCGGCAAGGGCTGT ACT

rs916336 AGGGTATTTGCTGTCTGGCTGTCTACT

rs916337 AAGGGCCTGTATGTAGGTTGAA ACT

rs916338 CCCTCTATGTCTCATGGATTTTCCACG

rs132697 CCTAGGGGAGCCCATATATCA ACT

rs12781 AGACAGCTCGAGAGATCC ACT

rs1053983 GCTGACTCAGATACACCCC ACG

rs1053982 GATGCTGGTAAGACAGGG ACG

rs2227167 CGTCAAAATCAAGTGCAAA ACT

rs2227168 ~ATTAAGGGACATTCTGC ~ AC~

dbSNP Extend Term rs# Primer Mix rs132700 ATCCTGTCTGTCATTGGCGTT ACT

rs3075364 GTTTAGGGAGTGGTTTTTGAAAG CGT

rs2227169 TGTCCTTTATTGGTACAGGGAAGAACT

rs2097466 TACAAGCATGAGCCACCGC ACT

rs2097467 TCCCAAAGTGCTGGGATTACA ACT

rs2413387 TACAGGCACTCACCACCAC ACT

rs132701 TGTACAAAACATATTTAACCTTGAACT

rs132702 CACCCAGTTAAGGAAAAATTCCT ACT

rs132703 GATCAATGTGTGTTCCCGGA ACT

rs2269595 GCCCCAGACAGCATCTCC ACT

rs2269596 TTGCTGGCAAGAGACCAGG ACT

rs132704 GGGCTGCCTGGAGGAGG ACG

rs2007468 TGGGCAATTCAGCCACACGCAC ACT

rs132705 TATAGACTGAATTGTGTGCCC ACG

rs2007706 GGAATTTACATAAGGGTCTATAG ACT

rs132706 GAACCCCCTCCACTGCCC ACT

rs132707 GCTCTCCCTCTGAAACAAGATG ACT

rs132708 GAGAGCTTCTTCCTTGGCC ACT

rs132709 CAGGGAAGATTAGAAGCTGAGAGCCGT

rs132710 GGGCAGGGAAGATTAGAAGC ACG

rs132711 TTTGCTGTCCAGGGCGGC ACG

rs132712 AACCCAGACGGAGGTGGC ACG

rs132713 GCCCCAACGGAACCCAGA ACG

rs132714 CCCCTTCTCTACTGAAAATACAAAACT

rs132716 TGAGGAGTCATTTACCATGAG ACG

rs132717 GCAGTTTTACGTGAAGGAGG ACT

rs132718 GTTTTATACCTAGAGCCACACT ACT

rs132719 TACCCAGTATTTCTTAACTTCC CGT

rs132720 CAGCTACAAAGTTGCTAATGG ACT

rs132721 ATGTTAGGAAAAGGTGGAGAG ACT
~

rs132722 CCTAACTGGGATGGGCCTGAA ACT

rs132723 TTCTGGGGCCCCCATGCA ACT

rs132724 ACCCAGTCCTGGGCAGCA ACT

rs132725 GGGAGTATGCAGAGGGGC ACT

rs132726 CAGTGAACAAAGCAGGAAGAAGG ACT

rs132727 GTCACACAGTGAACAAAGCAGGAAACT

rs132728 CATGGTGTTGAGATGGTTGCC ACG

rs132729 GCTCATGGTGTTGAGATGGTT ACT

rs132730 GTGACCCCCTAGGCCAAGGCA ACT

rs132731 GGCAACCATCTCAACACCAT ACT

rs132732 AACCATCTCAACACCATGAGCCA ACT

rs132733 ATCTCAACACCATGAGCCAG ACT

rs140575 GCTCTCTCCTGGTCCTCC ACG

rs132734 AGCCTCAACTAGGACACA ACT

rs132735 TCAACTAGGACACAGTGC ACT

rs80587 GCCAAGCTCACCAGATGCAGA ACT

rs132736 AGGGAGCTGCTTTGCTGAAA ACT

rs132737 CCTGCAGCCTGGGTGACA ACT

rs132738 GGCCAGGAGTTCAAGACAGCCTG ACT
~

dbSNP Extend Term rs# Primer Mix rs1807673 GGGCAACAGAGCGAGACTCC ACT

rs2014700 GAGCGAGACTCCATCTCA ACT

rs132739 GGGAGGTGACCTGGAGCC ACG

rs1812023 GCAATCAGACTCAAGCCTGG ACT

rs1812024 GGGATGGTGTGACCTCCC ACG

rs2005590 CAATGCCTGATTTTGTCACTGAAC ACT

rs132740 GGCATATGTGCATTTGTCTGAG ACG

rs3986001 TCCTTTTTCTAAACCCCTGCAA ACT

rs2413390 GGCTGAGCTCAAGGTTTTAAA ACT

rs132743 GGAGAAAGTGAGGAAGAAAATTA ACT

rs132744 TGGGGTTACAGTTGGTCATAACC ACT

rs2413391 TGATATGTTCAGCGGTGCAC ACT

rs132749 TCTTGATGTTTCTCCTATCCC ACG

rs132750 CCTGTGGAAACTCAGCAGC ACG

rs132741 GCACTAGATATTGAATTCTTTCC ACT

rs2413388 CAACCCCGTGACTGGAGATTC CGT

rs2413389 TTTCTCTCTCTAGTACTCTATTT ACT

Genetic Analysis [0324] AlleloTyping results from the discovery cohort are shown for cases and controls in Table 63.
The allele frequency for the A2 allele is noted in the fifth and sixth columns for osteoarthritis case pools and control pools, respectively, where "AF" is allele frequency. The allele frequency for the A1 allele can be easily calculated by subtracting the A2 allele frequency from 1 (Al AF
= 1-A2 AF). For example, the SNP rs2010605 has the following case and control allele frequencies: case A1 (A) = 0.19;
case A2 (G) = 0.81; control A1 (A) = 0.18; and control A2 (G) = 0.82, where the nucleotide is provided in paranthesis. Some SNPs are labeled "untyped" because of failed assays.

dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 13 rs3888818 201 34781551 C/T

rs2010605 425 34781775 A/G 0.81 0.82 0.782 rs743919 1095 34782445 G/T 0.10 0.11 0.502 rs1008134 2201 34783551 A/C

rs132607 7879 34789229 A/G 0.11 0.11 0.813 rs1476029 8395 34789745 C/T 0.15 0.15 0.983 rs1476030 8461 34789811 C/T 0.36 0.37 0.708 rs2413380 9503 34790853 C/T 0.29 0.29 0.900 rs2051609 10304 34791654 G/T

rs2413381 10695 34792045 C/T

rs1894604 16300 34797650 A/G 0.08 0.08 0.759 rs1894605 16444 34797794 G/T 0.08 0.09 0.468 rs132609 17591 34798941 C/T 0.68 0.67 0.777 rs 132610 17988 34799338 -/A

rs132611 19116 34800466 -/T 0.14 0.15 0.863 rs132612 19358 34800708 C/T 0.23 0.23 0.951 rs1008790 20300 34801650 A/G 0.03 0.10 0.007 rs23085 20669 34802019 A/T 0.31 0.32 0.738 rs105161 20891 34802241 A/G 0.76 0.77 0.826 rs132613 21451 34802801 C/T 0.80 0.81 0.619 rs132614 21978 34803328 C/T 0.16 0.14 0.434 dbSNP Position ChromosomeAllA2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID AF AF
NO: 13 rs132615 22785 34804135 C/G 0.32 0.31 0.740 rs132617 24248 34805598 C/T 0.35 0.36 0.825 rs386572424770 34806120 C/T 0.65 0.65 0.940 rs201965724844 34806194 A/G 0.20 0.20 0.857 rs386572525066 34806416 G/T

rs201936425096 34806446 C/T 0.40 0.39 0.767 rs200838325309 34806659 A/G 0.18 0.17 0.665 rs398600225344 34806694 A/C

rs388894225529 34806879 A/T

rs388894325537 34806887 A/G

rs388894425554 34806904 A/C

rs132618 27963 34809313 A/T 0.43 0.43 0.934 rs132619 28134 34809484 G/T

rs382734628356 34809706 A/G 0.84 0.84 0.976 rs132620 29648 34810998 -/A 0.29 0.29 0.879 rs 13262129986 34811336 A/G 0.32 0.31 0.867 rs80575 30217 34811567 G/T 0.27 0.27 0.948 rs80576 30267 34811617 A/G 0.26 0.25 0.443 rs80577 30315 34811665 A/G 0.26 0.23 0.191 rs80578 30585 34811935 C/T 0.49 0.48 0.548 rs80579 30724 34812074 A/C 0.23 0.25 0.574 rs80580 30897 34812247 C/T 0.31 0.31 0.878 rs132622 30931 34812281 C/T 0.29 0.30 0.943 rs132623 31080 34812430 G/T 0.60 0.59 0.806 rs132624 31246 34812596 C/T 0.36 0.37 0.772 rs132625 31373 34812723 A/T

rs132626 31463 34812813 A/G 0.89 0.84 0.082 rs132627 31467 34812817 A/G 0.12 0.11 0.836 rs180767232188 34813538 G/T 0.30 0.30 0.974 rs132628 32288 34813638 C/T 0.25 0.24 0.691 rs132629 32520 34813870 A/T 0.04 0.06 0.250 rs132630 32594 34813944 A/C 0.75 0.75 0.978 rs 13263132657 34814007 A/C 0.72 0.73 0.509 rs132632 32677 34814027 A/G 0.66 0.65 0.798 rs 13263332764 34814114 C/T 0.34 0.33 0.796 rs 13263432784 34814134 A/G 0.45 0.42 0.317 rs132635 32830 34814180 C/T 0.41 0.40 0.772 rs132636 32872 34814222 C/T 0.41 0.44 0.192 rs129603 33121 34814471 A/C

rs132637 33348 34814698 G/T 0.09 0.09 0.628 rs378851833952 34815302 C/G 0.17 0.19 0.297 rs132638 34184 34815534 C/G 0.56 0.58 0.509 rs132639 34361 34815711 A/T 0.13 0.12 0.561 rs132640 35026 34816376 A/G 0.32 0.30 0.388 rs132641 35192 34816542 A/G 0.48 0.51 0.287 rs132642 35600 34816950 A/T 0.15 0.14 0.732 rs132643 36033 34817383 C/T 0.44 0.46 0.360 rs132644 36289 34817639 C/T 0.53 0.58 0.075 rs1$2645 38869 34820219 A/G 0.19 0.18 0.572 rs201732939629 34820979 A/T 0.39 0.40 0.915 rs739198 40530 34821880 C/T 0.70 0.70 0.878 rs132647 41621 34822971 C/T 0.23 0.23 0.957 rs209746542379 34823729 C/T 0.54 0.51 0.344 rs210591542802 34824152 C/T 0.57 0.56 0.468 rs132648 42865 34824215 T/C

rs132649 43644 34824994 A/G 0.21 0.22 0.579 rs132650 45051 34826401 C/T 0.34 0.31 0.248 rs132651 45828 34827178 A/C

rs132652 45829 34827179 A/T

rs80584 46257 34827607 C/T 0.81 0.75 0.043 rs132653 47286 34828636 A/C 0.17 0.15 0.312 rs916334 47427 34828777 C/T 0.34 0.36 0.345 rs132654 47963 34829313 C/T 0.54 0.56 0.439 rs132655 48013 34829363 C/T 0.41 0.41 0.838 dbSNP Position ChromosomeAl/A2 F A2 F A2 F p-rs# in Position Allele Case Control Value SEQ ID NO: AF AF

rs132656 48229 34829579 C/T 0.37 0.36 0.813 rs3834684 48282 34829632 -/A 0.21 0.22 0.480 rs132657 48376 34829726 -/G 0.49 0.50 0.719 rs916335 48404 34829754 AIG 0.38 0.36 0.509 rs132659 49900 34831250 CIT

rs132660 52699 34834049 G/T 0.37 0.38 0.754 rs132661 52897 34834247 A/G 0.27 0.29 0.291 rs132662 53414 34834764 A/G 0.61 0.58 0.186 rs132663 53487 34834837 A/T 0.26 0.29 0.167 rs132664 54112 34835462 GIT 0.25 0.29 0.098 rs132667 55492 34836842 A/G 0.35 0.36 0.559 rs132670 59766 34841116 C/T

rs132671 60307 34841657 A/G 0.49 0.53 0.145 rs132672 60701 34842051 A/G 0.23 0.22 0.716 rs132673 60952 34842302 A/G 0.41 0.37 0.184 rs132674 61401 34842751 C/T 0.32 0.31 0.476 rs132675 62379 34843729 C/T 0.38 0.35 0.188 rs80585 62870 34844220 CIT 0.28 0.27 0.525 rs80586 62879 34844229 A/G 0.66 0.66 0.966 rs132676 63499 34844849 A/T 0.26 0.23 0.177 rs132677 64284 34845634 -/A 0.69 0.69 0.873 rs132678 64408 34845758 A/G 0.46 0.48 0.395 rs132680 64760 34846110 A/G 0.20 0.20 0.995 rs132681 65230 34846580 A/G 0.24 0.24 0.901 rs132683 66127 34847477 A/G 0.19 0.19 0.851 rs2269594 66634 34847984 C/T 0.70 0.67 0.332 rs132684 66686 34848036 A/G 0.21 0.20 0.756 rs132685 66694 34848044 C/G 0.30 0.28 0.553 rs132686 67113 34848463 A/G 0.46 0.48 0.398 rs132687 67257 34848607 A/G 0.96 0.96 0.767 rs132688 67403 34848753 A/G 0.24 0.23 0.553 rs132689 67609 34848959 A/G 0.61 0.63 0.564 rs132690 68418 34849768 -/A 0.16 0.17 0.672 rs132691 68610 34849960 C/G 0.52 0.52 0.976 rs132692 69629 34850979 C/T 0.63 0.62 0.800 rs132693 70024 34851374 A/G 0.58 0.58 0.868 rs132694 70848 34852198 A/G 0.17 0.16 0.583 rs132695 71428 34852778 C/G 0.23 0.22 0.616 rs1966266 71553 34852903 C/T 0.49 0.47 0.413 rs1966267 71633 34852983 A/G 0.40 0.41 0.773 rs106808 71768 34853118 A/C 0.68 0.67 0.617 rs132696 71769 34853119 A/G

rs2239829 73039 34854389 A/G 0.34 0.36 0.510 rs2285154 73325 34854675 A/G

rs2239830 73412 34854762 A/C 0.49 0.50 0.841 rs2239831 73547 34854897 C/T 0.52 0.50 0.564 rs3865722 73769 34855119 A/T 0.57 0.56 0.861 rs3865723 73806 34855156 A/G 0.59 0.58 0.722 rs3985996 74467 34855817 C/T 0.30 0.29 0.861 rs3985997 74472 34855822 C/T 0.89 0.90 0.527 rs3985998 74473 34855823 A/G

rs3985999 74482 34855832 C/T 0.19 0.19 0.968 rs3986000 74494 34855844 A/C

rs2413382 74592 34855942 A/G 0.61 0.59 0.618 rs2413383 74670 34856020 G/T

rs2413384 74672 34856022 G/T

rs2413385 74714 34856064 G/T 0.70 0.70 0.944 rs2413386 74723 34856073 A/T 0.70 0.71 0.816 rs1894606 74749 34856099 A/G

rs916336 74861 34856211 C/G

rs916337 74892 34856242 C/T

rs916338 74893 34856243 CIT 0.40 0.40 0.939 rs132697 75176 34856526 A/G 0.59 0.61 0.418 rs12781 75705 34857055 A/G

DEMANDE OU BREVET VOLUMINEUX
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PLUS D'UN TOME.

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Claims (71)

1. A method for identifying a subject at risk of osteoarthritis, which comprises detecting the presence or absence of one or more polymorphic variations associated with osteoarthritis in a nucleic acid sample from a subject, wherein the one or more polymorphic variations are detected in a nucleotide sequence in SEQ ID NO: 1-13, or referenced in Table B, or a substantially identical sequence thereof, or a fragment of the foregoing; whereby the presence of the polymorphic variation is indicative of the subject being at risk of osteoarthritis.

2. The method of claim 1, which further comprises obtaining the nucleic acid sample from the subject.

3. The method of claim 1, wherein the one or more polymorphic variations are detected within a region spanning chromosome positions 21233000 to 21243000 of chromosome 2 in human genomic DNA.

4. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 2 selected from the group consisting of 238, 294, 295, 347, 1425, 4891, 5087, 7041, 7121, 7219, 7443, 7485, 10939, 11367, 11571, 11839, 12551, 12646, 13469, 14913, 15205, 15246, 15695, 17473, 17610, 17828, 18130, 18281, 18623, 18890, 21561, 23 100, 23872, 24581, 24582, 24983, 27540, 30846, 31415, 31453, 31899, 37000, 38681, 39287, 42951, 45 648, 46222, 46687, 47020, 47593, 48513, 49723, 49986, 53018, 53296, 53547, 53899, 53916, 53933, 54305, 55327, 55895, 56143, 56640, 58486, 59576, 63048, 64008, 64018, 64859, 65995, 66905, 67183, 67942, 68101, 68521, 68664, 68988, 69178, 72143, 74183, 74312, 74407, 75518, 76153, 77398, 77615, 79092, 80000, 80125, 80595, 81061, 81151, 81918, 83072, 83137, 83235, 83263, 83279, 83280, 83533, 86856, 87186, 87189, 87727, 87978, 89129, 89556, 89702, 90233, 93060, 94779, 95367, 95844, 95942, 96884 , 96938, 97627, 97777, 97871, 98746 and 99663.

5. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 2 selected from the group consisting of 7219, 7485, 11839, 31899, 37000, 48513, 49986, 56640, 74407, 77398, 93060 and 97627.

6. The method of claim 1, wherein the one or more polymorphic variations are detected within a region spanning chromosome positions 102456500 to 102471500 of chromosome 2 in human genomic DNA.

7. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 3 selected from the group consisting of 225, 509, 860, 874, 939, 1483, 1798, 2189, 2215, 2282, 2340, 2963, 3369, 3481, 3564, 3653, 4860, 4941, 4975, 5321, 5346, 5541, 5633, 6007, 6317, 6378, 6382, 6426, 6479, 6641, 6703, 6705, 7963, 8525, 8526, 8598, 8624, 883, 8980, 13578, 16135, 16141, 16642, 16931, 17004, 17009, 17010, 18713, 18853, 20783, 21335, 22180, 22268, 22285, 25378, 25906, 26015, 26475, 26798, 27042, 27649, 27827, 27873, 28122, 28202, 28232, 28240, 29546, 29748, 30054, 30646, 31149, 36912, 36936, 37184, 39064, 39343, 40868, 40917, 41113, 47343, 47806, 47911, 48009, 48621, 49245, 49247, 49299, 49302, 49514, 49626, 49791, 50010, 50294, 51482, 51556, 51855, 51956 ,52155, 52448, 52458, 52511, 52607, 54049, 54224, 54567, 55052 55857, 55941, 56120, 56349, 56727, 57232, 58806, 61181, 63808, 64526, 64865, 64928, 64966, 65080, 65690, 66228, 66982, 72511, 74170, 74264, 74333, 74502, 74741, 75321, 82558, 85366, 85469, 86485, 87687, 89463, 89660, 95718 and 95821.

8. The method of claim l, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 3 selected from the group consisting of 2215, 3369, 16642, 20783, 52155, 55052, 55941, 74333, 74741, 85366, 85469, 87687, 89660 and 95718.

9. The method of claim 1, wherein the one or more polymorphic variations are detected within a region spanning chromosome positions 102570000 to 102583000 of chromosome 2 in human genomic DNA.

10. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 4 selected from the group consisting of 207, 6019, 641 4, 7341, 10984, 12351, 13335, 16584, 16737, 23897, 24057, 25145, 25300, 26262, 26312, 26589, 27302, 27358, 27451, 27552, 30731, 32085, 32139, 33184, 42382, 42569, 44823, 45217, 45548, 45601, 45722, 45967 ,47367, 47642, 48126, 49218, 49274, 49433, 49610, 51282, 51466, 53757, 53960, 54031, 54574, 55679, 56100, 56182, 59817, 60533, 60656, 72209, 72778, 74293, 77335, 78029, 78374, 78421, 78434-, 79174, 79397, 79562, 79700, 79730, 79904, 79920, 79938, 79972, 80125, 80368, 83484, 85536, 85829, 86425, 88083, 88770, 90622, 90924, 91634, 92029, 95152, 95348, 96145, 96793, 97015, 97064, 97711 , 97855 and 98708.

11. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 4 selected from the group consisting of 6414, 51282, 54574, 78374, 92029 and 96793.

12. The method of claim 1, wherein the one or more polymorphic variations are detected within a region spanning chromosome positions positions 175647734 to 175655734 of chromosome 2 in human genomic DNA.

13. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 5 selected from the group consisting of 209, 5908, 7460, 7733, 7855, 7904, 8869, 9480, 13820, 15152, 17713, 17804, 18220, 19083, 19123, 19605, 20247, 20592, 21907, 23273, 23299, 23623, 23669, 23844, 24190, 24486, 24896, 25118, 30551, 30844, 30900, 30942, 31699, 32081, 35078, 36196, 36541, 38356, 45578, 49634, 49774, 51119, 51181, 51652, 54467, 55762, 55999, 57865, 66613, 68377, 69754, 72859, 76512, 76717, 77722, 80998, 82033, 89658, 89960, 94155 and 95679.

14. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 5 selected from the group consisting of 19083, 30900, 38356, 76512 and 94155.

15. The method of claim 1, wherein the one or more polymorphic variations are detected within a region spanning chromosome positions 178746000 to 178751000 of chromosome 5 in human genomic DNA.

16. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 6 selected from the group consisting of 210, 3608, 3609, 4318, 5593, 5629, 5639, 5640, 8943, 17968, 19887, 21034, 21085,, 21596, 23379, 23432, 24007, 26121, 26273, 26755, 27411, 27710, 27842, 28379, 29603, 31232, 31504, 32583, 32794, 32840, 33044, 33150, 33218, 33513, 33959, 34486, 36289, 36570, 38247, 38477, 38518, 38529, 38667, 39781, 39856, 39927, 40506, 41869, 42452, 44788, 46059, 46846, 47712, 48796, 49441, 49602, 49723, 50050, 50171, 50477, 50818, 50833, 50881, 50882, 51386, 51534, 52317, 52368, 52970, 53023, 53356, 53882, 54553, 55475, 55530, 55691, 55848, 55879, 56316, 56911, 57320, 57391, 57437, 57478, 57500, 59111, 59333, 59715, 59804, 59851, 59929, 60052, 60240, 60359, 60381, 60456, 60724, 60875, 60968, 60978, 60998, 61557, 62091, 62645, 62943, 63131, 63145, 63406, 63427, 63554, 63661, 64093, 64153, 64409, 64544, 65257, 65626,65739 , 66392, 66720, 69177, 69336, 69636, 69823, 69928, 70547, 70633, 71805, 72181, 72200, 72474, 72567, 72973, 73468, 73889, 75730, 75970, 76114, 76342, 76449, 76465, 76791, 78042, 80758, 80778, 81356, 81576, 81689, 81759, 81950, 82562, 83591, 83700, 83821, 83842, 83923, 83929, 84021, 84175, 84417, 84747, 85746, 86129, 86335, 87315, 87648, 87764, 87770, 88221, 90474, 91148, 91150, 91160, 91733, 91772, 91785, 93140, 93148, 96080, 96157, 96313, 96759, 97026, 97320, 97732, 98713, 99707, 99959, 100009, 100020, 100065, 100086, 101270, 101276, 101371, 101376, 101439, 101820, 102392, 102602, 102604, 102896, 189104, 189134 and 189205.

17. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 6 selected from the group consisting of 5640, 33150, 38247, 38529, 46846, 49723, 50050, 63427, 73889, 189104 and rs428901.

18. The method of claim 1, wherein the one or more polymorphic variations are detected within a region spanning chromosome positions 105595000 to 105615000 of chromosome 6 in human genomic DNA.

19. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 7 selected from the group consisting of 241, 801, 899, 2091, 2290, 2440, 4959, 7914, 7969, 7972, 10831, 12399, 13841, 14461, 14680, 16808, 18231, 18394, 18505, 18684, 19257, 20263, 20656, 21499, 21563, 21612, 21834, 22406, 22408, 22685, 23303, 23306, 25139, 25211, 25364, 25381, 25414, 25835, 26214, 27224, 27526, 27934, 28550, 29015, 29879, 29979, 30030, 30585, 31753, 31934, 33227, 33228, 35172, 36901, 36921, 36932, 37061, 37570, 38745, 38970, 39725, 40070, 40460, 41470, 41562, 41956, 42047, 42280, 42358, 42629, 43075, 43387, 43393, 43438, 44115, 44537, 45642, 46629,47496, 47515, 48329, 48862, 48908, 49038, 49080, 50204, 50404, 50426, 50531, 50840, 50964, 50971,51378, 52610, 53906, 53951, 54111, 54149, 55563, 55999, 58415, 58961, 60447, 61377, 61528, 61606, 62140, 62461, 63826, 64950, 65076, 66121, 66406, 67051, 68860, 69014, 70796, 72325, 73414, 75258, 76347, 76839, 77358, 77822, 77946, 80002, 80024, 80285, 80397, 82075, 82153, 83981, 84184, 85089, 85288, 85330, 85581, 85642, 86433, 86904, 88391, 89042, 90828, 92676, 92881, 94227, 94585, 94616, 94712, 94738, 95253, 95522, 95869 and 97856.

20. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 7 selected from the group consisting of 25414, 25835, 38970, 41470, 44115, 47496, 49038, 50204, 50840, 50964, 50971, 53906, 54149, 58415, 70796, 72325, 75258, 77822, 80002, 85288, 85581, 86904, 90828, 94616, 94712, 95869 and 97856.

21. The method of claim 1, wherein the one or more polymorphic variations are detected within a region spanning chromosome positions 27052000 to 27066000 of chromosome 12 in human genomic DNA.

22. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 8 selected from the group consisting of 230, 231, 5330, 6334, 11372, 11456, 11501, 13393, 16666, 17596, 19710, 19800, 20297, 20967, 32514, 33159, 37600, 41259, 41329, 50060, 53292, 53393, 56417, 56435, 58847, 59595, 59661, 60355, 60407, 62357, 68230, 68516, 69055, 72603, 73928, 85897 and 91554.

23. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 8 selected from the group consisting of 56435, 59595, 53292, 33159 and 41329.

24. The method of claim 1, wherein the one or more polymorphic variations are detected within a region spanning chromosome positions 71957600 to 71962600 of chromosome 15 in human genomic DNA.

25. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 10 selected from the group consisting of 213, 249, 1824, 2057, 2306, 2869, 3976, 4288, 4290, 4434, 5298, 5467, 8486, 8487, 8831, 9036, 9058, 9131, 9732, 9862, 10191, 10270, 16167, 17620, 17751, 17764, 17787, 19401, 21021, 21902, 22173, 22416, 22653, 24945, 25011, 28563, 48574, 48710, 48880, 50194, 56343, 56455, 56729, 56759, 56895, 57036, 57702, 62515, 62629, 63501, 63547, 64876, 65073, 67149, 67549, 71660, 71906 and 71911.

26. The method of claim 1, wherein a polymorphic variation is detected at position 65073 in SEQ ID NO: 10.

27. The method of claim 1, wherein the one or more polymorphic variations are detected within a region spanning chromosome positions 76221000 to 76226000 of chromosome 16 in human genomic DNA.

28. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 11 selected from the group consisting of 205, 866, 4212, 5934, 11486, 16969, 22509, 22796, 28097, 28626, 28853, 28873, 30155, 30827, 31956, 32404, 32944, 35205, 35227, 35781, 41052, 45051, 46039, 47276, 47678, 47716, 51014, 54408, 54596, 56853, 61851, 62016, 62461, 68257, 69793, 73976, 73999, 74053, 75315, 75729, 76466, 77216, 77217, 79239, 80825, 81060, 81097, 81426, 84787, 84896, 85165, 86502, 86753, 86941, 88787 and 95598.

29. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 11 selected from the group consisting of 47716 and 69793.

30. The method of claim 1, wherein the one or more polymorphic variations are detected within a region spanning chromosome positions 34828750 and 34833750 of chromosome 22 in human genomic DNA.

31. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 13 selected from the group consisting of 201, 425, 1095, 2201, 7879, 8395, 8461, 9503, 10304, 10695, 16300, 16444, 17591, 17988, 19116, 19358, 20300, 20669, 20891, 21451, 21978, 22785, 24248, 24770, 24844, 25066, 25096, 25309, 25344, 25529, 25537, 25554, 27963, 28134, 28356, 29648, 29986, 30217, 30267, 30315, 30585, 30724, 30897, 30931, 31080, 31246, 31373, 31463, 31467, 32188, 32288, 32520, 32594, 32657, 32677, 32764, 32784, 32830, 32872, 33121, 33348, 33952, 34184, 34361, 35026, 35192, 35600, 36033, 36289, 38869, 39629, 40530, 41621, 42379, 42802, 42865, 43644, 45051, 45828, 45829, 46257, 47286, 47427, 47963, 48013, 48229, 48282, 48376, 48404, 49900, 52699, 52897, 53414, 53487, 54112, 55492, 59766, 60307, 60701, 60952, 61401, 62379, 62870, 62879, 63499, 64284, 64408, 64760, 65230, 66127, 6634, 66686, 66694, 67113, 67257, 67403, 67609, 68418, 68610, 69629, 70024, 70848, 71428, 71553, 71633, 71768, 71769, 73039, 73325, 73412, 73547, 73769, 73806, 74467, 74472, 74473, 74482, 74494, 74592, 74670, 74672, 74714, 74723, 74749, 74861, 74892, 74893, 75176, 75705, 75989, 76027, 77949, 77974, 78167, 78310, 78415, 78575, 78590, 78709, 78875, 79864, 81316, 81320, 81409, 81737, 81843, 82102, 82833, 83461, 83624, 83660, 83701, 83708, 83782, 85707, 85717, 86486, 86833, 87115, 87234, 87479, 87561, 87604, 87674, 87958, 87992, 88019, 88074, 88079, 88115, 88118, 88120, 88135, 88142, 88143, 88149, 88340, 88344, 88512, 88521, 88650, 88827, 89230, 89236, 90754, 90984, 91110, 92026, 92954, 93375, 93794, 94937, 95068, 96188, 97092 and 98812.

32. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO: 13 selected from the group consisting of 20300, 87958, 89236, 30267, 32657, 36289, 38869, 45051, 46257, 54112, 60307, 63499, 20891, 52699 and 71768.

33. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in Table B.

34. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in linkage disequilibrium with one or more positions in claim 4, 7, 10, 13, 16, 19, 22, 25, 28, 31 or 33.

35. The method of claim 1, wherein detecting the presence or absence of the one or more polymorphic variations comprises:
hybridizing an oligonucleotide to the nucleic acid sample, wherein the oligonucleotide is complementary to a nucleotide sequence in the nucleic acid and hybridizes to a region adjacent to the polymorphic variation;
extending the oligonucleotide in the presence of one or more nucleotides, yielding extension products; and detecting the presence or absence of a polymorphic variation in the extension products.

36. The method of claim 1, wherein the subject is a human.

37. The method of claim 36, wherein the subject is a human female.

38. The method of claim 36, wherein the subject is a human male.

39. A method for identifying a polymorphic variation associated with osteoarthritis proximal to an incident polymorphic variation associated with osteoarthritis, which comprises:
identifying a polymorphic variation proximal to the incident polymorphic variation associated with osteoarthritis, wherein the polymorphic variation is detected in a nucleotide sequence selected from the group consisting of:
(a) a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising a polymorphic variation;
determining the presence or absence of an association of the proximal polymorphic variant with osteoarthritis.

40. The method of claim 39, wherein the incident polymorphic variation is at one or more positions in claim 4, 7, 10, 13, 16, 19, 22, 25, 28, 31 or 33.

41. The method of claim 39, wherein the proximal polymorphic variation is within a region between about 5 kb 5' of the incident polymorphic variation and about 5 kb 3' of the incident polymorphic variation.

42. The method of claim 39, which further comprises determining whether the proximal polymorphic variation is in linkage disequilibrium with the incident polymorphic variation.

43. The method of claim 39, which further comprises identifying a second polymorphic variation proximal to the identified proximal polymorphic variation associated with osteoarthritis and determining if the second proximal polymorphic variation is associated with osteoarthritis.

44. The method of claim 43, wherein the second proximal polymorphic variant is within a region between about 5 kb 5' of the incident polymorphic variation and about 5 kb 3' of the proximal polymorphic variation associated with osteoarthritis.

45. An isolated nucleic acid comprising a nucleotide sequence selected from the group consisting of:
(a) a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising a polymorphic variation; and (e) a nucleotide sequence complementary to the nucleotide sequences of (a), (b), (c), or (d);
wherein the nucleotide sequence comprises a polymorphic variation associated with osteoarthritis selected from the group consisting of in SEQ ID NO: 2 an adenine at position 7219, a guanine at position 7485, an adenine at position 11839, a thymine at position 31899, an adenine at position 37000, a cytosine at position 48513, a guanine at position 49986, a guanine at position 56640, a cytosine at position 74407, a guanine at position 77398, an adenine at position 93060 and an adenine at position 97627; in SEQ ID
NO: 3 an adenine at position 2215, a deletion at position 3369, a deletion at position 16642, a cytosine at position 20783, a cytosine at position 52155, a cytosine at position 55052, a cytosine at position 55941, a thymine at position 74333, an adenine at position 74741, a deletion at position 85366, a thymine at position 85469, a thymine at position 87687, an adenine at position 89660 and a cytosine at position 95718; in SEQ ID NO: 4 an adenine at position 6414, an adenine at positoin 51282, a cytosine at position 54574, a thymine at position 92029 and an adenine at position 96793; in SEQ ID
NO: 5 a thymine at position 19083, a guanine at position 30900, an adenine at position 38356, an adenine at position 76512 and an adenine at position 94155; in SEQ ID NO: 6 a cytosine at position 5640, a cytosine at position 33150, an adenine at position 38247, a thymine at position 38529, an adenine at position 46846, a cytosine at position 49723, a cytosine at position 50050, a cytosine a position 63427, a guanine at position 73889, a thymine at position 189104, and an adenine at position rs428901; in SEQ ID NO: 7 an adenine at position 25414, a cytosine at position 25835, an adenine at position 38970, an adenine at position 41470, an adenine at position 44115, a guanine at position 47496, a cytosine at position 49038, an adenine at position 50204, a thymine at position 50840, a cytosine at position 50964, a cytosine at position 50971, an adenine at position 53906, a guanine at position 54149, a guanine at position 58415, a thymine at position 70796, a guanine at position 72325, a cytosine at position 75258, an adenine at position 77822, an adenine at position 80002, an adenine at position 85288, an adenine at position 85581, a guanine at position 86904, a guanine at position 90828, an adenine thymine adenine adenine sequence at position 94616, a cytosine at position 94712, a guanine at position 95869 and a cytosine at position 97856; in SEQ ID NO: 8 a thymine thymine repeat at position 56435, a thymine at position 59595, a cytosine at position 53292, a guanine at position 33159 and a thymine at position 41329; in SEQ ID NO:
a guanine at position 65073; in SEQ ID NO: 11 an adenine at position 47716 and a thymine at position 69793; in SEQ ID NO: 13 an adenine at position 20300, a thymine at position 46257, an adenine at position 89236, a guanine at position 30267, an adenine at position 32657, a cytosine at position 36289, a guanine at position 38869, a thymine at position 45051, a guanine at position 54112, an adenine at position 60307, a thymine at position 63499, a guanine at position 20891, a guanine at position 52699, and a cytosine at position 71768; and an allele associated with osteoporosis in Table B for positions rs910223, rs242392 and rs512294.

46. An oligonucleotide comprising a nucleotide sequence complementary to a portion of the nucleotide sequence of (a), (b), (c), or (d) in claim 45, wherein the 3' end of the oligonucleotide is adjacent to a polymorphic variation associated with osteoarthritis.

47. A microarray comprising an isolated nucleic acid of claim 45 linked to a solid support.

48. An isolated polypeptide encoded by the isolated nucleic acid sequence of claim 45.

49. A method for identifying a candidate therapeutic for treating osteoarthritis, which comprises:
(a) introducing a test molecule to a system which comprises a nucleic acid comprising a nucleotide sequence selected from the group consisting of:
(i) a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(ii) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(iii) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(iv) a fragment of a nucleotide sequence of (a), (b), or (c); or introducing a test molecule to a system which comprises a protein encoded by a nucleotide sequence of (i), (ii), (iii), or (iv); and (b) determining the presence or absence of an interaction between the test molecule and the nucleic acid or protein, whereby the presence of an interaction between the test molecule and the nucleic acid or protein identifies the test molecule as a candidate therapeutic for treating osteoarthritis.

50. The method of claim 49, wherein the system is an animal.

51. The method of claim 49, wherein the system is a cell.

52. The method of claim 49, wherein the nucleotide sequence comprises one or more polymorphic variations associated with osteoarthritis.

53. The method of claim 52, wherein the one or more polymorphic variations associated with osteoarthritis are at one or more positions in claim 4, 7, 10, 13, 16, 19, 22, 25, 28, 31 or 33.

54. A method for treating osteoarthritis in a subject, which comprises contacting one or more cells of a subject in need thereof with a nucleic acid, wherein the nucleic acid comprises a nucleotide sequence selected from the group consisting of:
(a) a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;

(d) a fragment of a nucleotide sequence of (a), (b), or (c); and (e) a nucleotide sequence complementary to the nucleotide sequences of (a), (b), (c), or (d);
whereby contacting the one or more cells of the subject with the nucleic acid treats the osteoarthritis in the subject.

55. The method of claim 54, wherein the nucleic acid is RNA or PNA.

56. The method of claim 55, wherein the nucleic acid is duplex RNA.

57. A method for treating osteoarthritis in a subject, which comprises contacting one or more cells of a subject in need thereof with a protein, wherein the protein is encoded by a nucleotide sequence which comprises a polynucleotide sequence selected from the group consisting of:
(a) a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(d) a fragment of a nucleotide sequence of (a), (b), or (c);
whereby contacting the one or more cells of the subject with the protein treats the osteoarthritis in the subject.

58. The method of claim 57, wherein the treatment comprises administration of an effective amount of a composition comprising an active ADAMTS2 polypeptide or fragment thereof, wherein the polypeptide fragment is selected from the group consisting of: 252-1211, 253-1211, 254-1211, 255-1211, 256-1211, 257-1211, 258-1211, 259-1211 or 260-1211 of SEQ ID NO: 44.

59. The method of claim 58, wherein the polypeptide or fragment has biological activity.

60. A method for treating osteoarthritis in a subject, which comprises:
detecting the presence or absence of one or more polymorphic variations associated with osteoarthritis in a nucleic acid sample from a subject, wherein the one or more polymorphic variation are detected in a nucleotide sequence selected from the group consisting of:
(a) a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;

(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising a polymorphic variation; and administering an osteoarthritis treatment to a subject in need thereof based upon the presence or absence of the one or more polymorphic variations in the nucleic acid sample.

61. The method of claim 60, wherein the one or more polymorphic variations are detected at one or more positions in claim 4, 7, 10, 13, 16, 19, 22, 25, 28, 31 or 33.

62. The method of claim 60, wherein the treatment is selected from the group consisting of administering a corticosteroid, a nonsteroidal anti-inflammatory drug (NSAID), a cyclooxygenase-2 (COX-2) inhibitor, an antibody, a glucocorticoid, hyaluronic acid, chondrotin sulfate, glucosamine or acetaminophen; prescribing a heat/cold regimen or a joint protection regimen;
performing joint surgery;
prescribing a weight control regimen; and combinations of the foregoing.

63. A method for detecting or preventing osteoarthritis in a subject, which comprises:
detecting the presence or absence of one or more polymorphic variations associated with osteoarthritis in a nucleic acid sample from a subject, wherein the polymorphic variation is detected in a nucleotide sequence selected from the group consisting of:
(a) a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising a polymorphic variation; and administering an osteoarthritis prevention or detection procedure to a subject in need thereof based upon the presence or absence of the one or more polymorphic variations in the nucleic acid sample.

64. The method of claim 63, wherein the one or more polymorphic variations are detected at one or more positions in claim 4, 7, 10, 13, 16, 19, 22, 25, 28, 31 or 33.

65. The method of claim 63, wherein the osteoarthritis prevention is selected from the group consisting of administering a corticosteroid, a nonsteroidal anti-inflammatory drug (NSAID), a cyclooxygenase-2 (COX-2) inhibitor, an antibody, a glucocorticoid, hyaluronic acid, chondrotin sulfate, glucosamine or acetaminophen; prescribing a heat/cold regimen or a joint protection regimen; performing joint surgery; prescribing a weight control regimen; and combinations of the foregoing.

66. A method of targeting information for preventing or treating osteoarthritis to a subject in need thereof, which comprises:
detecting the presence or absence of one or more polymorphic variations associated with osteoarthritis in a nucleic acid sample from a subject, wherein the polymorphic variation is detected in a nucleotide sequence selected from the group consisting of:
(a) a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B;
(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising a polymorphic variation; and directing information for preventing or treating osteoarthritis to a subject in need thereof based upon the presence or absence of the one or more polymorphic variations in the nucleic acid sample.

67. The method of claim 66, wherein the one or more polymorphic variations are detected at one or more positions in claim 4, 7, 10, 13, 16, 19, 22, 25, 28, 31 or 33.

68. A composition comprising a cell from a subject having osteoarthritis or at risk of osteoarthritis and an antibody that specifically binds to a protein, polypeptide or peptide encoded by a nucleotide sequence identical to or 90% or more identical to a nucleotide sequence in SEQ ID NO: 1-13 or referenced in Table B.

69. The composition of claim 68, wherein the antibody specifically binds to an epitope comprising an amino acid encoded by rs1367117, rs1041973 and rs398829.

70. A composition comprising a cell from a subject having osteoarthritis or at risk of osteoarthritis and a RNA, DNA, PNA or ribozyme molecule comprising a nucleotide sequence identical to or 90% or more identical to a portion of a nucleotide sequence in SEQ ID
NO: 1-13 or referenced in Table B.

71. The composition of claim 70, wherein the RNA molecule is a short inhibitory RNA
molecule.