NZ577804A - Genetic susceptibility variants of type 2 diabetes mellitus - Google Patents

Abstract

Provided is a method of determining a susceptibility to Type 2 diabetes in a human individual, comprising determining the presence or absence of at least one allele of at least one polymorphic marker in a nucleic acid sample obtained from the individual, or in a genotype dataset derived from the individual, wherein the at least one polymorphic marker is selected from rs7756992, and markers in linkage disequilibrium therewith, and wherein determination of the presence or absence of the at least one allele is indicative of a susceptibility to Type 2 diabetes.

Description

WO 2008/065682 PCT/IS2007/000020 1 GENETIC SUSCEPTIBILITY VARIANTS OF TYPE 2 DIABETES MELLITUS BACKGROUND OF THE INVENTION t Diabetes mellitus, a metabolic disease wherein carbohydrate utilization is reduced and lipid and protein utilization is enhanced, is caused by an absolute or relative deficiency of insulin. In the more severe cases, diabetes is characterized by chronic hyperglycemia, glycosuria, water and electrolyte loss, ketoacidosis and coma. Long term complications include development of neuropathy, retinopathy, nephropathy, generalized 10 degenerative changes in large and small blood vessels and increased susceptibility to infection. The most common form of diabetes is Type II, non-insulin-dependent diabetes that is characterized by hyperglycemia due to impaired insulin secretion and insulin resistance in target tissues. Both genetic and environmental factors contribute to the disease. For example, obesity plays a major role in the development of the disease. 15 Type 2 diabetes is often a mild form of diabetes mellitus of gradual onset.

The health implications of Type 2 diabetes are enormous. In 1995, there were 135 million adults with diabetes worldwide. It is estimated that close to 300 million will have diabetes in the year 2025. (King, H., et al., Diabetes Care, 21(9): 1414-1431 (1998)). The prevalence of Type 2 diabetes in the adult population in Iceland is 2.5% 20 (Vilbergsson, S., etal., Diabet. Med., 14(6): 491-498 (1997)), which comprises approximately 5,000 people over the age of 34 who have the disease.

Type 2 diabetes is characterized by hyperglycemia, which can occur through mechanisms such as impaired insulin secretion, insulin resistance in peripheral tissues and increased glucose output by the liver. Most Type 2 diabetes patients suffer serious 25 complications of chronic hyperglycemia including nephropathy, neuropathy, retinopathy and accelerated development of cardiovascular disease. The prevalence of Type 2 diabetes worldwide is currently 6% but is projected to rise over the next decade (Amos, A. F., McCarty, D. J., Zimmet, P., Diabet Med 14 Suppl 5, SI (1997)). This increase in prevalence of Type 2 diabetes is attributed to increasing age of the population and rise in 30 obesity.

There is evidence for a genetic component to the risk of Type 2 diabetes, including prevalence differences between various racial groups (Zimmet, P. eta/., Am J Epidemiol 118, 673 (1983), Knowler, W.C., Pettitt, D.J., Saad, M.F., Bennett, P.H., Diabetes Metab Rev 6, 1 (1990)), higher concordance rates among monozygotic than dizygotic twins WO 2008/065682 PCT/IS2007/000020 2 (Newman, B. etal., Diabetologia 30, 763 (1987), Barnett, A.H., Eff, C., Leslie, R.D., Pyke, D.A., Diabetologia 20, 87 (1981)) and a sibling relative risk (As) for Type 2 diabetes in European populations of approximately 3.5 (Gloyn, A.L., Ageing Res Rev 2, 111 (2003)).

Two approaches have thus far been used to search for genes associated with Type 5 2 diabetes. Single nucleotide polymorphisms (SNPs) within candidate genes have been tested for association and have, in general, not been replicated or confer only a modest risk of Type 2 diabetes - the most widely reported being a protective Prol2Ala polymorphism in the peroxisome proliferator activated receptor gamma gene (PPARG2) (Altshuler, D. eta/., Nat Genet 26, 76 (2000)) and an at risk polymorphism in the 10 potassium inwardly-rectifying channel, subfamily J, member 11 gene (KIR6.2) (Gloyn A.L. etal., Diabetes 52, 568 (2003)).

Genome-wide linkage scans in families with the common form of Type 2 diabetes have yielded several loci, and the primary focus of international research consortia has been on loci on chromosomes 1, 12 and 20 observed in many populations (Gloyn, A.L., 15 Ageing Res Rev 2, 111 (2003)). The genes in these loci have yet to be uncovered.

However, in Mexican Americans, the calpain 10 (CAPN10) gene was isolated out of a locus on chromosome 2q (Horikawa, Y. eta/., Nat Genet 26, 163 (2000)). The rare Mendelian forms of Type 2 diabetes, namely maturity-onset diabetes of the young (MODY), have yielded six genes by positional cloning (Gloyn, A.L., Ageing Res Rev 2, 111 (2003)).

Genome-wide significant linkage to chromosome 5q for Type 2 diabetes mellitus in the Icelandic population has been reported (Reynisdottir, I. et a/., Am J Hum Genet 73, 323 (2003)); in the same study, suggestive evidence of linkage to lOq and 12q was also reported. Linkage to the lOq region has also been observed in Mexican Americans (Duggirala, R. et a/., Am J Hum Genet 64, 1127 (1999)).

The transcription factor 7-like 2 gene (TCF7L2; formerly TCF4) has been associated with Type 2 diabetes (P = 2.1 x 10(-9)) (Grant, S.F. eta/., Nat Genet 38, 320 (2006)). The original finding in an Icelandic cohort of association of the microsatellite marker DG10S478 within intron 3 of the gene (P = 2.1 x 10(-9)) was replicated in a Danish cohort (P = 4.8 x 10(-3)) and in a US cohort (P = 3.3 x 10(-9)). Compared with 30 non-carriers, heterozygous and homozygous carriers of the at-risk alleles (38% and 7% of the population, respectively) have relative risks of 1.45 and 2.41. This corresponds to a population attributable risk of 21%. %. Association of the TCF7L2 variant has now been replicated in 10 independent studies with similar relative risk found in the different populations studied. The TCF7L2 gene product is a high mobility group box-containing 35 transcription factor previously implicated in blood glucose homeostasis. It is thought to act through regulation of proglucagon gene expression in enteroendocrine cells via the Wnt signaling pathway.

WO 2008/065682 PCT/IS2007/000020 3 Despite the advances in unravelling the genetics of Type 2 diabetes, the high prevalence of the disease and increasing population affected shows an unmet medical need to define additional genetic factors involved in Type 2 diabetes to more precisely define the associated risk factors. People with impaired fasting glucose or impaired 5 glucose tolerance are asymptomatic but are at a high risk of developing Type 2 diabetes. Currently there is very little information to distinguish those within this high risk group, where lifestyle intervention would be the best choice for disease prevention, from those individuals for whom preventive medication would be more appropriate. Identification of susceptibility genes will allow a better understanding of the pathophysiology of the 10 disease and as a direct benefit for the patient it will facilitate better approaches for diagnosis and treatment. Also needed are therapeutic agents for prevention of Type 2 diabetes.

SUMMARY OF THE INVENTION The present invention relates to methods of diagnosing an increased susceptibility to Type 2 diabetes, as well as methods of diagnosing a decreased susceptibility to Type 2 diabetes or diagnosing a protection against Type 2 diabetes, by evaluating certain markers or haplotypes that have been found to be associated with increased or decreased susceptibility of Type 2 diabetes.

In a first aspect, the present invention relates to a method of determining a susceptibility to Type 2 diabetes in a human individual, comprising determining the presence or absence of at least one allele of at least one polymorphic marker in a nucleic acid sample obtained from the individual, wherein the at least one polymorphic marker is selected from the markers set forth in Tables 10-12, and markers in linkage disequilibrium therewith, and wherein determination of the presence or absence of the at least one allele is indicative of a susceptibility to Type 2 diabetes. I one embodiment, the at least one polymorphic marker is selected from the markers set forth in Tables 10-12 and 14. In an alternative aspect the method of determining a susceptibility to Type 2 diabetes is a method of diagnosing a susceptibility to Type 2 diabetes.

In one embodiment, the at least one polymorphic marker is present within SEQ ID NO:l, SEQ ID NO:2 or SEQ ID NO:3. In another embodiment, the at least one polymorphic marker comprises at least one marker selected from rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), rsl860316 (SEQ ID WO 2008/065682 PCT/IS2007/000020 4 NO: 10), rsl981647 (SEQ ID NO: 11), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO: 13), rs9890889 (SEQ ID NO:31), and markers in linkage disequilibrium therewith. In another embodiment, the at least one polymorphic marker comprises at least one marker in strong linkage disequilibrium, as defined by numeric values for |D'| of greater than 0.8 5 and/or r2 of greater than 0.2, with one or more markers selected from the group consisting of the markers set forth in Table 22, Table 23 and Table 24. In one preferred embodiment, the at least one polymorphic marker is selected from markers rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 10 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), and markers in linkage disequilibrium therewith. In another preferred embodiment, the at least one polymorphic marker is selected from markers rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), and rs6931514 (SEQ ID NO:37). In one 15 embodiment, the at least one marker is selected from marker rs7756992 (SEQ ID NO: 21), and markers in linkage disequilibrium therewith. In another embodiment, the at least one markers is selected from the markers set forth in Table 22. In another embodiment, the at least one marker is selected from marker rsl0882091 (SEQ ID NO: 4), and markers in linkage disequilibrium therewith. In another embodiment, the at least 20 one markers is selected from the markers set forth in Table 23. In yet another embodiment, the at least one marker is selected from marker rs2191113 (SEQ ID NO: 13), and markers in linkage disequilibrium therewith. In another embodiment, the at least one markers is selected from the markers set forth in Table 24.

In one embodiment, the method of determining a susceptibility, or diagnosing a 25 susceptibility, of Type 2 diabetes, further comprises assessing the frequency of at least one haplotype in the individual. In one such embodiment, the at least one haplotype is selected from the haplotypes that comprise at least one polymorphic marker as set forth in Tables 1-6, and polymorphic markers in linkage disequilibrium therewith. In another embodiment, the at least one haplotype is selected from the haplotypes that comprise at 30 least one polymorphic marker selected from at least one marker selected from rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO:15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 35 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), rsl860316 (SEQ ID NO: 10), rsl981647 (SEQ ID NO: 11), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO: 13), rs9890889 (SEQ ID NO:31), and markers in linkage disequilibrium therewith. In another embodiment, the at least one haplotype is selected from the haplotypes set forth in Tables 1-6 and 14.

WO 2008/065682 PCT/IS2007/000020 In a second aspect, the invention relates to a method of determining a susceptibility to Type 2 diabetes in a human individual, comprising determining whether at least one at-risk allele in at least one polymorphic marker is present in a genotype dataset derived from the individual, wherein the at least one polymorphic marker is 5 selected from the markers set forth in Tables 10-12, and markers in linkage disequilibrium therewith, and wherein determination of the presence of the at least one at-risk allele is indicative of increased susceptibility to Type 2 diabetes in the individual. The genotype dataset comprises in one embodiment information about marker identity, and the allelic status of the individual, i.e. information about the identity of the two alleles 10 carried by the individual for the marker. The genotype dataset may comprise allelic information about one or more marker, including two or more markers, three or more markers, five or more markers, one hundred or more markers, etc. In some embodiments, the genotype dataset comprises genotype information from a whole-genome assessment of the individual including hundreds of thousands of markers, or even 15 one million or more markers.

In one embodiment, the at least one polymorphic marker is present within SEQ ID NO:l, SEQ ID NO:2 or SEQ ID NO:3. In another embodiment, the at least one polymorphic marker comprises at least one marker selected from rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID 20 NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO:19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), rsl860316 (SEQ ID NO: 10), rsl981647 (SEQ ID NO: 11), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID 25 NO: 13), rs9890889 (SEQ ID NO:31), and markers in linkage disequilibrium therewith. In another embodiment, the at least one polymorphic marker comprises at least one marker in strong linkage disequilibrium, as defined by numeric values for |D'| of greater than 0.8 and/or r2 of greater than 0.2, with one or more markers selected from the group consisting of the markers set forth in Table 22, Table 23 and Table 24. In one preferred 30 embodiment, the at least one polymorphic marker is selected from markers rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), and markers in linkage disequilibrium therewith. In another preferred embodiment, the at least one polymorphic marker is 35 selected from markers rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), and rs6931514 (SEQ ID NO:37). In one embodiment, the at least one marker is selected from marker rs7756992 (SEQ ID NO: 21), and markers in linkage disequilibrium therewith. In another embodiment, the at 40 least one markers is selected from the markers set forth in Table 22. In another WO 2008/065682 PCT/IS2007/000020 6 embodiment, the at least one marker is selected from marker rsl0882091 (SEQ ID NO: 4), and markers in linkage disequilibrium therewith. In another embodiment, the at least one markers is selected from the markers set forth in Table 23. In yet another embodiment, the at least one marker is selected from marker rs2191113 (SEQ ID NO: 5 13), and markers in linkage disequilibrium therewith. In another embodiment, the at least one markers is selected from the markers set forth in Table 24. In yet another embodiment, the at least one marker is selected from markers in linkage disequilibrium with the SLC30A gene on chromosome 8, between position 118,032,398 and 118,258,134 (NCBI Build 36 of the Human genome assembly). In one such embodiment, the at least 10 one marker is located within the SLC30A gene.

In one embodiment, the method of determining a susceptibility, or diagnosing a susceptibility, of Type 2 diabetes, further comprises assessing the frequency of at least one haplotype in the individual. In one such embodiment, the at least one haplotype is selected from the haplotypes that comprise at least one polymorphic marker as set forth 15 in Tables 1-6, and polymorphic markers in linkage disequilibrium therewith. In another embodiment, the at least one haplotype is selected from the haplotypes that comprise at least one polymorphic marker selected from at least one marker selected from rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 20 (SEQ ID NO:19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), rsl860316 (SEQ ID NO: 10), rsl981647 (SEQ ID NO: 11), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO: 13), rs9890889 (SEQ ID NO:31), and markers in linkage disequilibrium 25 therewith. In another embodiment, the at least one haplotype is selected from the haplotypes set forth in Tables 1-6 and 14.

In certain embodiments of the invention, determination of the presence of at least one at-risk allele of at least one polymorphic marker in a nucleic acid sample from the individual is indicative of an increased susceptibility to Type 2 diabetes. In one 30 embodiment, the increased susceptibility is characterized by a relative risk (RR) or odds ratio (OR) of at least 1.15. In another embodiment, the increased susceptibility is characterized by a relative risk (RR) or odds ratio (OR) of at least 1.20.

In some embodiments, the presence of rs2497304 allele A, rs947591 allele A, rsl0882091 allele C rs7914814 allele T, rs6583830 allele A, rs2421943 allele G, 35 rs6583826 allele G, rs7752906 allele A, rsl569699 allele C, rs7756992 allele G, rs9350271 allele A, rs9356744 allele C, rs9368222 allele A, rsl0440833 allele A, rs6931514 allele G, rsl860316 allele A, rsl981647 allele C, rsl843622 allele T, WO 2008/065682 PCT/IS2007/000020 7 rs2191113 allele A, and/or rs9890889 allele A is indicative of increased susceptibility of Type 2 diabetes.

In particular embodiments, the presence of at least one protective allele in a nucleic acid sample from the individual is indicative of a decreased susceptibility of Type 2 5 diabetes. In another embodiment, the absence of at least one at-risk allele in a nucleic acid sample from the individual is indicative of a decreased susceptibility of Type 2 diabetes.

Particular embodiments of the methods of the invention relate to the at least one marker or haplotype being further associated with insulin response and/or impaired 10 glucose tolerance in an individual.

In other embodiments, the presence of, or the determination of, at least one allele or haplotype in an at-risk marker is indicative of an increased susceptibility to Type 2 diabetes, and wherein the at least one allele or haplotype is further indicative of decreased insulin response and/or impaired glucose tolerance.

In certain embodiments of the invention, linkage disequilibrium is characterized by numeric values for |D'| of greater than 0.8 and/or r2 of greater than 0.2. However, other values for the r2and |D'| measures are also possible in other embodiments, and such embodiments are also within the scope of the claimed invention, as described in further detail herein.

Another aspect of the invention relates to a method of assessing a susceptibility to Type 2 diabetes in a human individual, comprising screening a nucleic acid from the individual for at least one polymorphic marker or haplotype in SEQ ID NO:l, SEQ ID NO:2 or SEQ ID NO:3, that correlates with increased occurrence of Type 2 diabetes in a human population, wherein the presence of an at-risk marker allele in the at least one 25 polymorphism or an at-risk haplotype in the nucleic acid identifies the individual as having elevated susceptibility to diabetes, and wherein the absence of the at least one at-risk marker allele or at-risk haplotype in the nucleic acid identifies the individual as not having the elevated susceptibility.

In one embodiment, the polymorphism or haplotype is selected from rs2497304 30 (SEQ ID NO:16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), rsl860316 35 (SEQ ID NO: 10), rsl981647 (SEQ ID NO: 11), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO: 13), rs9890889 (SEQ ID NO:31), and markers in linkage disequilibrium WO 2008/065682 PCT/IS2007/000020 8 therewith, as characterized by numeric values for |D'| of greater than 0.8 and/or r2 of greater than 0.2.

Certain embodiments of the invention further comprise a step of screening the nucleic acid for the presence of at least one at-risk genetic variant for Type 2 diabetes not 5 associated with LD Block C06 (SEQ ID NO:l), LD Block C10 (SEQ ID NO:2) and LD Block C17 (SEQ ID NO:3). Such additional genetic variants can in specific embodiments include any variant that has been identified as a susceptibility or risk variant for Type 2 diabetes, including other variants described herein. In one embodiment, the step comprises screening the nucleic acid for the presence or absence of at least one at-risk allele of at 10 least one at-risk variant for Type 2 diabetes in the TCF7L2 gene, wherein determination of the presence of the at least one at-risk allele is indicative of increased susceptibility of Type 2 diabetes. In another embodiment, the at least one at-risk variant in the TCF7L2 gene is selected from marker DG10S478, rsl2255372, rs7895340, rslll96205, rs7901695, rs7903146, rsl2243326 and rs4506565, and markers in linkage 15 disequilibrium therewith.

In another aspect of the present invention, the presence of the marker or haplotype found to be associated with Type 2 diabetes, and as such useful for determining a susceptibility to Type 2 diabetes, is indicative of a different response rate of the subject to a particular treatment modality for Type 2 diabetes.

In another aspect, the invention relates to a method of identification of a marker for use in assessing susceptibility to Type 2 diabetes in human individuals, the method comprising: identifying at least one polymorphic marker within SEQ ID NO:l, SEQ ID NO:2 or SEQ ID NO:3, or at least one polymorphic marker in linkage disequilibrium 25 therewith; determining the genotype status of a sample of individuals diagnosed with, or having a susceptibility to, Type 2 diabetes; and determining the genotype status of a sample of control individuals; wherein a significant difference in frequency of at least one allele in at least one 30 polymorphism in individuals diagnosed with, or having a susceptibility to, Type 2 diabetes, as compared with the frequency of the at least one allele in the control sample is indicative of the at least one polymorphism being useful for assessing susceptibility to Type 2 diabetes.

In one embodiment, "significant" is determined by statistical means, e.g. the 35 difference is statistically significant. In one such embodiment, statistical significance is WO 2008/065682 PCT/IS2007/000020 9 characterized by a P-vaiue of less than 0.05. In other embodiments, the statistical significance is characterized a P-value of less than 0.01, less than 0.001, less than 0.0001, less than 0.00001, less than 0.000001, less than 0.0000001, less than 0.0000000001, or less than 0.00000001.

In one embodiment, the at least one polymorphic marker is in linkage disequilibrium, as characterized by numerical values of r2 of greater than 0.2 and/or |D'| of greater than 0.8 with at least one marker selected from marker rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), 10 rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), rsl860316 (SEQ ID NO: 10), rsl981647 (SEQ ID NO:ll), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO:13), rs9890889 (SEQ ID NO:31).

In one embodiment, an increase in frequency of the at least one allele in the at least one polymorphism in individuals diagnosed with, or having a susceptibility to, Type 2 diabetes, as compared with the frequency of the at least one allele in the control sample, is indicative of the at least one polymorphism being useful for assessing increased susceptibility to Type 2 diabetes. In another embodiment, a decrease in frequency of the 20 at least one allele in the at least one polymorphism in individuals diagnosed with, or having a susceptibility to, Type 2 diabetes, as compared with the frequency of the at least one allele in the control sample is indicative of the at least one polymorphism being useful for assessing decreased susceptibility to, or protection against, Type 2 diabetes.

Another aspect of the invention relates to a method of genotyping a nucleic acid 25 sample obtained from a human individual, comprising determining the presence or absence of at least one allele of at least one polymorphic marker in the sample, wherein the at least one marker is selected rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), 30 rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), rsl860316 (SEQ ID N0:10), rsl981647 (SEQ ID NO:ll), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO: 13), rs9890889 (SEQ ID NO:31), and markers in linkage disequilibrium therewith, and wherein determination of the presence or 35 absence of the at least one allele of the at least one polymorphic marker is predictive of a susceptibility of Type 2 diabetes.

In one embodiment, genotyping comprises amplifying a segment of a nucleic acid that comprises the at least one polymorphic marker by Polymerase Chain Reaction (PCR), WO 2008/065682 PCT/IS2007/000020 using a nucleotide primer pair flanking the at least one polymorphic marker. In another embodiment, genotyping is performed using a process selected from allele-specific probe hybridization, allele-specific primer extension, allele-specific amplification, nucleic acid sequencing, 5'-exonuclease digestion, molecular beacon assay, oligonucleotide ligation 5 assay, size analysis, and single-stranded conformation analysis. In one particular embodiment, the process comprises allele-specific probe hybridization. In another embodiment, the process comprises DNA sequencing. In a preferred embodiment, the method comprises: 1) contacting copies of the nucleic acid with a detection oligonucleotide probe and 10 an enhancer oligonucleotide probe under conditions for specific hybridization of the oligonucleotide probe with the nucleic acid; wherein a) the detection oligonucleotide probe is from 5-100 nucleotides in length and specifically hybridizes to a first segment of the nucleic acid whose nucleotide sequence is given by SEQ ID NO:l, SEQ ID NO:2 or SEQ ID NO:3 that comprises at least one polymorphic site; b) the detection oligonucleotide probe comprises a detectable label at its 3' terminus and a quenching moiety at its 5' terminus; c) the enhancer oligonucleotide is from 5-100 nucleotides in length and is 20 complementary to a second segment of the nucleotide sequence that is 5' relative to the oligonucleotide probe, such that the enhancer oligonucleotide is located 3' relative to the detection oligonucleotide probe when both oligonucleotides are hybridized to the nucleic acid; and d) a single base gap exists between the first segment and the second 25 segment, such that when the oligonucleotide probe and the enhancer oligonucleotide probe are both hybridized to the nucleic acid, a single base gap exists between the oligonucleotides; 2) treating the nucleic acid with an endonuclease that will cleave the detectable label from the 3' terminus of the detection probe to release free detectable label when the detection probe is hybridized to the nucleic acid; and 3) measuring free detectable label, wherein the presence of the free detectable label indicates that the detection probe specifically hybridizes to the first segment of the nucleic acid, and indicates the sequence of the polymorphic site as the complement of the detection probe.

WO 2008/065682 PCT/IS2007/000020 11 In a particular embodiment, the copies of the nucleic acid are provided by amplification by Polymerase Chain Reaction (PCR). In another embodiment, the susceptibility determined is increased susceptibility. In another embodiment, the susceptibility determined is decreased susceptibility.

Another aspect of the invention relates to a method of assessing an individual for probability of response to a therapeutic agent for preventing and/or ameliorating symptoms associated with Type 2 diabetes, comprising: determining the presence or absence of at least one allele of at least one polymorphic marker in a nucleic acid sample obtained from the individual, wherein the at least one polymorphic marker is selected 10 from rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), 15 rsl860316 (SEQ ID NO: 10), rsl981647 (SEQ ID NO: 11), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO: 13), rs9890889 (SEQ ID NO:31), and markers in linkage disequilibrium therewith, wherein determination of the presence of the at least one allele of the at least one marker is indicative of a probability of a positive response to the Type 2 diabetes therapeutic agent. In one embodiment, the Type 2 diabetes therapeutic agent 20 is selected from the agents set forth in Agent Table 1 and Agent Table 2.

Yet another aspect of the invention relates to a method of predicting prognosis of an individual diagnosed with, Type 2 diabetes, the method comprising determining the presence or absence of at least one allele of at least one polymorphic marker in a nucleic acid sample obtained from the individual, wherein the at least one polymorphic marker is 25 selected from the group consisting of rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), rs 1569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), 30 rs6931514 (SEQ ID NO:37), rsl860316 (SEQ ID N0:10), rsl981647 (SEQ ID NO:ll), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO: 13), rs9890889 (SEQ ID NO:31), and markers in linkage disequilibrium therewith, wherein determination of the presence of the at least one allele is indicative of a worse prognosis of the Type 2 diabetes in the individual.

A further aspect of the invention relates to a method of monitoring progress of a treatment of an individual undergoing treatment for Type 2 diabetes, the method comprising determining the presence or absence of at least one allele of at least one polymorphic marker in a nucleic acid sample obtained from the individual, wherein the at least one polymorphic marker is selected from the group consisting of rs2497304 (SEQ ID WO 2008/065682 PCT/IS2007/000020 12 NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), rsl860316 (SEQ ID NO: 10), rsl981647 (SEQ ID NO:ll), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO:13), rs9890889 (SEQ ID NO:31), and markers in linkage disequilibrium therewith, wherein determination of the presence of the at least one allele is indicative of the treatment outcome of the individual.

In one embodiment, the method further comprises assessing at least one biomarker in a sample from the individual. In another embodiment, the method further comprises analyzing non-genetic information to make risk assessment, diagnosis, or prognosis of the individual. The non-genetic information is in one embodiment selected from age, gender, ethnicity, socioeconomic status, previous disease diagnosis, medical history of subject, family history of Type 2 diabetes, biochemical measurements, and clinical measurements. In a particular preferred embodiment, a further step comprising calculating overall risk is employed.

The invention also relates to a kit for assessing susceptibility to Type 2 diabetes in a human individual, the kit comprising reagents for selectively detecting the presence or absence of at least one allele of at least one polymorphic marker in the genome of the individual, wherein the polymorphic marker is selected from the group consisting of polymorphic markers within the nucleic acid segments whose sequences are set forth in SEQ ID NO:l, SEQ ID NO:2 and SEQ ID NO:3, and markers in linkage disequilibrium therewith, and wherein the presence of the at least one allele is indicative of a susceptibility to Type 2 diabetes.

In one embodiment, the at least one polymorphic marker is selected from the group of markers set forth in Tables 10 - 12, and markers in linkage disequilibrium therewith. In another embodiment, the at least one polymorphic marker is selected from the group of markers set forth in Tables 10 - 12 and Table 14, and markers in linkage disequilibrium therewith. In another embodiment, the at least one polymorphic markers is selected from rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), rsl860316 (SEQ ID N0:10), rsl981647 (SEQ ID NO:ll), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO:13), rs9890889 (SEQ ID NO:31), and markers in linkage disequilibrium therewith. In another embodiment, the at least one polymorphic markers is selected from rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID WO 2008/065682 PCT/IS2007/000020 13 NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), 5 rsl860316 (SEQ ID N0:10), rsl981647 (SEQ ID N0:11), rsl843622 (SEQ ID N0:9), rs2191113 (SEQ ID NO: 13), and rs9890889 (SEQ ID NO:31).

In one embodiment, the reagents comprise at least one contiguous oligonucleotide that hybridizes to a fragment of the genome of the individual comprising the at least one polymorphic marker, a buffer and a detectable label. In one embodiment, the reagents 10 comprise at least one pair of oligonucleotides that hybridize to opposite strands of a genomic nucleic acid segment obtained from the subject, wherein each oligonucleotide primer pair is designed to selectively amplify a fragment of the genome of the individual that includes one polymorphic marker, and wherein the fragment is at least 30 base pairs in size. In a particular embodiment the at least one oligonucleotide is completely 15 complementary to the genome of the individual. In another embodiment, the at least one oligonucleotide can comprise at least one mismatch to the genome of the individual. In one embodiment, the oligonucleotide is about 18 to about 50 nucleotides in length. In another embodiment, the oligonucleotide is 20-30 nucleotides in length.

In one preferred embodiment, the kit comprises: a detection oligonucleotide probe that is from 5-100 nucleotides in length; an enhancer oligonucleotide probe that is from 5-100 nucleotides in length; and an endonuclease enzyme; wherein the detection oligonucleotide probe specifically hybridizes to a first segment of the nucleic acid whose nucleotide sequence is given by SEQ ID NO:l, 25 SEQ ID NO:2 or SEQ ID NO:3 that comprises at least one polymorphic site; and wherein the detection oligonucleotide probe comprises a detectable label at its 3' terminus and a quenching moiety at its 5' terminus; wherein the enhancer oligonucleotide is from 5-100 nucleotides in length and is complementary to a second segment of the nucleotide sequence that is 5' relative to the 30 oligonucleotide probe, such that the enhancer oligonucleotide is located 3' relative to the detection oligonucleotide probe when both oligonucleotides are hybridized to the nucleic acid; wherein a single base gap exists between the first segment and the second segment, such that when the oligonucleotide probe and the enhancer oligonucleotide probe are both hybridized to the nucleic acid, a single 35 base gap exists between the oligonucleotides; and wherein treating the nucleic acid with the endonuclease will cleave the detectable label from the 3' terminus of the detection probe to release free detectable label when the detection probe is hybridized to the nucleic acid.

WO 2008/065682 PCT/IS2007/000020 14 A further aspect of the invention relates to the use of an oligonucleotide probe in the manufacture of a diagnostic reagent for diagnosing and/or assessing susceptibility to Type 2 diabetes in a human individual, wherein the probe hybridizes to a segment of a nucleic acid whose nucleotide sequence is given by SEQ ID NO: 1, SEQ ID NO:2 or SEQ 5 ID NO:3 that comprises at least one polymorphic site, wherein the fragment is 15-500 nucleotides in length. In one embodiment, the polymorphic site is selected from the polymorphic markers rs2497304 (SEQ ID NO:16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID N0:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), 10 rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), rsl860316 (SEQ ID NO: 10), rsl981647 (SEQ ID NO: 11), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO: 13), rs9890889 (SEQ ID NO:31), and polymorphisms in linkage disequilibrium therewith.

Yet another aspect of the invention relates to a computer-readable medium on which is stored: an identifier for at least one polymorphic marker; an indicator of the frequency of at least one allele of said at least one polymorphic marker in a plurality of individuals diagnosed with Type 2 diabetes; and an indicator of the frequency of the least one allele of said at least one polymorphic markers in a plurality of reference individuals; 20 wherein the at least one polymorphic marker is selected from the polymorphic markers rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID NO:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), 25 rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), rsl860316 (SEQ ID NO: 10), rsl981647 (SEQ ID NO: 11), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO: 13), rs9890889 (SEQ ID NO:31), and polymorphisms in linkage disequilibrium therewith. In one embodiment, linkage disequilibrium is defined as defined by numerical values of r2 of at least 0.2 and/or values of |D'| of at least 0.8.

In one embodiment, information about the ancestry of the plurality of individuals is included. In another embodiment, the plurality of individuals diagnosed with Type 2 diabetes and the plurality of reference individuals is of a specific ancestry.

Another aspect relates to an apparatus for determining a genetic indicator for Type 2 diabetes in a human individual, comprising: a computer readable memory; and a 35 routine stored on the computer readable memory; wherein the routine is adapted to be executed on a processor to analyze marker and/or haplotype information for at least one human individual with respect to at least one polymorphic marker selected from the markers rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), WO 2008/065682 PCT/IS2007/000020 rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), 5 rsl860316 (SEQ ID N0:10), rsl981647 (SEQ ID NO:ll), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO: 13), rs9890889 (SEQ ID N0:31), and markers in linkage disequilibrium therewith, as defined by numerical values of r2 of at least 0.2 and/or values of | D'| of at least 0.8, and generate an output based on the marker or haplotype information, wherein the output comprises a risk measure of the at least one marker or 10 haplotype as a genetic indicator of Type 2 diabetes for the human individual.

In one embodiment, the routine further comprises an indicator of the frequency of at least one allele of at least one polymorphic marker or at least one haplotype in a plurality of individuals diagnosed with Type 2 diabetes, and an indicator of the frequency of at the least one allele of at least one polymorphic marker or at least one haplotype in a 15 plurality of reference individuals, and wherein a risk measure is based on a comparison of the at least one marker and/or haplotype status for the human individual to the indicator of the frequency of the at least one marker and/or haplotype information for the plurality of individuals diagnosed with Type 2 diabetes.

In certain embodiments of the methods, uses, apparatus or kits of the invention, 20 linkage disequilibrium is characterized by numeric values for |D'| of greater than 0.8 and/or r2 of greater than 0.2. However, other values for the r2and |D'| measures are also possible in other embodiments and such embodiments are also within the scope of the claimed invention, as described in further detail herein.

In certain other embodiments of the methods, uses, apparatus or kits of the 25 invention, the individual is of a specific human ancestry. In one embodiment, the ancestry is selected from black African ancestry, Caucasian ancestry and Chinese ancestry. In another embodiment, the ancestry is black African ancestry. In another embodiment, the ancestry is European ancestry. In another embodiment, the ancestry is Caucasian ancestry. The ancestry is in certain embodiment self-reported by the individual 30 who undergoes genetic analysis or genotyping. In other embodiments, the ancestry is determined by genetic determination comprising detecting at least one allele of at least one polymorphic marker in a nucleic acid sample from the individual, wherein the presence or absence of the allele is indicative of the ancestry of the individual.

In particular other embodiments of the methods, uses, apparatus or kits of the 35 invention, the individual is obese. In other embodiments, the individual is non-obese.

Obesity is in one embodiment determined by values of BMI (Body Mass Index) of greater than 25. In another embodiment, obesity is defined by values of BMI greater than 30. Other cutoff integer or fractional values of BMI are also possible and within scope of the WO 2008/065682 PCT/IS2007/000020 16 invention, including, but not limited to BMI of greater than 23, 24, 25.5, 26, 26.5, 27, 27.5 and so on. Non-obese individuals are in one embodiment defined as all those individuals who do not fulfill the criteria of obesity by BMI. In other embodiments, non-obese individuals are those with a particular cutoff of BMI, such as BMI less than 25, less 5 than 24, less than 23, less than 22, less than 21 or less than 20. Non-integer cutoff values of BMI values are also useful for defining non-obese individuals. In general, the obese and non-obese groups do not overlap in terms of their BMI values. In certain embodiments, the cutoff employed to define the groups is the same, e.g., greater than or smaller than BMI of 25. In other embodiments, a different cutoff is used, e.g., greater 10 than 27 for obese individuals and smaller than 23 for non-obese individuals. All relevant ranges of BMI that are suitable for defining obese and non-obese individuals are also possible and within scope of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS The foregoing and other objects, features and advantages of the invention will be apparent from the following more particular description of preferred embodiments of the invention.

FIG 1 shows a plot linkage disequilibrium pattern in the region of chromosome 6p22.3 containing markers associated with Type 2 diabetes, (a) The X-axis shows positions with 20 respect to NCBI Build 35 genome assembly (identical to Build 36), and the Y-axis shows a measure of linkage disequilibrium in the region. The span of the CDKAL1 gene is indicated by the arrows, and the locations of exons by black bars perpendicular to the diagonal line. The SNP markers are plotted equidistantly rather than according to their physical positions. The figure shows the r2 measure of linkage disequilibrium, wherein the 25 shading is proportional to pair-wise values of r2 between markers, (b) A close-up of the 5' end of the CDKAL gene, showing the LD Block C06 region (SEQ ID NO: 1) within which several markers have been found to be associated with Type 2 diabetes. The location of several of the associated SNP markers is indicated on the figure.

FIG 2 shows linkage disequilibrium in the region of chromosome 10q23.33 containing 30 markers associated with Type 2 diabetes. The X-axis shows positions with respect to NCBI Build 35 genome assembly, and the Y-axis shows a measure of linkage disequilibrium in the region. The location of four associated SNP markers rs2497304, rs947591, rsl0882091 and rs7914814 is indicated as well as the span and exons of the three genes within the LD block, IDE, KIF11 and HHEX. The figure shows the r2 measure 35 of linkage disequilibrium, wherein the shading is proportional to pair-wise values of r2 between markers.

WO 2008/065682 PCT/IS2007/000020 17 FIG 3 shows linkage disequilibrium in the region of chromosome 17q24.3 containing markers associated with diabetes in non-obese and all patients. The location of five SNP markers, rsl860316, rsl981647, rsl843622, rs2191113 and rs9890889, is indicated. The figure shows the r2 measure of linkage disequilibrium, wherein the shading is 5 proportional to pair-wise values of r2 between markers.

FIG 4 shows a Q-Q plot of the 653,025 adjusted Chi2-statistics (circles) from the analysis of single SNPs and two marker haplotypes. The equiangular line (black line) is included in the plot for reference purpose. The dashed horizontal line indicates the threshold for genome-wide significance assuming a Bonferroni correction for the 653,025 SNPs / 10 haplotypes and three phenotypes tested.

FIG 5 presents a schematic view of the association of T2D to 6p22.3. a) The pair-wise correlation structure in a 1 Mb interval (20.5 - 21.5 Mb, NCBI Build34) on chromosome 6. The upper plot includes pair-wise D' for 1047 common SNPs (with MAF > 5%) from the HapMap release 19 for the CEU population, while the lower plot includes pair-wise r2 15 values for the same set of SNPs. b) Location of recombination hot-spots in this interval based on the HapMap dataset (Nature 437, 1299-1320 (27 October 2005))). c) Location of exons (vertical bars) of the two genes, E2F3 and CDKAL1, that map to the interval, d) Schematic view of the genome-wide association results in the interval for all T2D cases (black dots), non-obese T2D cases (open circles) and obese T2D cases (open triangles), 20 respectively. Plotted is -log P, where P is the adjusted P value, against the chromosomal location of the markers. All four panels use the same horizontal Mb scale indicated at the bottom of panel d).

FIG 6 shows CDKAL1 cDNA from INS-1 cells. Lanes 1 and 2 contain CDKAL1 cDNA amplified from exons 2 to 8 and exons 7 to 13, giving a band size of 596bp and 738bp, 25 respectively, p-actin (837bp) serves as a positive control in lane 3 and lane 4 is a negative control reaction without primers. Size standard is given on the left.

FIG 7 shows the association of rs7756992 and rsl3266634 to insulin secretion. Mean log-transformed insulin secretion levels, estimated by corrected insulin response (see Methods), for the three different genotypes of the two SNPs, rs7756992 and rsl3266634. 30 Results are shown for 3982 individuals (231 T2D cases and 3751 controls) from the Danish Inter99 study that had an oral glucose tolerance test. The number of individuals is included under each column, and the standard error (s.e.m.) is indicated as horizontal bars. The included P values are from regression of the log-transformed insulin secretion levels on genotype status, adjusting for age, sex and affection status, assuming either an 35 additive model (Padd) or a recessive model (Prec)- FIG 8 presents further analysis of association of rs7756992 and rsl3266634 with insulin secretion, a) Mean log-transformed insulin secretion levels, estimated by corrected WO 2008/065682 PCT/IS2007/000020 18 insulin response (CIR) for the three different genotypes for the SNP rs7756992. The insulin secretion levels are estimated for a group of 3938 individuals from the Danish Inter99 cohort (223 T2D cases and 3715 controls) that had an OGTT. Results are shown for all individuals (leftmost bars) and males (middle bars) and females (rightmost bars) 5 separately. The number of individuals behind each estimate is indicated in parenthesis below the columns together with the corresponding genotype. The standard error of the mean is indicated with a bar on top of each column, b) Corresponding estimates for the different genotypes of the SNP rsl3266634 for 3926 individuals (228 T2D cases and 3698 controls).

DETAILED DESCRIPTION OF THE INVENTION A description of preferred embodiments of the invention follows.

The present invention discloses polymorphic markers and haplotypes that have been found to be associated with Type 2 diabetes. Particular alleles at certain polymorphic SNP 15 markers and haplotypes comprising such alleles have been found to be associated with Type 2 diabetes. Such markers and haplotypes are useful for assessing susceptibility to Type 2 diabetes, as described in further detail herein. Further applications of the present invention include methods for assessing response to Type 2 diabetes therapeutic agents utilizing the polymorphic markers of the invention, as well as kits for assessing 20 susceptibility of an individual to Type 2 diabetes.

Definitions The following terms shall, in the present context, have the meaning as indicated: A "polymorphic marker", sometime referred to as a "marker", as described herein, 25 refers to a genomic polymorphic site. Each polymorphic marker has at least two sequence variations characteristic of particular alleles at the polymorphic site. Thus, genetic association to a polymorphic marker implies that there is association to at least one specific allele of that particular polymorphic marker. The marker can comprise any allele of any variant type found in the genome, including SNPs, microsatellites, insertions, 30 deletions, duplications and translocations.

An "allele" refers to the nucleotide sequence of a given locus (position) on a chromosome. A polymorphic marker allele thus refers to the composition (i.e., sequence) of the marker on a chromosome. Genomic DNA from an individual contains two alleles for any given polymorphic marker, representative of each copy of the marker on each WO 2008/065682 PCT/IS2007/000020 19 chromosome. Sequence codes for nucleotides used herein are: A = 1, C = 2, G = 3, T = 4.

Sequence conucleotide ambiguity as described herein is as proposed by IUPAC-IUB. These codes are compatible with the codes used by the EMBL, GenBank, and PIR 5 databases.

IUB Meaning A Adenosine C Cytidine G Guanine T Thymidine R G or A Y TorC K GorT M A or C S G or C W A orT B CGorT D AGorT H ACorT V A C or G N A C G or T (Any base) A nucleotide position at which more than one sequence is possible in a population (either a natural population or a synthetic population, e.g., a library of synthetic molecules) is referred to herein as a "polymorphic site".

A "Single Nucleotide Polymorphism" or "SNP" is a DNA sequence variation occurring when a single nucleotide at a specific location in the genome differs between members of a species or between paired chromosomes in an individual. Most SNP polymorphisms have two alleles. Each individual is in this instance either homozygous for one allele of the polymorphism (i.e. both chromosomal copies of the individual have the 15 same nucleotide at the SNP location), or the individual is heterozygous (i.e. the two sister chromosomes of the individual contain different nucleotides). The SNP nomenclature as reported herein refers to the official Reference SNP (rs) ID identification tag as assigned to each unique SNP by the National Center for Biotechnological Information (NCBI).

A "variant", as described herein, refers to a segment of DNA that differs from the 20 reference DNA. A "marker" or a "polymorphic marker", as defined herein, is a variant. Alleles that differ from the reference are referred to as "variant" alleles.

A "microsatellite" is a polymorphic marker that has multiple small repeats of bases that are 2-8 nucleotides in length (such as CA repeats) at a particular site, in which the number of repeat lengths varies in the general population. An "indel" is a common form WO 2008/065682 PCT/IS2007/000020 of polymorphism comprising a small insertion or deletion that is typically only a few nucleotides long.

A "haplotype," as described herein, refers to a segment of genomic DNA that is characterized by a specific combination of alleles arranged along the segment. For diploid 5 organisms such as humans, a haplotype comprises one member of the pair of alleles for each polymorphic marker or locus . In a certain embodiment, the haplotype can comprise two or more alleles, three or more alleles, four or more alleles, or five or more alleles. Haplotypes are described herein in the context of the marker name and the allele of the marker in that haplotype, e.g., "3 rs7758851" refers to the 3 allele of marker rs7758851 10 being in the haplotype, and is equivalent to "rs7758851 allele 3". Furthermore, allelic codes in haplotypes are as for individual markers, i.e. 1 = A, 2 = C, 3 = G and 4 = T.

The term "susceptibility", as described herein, encompasses both increased susceptibility and decreased susceptibility. Thus, particular alleles at polymorphic markers and/or haplotypes of the invention may be characteristic of increased 15 susceptibility (i.e., increased risk) of Type 2 diabetes, as characterized by a relative risk (RR) or odds ratio (OR) of greater than one for the particular allele or haplotype. Alternatively, the markers and/or haplotypes of the invention are characteristic of decreased susceptibility (i.e., decreased risk) of Type 2 diabetes, as characterized by a relative risk of less than one.

A "nucleic acid sample" is a sample obtained from an individuals that contains nucleic acid. In certain embodiments, i.e. the detection of specific polymorphic markers and/or haplotypes, the nucleic acid sample comprises genomic DNA. Such a nucleic acid sample can be obtained from any source that contains genomic DNA, including as a blood sample, sample of amniotic fluid, sample of cerebrospinal fluid, or tissue sample from 25 skin, muscle, buccal or conjunctival mucosa, placenta, gastrointestinal tract or other organs.

The term "Type 2 diabetes therapeutic agent" refers to an agent that can be used to ameliorate or prevent symptoms associated with Type 2 diabetes.

The term "Type 2 diabetes-associated nucleic acid", as described herein, refers to 30 a nucleic acid that has been found to be associated to Type 2 diabetes. This includes, but is not limited to, the markers and haplotypes described herein and markers and haplotypes in strong linkage disequilibrium (LD) therewith. In one embodiment, a Type 2 diabetes-associated nucleic acid refers to an LD-block found to be associated with Type 2 diabetes through at least one polymorphic marker located within the LD block.

The term "non-obese" refers, as described herein, to an individual with calculated Body Mass Index (BMI) below a pre-determined threshold, such as a threshold of 30 or WO 2008/065682 PCT/IS2007/000020 21 lower. Other thresholds useful for defining the term are also possible, as described in more detail herein. The formula for calculating BMI is given by [body weight (in kg)]/[height (in m)]2. The term "obese" refers to an individual with BMI above a certain pre-determined threshold, such as a threshold of 30.

The term "LD Block C06", as described herein, refers to the Linkage Disequilibrium (LD) block on Chromosome 6 between markers rs4429936 and rs6908425, corresponding to position 20,634,996 - 20,836,710 of NCBI (National Center for Biotechnology Information) Build 35 (SEQ ID NO:l).

The term "LD Block C10", as described herein, refers to the Linkage Disequilibrium 10 (LD) block on Chromosome 10 between markers rs2798253 and rslll87152, corresponding to position 94,192,885 - 94,490,091 of NCBI (National Center for Biotechnology Information) Build 35 (SEQ ID NO:2).

The term "LD Block C17", as described herein, refers to the Linkage Disequilibrium (LD) block on Chromosome 17 between markers rsl 1077501 and rs4793497, 15 corresponding to position 66,037,656 - 66,163,076 of NCBI (National Center for Biotechnology Information) Build 35 (SEQ ID NO:3).

The term "CDKAL1", as described herein, refers to the CDK5 regulatory subunit associated protein 1-like 1 gene, which spans locations 20,642,736 - 21,340,611 in NCBI Build 35 of the human genome.

The term "SLC30A8", as described herein, refers to the Solute Carrier Family 30, member 8, gene. This gene is located on chromosome 8, its longest isoform spanning as much as 225kb between positions 118,032,398 and 118,258,134 in NCBI Build 36 of the human genome assembly, corresponding to position 117,919,805 and 118,145,541, respectively in NCBI Build 34. In both these builds, the gene spans 225,736 bp of 25 genomic sequence.

Through genotyping of Icelandic Type 2 diabetes patients and population control individuals using the Illumina 330K chip that can be used to measure over 300,000 SNPs in the genome simultaneously, a number of variants associated with Type 2 diabetes have 30 been identified by the present invention. Association analysis using single SNPs, two marker haplotypes and extended haplotypes within areas of extensive linkage disequilibrium (LD blocks) was performed across the genome. After correcting the p-value for relatedness, 49 single markers and two marker haplotypes were initially identified at 21 loci (i.e. genetic susceptibility locations in the genome) that had a p-value 35 less than 5xl0"5 (Table 1). In addition, 10 extended haplotypes at 8 additional loci were WO 2008/065682 PCT/IS2007/000020 22 selected by the same criteria (Table 2). Within the patient group, 700 individuals were non-obese (BMI<30) and those were tested separately for association. After correcting the p-value for relatedness, 36 single markers and two marker haplotypes at 20 loci had a p-value less than 5xl0"5 (Table 3). Three of those loci were also identified when the total 5 group was analyzed. In addition, 6 extended haplotypes at 4 additional loci were selected by the same criteria (Table 4). The obese group of 531 patients (BMI >30) was also analyzed separately for association. After correcting the p-value for relatedness, 38 single markers and two marker haplotypes at 16 loci had a p-value less than 5xl0"5 (Table 5). One of those loci was also identified when the total group was analyzed but no 10 overlap was found between the non-obese and obese groups using this criteria. In addition 10 extended haplotypes at 7 additional loci had a p-value less than 5xl0"5 in association analysis of obese diabetics (Table 6).

These single-marker association and two-marker and extended haplotype association results represent evidence for multiple susceptibility variants for Type 2 15 diabetes. It should be noted that for single-marker SNP analysis as presented herein, susceptibility variants can be represented by increased risk, wherein one allele is overrepresented in the patient group compared with controls. Alternatively, the susceptibility variants can be represented by the other allele of the SNP in question - for that allele, under-representation in patients compared with controls is expected. This is a 20 natural consequence of association analysis to genetic elements comprising two alleles. For multi-marker haplotypes or for polymorphic markers comprising more than one marker, at-risk association may be observed to one (or more) at-risk allele or haplotype. Protective variants in form of association (with RR-values less than unity) to one (or more) protective variants or haplotypes may also be observed, depending on the genetic 25 composition and haplotype structure in the genetic region in question.

One of the most significant association signals was identified by two single markers (rsl569699 and rs7756992) and three 2 marker haplotypes mapping to chromosome 6p22.3 (3 rs7758851 2 rsl569699, 1 rs4712527 3 rs7756992, 1 rs7756992 3 rs9295478 ; see Table 3). These markers are located within an area of extensive LD 30 (LD block) between position 20634996 and 20836710 on chromosome 6 (NCBI Build 35; SEQ ID NO:l) between markers rs4429936 and rs6908425 (Figure 1). This region contains the 5' end including exons 1-5 of the gene CDK5 regulatory subunit associated protein 1-like 1 (CDKAL1) (NM_017774). The association of these markers was verified in two additional Type 2 diabetes cohorts (see Table 7).

Follow up studies of the association of rs7756992 allele G with increased risk of Type 2 diabetes have established association of the marker to Type 2 diabetes in individuals of European ancestry (allele specific odds ratio (OR) = 1.16; P = 3.9x10 10), in individuals from Hong Kong of Han Chinese ancestry (OR = 1.25; P = 0.00018) (see WO 2008/065682 PCT/IS2007/000020 23 Tables 14, 15 and 17). Additional variants within LD block C06 (SEQ ID NO:l) in LD with rs7756992 that have also been shown to be associated with Type 2 diabetes in European and Chinese populations include rsl569699, rs7752906, rs9350271, rs9356744, rs9368222, rsl0440833 and rs6931514 (Table 18). The genotype odds, ratio of the 5 rs77566992 allele G variant supports a nearly recessive mode of inheritance (Table 20). In particular, the OR for the homozygote is 1.45 and 1.55 in the European and Hong Kong groups, respectively. The rs77566992 allele G at-risk variant has been found to be correlated with decreased insulin response in carriers (Table 21, Figures 7 and 8). Homozygous carriers of the variant have been found to have an estimated 24% less 10 insulin response than heterozygotes or non-carriers suggesting that this variant confers risk of T2D through reduced insulin secretion. The rs7756992 marker, and markers in linkage disequilibrium therewith (including, but not limited to, rsl569699, rs7752906, rs9350271, rs9356744, rs9368222, rsl0440833 and rs6931514) can therefore be used to assess increased susceptibility to Type 2 diabetes in an individual.

The function of the gene product of CDKAL1 is not known. However, as implied in the gene name the protein product is similar to another protein, CDK5 regulatory subunit associated protein 1 (CDK5RAP1). CDK5RAP1 is expressed in neuronal tissues where it inhibits cyclin dependent kinase 5 (CDK5) activity by binding to the CDK5 regulatory subunit p35 (Ching, Y.P., Pang, A.S., Lam, W.H., Qi, R.Z. & Wang, J.H. J Biol Chem 277, 20 15237-40 (2002)). In pancreatic beta cells, CDK5 has been shown to play a role in the loss of beta cell function under glucotoxic conditions (Wei, F.Y. et al. Nat Med 11, 1104-8 (2005). Furthermore, inhibition of the CDK5/p35 complex prevents decrease of insulin gene expression that results from glucotoxicity (Ubeda, M., Rukstalis, J.M. & Habener, J.F. J Biol Chem 281, 28858-64 (2006)). CDKAL1 might play a role in the inhibition of 25 CDK5/p35 in pancreatic beta cells similar to that of CDK5RAP1 in neuronal tissue.

Reduced expression of CDKAL1 or reduced inhibitory function thus could lead to an impaired response to glucotoxicity. The present data shows that CDKAL1 is expressed in the rat pancreatic beta cell line INS-1 (Figure 6).

Based on the predicted function of CDKAL1 and known function of SLC30A8 we 30 would expect both rs7756992 and rsl3266634 to affect insulin secretion. To evaluate the effects of the two SNPs on insulin secretion we analyzed the effect of genotype status on corrected insulin response (CIR) in a set of individuals from the Inter99 study (part of Denmark B) that had undergone an oral glucose tolerance test (OGTT). For rs7756992, we demonstrated that the homozygote carriers of the risk allele had an estimated 24% 35 less CIR than the heterozygote carriers or non-carriers (P < 0.00001, Fig. 7). This observation is consistent with the variant's nearly recessive mode of inheritance with respect to disease risk. Furthermore, the effect observed on CIR is present in both males and females (Figure 8) and in T2D patients as well as controls, and adjusting for BMI status did not affect the results (Table 21). The effect of rsl3266634 on insulin response WO 2008/065682 PCT/IS2007/000020 24 was smaller but significant and for this risk variant the reduction in CIR was consistent with an additive effect. No effect on insulin sensitivity was observed for either variant (Table 21).

The identification of CDKAL1 as a susceptibility gene forT2D adds a new piece to 5 the puzzle of how genetic factors may predispose to T2D. Although the function of this gene remains to be elucidated we have shown that it is expressed in pancreatic beta cells and that a variant within the gene is correlated with insulin secretion. The similarity to CDK5RAP1 further indicates that CDKAL1 may facilitate insulin production under glucotoxic conditions through interaction with CDK5. In conclusion, we have identified a 10 variant in the CDKAL1 gene that in a nearly recessive manner blunts the insulin response and predisposes to T2D.

The present invention has identified seven single markers and seven two marker haplotypes in a region on chromosome 10q23.33 to be associated with Type 2 diabetes (Table 1). Most of those markers are also associated to diabetes with elevated RR values 15 when obese patients are analyzed separately (Table 5). These markers are located within one LD block between positions 94192885and 94490091 (NCBI Build 35), corresponding to the genomic segment bridged by markers rs2798253 and rslll87152 (Figure 2). This LD block contains three genes, Insulin-degrading enzyme (IDE) (NM_004969), Kinesin family member 11 (KIF11) (NM_004523) and Homeobox, hematopoietically expressed 20 (HHEX) (NM_002729).

IDE may belong to a protease family responsible for intercellular peptide signaling. Though its role in the cellular processing of insulin has not yet been defined, insulin-degrading enzyme is thought to be involved in the termination of the insulin response (Fakhrai-Rad et al, Human Molecular Genetics 9:2149-2158, 2000). Genetic analysis of 25 the diabetic GK rat has revealed 2 amino acid substitutions in the IDE gene (H18R and A890V) in the GK allele which reduced insulin-degrading activity by 31% in transfected cells. However, when the H18R and A890V variants were studied separately, no effects were observed, suggesting a synergistic effect of the 2 variants on insulin degradation. No effect on insulin degradation was observed in cell lysates, suggesting that the effect may 30 be coupled to receptor-mediated internalization of insulin. Congenic rats with the IDE GK allele displayed postprandial hyperglycemia, reduced lipogenesis in fat cells, blunted insulin-stimulated glucose transmembrane uptake, and reduced insulin degradation in isolated muscle. Analysis of additional rat strains demonstrated that the dysfunctional IDE allele was unique to GK rats. The authors concluded that IDE plays an important role in 35 the diabetic phenotype in GK rats. IDE has been studied as a candidate gene for Type 2 diabetes in humans with inconsistent results. Two large studies have recently analyzed the association of IDE to Type 2 diabetes by mutation screening and haplotype analysis using tagging SNPs over the gene (Groves et al, Diabetes 52:1300-1305, 2003; Florez et WO 2008/065682 PCT/IS2007/000020 al, Diabetes 55:128-135, 2006). Both studies conclude that common variants in IDE are unlikely to confer significant risk of Type 2 diabetes. These studies did however, not include the whole LD block as defined in figure 2 and at least some of the markers identified in our study as associated with Type 2 diabetes are outside the regions analyzed 5 in those previous studies. Based on the results reported here, markers in LD with IDE are associated with Type 2 diabetes, providing genetic evidence for the role of IDE in the etiology of Type 2 diabetes.

KIF11 encodes a motor protein that belongs to the kinesin-like protein family. Members of this protein family are known to be involved in various kinds of spindle 10 dynamics. The function of this gene product includes chromosome positioning, centrosome separation and establishing a bipolar spindle during cell mitosis. This gene is not a good functional candidate for diabetes but has to be considered as a positional candidate due to its location within the associated LD block.

HHEX encodes a member of the homeobox family of transcription factors, many of 15 which are involved in developmental processes. Expression in specific hematopoietic lineages suggests that this protein may play a role in hematopoietic differentiation. HHEX is essential for pancreatic development; in HHEX negative mouse embryos there is a complete failure in ventral pancreatic specification (Bort et al, Development 131, 797-806, 2004). Other transcription factors involved in pancreatic development include the 20 MODY genes as well as other factors that have been implicated in late onset diabetes. HHEX is also an essential effector of Wnt antagonist for heart induction (Foley and Mercola, GENES & DEVELOPMENT 19:387-396, 2005). This puts HHEX in the same pathway as the recently established Type 2 diabetes gene TCF7L2 and together these data make HHEX a functional as well as positional candidate for Type 2 diabetes.

The association of rs2497304, rs947591, rsl0882091 and rs7914814 to Type 2 diabetes was verified in a Danish Type 2 diabetes case - control cohort and also in a US Caucasian cohort Type 2 diabetes cohort from the PENN CATH study (Table 8). When the two cohorts are combined the association of rs947591 reaches significance at the 0.05 level, with a risk of 1.1 in the combined cohort. When all the cohorts are combined the 30 risk is 1.15 for the rs947591 marker. These results indicate that variants within the LD block on Chromosome 10 that includes IDE and HHEX are susceptibility variants for Type 2 diabetes.

Five single markers and two marker haplotypes in a region of chromosome 17q24.3 were furthermore found to be associated with Type 2 diabetes in non-obese 35 patients (Table 3). Some of these markers show the strongest association reported in Table 3 and association to this region was also observed when all diabetics were analyzed (Table 1). These markers are located within two adjacent LD blocks located between WO 2008/065682 PCT/IS2007/000020 26 positions 66037656 and 66163076 (NCBI Build 35) on chromosome 17, between markers rsll077501 and rs4793497 (Figure 3). The association is significant at the genome-wide level. No known genes are located within these LD blocks. However, it is possible that variants in this region affect genes in neighboring regions including KCNJ2 and KCNJ16.

Alternatively these variants may affect unknown genes within these LD blocks.

Further evidence for the association of rs7756992, and correlated markers within the LD block C06 that contains the 5' end including exons 1-5 of the CDKALlgene (NM_017774) on chromosome 6p22.3, with Type 2 diabetes has come from additional association studies. Two equivalent markers, rs7754840 and rsl0946398, highly 10 correlated with rs7756992 (r2 0,68; D' 0,95) were shown to be significantly associated with Type II diabetes in three large studies (Saxena, R et al. Science 2007;316:1331-6; Zeggini, E et al. Science 2007;316:1336-41; Scott, LJ et al. Science 2007;316:1341-5). These studies thus further support the involvement of the CDKAL gene in Type 2 diabetes.

Association of rsl0882091 and correlated markers on chromosome 10q23.33 with 15 Type II diabetes is also supported by recent publications. A highly correlated marker, rsllll875 (r2 0,51; D' = 1) was found to be significantly associated with Type II diabetes in four large studies (Sladek, R et al. Nature. 2007;445:828-30; Saxena, R et al. Science 2007;316:1331-6; Zeggini, E et al. Science 2007;316:1336-41; Scott, LJ et al. Science 2007;316:1341-5). Thus, recent studies provide additional support to the discoveries by 20 the present inventors that markers in the LD Block C10 region as described herein are risk factors for Type 2 diabetes.

The genomic sequence within populations is not identical when individuals are compared. Rather, the genome exhibits sequence variability between individuals at 25 many locations in the genome. Such variations in sequence are commonly referred to as polymorphisms, and there are many such sites within each genome For example, the human genome exhibits sequence variations which occur on average every 500 base pairs. The most common sequence variant consists of base variations at a single base position in the genome, and such sequence variants, or polymorphisms, are commonly 30 called Single Nucleotide Polymorphisms ("SNPs"). These SNPs are believed to have occurred in a single mutational event, and therefore there are usually two possible alleles possible at each SNP site; the original allele and the mutated allele. Due to natural genetic drift and possibly also selective pressure, the original mutation has resulted in a polymorphism characterized by a particular frequency of its alleles in any given 35 population. Many other types of sequence variants are found in the human genome, including microsatellites, insertions, deletions, inversions and copy number variations. A polymorphic microsatellite has multiple small repeats of bases (such as CA repeats, TG on WO 2008/065682 PCT/IS2007/000020 27 the complimentary strand) at a particular site in which the number of repeat lengths varies in the general population. In general terms, each version of the sequence with respect to the polymorphic site represents a specific allele of the polymorphic site. These sequence variants can all be referred to as polymorphisms, occurring at specific 5 polymorphic sites characteristic of the sequence variant in question. In general terms, polymorphisms can comprise any number of specific alleles. Thus in one embodiment of the invention, the polymorphism is characterized by the presence of two or more alleles in any given population. In another embodiment, the polymorphism is characterized by the presence of three or more alleles. In other embodiments, the polymorphism is 10 characterized by four or more alleles, five or more alleles, six or more alleles, seven or more alleles, nine or more alleles, or ten or more alleles. All such polymorphisms can be utilized in the methods and kits of the present invention, and are thus within the scope of the invention.

In some instances, reference is made to different alleles at a polymorphic site 15 without choosing a reference allele. Alternatively, a reference sequence can be referred to for a particular polymorphic site. The reference allele is sometimes referred to as the "wild-type" allele and it usually is chosen as either the first sequenced allele or as the allele from a "non-affected" individual (e.g., an individual that does not display a trait or disease phenotype).

Alleles for SNP markers as referred to herein refer to the bases A, C, G or T as they occur at the polymorphic site in the SNP assay employed. The allele codes for SNPs used herein are as follows: 1 = A, 2 =C, 3 =G, 4 =T. The person skilled in the art will however realise that by assaying or reading the opposite DNA strand, the complementary allele can in each case be measured. Thus, for a polymorphic site (polymorphic marker) 25 characterized by an A/G polymorphism, the assay employed may be designed to specifically detect the presence of one or both of the two bases possible, i.e. A and G. Alternatively, by designing an assay that is designed to detect the opposite strand on the DNA template, the presence of the complementary bases T and C can be measured. Quantitatively (for example, in terms of relative risk), identical results would be obtained 30 from measurement of either DNA strand (+ strand or - strand).

Typically, a reference sequence is referred to for a particular sequence. Alleles that differ from the reference are sometimes referred to as "variant" alleles. A variant sequence, as used herein, refers to a sequence that differs from the reference sequence but is otherwise substantially similar. Alleles at the polymorphic genetic markers 35 described herein are variants. Additional variants can include changes that affect a polypeptide. Sequence differences, when compared to a reference nucleotide sequence, can include the insertion or deletion of a single nucleotide, or of more than one nucleotide, resulting in a frame shift; the change of at least one nucleotide, resulting in a WO 2008/065682 PCT/IS2007/000020 28 change in the encoded amino acid; the change of at least one nucleotide, resulting in the generation of a premature stop codon; the deletion of several nucleotides, resulting in a deletion of one or more amino acids encoded by the nucleotides; the insertion of one or several nucleotides, such as by unequal recombination or gene conversion, resulting in an 5 interruption of the coding sequence of a reading frame; duplication of all or a part of a sequence; transposition; or a rearrangement of a nucleotide sequence,. Such sequence changes can alter the polypeptide encoded by the nucleic acid. For example, if the change in the nucleic acid sequence causes a frame shift, the frame shift can result in a change in the encoded amino acids, and/or can result in the generation of a premature 10 stop codon, causing generation of a truncated polypeptide. Alternatively, a polymorphism associated with a disease or trait can be a synonymous change in one or more nucleotides {i.e., a change that does not result in a change in the amino acid sequence). Such a polymorphism can, for example, alter splice sites, affect the stability or transport of mRNA, or otherwise affect the transcription or translation of an encoded polypeptide. It 15 can also alter DNA to increase the possibility that structural changes, such as amplifications or deletions, occur at the somatic level. The polypeptide encoded by the reference nucleotide sequence is the "reference" polypeptide with a particular reference amino acid sequence, and polypeptides encoded by variant alleles are referred to as "variant" polypeptides with variant amino acid sequences.

A haplotype refers to a segment of DNA that is characterized by a specific combination of alleles arranged along the segment. For diploid organisms such as humans, a haplotype comprises one member of the pair of alleles for each polymorphic marker or locus . In a certain embodiment, the haplotype can comprise two or more alleles, three or more alleles, four or more alleles, or five or more alleles, each allele 25 corresponding to a specific polymorphic marker along the segment. Haplotypes can comprise a combination of various polymorphic markers, e.g., SNPs and microsatellites, having particular alleles at the polymorphic sites. The haplotypes thus comprise a combination of alleles at various genetic markers.

Detecting specific polymorphic markers and/or haplotypes can be accomplished by 30 methods known in the art for detecting sequences at polymorphic sites. For example, standard techniques for genotyping for the presence of SNPs and/or microsatellite markers can be used, such as fluorescence-based techniques (Chen, X. eta/., Genome Res. 9(5)\ 492-98 (1999)), utilizing PCR, LCR, Nested PCR and other techniques for nucleic acid amplification. Specific methodologies available for SNP genotyping include, 35 but are not limited to, TaqMan genotyping assays and SNPlex platforms (Applied Biosystems), mass spectrometry (e.g., MassARRAY system from Sequenom), mini-sequencing methods, real-time PCR, Bio-Plex system (BioRad), CEQ and SNPstream systems (Beckman), Molecular Inversion Probe array technology (e.g., Affymetrix GeneChip), BeadArray Technologies (e.g., Illumina GoldenGate and Infinium assays) and WO 2008/065682 PCT/IS2007/000020 29 Centaurus assay (Nanogen). By these or other methods available to the person skilled in the art, one or more alleles at polymorphic markers, including microsatellites, SNPs or other types of polymorphic markers, can be identified.

In certain methods described herein, an individual who is at an increased. susceptibility (i.e., increased risk) for Type 2 diabetes, is an individual in whom at least one specific allele at one or more polymorphic marker or haplotype conferring increased susceptibility for Type 2 diabetes is identified (i.e., at-risk marker alleles or haplotypes). In one aspect, the at-risk marker or haplotype is one that confers a significant increased risk (or susceptibility) of Type 2 diabetes. In one embodiment, significance associated 10 with a marker or haplotype is measured by a relative risk (RR). In another embodiment, significance associated with a marker or haplotype is measured by an odds ratio (OR). In a further embodiment, the significance is measured by a percentage. In one embodiment, a significant increased risk is measured as a risk (relative risk and/or odds ratio) of at least 1.2, including but not limited to: at least 1.2, at least 1.3, at least 1.4, at 15 least 1.5, at least 1.6, at least 1.7, 1.8, at least 1.9, at least 2.0, at least 2.5, at least 3.0, at least 4.0, and at least 5.0. In a particular embodiment, a risk (relative risk and/or odds ratio) of at least 1.2 is significant. In another particular embodiment, a risk of at least 1.3 is significant. In yet another embodiment, a risk of at least 1.4 is significant. In a further embodiment, a relative risk of at least about 1.5 is significant. In another 20 further embodiment, a significant increase in risk is at least about 1.7 is significant.

However, other cutoffs are also contemplated, e.g. at least 1.15, 1.25, 1.35, and so on, and such cutoffs are also within scope of the present invention. In other embodiments, a significant increase in risk is at least about 20%, including but not limited to about 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 25 100%, 150%, 200%, 300%, and 500%. In one particular embodiment, a significant increase in risk is at least 20%. In other embodiments, a significant increase in risk is at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% and at least 100%. Other cutoffs or ranges as deemed suitable by the person skilled in the art to characterize the invention are however also contemplated, and those are also 30 within scope of the present invention.

An at-risk polymorphic marker or haplotype of the present invention is one where at least one allele of at least one marker or haplotype is more frequently present in an individual at risk for the disease or trait (affected), compared to the frequency of its presence in a comparison group (control), and wherein the presence of the marker or 35 haplotype is indicative of susceptibility to the disease or trait. The control group may in one embodiment be a population sample, i.e. a random sample from the general population. In another embodiment, the control group is represented by a group of individuals who are disease-free. Such disease-free control may in one embodiment be characterized by the absence of one or more specific disease-associated symptoms. In WO 2008/065682 PCT/IS2007/000020 another embodiment, the disease-free control group is characterized by the absence of one or more disease-specific risk factors. Such risk factors are in one embodiment at least one environmental risk factor. Representative environmental factors are natural products, minerals or other chemicals which are known to affect, or contemplated to 5 affect, the risk of developing the specific disease or trait. Other environmental risk factors are risk factors related to lifestyle, including but not limited to food and drink habits, geographical location of main habitat, and occupational risk factors. In another embodiment, the risk factors are at least one genetic risk factor.

As an example of a simple test for correlation would be a Fisher-exact test on a 10 two by two table. Given a cohort of chromosomes, the two by two table is constructed out of the number of chromosomes that include both of the markers or haplotypes, one of the markers or haplotypes but not the other and neither of the markers or haplotypes.

In other embodiments of the invention, an individual who is at a decreased susceptibility (i.e., at a decreased risk) for Type 2 diabetes is an individual in whom at least 15 one specific allele at one or more polymorphic marker or haplotype conferring decreased susceptibility for Type 2 diabetes is identified. The marker alleles and/or haplotypes conferring decreased risk are also said to be protective. In one aspect, the protective marker or haplotype is one that confers a significant decreased risk (or susceptibility) of the disease or trait. In another embodiment, the absence of an at-risk allele in a nucleic acid sample 20 from the individual is also indicative of a protection against disease, by virtue of the absence of at-risk alleles. In one embodiment, significant decreased risk is measured as a relative risk of less than 0.9, including but not limited to less than 0.9, less than 0.8, less than 0.7, less than 0.6, less than 0.5, less than 0.4, less than 0.3, less than 0.2 and less than 0.1. In one particular embodiment, significant decreased risk is less than 0.7. In another 25 embodiment, significant decreased risk is less than 0.5. In yet another embodiment, significant decreased risk is less than 0.3. In another embodiment, the decrease in risk (or susceptibility) is at least 20%, including but not limited to at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% and 30 at least 98%. In one particular embodiment, a significant decrease in risk is at least about 30%. In another embodiment, a significant decrease in risk is at least about 50%. In another embodiment, the decrease in risk is at least about 70%. Other cutoffs or ranges as deemed suitable by the person skilled in the art to characterize the invention are however also contemplated, and those are also within scope of the present invention.

The person skilled in the art will appreciate that for markers with two alleles present in the population being studied (such as SNPs), and wherein one allele is found in increased frequency in a group of individuals with a trait or disease in the population, compared with controls, the other allele of the marker will be found in decreased frequency in the group of WO 2008/065682 PCT/IS2007/000020 31 individuals with the trait or disease, compared with controls. In such a case, one allele of the marker (the one found in increased frequency in individuals with the trait or disease) will be the at-risk allele, while the other allele will be a protective allele.

Linkage Disequilibrium The natural phenomenon of recombination, which occurs on average once for each chromosomal pair during each meiotic event, represents one way in which nature provides variations in sequence (and biological function by consequence). It has been discovered that recombination does not occur randombly in the genome; rather, there are 10 large variations in the frequency of recombination rates, resulting in small regions of high recombination frequency (also called recombination hotspots) and larger regions of low recombination frequency, which are commonly referred to as Linkage Disequilibrium (LD) blocks (Myers, S. et al., Biochem Soc Trans 34:526-530 (2006); Jeffreys, A.J., et al.,Nature Genet 29:217-222 (2001); May, C.A., etal., Nature Genet 31:272-275(2002)).

Linkage Disequilibrium (LD) refers to a non-random assortment of two genetic elements. For example, if a particular genetic element (e.g., an allele of a polymorphic marker, or a haplotype) occurs in a population at a frequency of 0.50 (50%) and another element occurs at a frequency of 0.50 (50%), then the predicted occurrance of a person's having both elements is 0.25 (25%), assuming a random distribution of the elements. 20 However, if it is discovered that the two elements occur together at a frequency higher than 0.25, then the elements are said to be in linkage disequilibrium, since they tend to be inherited together at a higher rate than what their independent frequencies of occurrence (e.g., allele or haplotype frequencies) would predict. Roughly speaking, LD is generally correlated with the frequency of recombination events between the two 25 elements. Allele or haplotype frequencies can be determined in a population by genotyping individuals in a population and determining the frequency of the occurence of each allele or haplotype in the population. For populations of diploids, e.g., human populations, individuals will typically have two alleles for each genetic element (e.g., a marker, haplotype or gene).

Many different measures have been proposed for assessing the strength of linkage disequilibrium (LD). Most capture the strength of association between pairs of biallelic sites. Two important pairwise measures of LD are r2 (sometimes denoted A2) and |D'|. Both measures range from 0 (no disequilibrium) to 1 ('complete' disequilibrium), but their interpretation is slightly different. |D'| is defined in such a way that it is equal to 1 if just 35 two or three of the possible haplotypes are present, and it is <1 if all four possible haplotypes are present. Therefore, a value of |D'| that is <1 indicates that historical recombination may have occurred between two sites (recurrent mutation can also cause WO 2008/065682 PCT/IS2007/000020 32 |D'| to be <1, but for single nucleotide polymorphisms (SNPs) this is usually regarded as being less likely than recombination). The measure r2 represents the statistical correlation between two sites, and takes the value of 1 if only two haplotypes are present.

The r2 measure is arguably the most relevant measure for association mapping, 5 because there is a simple inverse relationship between r2 and the sample size required to detect association between susceptibility loci and SNPs. These measures are defined for pairs of sites, but for some applications a determination of how strong LD is across an entire region that contains many polymorphic sites might be desirable (e.g., testing whether the strength of LD differs significantly among loci or across populations, or 10 whether there is more or less LD in a region than predicted under a particular model). Measuring LD across a region is not straightforward, but one approach is to use the measure r, which was developed in population genetics. Roughly speaking, r measures how much recombination would be required under a particular population model to generate the LD that is seen in the data. This type of method can potentially also provide 15 a statistically rigorous approach to the problem of determining whether LD data provide evidence for the presence of recombination hotspots. For the methods, kits,procedures, media and apparati described herein, a significant r2 value can be at least 0.05, such as at least 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.91, 0.92, 0.93, 0.94, 0.95, 0.96, 0.97, 0.98, 0.99 or 1.0. In one preferred 20 embodiment, the significant r2 value can be at least 0.2. Alternatively, linkage disequilibrium as described herein, refers to linkage disequilibrium characterized by values of | D'| of at least 0.2, such as 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.85, 0.9, 0.95, 0.96, 0.97, 0.98, 0.99. Thus, linkage disequilibrium represents a correlation between alleles of distinct markers. It is measured by correlation coefficient or |D'| (r2 up to 1.0 and |D'| up 25 to 1.0). In certain embodiments, linkage disequilibrium is defined in terms of values for both the r2 and |D'| measures. In one such embodiment, a significant linkage disequilibrium is defined as r2 > 0.1 and |D'| >0.8. In another embodiment, a significant linkage disequilibrium is defined as r2 > 0.2 and |D'| >0.9. Other combinations and permutations of values of r2and |D'|for determining linkage disequilibrium are also 30 possible, and within the scope of the invention. Linkage disequilibrium can be determined in a single human population, as defined herein, or it can be determined in a collection of samples comprising individuals from more than one human population. In one embodiment of the invention, LD is determined in a sample from one or more of the HapMap populations (caucasian, african, japanese, Chinese), as defined 35 (http://www.hapmap.org). In one such embodiment, LD is determined in the CEU population of the HapMap samples. In another embodiment, LD is determined in the YRI population. In yet another embodiment, LD is determined in samples from the Icelandic population.

WO 2008/065682 PCT/IS2007/000020 33 If all polymorphisms in the genome were identical at the population level, then every single one of them would need to be investigated in association studies. However, due to linkage disequilibrium between polymorphisms, tightly linked polymorphisms are strongly correlated, which reduces the number of polymorphisms that need to be 5 investigated in an association study to observe a significant association. Another consequence of LD is that many polymorphisms may give an association signal due to the fact that these polymorphisms are strongly correlated.

Genomic LD maps have been generated across the genome, and such LD maps have been proposed to serve as framework for mapping disease-genes (Risch, N. & 10 Merkiangas, K, Science 273:1516-1517 (1996); Maniatis, N., etal., Proc Natl Acad Sci USA 99:2228-2233 (2002); Reich, DE etal, Nature 411:199-204 (2001)).

It is now established that many portions of the human genome can be broken into series of discrete haplotype blocks containing a few common haplotypes; for these blocks, linkage disequilibrium data provides little evidence indicating recombination (see, e.g., 15 Wall., J.D. and Pritchard, J.K., Nature Reviews Genetics 4:587-597 (2003); Daly, M. et al., Nature Genet. 29:229-232 (2001); Gabriel, S.B. etal., Science 296:2225-2229 (2002); Patil, N. etal., Science 294:1719-1723 (2001); Dawson, E. etal., Nature 418:544-548 (2002); Phillips, M.S. etal., Nature Genet. 33:382-387 (2003)).

There are two main methods for defining these haplotype blocks: blocks can be 20 defined as regions of DNA that have limited haplotype diversity (see, e.g., Daly, M. et al., Nature Genet. 29:229-232 (2001); Patil, N. etal., Science 294:1719-1723 (2001); Dawson, E. et al., Nature 418:544-548 (2002); Zhang, K. et al., Proc. Natl. Acad. Sci. USA 99:7335-7339 (2002)), or as regions between transition zones having extensive historical recombination, identified using linkage disequilibrium (see, e.g., Gabriel, S.B. et 25 al., Science 296:2225-2229 (2002); Phillips, M.S. etal., Nature Genet. 33:382-387 (2003); Wang, N. etal., Am. J. Hum. Genet. 71:1227-1234 (2002); Stumpf, M.P., and Goldstein, D.B., Curr. Biol. 13:1-8 (2003)). More recently, a fine-scale map of recombination rates and corresponding hotspots across the human genome has been generated (Myers, S., etal., Science 310:321-32324 (2005); Myers, S. et al., Biochem Soc Trans 34:526530 (2006)). The map reveals the enormous variation in recombination across the genome, with recombination rates as high as 10-60 cM/Mb in hotspots, while closer to 0 in intervening regions, which thus represent regions of limited haplotype diversity and high LD. The map can therefore be used to define haplotype blocks/LD blocks as regions flanked by recombination hotspots. As used herein, the terms 35 "haplotype block" or "LD block" includes blocks defined by any of the above described characteristics, or other alternative methods used by the person skilled in the art to define such regions.

WO 2008/065682 PCT/IS2007/000020 34 Haplotype blocks can be used to map associations between phenotype and haplotype status, using single markers or haplotypes comprising a plurality of markers. The main haplotypes can be identified in each haplotype block, and then a set of "tagging" SNPs or markers (the smallest set of SNPs or markers needed to distinguish among the 5 haplotypes) can then be identified. These tagging SNPs or markers can then be used in assessment of samples from groups of individuals, in order to identify association between phenotype and haplotype. If desired, neighboring haplotype blocks can be assessed concurrently, as there may also exist linkage disequilibrium among the haplotype blocks.

It has thus become apparent that for any given observed association to a 10 polymorphic marker in the genome, it is likely that additional markers in the genome also show association. This is a natural consequence of the uneven distribution of LD across the genome, as observed by the large variation in recombination rates. The markers used to detect association thus in a sense represent "tags" for a genomic region (i.e., a haplotype block or LD block) that is associating with a given disease or trait, and as such 15 are useful for use in the methods and kits of the present invention. One or more causative (functional) variants or mutations may reside within the region found to be associating to the disease or trait. Such variants may confer a higher relative risk (RR) or odds ratio (OR) than observed for the tagging markers used to detect the association. The present invention thus refers to the markers used for detecting association to the 20 disease, as described herein, as well as markers in linkage disequilibrium with the markers. Thus, in certain embodiments of the invention, markers that are in LD with the markers and/or haplotypes of the invention, as described herein, may be used as surrogate markers. The surrogate markers have in one embodiment relative risk (RR) and/or odds ratio (OR) values smaller than for the markers or haplotypes initially found to 25 be associating with the disease, as described herein. In other embodiments, the surrogate markers have RR or OR values greater than those initially determined for the markers initially found to be associating with the disease, as described herein. An example of such an embodiment would be a rare, or relatively rare (< 10% allelic population frequency) variant in LD with a more common variant (> 10% population 30 frequency) initially found to be associating with the disease, such as the variants described herein. Identifying and using such markers for detecting the association discovered by the inventors as described herein can be performed by routine methods well known to the person skilled in the art, and are therefore within the scope of the present invention.

It is possible that certain polymorphic markers in linkage disequilibrium witht the markers shown herein to be associated with Type 2 diabetes are located outside the physical boundaries of the LD block as defined. This is a consequence of the historical recombination rates in the region in question, which may have led to a region of strong LD (the LD block), with residual markers outside the block in LD with markers within the WO 2008/065682 PCT/IS2007/000020 block. Such markers are also within scope of the present invention, as they are equally useful for practicing the invention by virtue of their genetic relationship with the markers shown herein to be associated with Type 2 diabetes. Examples are shown in Table 22 (rsl7234378; SEQ ID NO:44), Table 23 (rs7086285; SEQ ID NO:43) and Table 24 5 (rs9890889; SEQ ID NO:31; rs2009802; SEQ ID NO:38; rsl7718938; SEQ ID NO:39; , rs2109050; SEQ ID NO:41; rsl962801; SEQ ID NO:42.

Determination of haplotype frequency The frequencies of haplotypes in patient and control groups can be estimated 10 using an expectation-maximization algorithm (Dempster A. et at., J. R. Stat. Soc. B, 39:1-38 (1977)). An implementation of this algorithm that can handle missing genotypes and uncertainty with the phase can be used. Under the null hypothesis, the patients and the controls are assumed to have identical frequencies. Using a likelihood approach, an alternative hypothesis is tested, where a candidate at-risk-haplotype, which can include 15 the markers described herein, is allowed to have a higher frequency in patients than controls, while the ratios of the frequencies of other haplotypes are assumed to be the same in both groups. Likelihoods are maximized separately under both hypotheses and a corresponding 1-df likelihood ratio statistic is used to evaluate the statistical significance.

To look for at-risk and protective markers and haplotypes within a region of 20 interest, for example, association of all possible combinations of genotyped markers is studied, provided those markers span a practical region. The combined patient and control groups can be randomly divided into two sets, equal in size to the original group of patients and controls. The marker and haplotype analysis is then repeated and the most significant p-value registered is determined. This randomization scheme can be repeated, 25 for example, over 100 times to construct an empirical distribution of p-values. In a preferred embodiment, a p-value of <0.05 is indicative of a significant marker and/or haplotype association.

Haplotype Analysis One general approach to haplotype analysis involves using likelihood-based inference applied to NEsted MOdels (Gretarsdottir S., eta/., Nat. Genet. 35:131-38 (2003)). The method is implemented in the program NEMO, which allows for many polymorphic markers, SNPs and microsatellites. The method and software are specifically designed for case-control studies where the purpose is to identify haplotype groups that 35 confer different risks. It is also a tool for studying LD structures. In NEMO, maximum WO 2008/065682 PCT/IS2007/000020 36 likelihood estimates, likelihood ratios and p-values are calculated directly, with the aid of the EM algorithm, for the observed data treating it as a missing-data problem.

Even though likelihood ratio tests based on likelihoods computed directly for the observed data, which have captured the information loss due to uncertainty in phase and 5 missing genotypes, can be relied on to give valid p-values, it would still be of interest to know how much information had been lost due to the information being incomplete. The information measure for haplotype analysis is described in Nicolae and Kong (Technical Report 537, Department of Statistics, University of Statistics, University of Chicago; Biometrics, 60(2):368-75 (2004)) as a natural extension of information measures defined 10 for linkage analysis, and is implemented in NEMO.

For single marker association to a disease or trait (e.g., Type 2 diabetes), the Fisher exact test can be used to calculate two-sided p-values for each individual allele. Usually, all p-values are presented unadjusted for multiple comparisons unless specifically indicated. The presented frequencies (for microsatellites, SNPs and haplotypes) are allelic frequencies as opposed to carrier frequencies. To minimize any bias due the relatedness of the patients who were recruited as families for the linkage analysis, first and second-degree relatives can be eliminated from the patient list. Furthermore, the test can be repeated for association correcting for any remaining relatedness among the patients, by extending a variance adjustment procedure described in Risch, N. &Teng, J. (Genome Res., 8:1273-1288 (1998)), DNA pooling (ibid) for sibships so that it can be applied to general familial relationships, and present both adjusted and unadjusted p-values for comparison. The differences are in general very small as expected. To assess the significance of single-marker association corrected for multiple testing we can carry out a randomization test using the same genotype data. Cohorts of patients and controls can be randomized and the association analysis redone multiple times (e.g., up to 500,000 times) and the p-value is the fraction of replications that produced a p-value for some marker allele that is lower than or equal to the p-value we observed using the original patient and control cohorts.

For both single-marker and haplotype analyses, relative risk (RR) and the 30 population attributable risk (PAR) can be calculated assuming a multiplicative model (haplotype relative risk model) (Terwilliger, J.D. & Ott, J., Hum. Hered. 42:337-46 (1992) and Falk, C.T. & Rubinstein, P, Ann. Hum. Genet. 51 (Pt 3):227-33 (1987)), i.e., that the risks of the two alleles/haplotypes a person carries multiply. For example, if RR is the risk of A relative to a, then the risk of a person homozygote AA will be RR times that of a 35 heterozygote Aa and RR2 times that of a homozygote aa. The multiplicative model has a nice property that simplifies analysis and computations— haplotypes are independent, i.e., in Hardy-Weinberg equilibrium, within the affected population as well as within the control population. As a consequence, haplotype counts of the affecteds and controls WO 2008/065682 PCT/IS2007/000020 37 each have multinomial distributions, but with different haplotype frequencies under the alternative hypothesis. Specifically, for two haplotypes, h, and hjt risk(/7,)/risk(/j;) = (fi/Pi)/(fj/Pj), where fand p denote, respectively, frequencies in the affected population and in the control population. While there is some power loss if the true model is not 5 multiplicative, the loss tends to be mild except for extreme cases. Most importantly, p-values are always valid since they are computed with respect to null hypothesis.

Risk assessment and Diagnostics As described herein, certain polymorphic markers and haplotypes comprising such 10 markers are found to be useful for risk assessment of Type 2 diabetes. Risk assessment can involve the use of the markers for diagnosing a susceptibility to Type 2 diabetes. Particular alleles of polymorphic markers are found more frequently in individuals with Type 2 diabetes, than in individuals without diagnosis of Type 2 diabetes. Therefore, these marker alleles have predictive value for detecting Type 2 diabetes, or a 15 susceptibility to Type 2 diabetes, in an individual. Tagging markers within haplotype blocks or LD blocks comprising at-risk markers, such as the markers of the present invention, can be used as surrogates for other markers and/or haplotypes within the haplotype block or LD block. Markers with values of r2 equal to 1 are perfect surrogates for the at-risk variants, i.e. genotypes for one marker perfectly predicts genotypes for the 20 other. Markers with smaller values of r2 than 1 can also be surrogates for the at-risk variant, or alternatively represent variants with relative risk values as high as or possibly even higher than the at-risk variant.

The at-risk variant identified may not be the functional variant itself, but is in this instance in linkage disequilibrium with the true functional variant. The present invention 25 encompasses the assessment of such surrogate markers for the markers as disclosed herein. Such markers are annotated, mapped and listed in public databases (e.g., dbSNP), as well known to the skilled person, or can alternatively be readily identified by sequencing the region or a part of the region identified by the markers of the present invention in a group of individuals, and identify polymorphisms in the resulting group of 30 sequences. As a consequence, the person skilled in the art can readily and without undue experimentation genotype surrogate markers in linkage disequilibrium with the markers and/or haplotypes as described herein. The tagging or surrogate markers in LD with the at-risk variants detected, also have predictive value for detecting association to Type 2 diabetes, or a susceptibility to Type 2 diabetes, in an individual.

The markers and haplotypes as described herein, e.g., the markers presented in Tables 1 - 24, may be useful for risk assessment and diagnostic purposes for, either alone or in combination. The markers and haplotypes can also be combined with other markers WO 2008/065682 PCT/IS2007/000020 38 conferring increased risk for Type 2 diabetes. Even in cases where the increase in risk by individual markers is relatively modest, i.e. on the order of 10-30%, the association may have significant implications. Thus, relatively common variants may have significant contribution to the overall risk (Population Attributable Risk is high), or combination of 5 markers can be used to define groups of individual who, based on the combined risk of the markers, is at significant combined risk of developing the disease. The markers described herein to be associated with Type 2 diabetes can therefore be combined with other polymorphic markers or haplotypes reported or found to be associated with Type 2 diabetes, so as to obtain an overall risk of the disease based on a plurality of genetic 10 markers.

In one such embodiment, the polymorphic markers or haplotypes described herein are assessed together with information about markers within the TCF7L2 gene.

Association of variants within this gene is well established (Grant S.F., et al., Nat Genet. -38:320-3 (2006)) and has been replicated in a large number of populations (Florez, J.C., 15 Curr Opin Clin Nutr Metabol Care 10:391-396 (2007). The marker rs7903146 within the TCF7L2 gene, or other markers in LD with the marker (e.g., rsl2255372) can be used to determine the genetic risk conferred by the at-risk variant in the gene (OR about 1.44).

Markers in other genes have recently been implicated in the etiology of Type 2 diabetes as risk factors, including PPARG (rsl801282), KCNJ11 (rs5215), TCF2 20 (rs4430796), WFS1 (rsl0010131), CDKN2A-2B (rsl081161), IGF2BP2 (rs4402960) and FTO (rs805136) (Frayling, T.M. Nature Reviews Genetics 8:657-662 (2007).. These markers, or markers in linkage disequilibrium therewith can likewise also be used in methods combining determination of the presence or absence of at-risk variants for Type 2 diabetes with the variants reported herein, so as to obtain an overall risk assessment of 25 Type 2 diabetes.

Thus, in one embodiment of the invention, a plurality of variants (genetic markers and/or biomarkers and/or haplotypes) is used for overall risk assessment. These variants are in one embodiment selected from the variants as disclosed herein. Other embodiments include the use of the variants of the present invention in combination with 30 other variants known to be useful for diagnosing a susceptibility to Type 2 diabetes. In such embodiments, the genotype status of a plurality of markers and/or haplotypes is determined in an individual, and the status of the individual compared with the population frequency of the associated variants, or the frequency of the variants in clinically healthy subjects, such as age-matched and sex-matched subjects. Methods known in the art, 35 such as multivariate analyses or joint risk analyses, may subsequently be used to determine the overall risk conferred based on the genotype status at the multiple loci. Assessment of risk based on such analysis may subsequently be used in the methods and kits of the invention, as described herein.

WO 2008/065682 PCT/IS2007/000020 39 As described in the above, the haplotype block structure of the human genome has the effect that a large number of variants (markers and/or haplotypes) in linkage disequilibrium with the variant originally associated with a disease or trait may be used as surrogate markers for assessing association to the disease or trait. The number of such 5 surrogate markers will depend on factors such as the historical recombination rate in the region, the mutational frequency in the region (i.e., the number of polymorphic sites or markers in the region), and the extent of LD (size of the LD block) in the region. These markers are usually located within the physical boundaries of the LD block or haplotype block in question as defined using the methods described herein, or by other methods 10 known to the person skilled in the art. However, sometimes marker and haplotype association is found to extend beyond the physical boundaries of the haplotype block as defined. Such markers and/or haplotypes may in those cases be also used as surrogate markers and/or haplotypes for the markers and/or haplotypes physically residing within the haplotype block as defined. As a consequence, markers and haplotypes in LD 15 (typically characterized by r2 greater than 0.1, such as r2 greater than 0.2, including r2 greater than 0.3, also including r2 greater than 0.4) with the markers and haplotypes of the present invention are also within the scope of the invention, even if they are physically located beyond the boundaries of the haplotype block as defined. This includes markers that are described herein (e.g., markers listed in Tables 22, 23 and 24), but may 20 also include other markers that are in linkage disequilibrium (e.g., characterized by r2 greater than 0.2 and/or |D'| > 0.8) with one or more of the markers listed in Tables 22, 23 and 24.

For the SNP markers described herein, the opposite allele to the allele found to be in excess in patients (at-risk allele) is found in decreased frequency in Type 2 diabetes. 25 These markers and haplotypes in LD and/or comprising such markers, are thus protective for Type 2 diabetes, i.e. they confer a decreased risk or susceptibility of individuals carrying these markers and/or haplotypes developing Type 2 diabetes. Alternatively speaking, the absence of at-risk alleles of at-risk variants implies the presence of the alternate allele for biallelic markers such as SNPs. Thus, the absence of at-risk variants 30 as described herein is indicative of a protection against Type 2 diabetes.

As described herein, haplotypes comprising a combination of genetic markers, e.g., SNPs and microsatellites, can be useful for risk assessment. Detecting haplotypes can be accomplished by methods known in the art and/or described herein for detecting sequences at polymorphic sites. Furthermore, correlation between certain haplotypes or 35 sets of markers and disease phenotype can be verified using standard techniques. A representative example of a simple test for correlation would be a Fisher-exact test on a two by two table.

WO 2008/065682 PCT/IS2007/000020 40 In specific embodiments, a marker or haplotype found to be associated with Type 2 diabetes, is one in which a marker or haplotype is more frequently present in an individual at risk for Type 2 diabetes (e.g., an affected person), compared to the frequency of its presence in a healthy individual (control) or in a randomly selected 5 individual from the population (population control), wherein the presence of the marker allele or haplotype is indicative of Type 2 diabetes or a susceptibility to Type 2 diabetes. In other embodiments, at-risk markers in linkage disequilibrium with one or more markers found to be associated with Type 2 diabetes are tagging markers that are more frequently present in an individual at risk for Type 2 diabetes (e.g., affected individuals), 10 compared to the frequency of their presence in controls, wherein the presence of the tagging markers is indicative of increased susceptibility to Type 2 diabetes. In a further embodiment, at-risk markers alleles (i.e. conferring increased susceptibility) in linkage disequilibrium with one or more markers found to be associated with Type 2 diabetes are markers comprising one or more allele that is more frequently present in an individual at 15 risk for Type 2 diabetes, compared to the frequency of their presence in controls, wherein the presence of the markers is indicative of increased susceptibility to Type 2 diabetes.

Study population In a general sense, the methods and kits of the invention can be utilized from 20 samples containing genomic DNA from any source, i.e. any individual. In preferred embodiments, the individual is a human individual. The individual can be an adult, child, or fetus. The present invention also provides for assessing markers and/or haplotypes in individuals who are members of a target population. Such a target population is in one embodiment a population or group of individuals at risk of developing the disease, based 25 on other genetic factors, biomarkers, biophysical parameters (e.g., weight, BMD, blood pressure), or general health and/or lifestyle parameters (e.g., history of disease or related diseases, previous diagnosis of disease, family history of disease).

The invention provides for embodiments that include individuals from specific age subgroups, such as those over the age of 40, over age of 45, or over age of 50, 55, 60, 30 65, 70, 75, 80, or 85. Other embodiments of the invention pertain to other age groups, such as individuals aged less than 85, such as less than age 80, less than age 75, or less than age 70, 65, 60, 55, 50, 45, 40, 35, or age 30. Other embodiments relate to individuals with age at onset of the disease in any of the age ranges described in the above. It is also contemplated that a range of ages may be relevant in certain 35 embodiments, such as age at onset at more than age 45 but less than age 60. Other age ranges are however also contemplated, including all age ranges bracketed by the age WO 2008/065682 PCT/IS2007/000020 41 values listed in the above. The invention furthermore relates to individuals of either gender, males or females.

The Icelandic population is a Caucasian population of Northern European ancestry. A large number of studies reporting results of genetic linkage and association in the 5 Icelandic population have been published in the last few years. Many of those studies show replication of variants, originally identified in the Icelandic population as being associating with a particular disease, in other populations (Stacey, S.N., et al., Nat Genet. May 27 2007 (Epub ahead of print; Helgadottir, A., et al., Science 316:1491-93 (2007); Steinthorsdottir, V., etal., Nat Genet. 39:770-75 (2007); Gudmundsson, J., etal., Nat 10 Genet. 39:631-37 (2007); Amundadottir, L.T., etal., Nat Genet. 38:652-58 (2006); Grant, S.F., et al., Nat Genet. 38:320-23 (2006)). Thus, genetic findings in the Icelandic population have in general been replicated in other populations, including populations from Africa and Asia. The variants described herein to be associated to the CDKAL gene, in particular the LD Block C06 (SEQ ID NO:l) have been replicated in several populations 15 of European, American, and Chinese (Hong Kong) origin. This supports the belief that these variants (rs7756992 and markers in linkage disequilibrium therewith) are at-risk variants for Type 2 diabetes in most populations.

Particular embodiments comprising individual human populations are thus also contemplated and within the scope of the present invention. Such embodiments relate to human subjects that are from one or more human population including, but not limited to, Caucasian populations, European populations, American populations, Eurasian populations, Asian populations, Central/South Asian populations, East Asian populations, Middle Eastern populations, African populations, Hispanic populations, and Oceanian populations. European populations include, but are not limited to, Swedish, Norwegian, Finnish, Russian, Danish, Icelandic, Irish, Kelt, English, Scottish, Dutch, Belgian, French, German, Spanish, Portuguese, Italian, Polish, Bulgarian, Slavic, Serbian, Bosnian, Czech, Greek and Turkish populations. The invention furthermore in other embodiments can be practiced in specific human populations that include Bantu, Mandenk, Yoruba, San, Mbuti Pygmy, Orcadian, Adygei, Russian, Sardinian, Tuscan, Mozabite, Bedouin, Druze, Palestinian, Balochi, Brahui, Makrani, Sindhi, Pathan, Burusho, Hazara, Uygur, Kalash, Han, Dai, Daur, Hezhen, Lahu, Miao, Oroqen, She, Tujia, Tu, Xibo, Yi, Mongolan, Naxi, Cambodian, Japanese, Yakut, Melanesian, Papuan, Karitianan, Surui, Columbian, Maya and Pima.

In one preferred embodiment, the invention relates to populations that include 35 black African ancestry such as populations comprising persons of African descent or lineage. Black African ancestry may be determined by self reporting as African-Americans, Afro-Americans, Black Americans, being a member of the black race or being a member of the negro race. For example, African Americans or Black Americans are WO 2008/065682 PCT/IS2007/000020 42 those persons living in North America and having origins in any of the black racial groups of Africa. In another example, self-reported persons of black African ancestry may have at least one parent of black African ancestry or at least one grandparent of black African ancestry.

The racial contribution in individual subjects may also be determined by genetic analysis. Genetic analysis of ancestry may be carried out using unlinked microsatellite markers such as those set out in Smith et al. (Am J Hum Genet 74, 1001-13 (2004)).

In certain embodiments, the invention relates to markers and/or haplotypes identified in specific populations, as described in the above. The person skilled in the art 10 will appreciate that measures of linkage disequilibrium (LD) may give different results when applied to different populations. This is due to different population history of different human populations as well as differential selective pressures that may have led to differences in LD in specific genomic regions. It is also well known to the person skilled in the art that certain markers, e.g. SNP markers, have different population frequency in 15 different populations, or are polymorphic in one population but not in another. The person skilled in the art will however apply the methods available and as thought herein to practice the present invention in any given human population. This may include assessment of polymorphic markers in the LD region of the present invention, so as to identify those markers that give strongest association within the specific population. 20 Thus, the at-risk variants of the present invention may reside on different haplotype background and in different frequencies in various human populations. However, utilizing methods known in the art and the markers of the present invention, the invention can be practiced in any given human population.

Utility of Genetic Testing The knowledge about a genetic variant that confers a risk of developing Type 2 diabetes offers the opportunity to apply a genetic test to distinguish between individuals with increased risk of developing the disease (i.e. carriers of the at-risk variant) and those with decreased risk of developing the disease (i.e. carriers of the protective variant). The 30 core values of genetic testing, for individuals belonging to both of the above mentioned groups, are the possibilities of being able to diagnose the disease at an early stage and provide information to the clinician about prognosis/aggressiveness of the disease in order to be able to apply the most appropriate treatment.

For example, the application of a genetic test for Type 2 diabetes can identify high risk individuals among people with impaired fasting glucose (IFG) or impaired glucose tolerance (IGT). It is well established that while around a third of people who are found to WO 2008/065682 PCT/IS2007/000020 43 have IFG/IGT develop Type 2 diabetes, glucose levels return to normal for an equal proportion of individuals. Identification of individuals within this group that are carriers of genetic risk variants will allow targeting of those individuals by preventive measures. For example, these individuals may benefit from a closer monitoring of blood glucose levels to 5 aid in early diagnosis. They may also need more stringent lifestyle intervention advice since individuals with certain genetic risk factors develop Type 2 diabetes at lower BMI levels than those without those factors.

Individuals with a family history of Type 2 diabetes and carriers of at-risk variants may benefit from genetic testing since the knowledge of the presence of a genetic risk 10 factor, or evidence for increased risk of being a carrier of one or more risk factors, may provide increased incentive for implementing a healthier lifestyle. Furthermore, closer monitoring of glucose levels should be advised for such individuals, facilitating early diagnosis and/or preventative treatment.

Genetic testing of Type 2 diabetes patients may furthermore give valuable 15 information about the primary cause of the disease and can aid the clinician in selecting the best treatment options and medication for each individual. For instance, patients with genetic risk factors for reduced insulin secretion may be likely to benefit from medication increasing insulin secretion while increasing insulin sensitivity in those individuals may be less effective.

METHODS OF THE INVENTION Methods for risk assessment of Type 2 diabetes are described herein and are encompassed by the invention. The invention also encompasses methods of assessing an individual for probability of response to a therapeutic agent for Type 2 diabetes, as well as 25 methods for predicting the effectiveness of a therapeutic agent for Type 2 diabetes. Kits for assaying a sample from a subject to detect susceptibility to Type 2 diabetes are also encompassed by the invention.

DIAGNOSTIC AND SCREENING ASSAYS OF THE INVENTION In certain embodiments, the present invention pertains to methods of assessing risk or diagnosing, or aiding in risk assessment or diagnosis of, Type 2 diabetes or a susceptibility to Type 2 diabetes, by detecting particular alleles at genetic markers that appear more frequently in Type 2 diabetes subjects or subjects who are susceptible to Type 2 diabetes. In a particular embodiment, the invention is a method of assessing 35 susceptibility to Type 2 diabetes by detecting at least one allele of at least one WO 2008/065682 PCT/IS2007/000020 44 polymorphic marker (e.g., the markers described herein). The present invention describes methods whereby detection of particular alleles of particular markers or haplotypes is indicative of a susceptibility to Type 2 diabetes. Such prognostic or predictive assays can also be used to determine prophylactic treatment of a subject prior 5 to the onset of symptoms of Type 2 diabetes.

The present invention pertains in some embodiments to methods of clinical applications of diagnosis, e.g., diagnosis performed by a medical professional, which may include an assessment or determination of genetic risk variants. In other embodiments, the invention pertains to methods of risk assessment (or diagnosis) performed by a 10 layman. Recent technological advances in genotyping technologies, including high-throughput genotyping of SNP markers, such as Molecular Inversion Probe array technology (e.g., Affymetrix GeneChip), and BeadArray Technologies (e.g., Illumina GoldenGate and Infinium assays) have made it possible for individuals to have their own genome assessed for up to one million SNPs. The resulting genotype information, made 15 available to the individual can be compared to information from the public literature about disease or trait risk associated with various SNPs. The diagnostic application of disease-associated alleles as described herein, can thus be performed either by a health professional based on results of a clinical test or by a layman, including an individual providing service for performing an whole-genome assessment of SNPs. In other words, 20 the diagnosis or assessment of a susceptibility based on genetic risk can be made by health professionals, genetic counselors, genotype services providers or by the layman, based on information about his/her genotype and publications on various risk factors. In the present context, the term "diagnosing", and "diagnose a susceptibility", is meant to refer to any available diagnostic method, including those mentioned above.

In addition, in certain other embodiments, the present invention pertains to methods of diagnosing, or aiding in the diagnosis of, a decreased susceptibility to Type 2 diabetes, by detecting particular genetic marker alleles or haplotypes that appear less frequently in Type 2 diabetes patients than in individual not diagnosed with Type 2 diabetes or in the general population.

As described and exemplified herein, particular marker alleles or haplotypes (e.g. the markers and haplotypes as listed in Tables 1-24, e.g., the markers and haplotypes as listed in Tables 1-6 and Tables 9-12, and markers in linkage disequilibrium therewith) are associated with Type 2 diabetes. In one embodiment, the marker allele or haplotype is one that confers a significant risk or susceptibility to Type 2 diabetes. In another 35 embodiment, the invention relates to a method of diagnosing a susceptibility to Type 2 diabetes in a human individual, the method comprising determining the presence or absence of at least one allele of at least one polymorphic marker in a nucleic acid sample obtained from the individual, wherein the at least one polymorphic marker is selected WO 2008/065682 PCT/IS2007/000020 45 from the group consisting of the polymorphic markers listed in Table 9, Table 10, Table 11, and Table 12, and markers in linkage disequilibrium (defined as r2 > 0.2) therewith. In another embodiment, the invention pertains to methods of diagnosing or assessing a susceptibility to Type 2 diabetes in a human individual, by screening for at least one 5 marker allele or haplotype as listed in Tables 1-6 and 9 - 12, or markers in linkage disequilibrium therewith. In another embodiment, the marker allele or haplotype is more frequently present in a subject having, or who is susceptible to, Type 2 diabetes (affected), as compared to the frequency of its presence in a healthy subject (control, such as population controls). In certain embodiments, the significance of association of 10 the at least one marker allele or haplotype is characterized by a p value < 0.05. In other embodiments, the significance of association is characterized by smaller p-values, such as < 0.01, <0.001, <0.0001, <0.00001, <0.000001, <0.0000001, <0.00000001 or <0.000000001.

In these embodiments, the presence of the at least one marker allele or 15 haplotype is indicative of a susceptibility to Type 2 diabetes. These diagnostic methods involve detecting the presence or absence of at least one marker allele or haplotype that is associated with Type 2 diabetes. The haplotypes described herein include combinations of alleles at various genetic markers (e.g., SNPs, microsatellites). The detection of the particular genetic marker alleles that make up the particular haplotypes can be performed 20 by a variety of methods described herein and/or known in the art. For example, genetic markers can be detected at the nucleic acid level (e.g., by direct nucleotide sequencing or by other means known to the skilled in the art) or at the amino acid level if the genetic marker affects the coding sequence of a protein encoded by a Type 2 diabetes -associated nucleic acid (e.g., by protein sequencing or by immunoassays using antibodies that 25 recognize such a protein). The marker alleles or haplotypes of the present invention correspond to fragments of a genomic DNA sequence associated with Type 2 diabetes. Such fragments encompass the DNA sequence of the polymorphic marker or haplotype in question, but may also include DNA segments in strong LD (linkage disequilibrium) with the marker or haplotype (e.g., as determined by a value of ^greater than 0.2 and/or |D'| 30 > 0.8).

In one embodiment, diagnosis or assessment of a susceptibility to Type 2 diabetes can be accomplished using hybridization methods, such as Southern analysis, Northern analysis, and/or in situ hybridizations (see Current Protocols in Molecular Biology, Ausubel, F. et ai., eds., John Wiley & Sons, including all supplements). The presence of a 35 specific marker allele can be indicated by sequence-specific hybridization of a nucleic acid probe specific for the particular allele. The presence of more than specific marker allele or a specific haplotype can be indicated by using several sequence-specific nucleic acid probes, each being specific for a particular allele. In one embodiment, a haplotype can be indicated by a single nucleic acid probe that is specific for the specific haplotype (i.e., WO 2008/065682 PCT/IS2007/000020 46 hybridizes specifically to a DNA strand comprising the specific marker alleles characteristic of the haplotype). A sequence-specific probe can be directed to hybridize to genomic DNA, RNA, or cDNA. A "nucleic acid probe", as used-tierein, can be a DNA probe or an RNA probe that hybridizes to a complementary sequence. One of skill in the art would 5 know how to design such a probe so that sequence specific hybridization will occur only if a particular allele is present in a genomic sequence from a test sample.

To diagnose a susceptibility to Type 2 diabetes, a hybridization sample is formed by contacting the test sample containing an Type 2 diabetes -associated nucleic acid, such as a genomic DNA sample, with at least one nucleic acid probe. A non-limiting example of 10 a probe for detecting mRNA or genomic DNA is a labeled nucleic acid probe that is capable of hybridizing to mRNA or genomic DNA sequences described herein. The nucleic acid probe can be, for example, a full-length nucleic acid molecule, or a portion thereof, such as an oligonucleotide of at least 15, 30, 50, 100, 250 or 500 nucleotides in length that is sufficient to specifically hybridize under stringent conditions to appropriate mRNA or 15 genomic DNA. For example, the nucleic acid probe can comprise all or a portion of the nucleotide sequence of LD Block C06 (SEQ ID NO:l), LD Block C10 (SEQ ID NO:2) (e.g., the nucleotide sequence encoding the IDE, KIFll and/or the HHEX genes), LD Block C17 (SEQ ID NO:3) or the CDKAL1 gene, or the SLC30A8 gene, as described herein, optionally comprising at least one allele of a marker described herein, or at least one haplotype 20 described herein, or the probe can be the complementary sequence of such a sequence. In a particular embodiment, the nucleic acid probe is a portion of the nucleotide sequence of LD Block C06 (SEQ ID NO:l), LD Block C10 (SEQ ID NO:2) (e.g., the nucleotide sequence encoding the IDE, KIFll and/or the HHEX genes), LD Block C17 (SEQ ID NO:3) or the CDKAL1 gene, or the SLC30A8 gene as described herein, optionally comprising at 25 least one allele of a marker described herein , or at least one allele contained in the haplotypes described herein, or the probe can be the complementary sequence of such a sequence. Other suitable probes for use in the diagnostic assays of the invention are described herein. Hybridization can be performed by methods well known to the person skilled in the art (see, e.g., Current Protocols in Molecular Biology, Ausubel, F. eta/., eds., 30 John Wiley & Sons, including all supplements). In one embodiment, hybridization refers to specific hybridization, i.e., hybridization with no mismatches (exact hybridization). In one embodiment, the hybridization conditions for specific hybridization are high stringency.

Specific hybridization, if present, is detected using standard methods. If specific 35 hybridization occurs between the nucleic acid probe and the nucleic acid in the test sample, then the sample contains the allele that is complementary to the nucleotide that is present in the nucleic acid probe. The process can be repeated for any markers of the present invention, or markers that make up a haplotype of the present invention, or multiple probes can be used concurrently to detect more than one marker alleles at a WO 2008/065682 PCT/IS2007/000020 47 time. It is also possible to design a single probe containing more than one marker alleles of a particular haplotype (e.g., a probe containing alleles complementary to 2, 3, 4, 5 or all of the markers that make up a particular haplotype). Detection of the particular markers of the haplotype in the sample is indicative that the source of the sample has the 5 particular haplotype (e.g., a haplotype) and therefore is susceptible to DISEASE.

In one preferred embodiment, a method utilizing a detection oligonucleotide probe comprising a fluorescent moiety or group at its 3' terminus and a quencher at its 5' terminus, and an enhancer oligonucleotide, is employed, as described by Kutyavin et at. (Nucleic Acid Res. 34:el28 (2006)). The fluorescent moiety can be Gig Harbor Green or 10 Yakima Yellow, or other suitable fluorescent moieties. The detection probe is designed to hybridize to a short nucleotide sequence that includes the SNP polymorphism to be detected. Preferably, the SNP is anywhere from the terminal residue to -6 residues from the 3' end of the detection probe. The enhancer is a short oligonucleotide probe which hybridizes to the DNA template 3' relative to the detection probe. The probes are 15 designed such that a single nucleotide gap exists between the detection probe and the enhancer nucleotide probe when both are bound to the template. The gap creates a synthetic abasic site that is recognized by an endonuclease, such as Endonuclease IV. The enzyme cleaves the dye off the fully complementary detection probe, but cannot cleave a detection probe containing a mismatch. Thus, by measuring the fluorescence of 20 the released fluorescent moiety, assessment of the presence of a particular allele defined by nucleotide sequence of the detection probe can be performed.

The detection probe can be of any suitable size, although preferably the probe is relatively short. In one embodiment, the probe is from 5-100 nucleotides in length. In another embodiment, the probe is from 10-50 nucleotides in length, and in another 25 embodiment, the probe is from 12-30 nucleotides in length. Other lengths of the probe are possible and within scope of the skill of the average person skilled in the art. In a preferred embodiment, the DNA template containing the SNP polymorphism is amplified by Polymerase Chain Reaction (PCR) prior to detection. In such an embodiment, the amplified DNA serves as the template for the detection probe and the enhancer probe.

Certain embodiments of the detection probe, the enhancer probe, and/or the primers used for amplification of the template by PCR include the use of modified bases, including modified A and modified G. The use of modified bases can be useful for adjusting the melting temperature of the nucleotide molecule (probe and/or primer) to the template DNA, for example for increasing the melting temperature in regions 35 containing a low percentage of G or C bases, in which modified A with the capability of forming three hydrogen bonds to its complementary T can be used, or for decreasing the melting temperature in regions containing a high percentage of G or C bases, for example by using modified G bases that form only two hydrogen bonds to their complementary C WO 2008/065682 PCT/IS2007/000020 48 base in a double stranded DNA molecule. In a preferred embodiment, modified bases are used in the design of the detection nucleotide probe. Any modified base known to the skilled person can be selected in these methods, and the selection of suitable bases is well within the scope of the skilled person based on the teachings herein and known bases available from commercial sources as known to the skilled person.

In another hybridization method, Northern analysis (see Current Protocols in Molecular Biology, Ausubel, F. et al., eds., John Wiley & Sons, supra) is used to identify the presence of a polymorphism associated with Type 2 diabetes. For Northern analysis, a test sample of RNA is obtained from the subject by appropriate means. As described herein, specific hybridization of a nucleic acid probe to RNA from the subject is indicative of a particular allele complementary to the probe. For representative examples of use of nucleic acid probes, see, for example, U.S. Patent Nos. 5,288,611 and 4,851,330.

Additionally, or alternatively, a peptide nucleic acid (PNA) probe can be used in addition to, or instead of, a nucleic acid probe in the hybridization methods described herein. A PNA is a DNA mimic having a peptide-like, inorganic backbone, such as N-(2-aminoethyl)glycine units, with an organic base (A, G, C, T or U) attached to the glycine nitrogen via a methylene carbonyl linker (see, for example, Nielsen, P., eta/., Bioconjug. Chem. 5:3-7 (1994)). The PNA probe can be designed to specifically hybridize to a molecule in a sample suspected of containing one or more of the marker alleles or haplotypes that are associated with Type 2 diabetes. Hybridization of the PNA probe is thus diagnostic for Type 2 diabetes or a susceptibility to Type 2 diabetes.

In one embodiment of the methods of the invention, diagnosis of Type 2 diabetes or a susceptibility to Type 2 diabetes is accomplished through enzymatic amplification of a nucleic acid from the subject. For example, a test sample containing genomic DNA can be obtained from the subject and the polymerase chain reaction (PCR) can be used to amplify a fragment comprising one ore more markers or haplotypes of the present invention found to be associated with Type 2 diabetes. As described herein, identification of a particular marker allele or haplotype associated with Type 2 diabetes can be accomplished using a variety of methods (e.g., sequence analysis, analysis by restriction digestion, specific hybridization, single stranded conformation polymorphism assays (SSCP), electrophoretic analysis, etc.). In another embodiment, diagnosis is accomplished by expression analysis using quantitative PCR (kinetic thermal cycling).

This technique can, for example, utilize commercially available technologies, such as TaqMan® (Applied Biosystems, Foster City, CA), to allow the identification of polymorphisms and haplotypes. The technique can assess the presence of an alteration in the expression or composition of a polypeptide or splicing variant(s) that is encoded by a Type 2 diabetes-associated nucleic acid. Further, the expression of the variant(s) can be quantified as physically or functionally different.

WO 2008/065682 PCT/IS2007/000020 49 In another embodiment of the methods of the invention, analysis by restriction digestion can be used to detect a particular allele if the allele results in the creation or elimination of a restriction site relative to a reference sequence. A test sample containing genomic DNA is obtained from the subject. PCR can be used to amplify particular regions 5 that are associated with Type 2 diabetes (e.g. the polymorphic markers and haplotypes of Tables 1-21, e.g., the polymorphic markers and haplotypes of Tables 1-6 and Tables 9-12, and markers in linkage disequilibrium therewith) nucleic acid in the test sample from the test subject. Restriction fragment length polymorphism (RFLP) analysis can be conducted, e.g., as described in Current Protocols in Molecular Biology, supra. The 10 digestion pattern of the relevant DNA fragment indicates the presence or absence of the particular allele in the sample.

Sequence analysis can also be used to detect specific alleles at polymorphic sites associated with Type 2 diabetes (e.g. the polymorphic markers and haplotypes of Tables 1-24, e.g., the polymorphic markers and haplotypes of Tables 1-6 and Tables 9-12, and 15 markers in linkage disequilibrium therewithe, e.g., the markers set forth in Tables 22, 23 and 24). Therefore, in one embodiment, determination of the presence or absence of a particular marker alleles or haplotypes comprises sequence analysis. For example, a test sample of DNA or RNA can be obtained from the test subject. PCR or other appropriate methods can be used to amplify a portion of a Type 2 diabetes-associated nucleic acid, 20 and the presence of a specific allele can then be detected directly by sequencing the polymorphic site (or multiple polymorphic sites) of the genomic DNA in the sample.

Allele-specific oligonucleotides can also be used to detect the presence of a particular allele at a Type 2 diabetes-associated nucleic acid (e.g. the polymorphic markers and haplotypes of Tables 1-21, e.g., the polymorphic markers and haplotypes of 25 Tables 1-6 and Tables 9-12, and markers in linkage disequilibrium therewith), through the use of dot-blot hybridization of amplified oligonucleotides with allele-specific oligonucleotide (ASO) probes (see, for example, Saiki, R. etal., Nature, 324:163-166 (1986)). An "allele-specific oligonucleotide" (also referred to herein as an "allele-specific oligonucleotide probe") is an oligonucleotide of approximately 10-50 base pairs or 30 approximately 15-30 base pairs, that specifically hybridizes to a Type 2 diabetes- associated nucleic acid, and which contains a specific allele at a polymorphic site (e.g., a polymorphism described herein). An allele-specific oligonucleotide probe that is specific for one or more particular a Type 2 diabetes-associated nucleic acid can be prepared using standard methods (see, e.g., Current Protocols in Molecular Biology, supra). PCR 35 can be used to amplify the desired region a Type 2 diabetes-associated nucleic acid. The DNA containing the amplified region can be dot-blotted using standard methods (see, e.g., Current Protocols in Molecular Biology, supra), and the blot can be contacted with the oligonucleotide probe. The presence of specific hybridization of the probe to the amplified region can then be detected. Specific hybridization of an allele-specific WO 2008/065682 PCT/IS2007/000020 50 oligonucleotide probe to DNA from the subject is indicative of a specific allele at a polymorphic site associated with Type 2 diabetes (see, e.g., Gibbs, R. et al., Nucleic Acids Res., 17:2437-2448 (1989) and WO 93/22456).

In another embodiment, arrays of oligonucleotide probes that are complementary 5 to target nucleic acid sequence segments from a subject, can be used to identify polymorphisms in a Type 2 diabetes-associated nucleic acid (e.g. the polymorphic markers and haplotypes of Tables 1-24, e.g. the polymorphic markers and haplotypes of Tables 1-6 and Tables 9-12, and markers in linkage disequilibrium therewith). For example, an oligonucleotide array can be used. Oligonucleotide arrays typically comprise 10 a plurality of different oligonucleotide probes that are coupled to a surface of a substrate in different known locations. These oligonucleotide arrays, also described as "Genechips™," have been generally described in the art (see, e.g., U.S. Patent No. 5,143,854, PCT Patent Publication Nos. WO 90/15070 and 92/10092). These arrays can generally be produced using mechanical synthesis methods or light directed synthesis 15 methods that incorporate a combination of photolithographic methods and solid phase oligonucleotide synthesis methods (Fodor, S. eta/., Science, 251:767-773 (1991); Pirrung et al., U.S. Patent No. 5,143,854 (see also published PCT Application No. WO 90/15070); and Fodor. S. et al., published PCT Application No. WO 92/10092 and U.S. Patent No. 5,424,186, the entire teachings of each of which are incorporated by reference herein). 20 Techniques for the synthesis of these arrays using mechanical synthesis methods are described in, e.g., U.S. Patent No. 5,384,261; the entire teachings of which are incorporated by reference herein. In another example, linear arrays can be utilized.

Additional descriptions of use of oligonucleotide arrays for detection of polymorphisms can be found, for example, in U.S. Patent Nos. 5,858,659 and 5,837,832, 25 the entire teachings of both of which are incorporated by reference herein. Other methods of nucleic acid analysis can be used to detect a particular allele at a polymorphic site associated with Type 2 diabetes (e.g. the polymorphic markers and haplotypes of Tables 1-24, e.g. the polymorphic markers and haplotypes of Tables 1-6 and Tables 9-12, and markers in linkage disequilibrium therewith). Representative methods include, for 30 example, direct manual sequencing (Church and Gilbert, Proc. Natl. Acad. Sci. USA, 81: 1991-1995 (1988); Sanger, F., etal., Proc. Natl. Acad. Sci. USA, 74:5463-5467 (1977); Beavis, et al., U.S. Patent No. 5,288,644); automated fluorescent sequencing; single-stranded conformation polymorphism assays (SSCP); clamped denaturing gel electrophoresis (CDGE); denaturing gradient gel electrophoresis (DGGE) (Sheffield, V., et 35 al., Proc. Natl. Acad. Sci. USA, 86:232-236 (1989)), mobility shift analysis (Orita, M., et al., Proc. Natl. Acad. Sci. USA, 86:2766-2770 (1989)), restriction enzyme analysis (Flavell, R., etal., Cell, 15:25-41 (1978); Geever, R., eta/., Proc. Natl. Acad. Sci. USA, 78:5081-5085 (1981)); heteroduplex analysis; chemical mismatch cleavage (CMC) (Cotton, R., etal., Proc. Natl. Acad. Sci. USA, 85:4397-4401 (1985)); RNase protection WO 2008/065682 PCT/IS2007/000020 51 assays (Myers, R., eta/., Science, 230:1242-1246 (1985); use of polypeptides that recognize nucleotide mismatches, such as E. coli mutS protein; and allele-specific PCR.

In another embodiment of the invention, diagnosis of Type 2 diabetes or a susceptibility to Type 2 diabetes can be made by examining expression and/or 5 composition of a polypeptide encoded by Type 2 diabetes-associated nucleic acid in those instances where the genetic marker(s) or haplotype(s) of the present invention result in a change in the composition or expression of the polypeptide. Thus, diagnosis of a susceptibility to Type 2 diabetes can be made by examining expression and/or composition of one of these polypeptides, or another polypeptide encoded by a Type 2 10 diabetes-associated nucleic acid, in those instances where the genetic marker or haplotype of the present invention results in a change in the composition or expression of the polypeptide. The haplotypes and markers of the present invention that show association to Type 2 diabetes may play a role through their effect on one or more of these nearby genes. Possible mechanisms affecting these genes include, e.g., effects on 15 transcription, effects on RNA splicing, alterations in relative amounts of alternative splice forms of mRNA, effects on RNA stability, effects on transport from the nucleus to cytoplasm, and effects on the efficiency and accuracy of translation.

A variety of methods can be used to make such a detection, including enzyme linked immunosorbent assays (ELISA), Western blots, immunoprecipitation and 20 immunofluorescence. A test sample from a subject is assessed for the presence of an alteration in the expression and/or an alteration in composition of the polypeptide encoded by a Type 2 diabetes-associated nucleic acid. An alteration in expression of a polypeptide encoded by a Type 2 diabetes-associated nucleic acid can be, for example, an alteration in the quantitative polypeptide expression (i.e., the amount of polypeptide 25 produced). An alteration in the composition of a polypeptide encoded by a Type 2 diabetes-associated nucleic acid is an alteration in the qualitative polypeptide expression (e.g., expression of a mutant polypeptide or of a different splicing variant). In one embodiment, diagnosis of a susceptibility to Type 2 diabetes is made by detecting a particular splicing variant encoded by a Type 2 diabetes-associated nucleic acid, or a 30 particular pattern of splicing variants.

Both such alterations (quantitative and qualitative) can also be present. An "alteration" in the polypeptide expression or composition, as used herein, refers to an alteration in expression or composition in a test sample, as compared to the expression or composition of polypeptide encoded by a Type 2 diabetes-associated nucleic acid in a 35 control sample. A control sample is a sample that corresponds to the test sample (e.g., is from the same type of cells), and is from a subject who is not affected by, and/or who does not have a susceptibility to, Type 2 diabetes (e.g., a subject that does not possess a marker allele or haplotype as described herein). Similarly, the presence of one or more WO 2008/065682 PCT/IS2007/000020 52 different splicing variants in the test sample, or the presence of significantly different amounts of different splicing variants in the test sample, as compared with the control sample, can be indicative of a susceptibility to Type 2 diabetes. An alteration in the expression or composition of the polypeptide in the test sample, as compared with the control sample, can be indicative of a specific allele in the instance where the allele alters a splice site relative to the reference in the control sample. Various means of examining expression or composition of a polypeptide encoded by a Type 2 diabetes-associated nucleic acid can be used, including spectroscopy, colorimetry, electrophoresis, isoelectric focusing, and immunoassays (e.g., David et al., U.S. Pat. No. 4,376,110) such as immunoblotting (see, e.g., Current Protocols in Molecular Biology, particularly chapter 10, supra).

For example, in one embodiment, an antibody (e.g., an antibody with a detectable label) that is capable of binding to a polypeptide encoded by a Type 2 diabetes-associated nucleic acid can be used. Antibodies can be polyclonal or monoclonal. An intact antibody, or a fragment thereof (e.g., Fv, Fab, Fab', F(ab')2) can be used. The term "labeled", with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled. Examples of indirect labeling include detection of a primary antibody using a labeled secondary antibody (e.g., a fluorescently-labeled secondary antibody) and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently-labeled streptavidin.

In one embodiment of this method, the level or amount of polypeptide encoded by a Type 2 diabetes-associated nucleic acid in a test sample is compared with the level or 25 amount of the polypeptide encoded by a Type 2 diabetes-associated nucleic acid in a control sample. A level or amount of the polypeptide in the test sample that is higher or lower than the level or amount of the polypeptide in the control sample, such that the difference is statistically significant, is indicative of an alteration in the expression of the polypeptide encoded by the Type 2 diabetes-associated nucleic acid, and is diagnostic for 30 a particular allele or haplotype responsible for causing the difference in expression.

Alternatively, the composition of the polypeptide encoded by a Type 2 diabetes-associated nucleic acid in a test sample is compared with the composition of the polypeptide encoded by a Type 2 diabetes-associated nucleic acid in a control sample. In another embodiment, both the level or amount and the composition of the polypeptide can be 35 assessed in the test sample and in the control sample.

In another embodiment, the diagnosis of a susceptibility to Type 2 diabetes is made by detecting at least one Type 2 diabetes-associated marker allele or haplotype (e.g., associated alleles or haplotypes of the markers listed in Tables 1-21, such as Tables WO 2008/065682 PCT/IS2007/000020 53 1-6 and Tables 9-12), in combination with an additional protein-based, RNA-based or DNA-based assay. The methods of the invention can also be used in combination with an analysis of a subject's family history and risk factors (e.g., environmental risk factors, lifestyle risk factors).

Kits Kits useful in the methods of the invention comprise components useful in any of the methods described herein, including for example, primers for nucleic acid amplification, hybridization probes, restriction enzymes (e.g., for RFLP analysis), allele-10 specific oligonucleotides, antibodies that bind to an altered polypeptide encoded by a nucleic acid of the invention as described herein (e.g., a genomic segment comprising at least one polymorphic marker and/or haplotype of the present invention) or to a non-altered (native) polypeptide encoded by a nucleic acid of the invention as described herein, means for amplification of a nucleic acid associated with Type 2 diabetes, means 15 for analyzing the nucleic acid sequence of a nucleic acid associated with Type 2 diabetes, means for analyzing the amino acid sequence of a polypeptide encoded by a nucleic acid associated with Type 2 diabetes (e.g., the Type 2 diabetes protein encoded by the Type 2 diabetes gene), etc. The kits can for example include necessary buffers, nucleic acid primers for amplifying nucleic acids of the invention (e.g., a nucleic acid segment 20 comprising one or more of the polymorphic markers as described herein), and reagents for allele-specific detection of the fragments amplified using such primers and necessary enzymes (e.g., DNA polymerase). Additionally, kits can provide reagents for assays to be used in combination with the methods of the present invention, e.g., reagents for use with other Type 2 diabetes diagnostic assays.

In one embodiment, the invention is a kit for assaying a sample from a subject to detect the presence of Type 2 diabetes, symptoms associated with Type 2 diabetes, or a susceptibility to Type 2 diabetes in a subject, wherein the kit comprises reagents necessary for selectively detecting at least one allele of at least one polymorphism of the present invention in the genome of the individual. In a particular embodiment, the 30 reagents comprise at least one contiguous oligonucleotide that hybridizes to a fragment of the genome of the individual comprising at least one polymorphism of the present invention. In another embodiment, the reagents comprise at least one pair of oligonucleotides that hybridize to opposite strands of a genomic segment obtained from a subject, wherein each oligonucleotide primer pair is designed to selectively amplify a 35 fragment of the genome of the individual that includes at least one polymorphism, wherein the polymorphism is selected from the group consisting of the polymorphisms as listed in Tables 1-6 and 9-12, and polymorphic markers in linkage disequilibrium WO 2008/065682 PCT/IS2007/000020 54 therewith (e.g., the markers set forth in Tables 22, 23 and 24). In yet another embodiment the fragment is at least 20 base pairs in size. Such oligonucleotides or nucleic acids (e.g., oligonucleotide primers) can be designed using portions of the nucleic acid sequence flanking polymorphisms (e.g., SNPs or microsatellites) that are indicative of 5 Type 2 diabetes. In another embodiment, the kit comprises one or more labeled nucleic acids capable of allele-specific detection of one or more specific polymorphic markers or haplotypes associated with Type 2 diabetes, and reagents for detection of the label. Suitable labels include, e.g., a radioisotope, a fluorescent label, an enzyme label, an enzyme co-factor label, a magnetic label, a spin label, an epitope label.

In particular embodiments, the polymorphic marker or haplotype to be detected by the reagents of the kit comprises one or more markers, two or more markers, three or more markers, four or more markers or five or more markers selected from the group consisting of the markers set forth in Tables 9-12. In another embodiment, the marker or haplotype to be detected comprises the markers set forth in Tables 22-24. In another 15 embodiment, the marker or haplotype to be detected comprises markers rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID 20 NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), rsl860316 (SEQ ID NO: 10), rsl981647 (SEQ ID NO:ll), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO: 13), and rs9890889 (SEQ ID NO:31), and markers in linkage disequilibrium therewith. In one such embodiment, linkage disequilibrium is defined by values of r2 greater than 0.2.

In one preferred embodiment, the kit for detecting the markers of the invention comprises a detection oligonucleotide probe, that hybridizes to a segment of template DNA containing a SNP polymorphisms to be detected, an enhancer oligonucleotide probe and an endonuclease. As explained in the above, the detection oligonucleotide probe comprises a fluorescent moiety or group at its 3' terminus and a quencher at its 5' 30 terminus, and an enhancer oligonucleotide, is employed, as described by Kutyavin eta/. (Nucleic Acid Res. 34:el28 (2006)). The fluorescent moiety can be Gig Harbor Green or Yakima Yellow, or other suitable fluorescent moieties. The detection probe is designed to hybridize to a short nucleotide sequence that includes the SNP polymorphism to be detected. Preferably, the SNP is anywhere from the terminal residue to -6 residues from 35 the 3' end of the detection probe. The enhancer is a short oligonucleotide probe which hybridizes to the DNA template 3' relative to the detection probe. The probes are designed such that a single nucleotide gap exists between the detection probe and the enhancer nucleotide probe when both are bound to the template. The gap creates a synthetic abasic site that is recognized by an endonuclease, such as Endonuclease IV.

WO 2008/065682 PCT/IS2007/000020 55 The enzyme cleaves the dye off the fully complementary detection probe, but cannot cleave a detection probe containing a mismatch. Thus, by measuring the fluorescence of the released fluorescent moiety, assessment of the presence of a particular allele defined by nucleotide sequence of the detection probe can be performed.

The detection probe can be of any suitable size, although preferably the probe is relatively short. In one embodiment, the probe is from 5-100 nucleotides in length. In another embodiment, the probe is from 10-50 nucleotides in length, and in another embodiment, the probe is from 12-30 nucleotides in length. Other lengths of the probe are possible and within scope of the skill of the average person skilled in the art.

In a preferred embodiment, the DNA template containing the SNP polymorphism is amplified by Polymerase Chain Reaction (PCR) prior to detection, and primers for such amplification are included in the reagent kit. In such an embodiment, the amplified DNA serves as the template for the detection probe and the enhancer probe.

Certain embodiments of the detection probe, the enhancer probe, and/or the primers used for amplification of the template by PCR include the use of modified bases, including modified A and modified G. The use of modified bases can be useful for adjusting the melting temperature of the nucleotide molecule (probe and/or primer) to the template DNA, for example for increasing the melting temperature in regions containing a low percentage of G or C bases, in which modified A with the capability of forming three hydrogen bonds to its complementary T can be used, or for decreasing the melting temperature in regions containing a high percentage of G or C bases, for example by using modified G bases that form only two hydrogen bonds to their complementary C base in a double stranded DNA molecule. In a preferred embodiment, modified bases are used in the design of the detection nucleotide probe. Any modified base known to the skilled person can be selected in these methods, and the selection of suitable bases is well within the scope of the skilled person based on the teachings herein and known bases available from commercial sources as known to the skilled person.

In one such embodiments, the presence of the marker or haplotype is indicative of a susceptibility (increased susceptibility or decreased susceptibility) to Type 2 diabetes. In another embodiment, the presence of the marker or haplotype is indicative of response to a Type 2 diabetes therapeutic agent. In another embodiment, the presence of the marker or haplotype is indicative of prognosis of Type 2 diabetes. In yet another embodiment, the presence of the marker or haplotype is indicative of progress of treatment of Type 2 diabetes. Such treatment may include intervention by surgery, medication or by other means (e.g., lifestyle changes).

WO 2008/065682 PCT/IS2007/000020 56 Therapeutic agents for Type 2 diabetes Currently available Type 2 diabetes medication (apart from insulin) falls into six main classes of drugs: sulfonylureas, meglitinides, biguanides, thiazolidinediones, alpha-glucosidase inhibitors and a new class of drugs called DPP-4 inhibitors. These classes of drugs work in different ways to lower blood glucose levels. 1. Sulfonylureas. Sulfonylureas stimulate the beta cells of the pancreas to release more insulin. 2. Meglitinides. Meglitinides are drugs that also stimulate the beta cells to release 10 insulin. 3. Biguanides. Biguanides lower blood glucose levels primarily by decreasing the amount of glucose produced by the liver. Metformin also helps to lower blood glucose levels by making muscle tissue more sensitive to insulin so glucose can be absorbed. 4. Thiazolidinediones. These drugs help insulin work better in the muscle and fat and 15 also reduce glucose production in the liver.

. Alpha-glucosidase inhibitors. These drugs help the body to lower blood glucose levels by blocking the breakdown of starches, such as bread, potatoes, and pasta in the intestine. They also slow the breakdown of some sugars, such as table sugar. Their action slows the rise in blood glucose levels after a meal. They should be taken with the first bite of a meal. 6: DPP-4 Inhibitors. A new class of medications called DPP-4 inhibitors help improve AlC without causing hypoglycemia. They work by preventing the breakdown of a naturally occurring compound in the body, GLP-1. GLP-1 reduces blood glucose levels in the body, but is broken down very quickly so it does not work well when injected as a drug itself. 25 By interfering in the process that breaks down GLP-1, DPP-4 inhibitors allow it to remain active in the body longer, lowering blood glucose levels only when they are elevated.

Examples of available drugs in these classes are listed in Agent Table 1.

Agent Table 1.

Drug Class Generic name Brand name Biguanides metformin Glucophage, Glucophage XR, Glycon metformin plus qlyburide Glucovance Thiazolidinediones pioglitazone Actos rosiglitazone Avandia Sulfonylureas acetohexamide Dymelor 57 Drug Class Generic name Brand name chlorpropamide Diabinese gliclazide Diamicron Diamicron MR glimepiride Amaryl glipizide Glucotrol.Glucotrol XL glyburide Micronase, DiaBeta, Glynase PresTab glyburide plus metformin Glucovance tolazamide Tolinase tolbutamide Orinase, Tol-Tab Meglitinides nateglinide Starlix repaglinide Prandin, Gluconorm Alpha-glucosidase inhibitors acarbose Precose, Prandase miglitol Glyset DPP-4 Inhibitors sitagliptin Januvia Additionally, a combination therapy comprising Biguanide and Sulphonylureas has bee used for treatment of Type 2 diabetes.

Additional Type 2 diabetes drugs are listed Agent Table 2.

Agent Table 2 Compound name(s) Compound name (generated using Autonom, ISIS Draw version 2.5 from MDL Information Systems) Company Compound Reference Indications AR-0133418 (SN-4521) 1 -(4-Methoxy-benzyl)-3-(5-nitro-thiazol-2-yl)-urea AstraZeneca AD AR-025028 NSD AstraZeneca CT-98023 N-[4-(2,4-Dichloro-phenyl)-5-(1 H-imidazol-2-yl)-pyrimidin-2-yl]-N'-(5-nitro-pyridin-2-yl)-ethane-1,2-diamine Chiron Corp non-insulin dependent diabetes CT-20026 NSD Chiron Corp Wagman et al., Curr Pharm. Des 2004: 10(10) 1105-37 non-insulin dependent diabetes CT-21022 NSD Chiron Corp non-insulin dependent diabetes CT-20014 NSD Chiron Corp non-insulin dependent diabetes CT-21018 NSD Chiron Corp non-insulin dependent diabetes CHIR-98025 NSD Chiron Corp non-insulin dependent diabetes CHIR-99021 NSD Chiron Corp Wagman et al., Curr Pharm. Des 2004: 10(10) 1105-37 non-insulin dependent diabetes CG-100179 NSD CrystalGenomics and Yuyu WO- 2004065370 diabetes mellitus (Korea) 58 Compound name(s) Compound name (generated using Autonom, ISIS Draw version 2.5 from MDL Information Systems) Company Compound Reference Indications 4-[2-(4-Dimethylamino-3-nitro-phenylamino)-pyrimidin-4-yl]-3,5-dimethyl-1 H-pyrrole-2-carbonitrile Cyclacel Ltd. non-insulin dependent diabetes, among others.

NP-01139, NP-031112, NP-03112, NP-00361 4-Benzyl-2-methyl-[1,2,4]thiadiazolidine-3,5-dione Neuropharma SA CNS disorders, AD 3-[9-Fluoro-2-(piperidine-1-carbonyl)-1,2,3,4-tetrahydro-[1,4]diazepino[6,7,1-hi]indol-7-yl]-4-imidazo[1,2-a]pyridin-3-yl-pyrrole-2,5-dione Eli Lilly & Co non-insulin dependent diabetes GW-784752x, GW-784775, SB-216763, SB-415286 Cyclopentanecarboxylic acid (6-pyridin-3-yl-furo[2,3- d]pyrimidin-4-yl)-amide GSK W003024447 (compound referenced: 4-[2-(2- bromophenyl)-4-(4-fluorophenyl)-1H-imidazol-5-yljpyridine non-insulin dependent diabetes, neurodegenerative disease NNC-57-0511, NNC-57-0545, NNC-57-0588 1 -(4-Amino-furazan-3-yl)-5-piperidin-1-ylmethyl-1H-[1,2,3]triazole-4-carboxylic acid [1-pyridin-4-yl-meth-(E)-ylidene]-hydrazide Novo Nordisk non-insulin dependent diabetes, CP-70949 NSD Pfizer Hypoglycemic agent VX-608 NSD Cerebrovascular ischemia, non-insulin dependent diabetes KP-403 class NSD Kinetek Nuclear factor kappa B modulator, Antiinflammatory, Cell cycle inhibitor, Glycogen synthase kinase-3 beta inhibitor BYETTA (exenatide) Exenatide: C184H282N50O60S - Amino acid sequence:H-His- Gly-Glu-Gly-Thr-Phe-Thr- Ser-Asp-Leu-Ser-Lys-Gln- Met-Glu-Glu-Glu-Ala-Val- Arg-Leu-Phe-lle-Glu-Trp- Leu-Lys-Asn-Gly-Gly-Pro- Ser-Ser-Gly-Ala-Pro-Pro- Pro-Ser-NH2 Amylin / Eli Lilly & Co non-insulin dependent diabetes Vildagliptin (LAF237) NSD Novartis non-insulin dependent diabetes -DPP-4 inhibitor WO 2008/065682 PCT/IS2007/000020 59 Therapeutic agents of the invention Variants of the present invention {e.g., the markers and/or haplotypes as described herein) can be used to identify novel therapeutic targets for Type 2 diabetes.

For example, genes containing, or in linkage disequilibrium with, variants (markers and/or haplotypes) associated with Type 2 diabetes, or their products, as well as genes or their products that are directly or indirectly regulated by or interact with these variant genes or their products, can be targeted for the development of therapeutic agents to'treat Type 2 diabetes, or prevent or delay onset of symptoms associated with Type 2 diabetes. 10 Therapeutic agents may comprise one or more of, for example, small non-protein and non-nucleic acid molecules, proteins, peptides, protein fragments, nucleic acids (DNA, RNA), PNA (peptide nucleic acids), or their derivatives or mimetics which can modulate the function and/or levels of the target genes or their gene products.

The nucleic acids and/or variants of the invention, or nucleic acids comprising their 15 complementary sequence, may be used as antisense constructs to control gene expression in cells, tissues or organs. The methodology associated with antisense techniques is well known to the skilled artisan, and is described and reviewed in AntisenseDrug Technology: Principles, Strategies, and Applications, Crooke, ed., Marcel Dekker Inc., New York (2001). In general, antisense nucleic acid molecules are designed 20 to be complementary to a region of mRNA expressed by a gene, so that the antisense molecule hybridizes to the mRNA, thus blocking translation of the mRNA into protein. Several classes of antisense oligonucleotide are known to those skilled in the art, including cleavers and blockers. The former bind to target RNA sites, activate intracellular nucleases (e.g., RnaseH or Rnase L), that cleave the target RNA. Blockers bind to target 25 RNA, inhibit protein translation by steric hindrance of the ribosomes. Examples of blockers include nucleic acids, morpholino compounds, locked nucleic acids and methylphosphonates (Thompson, Drug Discovery Today, 7:912-917 (2002)). Antisense oligonucleotides are useful directly as therapeutic agents, and are also useful for determining and validating gene function, for example by gene knock-out or gene knock-30 down experiments. Antisense technology is further described in Lavery et at., Curr. Opin. Drug Discov. Devel. 6:561-569 (2003), Stephens et al., Curr. Opin. Mol. Ther. 5:118-122 (2003), Kurreck, Eur. J. Biochem. 270:1628-44 (2003), Dias et al., Mol. Cancer Ter. 1:347-55 (2002), Chen, Methods Mol. Med. 75:621-636 (2003), Wang etal., Curr. Cancer Drug Targets 1:177-96 (2001), and Bennett, Antisense Nucleic Acid Drug.Dev. 12:215-24 35 (2002) The variants described herein can be used for the selection and design of antisense reagents that are specific for particular variants. Using information about the variants described herein, antisense oligonucleotides or other antisense molecules that WO 2008/065682 PCT/IS2007/000020 60 specifically target mRNA molecules that contain one or more variants of the invention can be designed. In this manner, expression of mRNA molecules that contain one or more variant of the present invention (markers and/or haplotypes) can be inhibited or blocked. In one embodiment, the antisense molecules are designed to specifically bind a particular 5 allelic form (i.e., one or several variants (alleles and/or haplotypes)) of the target nucleic acid, thereby inhibiting translation of a product originating from this specific allele or haplotype, but which do not bind other or alternate variants at the specific polymorphic sites of the target nucleic acid molecule.

As antisense molecules can be used to inactivate mRNA so as to inhibit gene 10 expression, and thus protein expression, the molecules can be used to treat a disease or disorder, such as Type 2 diabetes. The methodology can involve cleavage by means of ribozymes containing nucleotide sequences complementary to one or more regions in the mRNA that attenuate the ability of the mRNA to be translated. Such mRNA regions include, for example, protein-coding regions, in particular protein-coding regions 15 corresponding to catalytic activity, substrate and/or ligand binding sites, or other functional domains of a protein.

The phenomenon of RNA interference (RNAi) has been actively studied for the last decade, since its original discovery in C. elegans (Fire et al.,Nature 391:806-11 (1998)), and in recent years its potential use in treatment of human disease has been actively 20 pursued (reviewed in Kim & Rossi, Nature Rev. Genet. 8:173-204 (2007)). RNA interference (RNAi), also called gene silencing, is based on using double-stranded RNA molecules (dsRNA) to turn off specific genes. In the cell, cytoplasmic double-stranded RNA molecules (dsRNA) are processed by cellular complexes into small interfering RNA (siRNA). The siRNA guide the targeting of a protein-RNA complex to specific sites on a 25 target mRNA, leading to cleavage of the mRNA (Thompson, Drug Discovery Today, 7:912-917 (2002)). The siRNA molecules are typically about 20, 21, 22 or 23 nucleotides in length. Thus, one aspect of the invention relates to isolated nucleic acid molecules, and the use of those molecules for RNA interference, i.e. as small interfering RNA molecules (siRNA). In one embodiment, the isolated nucleic acid molecules are 18-26 nucleotides in 30 length, preferably 19-25 nucleotides in,length, more preferably 20-24 nucleotides in length, and more preferably 21, 22 or 23 nucleotides in length.

Another pathway for RNAi-mediated gene silencing originates in endogenously encoded primary microRNA (pri-miRNA) transcripts, which are processed in the cell to generate precursor miRNA (pre-miRNA). These miRNA molecules are exported from the 35 nucleus to the cytoplasm, where they undergo processing to generate mature miRNA molecules (miRNA), which direct translational inhibition by recognizing target sites in the 3' untranslated regions of mRNAs, and subsequent mRNA degradation by processing P-bodies (reviewed in Kim & Rossi, Nature Rev. Genet. 8:173-204 (2007)).

WO 2008/065682 PCT/IS2007/000020 61 Clinical applications of RNAi include the incorporation of synthetic siRNA duplexes, which preferably are approximately 20-23 nucleotides in size, and preferably have 3' overlaps of 2 nucleotides. Knockdown of gene expression is established by sequence-specific design for the target mRNA. Several commercial sites for optimal design and 5 synthesis of such molecules are known to those skilled in the art.

Other applications provide longer siRNA molecules (typically 25-30 nucleotides in length, preferably about 27 nucleotides), as well as small hairpin RNAs (shRNAs; typically about 29 nucleotides in length). The latter are naturally expressed, as described in Amarzguioui et al. (FEBS Lett. 579:5974-81 (2005)). Chemically synthetic siRNAs and 10 shRNAs are substrates for in vivo processing, and in some cases provide more potent gene-silencing than shorter designs (Kim et al., Nature Biotechnol. 23:222-226 (2005); Siolas et al., Nature Biotechnol. 23:227-231 (2005)). In general siRNAs provide for transient silencing of gene expression, because their intracellular concentration is diluted by subsequent cell divisions. By contrast, expressed shRNAs mediate long-term, stable 15 knockdown of target transcripts, for as long as transcription of the shRNA takes place (Marques et al., Nature Biotechnol. 23:559-565 (2006); Brummelkamp et al., Science 296: 550-553 (2002)).

Since RNAi molecules, including siRNA, miRNA and shRNA, act in a sequence-dependent manner, the variants of the present invention (e.g., the markers and 20 haplotypes as described herein) can be used to design RNAi reagents that recognize specific nucleic acid molecules comprising specific alleles and/or haplotypes (e.g., the alleles and/or haplotypes of the present invention), while not recognizing nucleic acid molecules comprising other alleles or haplotypes. These RNAi reagents can thus recognize and destroy the target nucleic acid molecules. As with antisense reagents, RNAi 25 reagents can be useful as therapeutic agents (i.e., for turning off disease-associated genes or disease-associated gene variants), but may also be useful for characterizing and validating gene function (e.g., by gene knock-out or gene knock-down experiments).

Delivery of RNAi may be performed by a range of methodologies known to those skilled in the art. Methods utilizing non-viral delivery include cholesterol, stable nucleic 30 acid-lipid particle (SNALP), heavy-chain antibody fragment (Fab), aptamers and nanoparticles. Viral delivery methods include use of lentivirus, adenovirus and adeno-associated virus. The siRNA molecules are in some embodiments chemically modified to increase their stability. This can include modifications at the 2' position of the ribose, including 2'-0-methylpurines and 2'-fluoropyrimidines, which provide resistance to Rnase 35 activity. Other chemical modifications are possible and known to those skilled in the art.

The following references provide a further summary of RNAi, and possibilities for targeting specific genes using RNAi: Kim & Rossi, Nat. Rev. Genet. 8:173-184 (2007), WO 2008/065682 PCT/IS2007/000020 62 Chen & Rajewsky, Nat. Rev. Genet. 8: 93-103 (2007), Reynolds, eta/., Nat. Biotechnol. 22:326-330 (2004), Chi etal., Proc. Natl. Acad. Sci. USA 100:6343-6346 (2003), Vickers eta/., J. Biol. Chem. 278:7108-7118 (2003), Agami, Curr. Opin. Chem. Biol. 6:829-834 (2002), Lavery, eta/., Curr. Opin. Drug Discov. Devel. 6:561-569 (2003), Shi, Trends 5 Genet. 19:9-12 (2003), Shuey eta/., Drug Discov. Today 7:1040-46 (2002), McManus et al., Nat. Rev. Genet. 3:737-747 (2002), Xia etal., Nat. Biotechnol. 20:1006-10 (2002), Plasterk et al., curr. Opin. Genet. Dev. 10:562-7 (2000), Bosher et al., Nat. Cell Biol. 2:E31-6 (2000), and Hunter, Curr. Biol. 9:R440-442 (1999).

A genetic defect leading to increased predisposition or risk for development of a 10 disease, including Type 2 diabetes, or a defect causing the disease, may be corrected permanently by administering to a subject carrying the defect a nucleic acid fragment that incorporates a repair sequence that supplies the normal/wild-type nucleotide(s) at the site of the genetic defect. Such site-specific repair sequence may concompass an RNA/DNA oligonucleotide that operates to promote endogenous repair of a subject's genomic DNA. 15 The administration of the repair sequence may be performed by an appropriate vehicle, such as a complex with polyethelenimine, encapsulated in anionic liposomes, a viral vector such as an adenovirus vector, or other pharmaceutical compositions suitable for promoting intracellular uptake of the adminstered nucleic acid. The genetic defect may then be overcome, since the chimeric oligonucleotides induce the incorporation of the 20 normal sequence into the genome of the subject, leading to expression of the normal/wild-type gene product. The replacement is propagated, thus rendering a permanent repair and alleviation of the symptoms associated with the disease or condition.

The present invention provides methods for identifying compounds or agents that 25 can be used to treat Type 2 diabetes. Thus, the variants of the invention are useful as targets for the identification and/or development of therapeutic agents. Such methods may include assaying the ability of an agent or compound to modulate the activity and/or expression of a nucleic acid that includes at least one of the variants (markers and/or haplotypes) of the present invention, or the encoded product of the nucleic acid. This in 30 turn can be used to identify agents or compounds that inhibit or alter the undesired activity or expression of the encoded nucleic acid product. Assays for performing such experiments can be performed in cell-based systems or in cell-free systems, as known to the skilled person. Cell-based systems include cells naturally expressing the nucleic acid molecules of interest, or recombinant cells that have been genetically modified so as to 35 express a certain desired nucleic acid molecule.

Variant gene expression in a patient can be assessed by expression of a variant-containing nucleic acid sequence (for example, a gene containing at least one variant of the present invention, which can be transcribed into RNA containing the at least one WO 2008/065682 PCT/IS2007/000020 63 variant, and in turn translated into protein), or by altered expression of a normal/wild-type nucleic acid sequence due to variants affecting the level or pattern of expression of the normal transcripts, for example variants in the regulatory or control region of the gene. Assays for gene expression include direct nucleic acid assays (mRNA), assays for 5 expressed protein levels, or assays of collateral compounds involved in a pathway, for example a signal pathway. Furthermore, the expression of genes that are up- or down-regulated in response to the signal pathway can also be assayed. One embodiment includes operably linking a reporter gene, such as luciferase, to the regulatory region of the gene(s) of interest.

Modulators of gene expression can in one embodiment be identified when a cell is contacted with a candidate compound or agent, and the expression of mRNA is determined. The expression level of mRNA in the presence of the candidate compound or agent is compared to the expression level in the absence of the compound or agent.

Based on this comparison, candidate compounds or agents for treating Type 2 diabetes 15 can be identified as those modulating the gene expression of the variant gene. When expression of mRNA or the encoded protein is statistically significantly greater in the presence of the candidate compound or agent than in its absence, then the candidate compound or agent is identified as a stimulator or up-regulator of expression of the nucleic acid. When nucleic acid expression or protein level is statistically significantly less 20 in the presence of the candidate compound or agent than in its absence, then the candidate compound is identified as an inhibitor or down-regulator of the nucleic acid expression.

The invention further provides methods of treatment using a compound identified through drug (compound and/or agent) screening as a gene modulator (i.e. stimulator 25 and/or inhibitor of gene expression).

In a further aspect of the present invention, a pharmaceutical pack (kit) is provided, the pack comprising a therapeutic agent and a set of instructions for administration of the therapeutic agent to humans diagnostically tested for one or more variants of the present invention, as disclosed herein. The therapeutic agent can be a 30 small molecule drug, an antibody, a peptide, an antisense or RNAi molecule, or other therapeutic molecules. In one embodiment, an individual identified as a carrier of at least one variant of the present invention is instructed to take a prescribed dose of the therapeutic agent. In one such embodiment, an individual identified as a homozygous carrier of at least one variant of the present invention is instructed to take a prescribed 35 dose of the therapeutic agent. In another embodiment, an individual identified as a non-carrier of at least one variant of the present invention is instructed to take a prescribed dose of the therapeutic agent. 64 Methods of assessing probability of response to therapeutic agents, methods of monitoring progress of treatment and methods of treatment As is known in the art, individuals can have differential responses to a particular 5 therapy (e.g., a therapeutic agent or therapeutic method). Pharmacogenomics addresses the issue of how genetic variations (e.g., the variants (markers and/or haplotypes) of the present invention) affect drug response, due to altered drug disposition and/or abnormal or altered action of the drug . Thus, the basis of the differential response may be genetically determined in part. Clinical outcomes due to genetic variations affecting drug 10 response may result in toxicity of the drug in certain individuals (e.g., carriers or non-carriers of the genetic variants of the present invention), or therapeutic failure of the drug. Therefore, the variants of the present invention may determine the manner in which a therapeutic agent and/or method acts on the body, or the way in which the body metabolizes the therapeutic agent.

Accordingly, in one embodiment, the presence of a particular allele at a polymorphic site or haplotype is indicative of a different, e.g. a different response rate, to a particular treatment modality. This means that a patient diagnosed with Type 2 diabetes, and carrying a certain allele at a polymorphic or haplotype of the present invention (e.g., the at-risk and protective alleles and/or haplotypes of the invention) 20 would respond better to, or worse to, a specific therapeutic, drug and/or other therapy used to treat the disease. Therefore, the presence or absence of the marker allele or haplotype could aid in deciding what treatment should be used for a the patient. For example, for a newly diagnosed patient, the presence of a marker or haplotype of the present invention may be assessed (e.g., through testing DNA derived from a blood 25 sample, as described herein). If the patient is positive for a marker allele or haplotype at (that is, at least one specific allele of the marker, or haplotype, is present), then the physician recommends one particular therapy, while if the patient is negative for the at least one allele of a marker, or a haplotype, then a different course of therapy may be recommended (which may include recommending that no immediate therapy, other than 30 serial monitoring for progression of the disease, be performed). Thus, the patient's carrier status could be used to help determine whether a particular treatment modality should be administered. The value lies within the possibilities of being able to diagnose the disease at an early stage, to select the most appropriate treatment, and provide information to the clinician about prognosis/aggressiveness of the disease in order to be 35 able to apply the most appropriate treatment.

In some embodiments, the treatment modality comprises adminstering at least one of the therapeutic agents set forth in Agent Table 1 and Agent Table 2. In one WO 2008/065682 PCT/IS2007/000020 65 embodiment, the therapeutic agent is selected from Biguanides, Thiazolidinediones, Sulfonylureas, Meglitinides, Alpha-glucosidase inhibitors and DPP-4 inhibitors. In one embodiment, the Biguanide is metformin or metformin plus glyburide. Other combination therapies comprising metformin, including combinations with thiazolidinediones, are also 5 contemplated and within the scope of the invention. In another embodiment, the Sulfunylurea is selected from acetohexamide, chlorpropamide, gliclazide Diamicron, glimepiride, glipizide, glyburide, tolazamide and tolbutamide. In another embodiment, the Thiazolidinedione is selected from pioglitazone, rosiglitazone and mitoglitazone or other thiazolidinedione derivatives. In another embodiment, the therapeutic agent is 10 selected from the agents set forth in Agent Table 2.

The present invention also relates to methods of monitoring progress or effectiveness of a treatment for Type 2 diabetes. This can be done based on the genotype and/or haplotype status of the markers and haplotypes of the present invention, i.e., by assessing the absence or presence of at least one allele of at least one polymorphic 15 marker as disclosed herein, or by monitoring expression of genes that are associated with the variants (markers and haplotypes) of the present invention. The risk gene mRNA or the encoded polypeptide can be measured in a tissue sample (e.g., a peripheral blood sample, or a biopsy sample). Expression levels and/or mRNA levels can thus be determined before and during treatment to monitor its effectiveness. Alternatively, or 20 concomitantly, the genotype and/or haplotype status of at least one risk variant for Type 2 diabetes presented herein is determined before and during treatment to monitor its effectiveness. Alternatively, biological networks or metabolic pathways related to the markers and haplotypes of the present invention can be monitored by determining mRNA and/or polypeptide levels. This can be done for example, by monitoring expression levels 25 or polypeptides for several genes belonging to the network and/or pathway, in samples taken before and during treatment. Alternatively, metabolites belonging to the biological network or metabolic pathway can be determined before and during treatment. Effectiveness of the treatment is determined by comparing observed changes in expression levels/metabolite levels during treatment to corresponding data from healthy 30 subjects.

The progress of therapy in individuals carrying at least one at-risk allele of at least one marker found to be associated with increased susceptibility or risk of Type 2 diabetes is thus monitored based on the genotype status of the individual. Individuals carrying at-risk variants as described herein may benefit from closer or more frequent monitoring of 35 progress of therapy than non-carriers, alternatively in combination with a particular treatment modality or therapeutic agent being adminstered, as described in the above.

In a further aspect, the markers of the present invention can be used to increase power and effectiveness of clinical trials. Thus, individuals who are carriers of at least one WO 2008/065682 PCT/IS2007/000020 66 at-risk variant of the present invention, i.e. individuals who are carriers of at least one allele of at least one polymorphic marker conferring increased risk of developing Type 2 diabetes may be more likely to respond to a particular treatment modality. In one embodiment, individuals who carry at-risk variants for gene(s) in a pathway and/or 5 metabolic network for which a particular treatment (e.g., small molecule drug) is targeting, are more likely to be responders to the treatment. In another embodiment, individuals who carry at-risk variants for a gene, which expression and/or function is altered by the at-risk variant, are more likely to be responders to a treatment modality targeting that gene, its expression or its gene product. This application can improve the 10 safety of clinical trials, but can also enhance the chance that a clinical trial will demonstrate statistically significant efficacy, which may be limited to a certain sub-group of the population, e.g., individuals that are either carriers or non-carriers of the at-risk variants described herein. Thus, one possible outcome of such a trial is that carriers of certain genetic variants, e.g., the markers and haplotypes of the present invention, are 15 statistically significantly likely to show positive response to the therapeutic agent, i.e. experience alleviation of symptoms associated with Type 2 diabetes when taking the therapeutic agent or drug as prescribed.

In a further aspect, the markers and haplotypes of the present invention can be used for targeting the selection of pharmaceutical agents for specific individuals. 20 Personalized selection of treatment modalities, lifestyle changes or combination of the two, can be realized by the utilization of the at-risk variants of the present invention. Thus, the knowledge of an individual's status for particular markers of the present invention, can be useful for selection of treatment options that target genes or gene products affected by the at-risk variants of the invention. Certain combinations of 25 variants may be suitable for one selection of treatment options, while other gene variant combinations may target other treatment options. Such combination of variant may include one variant, two variants, three variants, or four or more variants, as needed to determine with clinically reliable accuracy the selection of treatment module.

In addition to the diagnostic and therapeutic uses of the variants of the present 30 invention, the variants (markers and haplotypes) can also be useful markers for human identification, and as such be useful in forensics, paternity testing and in biometrics. The specific use of SNPs for forensic purposes is reviewed by Gill {Int. J. Legal Med. 114:204-10 (2001)). Genetic variations in genomic DNA between individuals can be used as genetic markers to identify individuals and to associate a biological sample with an 35 individual. Genetic markers, including SNPs and microsatellites, can be useful to distinguish individuals. The more markers that are analyzed, the lower the probability that the allelic combination of the markers in any given individual is the same as in an unrelated individual (assuming that the markers are unrelated, i.e. that the markers are in perfect linkage equilibrium). Thus, the variants used for these purposes are preferably WO 2008/065682 PCT/IS2007/000020 67 unrelated, i.e. they are inherited independently. Thus, preferred markers can be selected from available markers, such as the markers of the present invention, and the selected markers may comprise markers from different regions in the human genome, including markers on different chromosomes.

In certain applications, the SNPs useful for forensic testing are from degenerate codon positions (i.e., the third position in certain codons such that the variation of the SNP does not affect the amino acid encoded by the codon). In other applications, such for applications for predicting phenotypic characteristics including race, ancestry or physical characteristics, it may be more useful and desirable to utilize SNPs that affect the amino 10 acid sequence of the encoded protein. In other such embodiments, the variant (SNP or other polymorphic marker) affects the expression level of a nearby gene, thus leading to altered protein expression.

The present invention also relates to computer-implemented applications of the polymorphic markers and haplotypes described herein to be associated with Type 2 diabetes. Such applications can be useful for storing, manipulating or otherwise analyzing genotype data that is useful in the methods of the invention. One example pertains to storing genotype information derived from an individual on readable media, so as to be able to provide the genotype information to a third party (e.g., the individual), or for deriving information from the genotype data, e.g., by comparing the genotype data to information about genetic risk factors contributing to increased susceptibility to Type 2 diabetes, and reporting results based on such comparison.

One such aspect relates to computer-readable media. In general terms, such medium has capabilities of storing (i) identifer information for at least one polymorphic marker or a haplotye; (ii) an indicator of the frequency of at least one allele of said at least one marker, or the frequency of a haplotype, in individuals with Type 2 diabetes; and an indicator of the frequency of at least one allele of said at least one marker, or the frequency of a haplotype, in a reference population. The reference population can be a disease-free population of individuals. Alternatively, the reference population is a random sample from the general population, and is thus representativ of the population at large. The frequency indicator may be a calculated frequency, a count of alleles and/or haplotype copies, or normalized or otherwise manipulated values of the actual frequencies that are suitable for the particular medium.

Additional information about the individual can be stored on the medium, such as ancestry information, information about sex, physical attributes or charactersitics 35 (including height and weight), biochemical measurements (such as blood pressure, blood lipid levels, fasting glucose levels, insulin response measurements), or other useful WO 2008/065682 PCT/IS2007/000020 68 information that is desirable to store or manipulate in the context of the genotype status of a particular individual.

The invention furthermore relates to an apparatus that is suitable for determination or manipulation of genetic data useful for determining a susceptibility to 5 Type 2 diabetes in a human individual. Such an apparatus can include a computer-readable memory, a routine for manipulating data stored on the computer-readable memory, and a routine for generating an output that includes a measure of the genetic data. Such measure can include values such as allelic or haplotype frequencies, genotype counts, sex, age, phenotype information, values for odds ratio (OR) or relative risk (RR), 10 population attributable risk (PAR), or other useful information that is either a direct statistic of the original genotype data or based on calculations based on the genetic data.

The above-described applications can all be practiced with the markers and haplotypes of the invention that have in more detail been described with respect to methods of assessing susceptibility to Type 2 diabetes. Thus, these applications can in 15 general be reduced to practice using markers listed in Tables 1-6, and markers in linkage disequilibrium therewith, e.g. the markers set forth in Tables 22, 23 and 24. In one embodiment, the markers or haplotypes are present within the genomic segments whose sequences are set forth in SEQ ID NO:l, SEQ ID NO:2 or SEQ ID NO:3. In another embodiment, the markers and haplotypes comprise at least one marker selected from 20 rs2497304 (SEQ ID NO: 16), rs947591 (SEQ ID N0:30), rsl0882091 (SEQ ID NO:4), rs7914814 (SEQ ID NO:24), rs6583830 (SEQ ID N0:20), rs2421943 (SEQ ID NO: 15), rs6583826 (SEQ ID NO: 19), rs7752906 (SEQ ID NO:32), rsl569699 (SEQ ID NO:6), rs7756992 (SEQ ID NO:21), rs9350271 (SEQ ID NO:33), rs9356744 (SEQ ID NO:34), rs9368222 (SEQ ID NO:35), rsl0440833 (SEQ ID NO:36), rs6931514 (SEQ ID NO:37), 25 rsl860316 (SEQ ID NO: 10), rsl981647 (SEQ ID NO: 11), rsl843622 (SEQ ID NO:9), rs2191113 (SEQ ID NO: 13), and rs9890889 (SEQ ID NO:31), optionally including markers in linkage disequilibrium therewith, wherein linkage disequilibrium is defined by numerical values for r2 of greater than 0.2. In another embodiment, the marker or haplotype comprises at least one marker selected from rs2497304 allele A, rs947591 allele A, 30 rsl0882091 allele C rs7914814 allele T, rs6583830 allele A, rs2421943 allele G, rs6583826 allele G, rs7752906 allele A, rsl569699 allele C, rs7756992 allele G, rs9350271 allele A, rs9356744 allele C, rs9368222 allele A, rsl0440833 allele A, rs6931514 allele G, rsl860316 allele A, rsl981647 allele C, rsl843622 allele T, rs2191113 allele A, and rs9890889 allele A. In yet another embodiment, the at least one 35 marker or haplotype comprises at least one marker selected from the markers set forth in Tables 22, 23 and 24.

WO 2008/065682 Nucleic acids and polypeptides 69 The nucleic acids and polypeptides described herein can be used in methods of diagnosis of a susceptibility to Type 2 diabetes, as well as in kits useful for such diagnosis.

An "isolated" nucleic acid molecule, as used herein, is one that is separated from 5 nucleic acids that normally flank the gene or nucleotide sequence (as in genomic sequences) and/or has been completely or partially purified from other transcribed sequences (e.g., as in an RNA library). For example, an isolated nucleic acid of the invention can be substantially isolated with respect to the complex cellular milieu in which it naturally occurs, or culture medium when produced by recombinant techniques, or 10 chemical precursors or other chemicals when chemically synthesized. In some instances, the isolated material will form part of a composition (for example, a crude extract containing other substances), buffer system or reagent mix. In other circumstances, the material can be purified to essential homogeneity, for example as determined by polyacrylamide gel electrophoresis (PAGE) or column chromatography (e.g., HPLC). An 15 isolated nucleic acid molecule of the invention can comprise at least about 50%, at least about 80% or at least about 90% (on a molar basis) of all macromolecular species present. With regard to genomic DNA, the term "isolated" also can refer to nucleic acid molecules that are separated from the chromosome with which the genomic DNA is naturally associated. For example, the isolated nucleic acid molecule can contain less than 20 about 250 kb, 200 kb, 150 kb, 100 kb, 75 kb, 50 kb, 25 kb, 10 kb, 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb of the nucleotides that flank the nucleic acid molecule in the genomic DNA of the cell from which the nucleic acid molecule is derived.

The nucleic acid molecule can be fused to other coding or regulatory sequences and still be considered isolated. Thus, recombinant DNA contained in a vector is included 25 in the definition of "isolated" as used herein. Also, isolated nucleic acid molecules include recombinant DNA molecules in heterologous host cells or heterologous organisms, as well as partially or substantially purified DNA molecules in solution. "Isolated" nucleic acid molecules also encompass in vivo and in vitro RNA transcripts of the DNA molecules of the present invention. An isolated nucleic acid molecule or nucleotide sequence can include a 30 nucleic acid molecule or nucleotide sequence that is synthesized chemically or by recombinant means. Such isolated nucleotide sequences are useful, for example, in the manufacture of the encoded polypeptide, as probes for isolating homologous sequences (e.g., from other mammalian species), for gene mapping (e.g., by in situ hybridization with chromosomes), or for detecting expression of the gene in tissue (e.g., human 35 tissue), such as by Northern blot analysis or other hybridization techniques.

The invention also pertains to nucleic acid molecules that hybridize under high stringency hybridization conditions, such as for selective hybridization, to a nucleotide WO 2008/065682 PCT/IS2007/000020 70 sequence described herein (e.g., nucleic acid molecules that specifically hybridize to a nucleotide sequence containing a polymorphic site associated with a haplotype described herein). In one embodiment, the invention includes variants that hybridize under high stringency hybridization and wash conditions (e.g., for selective hybridization) to a 5 nucleotide sequence that comprises the nucleotide sequence of LD Block C06 (SEQ ID NO:l), LD Block CIO (SEQ ID NO:2; e.g., the nucleotide sequence encoding the IDE, KIFll and/or the HHEX genes) and LD Block C17 (SEQ ID NO:3), or the CDKALl gene or a fragment thereof (or a nucleotide sequence comprising the complement of the nucleotide sequence of LD Block C06 (SEQ ID NO:l), LD Block CIO (SEQ ID NO:2; e.g., 10 the nucleotide sequence encoding the IDE, KIFll and/or the HHEX genes) and LD Block C17 (SEQ ID NO:3), or the CDKALl gene or a fragment thereof), wherein the nucleotide sequence comprises at least one polymorphic allele contained in the haplotypes (e.g., haplotypes) described herein.

Such nucleic acid molecules can be detected and/or isolated by allele- or 15 . sequence-specific hybridization (e.g., under high stringency conditions). Stringency conditions and methods for nucleic acid hybridizations are explained on pages 2.10.1-2.10.16 and pages 6.3.1-6.3.6 in Current Protocols in Molecular Biology (Ausubel, F. et al., "Current Protocols in Molecular Biology", John Wiley & Sons, (1998)), and Kraus, M. and Aaronson, S., Methods Enzymol., 200:546-556 (1991), the entire teachings of which 20 are incorporated by reference herein.

The percent identity of two nucleotide or amino acid sequences can be determined by aligning the sequences for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first sequence). The nucleotides or amino acids at corresponding positions are then compared, and the percent identity between the two sequences is a 25 function of the number of identical positions shared by the sequences (i.e., % identity = # of identical positions/total # of positions x 100). In certain embodiments, the length of a sequence aligned for comparison purposes is at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%, of the length of the reference sequence. The actual comparison of the two sequences can be 30 accomplished by well-known methods, for example, using a mathematical algorithm. A non-limiting example of such a mathematical algorithm is described in Karlin, S. and Altschul, S., Proc. Natl. Acad. Sci. USA, 90:5873-5877 (1993). Such an algorithm is incorporated into the NBLAST and XBLAST programs (version 2.0), as described in Altschul, S. et al., Nucleic Acids Res., 25:3389-3402 (1997). When utilizing BLAST and 35 Gapped BLAST programs, the default parameters of the respective programs (e.g., NBLAST) can be used. See the website on the world wide web at ncbi.nlm.nih.gov. In one embodiment, parameters for sequence comparison can be set at score=100, wordlength = 12, or can be varied (e.g., W=5 or W=20).

WO 2008/065682 PCT/IS2007/000020 71 Other examples include the algorithm of Myers and Miller, CABIOS (1989), ADVANCE and ADAM as described in Torellis, A. and Robotti, C., Comput. Appl. Biosci. 10:3-5 (1994); and FASTA described in Pearson, W. and Lipman, D., Proc. Natl. Acad. Sci. USA, 85:2444-48 (1988). In another embodiment, the percent identity between two 5 amino acid sequences can be accomplished using the GAP program in the GCG software package (Accelrys, Cambridge, UK).

The present invention also provides isolated nucleic acid molecules that contain a fragment or portion that hybridizes under highly stringent conditions to a nucleic acid that comprises, or consists of, the nucleotide sequence of LD Block C06 (SEQ ID NO:l), LD 10 Block CIO (SEQ ID NO:2; e.g., the nucleotide sequence encoding the IDE, KIFll and/or the HHEX genes) and LD Block C17 (SEQ ID NO: 3), or the CDKALl gene or a fragment thereof (or a nucleotide sequence comprising, or consisting of, the complement of the nucleotide sequence of LD Block C06 (SEQ ID NO:l), LD Block CIO (SEQ ID NO:2; e.g., the nucleotide sequence encoding the IDE, KIFll and/or the HHEX genes)and LD Block 15 C17 (SEQ ID NO:3), or the CDKALl gene or a fragment thereof), wherein the nucleotide sequence comprises at least one polymorphic allele contained in the haplotypes (e.g., haplotypes) described herein. The nucleic acid fragments of the invention are at least about 15, at least about 18, 20, 23 or 25 nucleotides, and can be 30, 40, 50, 100, 200, 500, 1000, 10,000 or more nucleotides in length.

The nucleic acid fragments of the invention are used as probes or primers in assays such as those described herein. "Probes" or "primers" are oligonucleotides that hybridize in a base-specific manner to a complementary strand of a nucleic acid molecule.

In addition to DNA and RNA, such probes and primers include polypeptide nucleic acids (PNA), as described in Nielsen, P. et al., Science 254:1497-1500 (1991). A probe or primer comprises a region of nucleotide sequence that hybridizes to at least about 15, typically about 20-25, and in certain embodiments about 40, 50 or 75, consecutive nucleotides of a nucleic acid molecule. In one embodiment, the probe or primer comprises at least one allele of at least one polymorphic marker or at least one haplotype described herein, or the complement thereof. In particular embodiments, a probe or primer can comprise 100 or fewer nucleotides; for example, in certain embodiments from 6 to 50 nucleotides, or, for example, from 12 to 30 nucleotides. In other embodiments, the probe or primer is at least 70% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical, to the contiguous nucleotide sequence or to the complement of the contiguous nucleotide sequence. In another embodiment, the probe or primer is capable of selectively hybridizing to the contiguous nucleotide sequence or to the complement of the contiguous nucleotide sequence. Often, the probe or primer further comprises a label, e.g., a radioisotope, a fluorescent label, an enzyme label, an enzyme co-factor label, a magnetic label, a spin label, an epitope label.

WO 2008/065682 PCT/IS2007/000020 72 The nucleic acid molecules of the invention, such as those described above, can be identified and isolated using standard molecular biology techniques well known to the skilled person. The amplified DNA can be labeled (e.g., radiolabeled) and used as a probe for screening a cDNA library derived from human cells. The cDNA can be derived from 5 mRNA and contained in a suitable vector. Corresponding clones can be isolated, DNA can obtained following In vivo excision, and the cloned insert can be sequenced in either or both orientations by art-recognized methods to identify the correct reading frame encoding a polypeptide of the appropriate molecular weight. Using these or similar methods, the polypeptide and the DNA encoding the polypeptide can be isolated, 10 sequenced and further characterized.

In general, the isolated nucleic acid sequences of the invention can be used as molecular weight markers on Southern gels, and as chromosome markers that are labeled to map related gene positions. The nucleic acid sequences can also be used to compare with endogenous DNA sequences in patients to identify Type 2 diabetes or a susceptibility 15 to Type 2 diabetes, and as probes, such as to hybridize and discover related DNA sequences or to subtract out known sequences from a sample (e.g., subtractive hybridization). The nucleic acid sequences can further be used to derive primers for genetic fingerprinting, to raise anti-polypeptide antibodies using immunization techniques, and/or as an antigen to raise anti-DNA antibodies or elicit immune responses.

Antibodies Polyclonal antibodies and/or monoclonal antibodies that specifically bind one form of the gene product but not to the other form of the gene product are also provided. Antibodies are also provided which bind a portion of either the variant or the reference 25 gene product that contains the polymorphic site or sites. The term "antibody" as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain antigen-binding sites that specifically bind an antigen. A molecule that specifically binds to a polypeptide of the invention is a molecule that binds to that polypeptide or a fragment thereof, but does not 30 substantially bind other molecules in a sample, e.g., a biological sample, which naturally contains the polypeptide. Examples of immunologically active portions of immunoglobulin molecules include F(ab) and F(ab')2 fragments which can be generated by treating the antibody with an enzyme such as pepsin. The invention provides polyclonal and monoclonal antibodies that bind to a polypeptide of the invention. The term "monoclonal 35 antibody" or "monoclonal antibody composition", as used herein, refers to a population of antibody molecules that contain only one species of an antigen binding site capable of immunoreacting with a particular epitope of a polypeptide of the invention. A monoclonal WO 2008/065682 PCT/IS2007/000020 73 antibody composition thus typically displays a single binding affinity for a particular polypeptide of the invention with which it immunoreacts.

Polyclonal antibodies can be prepared as described above by immunizing a suitable subject with a desired immunogen, e.g., polypeptide of the invention or a 5 fragment thereof. The antibody titer in the immunized subject can be monitored over time by standard techniques, such as with an enzyme linked immunosorbent assay (ELISA) using immobilized polypeptide. If desired, the antibody molecules directed against the polypeptide can be isolated from the mammal (e.g., from the blood) and further purified by well-known techniques, such as protein A chromatography to obtain 10 the IgG fraction. At an appropriate time after immunization, e.g., when the antibody titers are highest, antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as the hybridoma technique originally described by Kohler and Milstein, Nature 256:495-497 (1975), the human B cell hybridoma technique (Kozbor et al., Immunol. Today 4: 72 (1983)), the EBV-hybridoma 15 technique (Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss,1985, Inc., pp. 77-96) or trioma techniques. The technology for producing hybridomas is well known (see generally Current Protocols in Immunology (1994) Coligan et al., (eds.) John Wiley & Sons, Inc., New York, NY). Briefly, an immortal cell line (typically a myeloma) is fused to lymphocytes (typically splenocytes) from a mammal immunized with an immunogen as 20 described above, and the culture supernatants of the resulting hybridoma cells are screened to identify a hybridoma producing a monoclonal antibody that binds a polypeptide of the invention.

Any of the many well known protocols used for fusing lymphocytes and immortalized cell lines can be applied for the purpose of generating a monoclonal antibody 25 to a polypeptide of the invention (see, e.g., Current Protocols in Immunology, supra; Galfre eta/., Nature 266:55052 (1977); R.H. Kenneth, in Monoclonal Antibodies: A New Dimension In Biological Analyses, Plenum Publishing Corp., New York, New York (1980); and Lemer, Yale J. Biol. Med. 54:387-402 (1981)). Moreover, the ordinarily skilled worker will appreciate that there are many variations of such methods that also would be 30 useful.

Alternative to preparing monoclonal antibody-secreting hybridomas, a monoclonal antibody to a polypeptide of the invention can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with the polypeptide to thereby isolate immunoglobulin library members that bind 35 the polypeptide. Kits for generating and screening phage display libraries are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene Su/fZAP™ Phage Display Kit, Catalog No. 240612). Additionally, examples of methods and reagents particularly amenable for use WO 2008/065682 PCT/IS2007/000020 74 in generating and screening antibody display library can be found in, for example, U.S. Patent No. 5,223,409; PCT Publication No. WO 92/18619; PCT Publication No. WO 91/17271; PCT Publication No. WO 92/20791; PCT Publication No. WO 92/15679; PCT Publication No. WO 93/01288; PCT Publication No. WO 92/01047; PCT Publication No. WO 5 92/09690; PCT Publication No. WO 90/02809; Fuchs etal., Bio/Technology 9: 1370-1372 (1991); Hay etal., Hum. Antibod. Hybridomas 3:81-85 (1992); Huse et al., Science 246: 1275-1281 (1989); and Griffiths et al., EMBO J. 12:725-734 (1993).

Additionally, recombinant antibodies, such as chimeric and humanized monoclonal antibodies, comprising both human and non-human portions, which can be made using 10 standard recombinant DNA techniques, are within the scope of the invention. Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art.

In general, antibodies (e.g., a monoclonal antibody) can be used to isolate a polypeptide of the invention by standard techniques, such as affinity chromatography or 15 immunoprecipitation. A polypeptide-specific antibody can facilitate the purification of natural polypeptide from cells and of recombinantly produced polypeptide expressed in host cells. Moreover, an antibody specific for a polypeptide of the invention can be used to detect the polypeptide (e.g., in a cellular lysate, cell supernatant, or tissue sample) in order to evaluate the abundance and pattern of expression of the polypeptide. Antibodies 20 can be used diagnostically to monitor protein levels in tissue as part of a clinical testing procedure, e.g., to, for example, determine the efficacy of a given treatment regimen. The antibody can be coupled to a detectable substance to facilitate its detection.

Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, biolumihescent materials, and radioactive 25 materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-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 30 example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include 125I, 131I, 35S or 3H.

Antibodies may also be useful in pharmacogenomic analysis. In such embodiments, antibodies against variant proteins encoded by nucleic acids as described 35 herein, such as variant proteins that are encoded by nucleic acids that contain at least one polymorpic marker of the invention, can be used to identify individuals that require modified treatment modalities.

WO 2008/065682 PCT/IS2007/000020 75 Antibodies can furthermore be useful for assessing expression of variant proteins in disease states, such as in active stages of Type 2 diabetes, or in an individual with a predisposition to Type 2 diabetes that is related to the function of the protein. Antibodies specific for a variant protein of the present invention that is encoded by a nucleic acid that 5 comprises at least one polymorphic marker or haplotype as described herein can be used to screen for the presence of the variant protein, for example to screen for a predisposition to Type 2 diabetes as indicated by the presence of the variant protein.

Antibodies can be used in other methods. Thus, antibodies are useful as diagnostic tools for evaluating proteins, such as variant proteins of the invention, in 10 conjunction with analysis by electrophoretic mobility, isoelectric point, tryptic or other protease digest, or for use in other physical assays known to those skilled in the art. Antibodies may also be used in tissue typing. In one such embodiment, a specific variant protein has been correlated with expression in a specific tissue type, and antibodies specific for the variant protein can then be used to identify the specific tissue type.

Subcellular localization of proteins, including variant proteins, can also be determined using antibodies, and can be applied to assess aberrant subcellular localization of the protein in cells in various tissues. Such use can be applied in genetic testing, but also in monitoring a particular treatment modality. In the case where treatment is aimed at correcting the expression level or presence of the variant protein or 20 aberrant tissue distribution or developmental expression of the variant protein, antibodies specific for the variant protein or fragments thereof can be used to monitor therapeutic efficacy.

Antibodies are further useful for inhibiting variant protein function, for example by blocking the binding of a variant protein to a binding molecule or partner. Such uses can 25 also be applied in a therapeutic context in which treatment involves inhibiting a variant protein's function. An antibody can be for example be used to block or competitively inhibit binding, thereby modulating (i.e., agonizing or antagonizing) the activity of the protein. Antibodies can be prepared against specific protein fragments containing sites required for specific function or against an intact protein that is associated with a cell or 30 cell membrane. For administration in vivo, an antibody may be linked with an additional therapeutic payload, such as radionuclide, an enzyme, an immunogenic epitope, or a cytotoxic agent, including bacterial toxins (diphtheria or plant toxins, such as ricin). The in vivo half-life of an antibody or a fragment thereof may be increased by pegylation through conjugation to polyethylene glycol.

The present invention will now be exemplified by the following non-limiting examples.

EXEMPLIFICATION 76 EXAMPLE 1 The following contains description of the identifiction of susceptibility factors found to be associated with Type 2 diabetes through single-point and haplotype analysis of SNP markers.

METHODS Icelandic cohort The Data Protection Authority of Iceland and the National Bioethics Committee of Iceland approved the study. All participants in the study gave informed consent. All personal identifiers associated with blood samples, medical information and genealogy were first encrypted by the Data Protection Authority, using a third-party encryption system. 15 For this study, 2400 Type 2 diabetes patients were identified who were diagnosed either through a long-term epidemiologic study done at the Icelandic Heart Association over the past 30 years or at one of two major hospitals in Reykjavik over the past 12 years. Two-thirds of these patients were alive, representing about half of the population of known Type 2 diabetes patients in Iceland today. The majority of these patients were contacted for this 20 study, and the cooperation rate exceeded 80%. All participants in the study visited the Icelandic Heart Association where they answered a questionnaire, had blood drawn and a fasting plasma glucose measurements taken. Questions about medication and age at diagnosis were included. The Type 2 diabetes patients in this study were diagnosed as described in our previously published linkage study (Reynisdottir et al., Am J Hum Genet 73, 25 323 (2003). In brief, the diagnosis of Type 2 diabetes was confirmed by study physicians through previous medical records, medication history, and/or new laboratory measurements. For previously diagnosed Type 2 diabetes patients, reporting of the use of oral glucose-lowering agent confirmed Type 2 diabetes. Individuals who were currently treated with insulin were classified as having Type 2 diabetes if they were also using or had previously used oral 30 glucose-lowering agents. In this cohort the majority of patients on medication take oral glucose-lowering agents and only a small portion (9%) require insulin. For hitherto undiagnosed individuals, the diagnosis of Type 2 diabetes and impaired fasting glucose (IFG) was based on the criteria set by the American Diabetes Association (Expert Committee on the Diagnosis and Classification of Diabetes Mellitus 1997). The average age of the Type 2 35 diabetes patients in this study was 69.7 years.

WO 2008/065682 PCT/IS2007/000020 77 Replication cohorts The Danish study group was a set of Type 2 diabetes patients from the Steno Diabetes Center in Copenhagen (N = 1,018) and from the Inter99 population-based sample of 30-60 year old individuals living in the greater Copenhagen area and sampled at 5 Research Centre for Prevention and Health28 (N = 359). Diabetes and pre-diabetes categories were diagnosed according to the 1999 World Health Organization (WHO) criteria. An effectively random subset (N=2,400) of Danish controls with BMI measurements were obtained from the Inter99 collection. Informed written consent was obtained from all subjects before participation. The study was approved by the Ethical 10 Committee of Copenhagen County and was in accordance with the principles of the Helsinki Declaration.

The PENN CATH study in the US is a cross sectional study of the association of biochemical and genetic factors with coronary atherosclerosis in a consecutive cohort of patients undergoing cardiac catheterization at the University of Pennsylvania Medical 15 Center between July 1998 and March 2003. Type 2 diabetes was defined as history of fasting blood glucose >126mg/dl, 2-hour post-prandial glucose >200mg/dl, use of oral hypoglycemic agents, or insulin and oral hypoglycemic in a subject greater than age 40. The University of Pennsylvania Institutional Review Board approved the study protocol and all subjects gave written informed consent. Ethnicity was determined through self-20 report. A total of 468 Caucasian Type 2 diabetes cases were derived from this cohort. Additionally, 1024 unaffected (with respect to Type 2 diabetes) Caucasian controls were randomly drawn from the same study.

The DNA used for genotyping was the product of whole-genome amplification, by use of the GenomiPhi Amplification kit (Amersham), of DNA isolated from the peripheral 25 blood of the Danish and US Type 2 diabetes patients and controls.

Genotyping A genome-wide scan of 1399 Icelandic diabetes patients was performed using Infinium HumanHap300 SNP chips from Illumina for assaying approximately 317,000 30 single nucleotide polymorphisms (SNPs) on a single chip (Illumina, San Diego, CA, USA). SNP genotyping for replication in other case-control cohorts was carried using the Centaurus platform (Nanogen).

Statistical Methods for Association Analysis For single marker association to Type 2 diabetes, we used a likelihood ratio test to calculate a two-sided p-value for each allele. We calculated relative risk (RR) and population attributable risk (PAR) assuming a multiplicative model (C. T. Falk, P. Rubinstein, Ann Hum Genet 51 (Pt 3), 227 (1987); J. D. Terwilliger, J. Ott, Hum Hered 42, 337 (1992)). For the CEPH Caucasian HapMap data, we calculated LD between pairs 40 of SNPs using the standard definition of D' (R. C. Lewontin, Genetics 50, 757 (1964)) and WO 2008/065682 PCT/IS2007/000020 78 R2 W. G. Hill, A. Robertson, Genetics 60, 615 (Nov, 1968). When plotting all SNP combinations to elucidate the LD structure in a particular region, we plotted D' in the upper left corner and p-values in the lower right corner. In the LD plots we present, the markers are plotted equidistantly rather than according to their physical positions.

RESULTS Genome-wide association study We successfully genotyped 1399 Icelandic Type 2 diabetes patients and 5275 10 population control individuals using the Illumina 330K chip. Association analysis was performed using single SNPs, two marker haplotypes and extended haplotypes within LD blocks. After correcting the p-value for relatedness we identified 49 single markers and two marker haplotypes at 21 loci (i.e. genetic susceptibility locations in the genome) that had a p-value less than 5xl0"5 (Table 1). In addition, 10 extended haplotypes at 8 15 additional loci were selected by the same criteria (Table 2). Within the patient group, 700 individuals were non-obese (BMI<30) and those were tested separately for association. After correcting the p-value for relatedness, 36 single markers and two marker haplotypes at 20 loci had a p-value less than 5xl0"5 (Table 3). Three of those loci were also identified when the total group was analysed. In addition 6 extended haplotypes at 4 additional loci 20 were selected by the same criteria (Table 4). The obese group of 531 patients (BMI >30) was also analysed separately for association. After correcting the p-value for relatedness 38 single markers and two marker haplotypes at 16 loci had a p-value less than 5xl0"5 (Table 5). One of those loci was also identified when the total group was analysed but no overlap was found between the non-obese and obese groups using this criteria. In 25 addition 10 extended haplotypes at 7 additional loci had a p-value less than 5xl0"5 in association analysis of obese diabetics (Table 6).

The single-marker association and two-marker and extended haplotype association analysis presented in Tables 1-6 thus represents evidence for multiple susceptibility variants for Type 2 diabetes. It should be noted that for single-marker SNP analysis as 30 presented herein, susceptibility variants can either be represented by increased risk, wherein one allele is overrepresented in the patient group compared with controls. Alternatively, the susceptibility variants can be represented by the other allele of the SNP in question - for that allele, under-representation in patients compared with controls is expected. This is a natural consequence of association analysis to genetic elements 35 comprising two alleles. For multi-marker haplotypes or for polymorphic markers comprising more than one marker, at-risk association may be observed to one (or more) at-risk allele or haplotype. Protective variants in form of association (with RR-values less than unity) to one (or more) protective variants or haplotypes may also be observed, depending on the genetic composition and haplotype structure in the genetic region in 40 question.

Table 1. Single markers and two marker haplotypes associated with Type 2 Diabetes. Associating alleles are indicated in front of each marker (Allelic code: A=l, C=2, G=3, T=4) Chr Pos Punadj Padj Rrisk Aff.frq Ctrl.frq Haplotype chrl 151511890 4.01 E-06 4.49E-05 1.223 0.407 0.360 3 rs3738028 chr2 40560735 2.41 E-06 3.06E-05 1.225 0.593 0.543 1 rs13414307 chr2 40560735 4.59E-07 8.27E-06 1.243 0.571 0.517 1 rs13414307 3 rs1990609 chr2 54969849 .53E-08 1.56E-06 1.287 0.335 0.281 3 rs930493 4 rs10173697 chr2 54977961 3.12E-06 3.75E-05 1.224 0.553 0.503 4 rs10173697 chr3 89323970 2.60E-06 3.25E-05 1.380 0.904 0.872 4 rs12486049 chr6 6965113 1.00E-06 1.53E-05 1.705 0.072 0.044 1 rs490213 3 rs814174 chr6 31556294 3.22 E-06 3.78E-05 1.232 0.372 0.325 2 rs2516424 chr6 31556294 1.93E-06 2.57E-05 1.240 0.368 0.320 2 rs2516424 2 rs4947324 chr6 132422361 3.10E-06 3.74E-05 1.262 0.278 0.234 3 rs9483377 2 rs997607 chr6 132422361 3.97E-06 4.54E-05 1.252 0.276 0.233 3 rs9483377 3 rs7745875 chr6 132422361 7.98E-07 1.25E-05 1.249 0.356 0.307 3 rs9483377 chr6 150460378 .01 E-07 8.86E-06 1.293 0.794 0.749 1 rs11155700 chr6 150461077 .15E-07 9.05E-06 1.292 0.794 0.749 2 rs12213837 chr6 164474219 3.07E-06 3.63E-05 0.813 0.479 0.531 4 rs206732 2 rs933251 chr7 87951463 4.36E-06 4.89E-05 1.273 0.753 0.705 1 rs2192319 chr8 124196776 1.21 E-06 1.78E-05 1.253 0.721 0.673 3 rs952656 chr8 124202699 .97E-07 9.96E-06 0.722 0.108 0.143 4 rs13252935 3 rs7824293 chr9 90164936 2.03E-06 2.62E-05 1.304 0.192 0.154 1 rs10993008 chr9 95493692 2.38E-06 3.03E-05 1.253 0.309 0.263 3 rs10990568 3 rs4743148 chr9 95510129 .85E-07 9.80E-06 1.252 0.365 0.315 3 rs4743148 chr10 53058229 1.39E-06 1.98E-05 1.240 0.377 0.328 4 rs7915186 4 rs3829170 chr10 53063104 1.37E-06 1.96E-05 1.239 0.386 0.336 4 rs3829170 3 rs7922112 chr10 94301795 2.54E-08 8.44E-07 1.276 0.614 0.555 3 rs2421943 chr10 94301795 2.11E-09 1.19E-07 1.297 0.585 0.521 3 rs2421943 2 rs7917359 chr10 94304784 1.49E-07 3.32E-06 0.797 0.443 0.499 3 rs7908111 3 rs2497304 chr10 94309972 6.60E-09 2.85E-07 0.779 0.455 0.517 3 rs1999763 4 rs10882091 chr10 94309972 6.60E-09 2.85E-07 0.779 0.455 0.517 . 3 rs1999763 3 rs6583830 chr10 94337810 1.36E-06 1.91E-05 1.228 0.518 0.467 3 rs6583826 chr10 94337810 7.18E-08 1.91 E-06 1.262 0.449 0.393 3 rs6583826 2 rs10882091 chr10 94364357 7.76E-08 2.04E-06 1.259 0.466 0.410 2 rs10882091 3 rs7923837 chr10 94364357 9.33E-08 2.30E-06 1.256 0.472 0.415 2 rs10882091 chr10 94372930 9.81 E-08 2.40E-06 1.256 0.472 0.415 4 rs7914814 chr10 94388098 9.33E-08 2.30E-06 1.256 0.472 0.415 1 rs6583830 chr10 94442410 8.41 E-08 2.17E-06 1.256 0.527 0.470 1 rs2275729 3 rs1111875 chr10 94482696 7.56E-08 1.95E-06 1.258 0.542 0.485 1 rs2497304 chr10 94485733 1.64E-06 2.21 E-05 1.225 0.526 0.475 1 rs947591 chr12 33373479 3.87E-06 4.37E-05 1.391 0.110 0.082 4 rs1905421 chr15 98156854 3.80E-06 4.30E-05 0.815 0.469 0.521 1 rs9920347 3 rs11635811 chr16 22705353 2.93E-06 3.57E-05 1.264 0.781 0.738 4 rs724466 chr16 72066252 4.23E-06 4.68E-05 0.625 0.038 0.059 2 rs1862773 4 rs825842 chr16 72086481 .86E-07 9.82E-06 0.612 0.043 0.069 4 rs2432543 3 rs4887826 chr17 66072384 7.34E-07 1.20E-05 1.236 " 0.564 0.511 3 rs17763769 1 rs1860316 chr17 66117911 1.18E-07 2.77E-06 0.781 0.282 0.335 3 rs1860316 2 rs17763811 chr17 66117911 6.79E-08 1.83E-06 1.281 0.707 0.653 1 rs1860316 chr17 66132788 chr17 66149102 chr17 66159416 chr20 36391335 1.80E-06 2.43E-05 1.39E-06 1.99E-05 7.32E-07 1.19E-05 2.09E-07 4.45E-06 1.226 0.563 1.239 0.665 1.266 0.744 1.250 0.550 0.513 2 rs1981647 0.615 4 rs1843622 0.696 1 rs2191113 0.495 3 rs4592915 2 rs2232580 Table 2. Multi - marker haplotypes associated with Type 2 Diabetes. Chr Pos Punadj Padj Rrisk Aff.frq Ctrl.frq Haplotype* Chr2 19652497 2.00E-08 6.98E-07 2.492 0.027 0.011 3 rs1593746 3 rs4666491 3 re12710718 4 rs1579204 1 rs824506 2 rs1344652 1 rs4109456 3 rs1427547 2 rs1522490 1 rs6757410 4 rs1863776 Chr2 74747736 1.95E-06 2.59E-05 1.903 0.036 0.019 2 rs363674 2 rs759075 1 rs4853033 1 rs205651 4 rs363608 1 rs1063588 2 rs363612 1 rs150139 2 rs363617 4 rs1137 4 rs828902 1 rs205627 chr9 29300367 5.32E-07 9.29E-06 1.813 0.042 0.024 1 rs4879332 2 rs1928663 4 rs2183357 2 rs10813050 2 rs1928661 4 rs10491662 2 rs1169758 2 rs1169757 3 rs12378755 chr9 32290296 4.13E-06 4.68E-05 1.489 0.075 0.052 3 rs1537156 2 rs7024902 4 rs7037573 4 rs3928808 4 rs10970902 3 rs1331226 3 rs10758127 1 rs1331231 1 rs992710 2 rs1411866 3 rs10511901 3 rs2094703 1 rs7854942 4 rs2150637 Chr11 22912998 7.25E-07 1.19E-05 1.687 0.059 0.036 3 rs11026796 1 rs1019216 2 rs2302423 4 rs4923035 1 rs2429777 4 rs12575930 3 rs887567 2 rs733295 3 rs7113718 1 rs7934814 4 rs3909703 4 rs3862134 3 rs10833917 1 rs6483890 2 rs2433454 chr13 60726830 1.52E-06 2.12E-05 1.481 0.108 0.075 4 rs1411145 4 rs9539100 3 rs991666 3 rs1026924 3 rs4886330 3 rs1411568 3 rs1028965 1 rs9670441 chr16 72082296 1.71 E-06 2.29E-05 0.595 0.033 0.054 4 rs1424011 2 rs1862778 1 rs4888373 4 rs8053178 4 rs825842 4 rs2432543 2 rs6564272 3 rs4887826 3 rs825851 chr17 66118095 3.46E-08 1.05E-06 0.762 0.229 0.281 2 rs16913 2 rs10512540 3 rs17763769 1 rs2109051 3 rs1860316 3 rs9904090 4 rs1981647 2 rs1843622 2 rs4584866 3 rs17791650 3 rs9891997 3 rs2191113 Chr18 67477090 1.12E-06 1.64E-05 0.547 0.033 0.059 2 rs9956771 4 rs8088887 2 rs10514019 4 rs719328 4 rs1942399 2 rs1942396 4 rs948665 3 rs11151691 chrX 56884473 4.32E-06 4.85E-05 1.184 0.709 0.673 1 rs12858633 1 rs5960235 3 rs5914036 3 rs6612746 * Associating alleles are indicated in front of each marker (Allelic code: A=l, C=2, G=3, T=4) 82 Table 3. Single markers and two marker haplotypes associated with Type 2 Diabetes in non-obese patients Chr Pos Punadj Padj Rrisk Aff.frq Ctrl.frq Haplotype* chrl 29759353 .23E-06 3.18E-05 0.661 0.104 0.149 4 rs4949283 2 rs502545 chr2 53360168 8.51 E-06 4.70E-05 1.411 0.855 0.807 1 rs1424963 chr5 87772535 1.95E-06 1.36E-05 1.394 0.244 0.188 3 rs10505855 2 rs12514611 chr6 6965113 .76E-06 3.39E-05 1.891 0.080 0.044 1 rs490213 3 rs814174 chr6 20650200 8.46E-06 4.68E-05 1.327 0.307 0.250 3 rs7758851 2 rs1569699 chr6 20771314 1.06E-06 8.14E-06 1.369 0.292 0.232 1 rs4712527 3 rs7756992 chr6 20787289 4.47E-06 2.79E-05 1.333 0.315 0.256 2 rs1569699 chr6 20787688 1.78E-06 1.28E-05 0.741 0.682 0.743 1 rs7756992 3 rs9295478 chr6 20787688 1.11 E-06 8.61 E-06 1.368 0.292 0.232 3 rs7756992 chr9 95447272 6.08E-06 3.61 E-05 0.764 0.469 0.536 2 rs10818991 2 rs10990303 chr11 23939149 3.05E-06 2.02E-05 1.525 0.128 0.088 4 rs1879230 chr11 130184827 9.00E-06 4.93E-05 1.303 0.416 0.353 4 rs11222327 1 rs1939905 chr13 26578564 2.15E-06 1.51 E-05 0.723 0.220 0.281 1 rs565707 1 rs6491198 chr13 26578564 8.29E-07 6.63E-06 1.381 0.763 0.700 2 rs565707 chr13 26635031 3.14E-06 2.03E-05 1.309 0.606 0.540 2 rs7984685 chr13 26637643 3.37E-06 2.15E-05 1.308 0.606 0.540 2 rs7998347 chr13 26801814 9.09E-06 4.97E-05 1.340 0.771 0.716 1 rs1333350 chr13 26801814 1.29E-06 9.76E-06 0.709 0.195 0.254 3 rs1333350 4 rs7987436 chr13 108034018 9.08E-06 4.97E-05 1.322 0.732 0.674 2 rs4771591 chr16 12697094 8.10E-06 4.59E-05 0.616 0.068 0.105 2 rs6498353 3 rs9941146 chr17 66072384 2.10E-07 2.09E-06 1.347 0.585 0.511 3 rs17763769 1 rs1860316 chr17 66117911 1.01E-09 2.42E-08 0.677 0.254 0.335 3 rs1860316 2 rs17763811 chr17 66117911 1.20E-09 2.73E-08 1.462 0.734 0.653 1 rs1860316 chr17 66132788 7.18E-07 .88E-06 1.329 0.583 0.513 2 rs1981647 chr17 66149102 4.33E-07 3.84E-06 1.355 0.684 0.615 4 rs1843622 chr17 66159416 4.49E-09 8.28E-08 1.467 0.771 0.696 1 rs2191113 chr17 66173475 4.75E-06 2.88E-05 1.472 0.885 0.839 1 rs9890889 chr18 41053807 4.27E-06 2.68E-05 1.389 0.218 0.167 3 rs10502860 chr18 63441694 8.25E-06 4.66E-05 0.687 0.121 0.167 4 rs764133 4 rs7237209 chr18 63465082 4.35E-06 2.67E-05 1.443 0.867 0.819 2 rs7237209 chr19 3316583 7.55E-06 4.33E-05 1.370 0.227 0.176 1 rs3810420 chr20 36391335 8.38E-06 4.65E-05 1.292 0.558 0.495 3 rs4592915 2 rs2232580 chr21 13769165 3.83E-06 2.40E-05 1.599 0.927 0.888 1 rs468601 chr21 33298252 1.17E-06 9.03E-06 1.358 0.311 0.249 3 rs2834061 chr21 39374906 4.04E-06 2.51 E-05 1.308 0.631 0.566 4 rs369906 chr22 29580921 8.60E-06 4.75E-05 1.347 0.265 0.212 3 rs8142410 3 rs5994353 *Associating alleles are indicated in front of each marker (Allelic code: A=l, C=2, G=3, T=4) Table 4. Multi- marker haplotypes associated with Type 2 Diabetes in non-obese patients Chr Pos Punadj Padj Rrisk Aff.frq Ctrl.frq Haplotype* chr2 19652497 3.14E-07 2.93E-06 2.859 0.031 0.011 3 rs1593746 3 rs4666491 3 rs12710718 4 rs1579204 1 rs824506 2 rs1344652 1 rs4109456 3 rs1427547 2 rs1522490 1 rs6757410 4 rs1863776 chr5 2458281 6.12E-06 3.62E-05 0.077 0.001 0.017 3 rs931283 1 rs160730 3 rs468085 4 rs464716 3 rs10052956 2 rs160729 3 rs315914 1 rs1039096 chr6 137323498 6.46E-06 3.73E-05 2.566 0.040 0.016 2 rs6570118 4 rs7743308 3 rs6928748 2 rs12214917 2 rs6936698 2 rs4896224 2 rs10872468 chr11 32116221 4.15E-06. 2.57E-05 1.362 . 0.266 0.211 1 rs224633 3 rs581573 4 rs223070 4 rs10488686 4 rs4922579 2 rs110688 4 rs1605271 3 rs4922901 3 rs7950374 1 rs1033584 1 rs12788147 3 rs11031625 2 rs880587 4 rs989570 2 rs10835861 chr17 66118095 7.82E-10 1.95E-08 0.660 0.205 0.281 2 rs16913 2 rs10512540 3 rs17763769 1 rs2109051 3 rs1860316 3 rs9904090 4 rs1981647 2 rs1843622 2 rs4584866 3 rs17791650 3 rs9891997 3 rs2191113 chr17 66204022 6.39E-06 3.76E-05 0.683 0.115 0.160 2 rs9890889 4 rs2367005 2 rs2109054 3 rs17792120 1 rs7221340 4 rs1486293 2 rs1486296 2 rs17763811 4 rs9807096 3 rs10512541 3 rs8065001 2 rs4793501 3 rs929474 3 rs9907514 *Associating alleles are indicated in front of each marker (Allelic code: A=l, C=2, G=3, T=4) 84 Table 5. Single markers and two marker haplotypes associated with Type 2 Diabetes in obese patients Chr Pos Punadj Padj Rrisk Aff.frq Ctrl.frq Haplotype* chrl 104818519 .60E-06 2.85E-05 1.343 0.466 0.394 2 rs7553985 chrl 104824377 4.76E-06 2.48E-05 1.346 0.466 0.393 4 rs2166890 chrl 104825870 6.28E-06 3.14E-05 1.355 0.396 0.317 4 rs7552405 chr3 147025256 7.11 E-06 3.49E-05 1.696 0.097 0.059 3 rs7630694 chr3 197065940 2.81 E-06 1.58E-05 1.396 0.737 0.668 1 rs9858622 chr4 140287637 4.41 E-06 2.32E-05 1.431 0.804 0.741 1 rs13116075 1 rs6824182 chr4 140364285 1.05 E-05 4.86E-05 0.708 0.194 0.254 4 rs2292837 2 rs11725721 chr4 140397800 8.21 E-06 3.95E-05 0.704 0.194 0.254 3 rs3762864 2 rs11725721 chr5 76586085 9.46E-06 4.46E-05 0.750 0.438 0.510 1 rs832785 1 rs2859576 chr5 76586766 8.97E-06 4.26E-05 1.333 0.562 0.491 4 rS4704400 chrf> 9509965 7.50E-06 3.66E-05 1.335 0.495 0.424 4 rs214447 chr6 22837279 1.03E-05 4.80E-05 1.430 0.824 0.766 2 rs10498713 3 rs4426986 chr6 41191330 3.22E-06 1.77E-05 1.360 0.637 0.563 1 rs10456499 chr8 128358773 4.94E-06 2.56E-05 0.692 0.190 0.254 2 rs283710 2 rs412835 chr8 128362648 6.35E-07 4.42E-06 1.495 0.822 0.755 3 rs185852 chr8 128376264 1.57E-06 9.59E-06 0.680 0.189 0.255 2 rs283718 1 rs283720 chr9 126494483 2.67E-06 1.51 E-05 1.591 0.139 0.092 4 rs3814120 chr10 94301795 .53E-07 3.93E-06 1.393 0.602 0.521 3 rs2421943 2 rs7917359 chr10 94304784 8.39E-06 4.02E-05 0.747 0.427 0.499 3 rs7908111 3 rs2497304 chr10 94309972 3.74E-06 2.01 E-05 0.739 0.442 0.518 3 rs1999763 4 rs10882091 chr10 94309972 3.74E-06 2.01 E-05 0.739 0.442 0.518 3 rs1999763 3 rs6583830 chr10 94337810 1.89E-06 1.12E-05 1.364 0.469 0.393 3 rs6583826 2 rs10882091 chr10 94364357 1.76E-06 1.05E-05 1.363 0.486 0.410 2 rs10882091 3 rs7923837 chr10 94364357 2.58E-06 1.47E-05 1.355 0.491 0.415 2 rs10882091 chr10 94372930 2.66E-06 1.51 E-05 1.355 0.491 0.416 4 rs7914814 chr10 94388098 2.58E-06 1.47E-05 1.355 0.491 0.415 1 rs6583830 chr10 94482696 1.62E-06 9.85E-06 1.363 0.562 0.485 1 rs2497304 chr10 118562511 8.21 E-06 3.95E-05 1.384 0.302 0.238 4 rs1681748 4 rs2170862 chr10 118610986 9.43E-06 4.45E-05 1.367 0.320 0.256 4 rs2170862 chr10 118880683 3.29E-06 1.80E-05 1.379 0.347 0.278 3 rs10787760 chr11 106441899 8.79E-06 4.18E-05 1.533 0.142 0.097 4 rs1455593 chr12 30340321 4.54E-06 2.38E-05 0.723 0.296 0.368 1 rs1429622 3 rs1506382 chr14 81787150 3.94E-06 2.10E-05 1.363 0.439 0.365 1 rs799099 3 rs4899801 chr14 81843593 8.25E-06 3.97E-05 1.339 0.437 0.367 3 rs2066041 chr14 81899972 9.32E-06 4.40E-05 1.331 0.530 0.459 1 rs10483957 chr14 87823315 9.69E-07 6.35E-06 1.605 0.891 0.836 3 rs419028 chr16 24287484 6.15E-06 3.08E-05 1.388 0.372 0.300 1 rs11074618 2 rs985729 chr19 3065864 1.02 E-05 4.77E-05 1.433 0.825 0.767 3 rs3746069 *Associating alleles T=4) are indicated in front of each marker (Allelic code: A=l, C=2, G=3, Table 6. Multi- marker haplotypes associated with Type 2 Diabetes in obese patients ® o o 00 Chr Pos Punadj Padj Rrisk Aff.frq Ctrl.frq Haplotype* ® •j\ chr2 2591675 4.35E-06 2.29E-05 0.654 0.126 0.181 S 4 rs7576292 4 rs6548079 4 rs1451199 1 rs2385306 2 rs1020530 1 rs12714359 2 rs7556672 3 rs1451198 chr4 112032007 7.13E-06 3.50E-05 1.699 0.097 0.060 2 rsl 6997168 4 rs2723316 1 rs6419178 3 rs1448817 3 rs2634073 2 rs2200733 2 rs2220427 2 rsl 3105878 3 rsl 0033464 Chr8 128361033 7.34E-07 5.01E-06 0.671 0.178 0.244 3 rs283709 2 rs283710 2 rs4871780 1 rsl 85852 2 rs412835 Chr10 68829632 4.50E-06 2.36E-05 2.428 0.039 0.017 4 rs7094426 1 rs1904614 3 rs10823028 3 rs2620924 1 rs12359451 2 rs11815372 3 rs7083570 3 rs2394375 2 rs1875151 4 rs10823057 4 rs6480272 3 rs1911356 chr11 106076550 9.88E-06 4.63E-05 0.655 0.114 0.164 3 rs1791587 3 rsl 793083 2 rs1791597 4 rs7104111 2 rsl 793064 1 rs4523664 2 rs623018 4 rs631214 3 rs602159 2 rsl 0890568 2 rs4553343 4 rsl 487906 3 rs4.121676 1 rs4121677 4 rs6588924 Chr13 94045239 4.93E-06 2.55E-05 0.058 0.001 0.012 1 rs726298 2 rs7339106 1 rs9556403 2 rs9590039 2 rs6492722 1 rs1572935 3 rs6492725 ,J' chr14 81810554 9.82E-07 6.42E-06 1.408 0.341 0.269 4 rs9323719 2 rs7143860 3 rs709900 2 rs10135954 1 rs799103 1 rs799099 3 rs8018202 4 rs709915 3 rs709918 3 rs2066041 1 rs1457990 3 rs4899801 1 rs10483957 chr15 63410029 6.68E-06 3.31 E-05 2.395 0.047 0.020 4 rs2019185 2 rs920688 1 rs894494 3 rs665287 1 rs626163 2 rs639812 2 rs894491 1 rs581427 4 rs603439 1 rs678113 2 rs602192 3 rs7182756 1 rs2280345 3 rs11071841 1 rs2277582 chr15 95944049 4.24E-06 2.25E-05 0.593 0.079 0.127 2 rs8029926 4 rs649034 4 rs2036348 chr18 38114511 4.94E-06 2.56E-05 0.555 0.055 0.094 4 rs9304267 3 rs3763494 1 rs882291 2 rs898785 3 rsl 1082268 4 rs8088748 2 rsl 0502781 3 rs717127 chr20 45233401 3.10E-06 1.71 E-05 1.397 0.322 0.254 1 rs6063073 4 rs6066209 3 rs2018876 2 rs3092781 4 rs6122563 3 rs8126262 1 rs6063083 3 rs6018337 4 rs7262634 pS *Associating alleles are indicated in front of each marker (Allelic code: A=l, C=2, G=3, T=4) H in o o © o o o In) O 86 Chromosome 6d22.3 locus One of the most significant association signals for non-obese diabetic patients was identified by two single markers (rsl569699 and rs7756992) and two 2 marker haplotypes mapping to chromosome 6p22.3 (Table 3). These markers are located within one LD block at position 20634996-20836710 bases (NCBI Build 35) between markers rs4429936 and rs6908425 (SEQ ID NO:l; Figure 1). This LD block contains the 5' end including exons 1-5 of the gene CDK5 regulatory subunit associated protein 1-like 1 (CDKALl) (NM_017774). The CDKALl protein has catalytic activity as well as iron ion binding activity but the in vivo function in unknown. It is widely expressed including expression in pancreas.

To verify the association of rsl569699 and rs7756992 to Type 2 diabetes the two markers were genotyped in a Danish Type 2 diabetes case - control cohort and also in a US Caucasian cohort Type 2 diabetes cohort from the PENN CATH study (Table 7). The results show that the two markers are significantly associated with Type 2 diabetes in the Danish cohort and that it confers a similar risk in the US UPenn. cohort although the results do not reach statistical significance. When the two replication cohorts are combined the results are significant with a risk of around 1.2. When all the cohorts are combined the risk for each marker is over 1.2 comparing a group of nearly 3000 Type 2 diabetes patients (not accounting for BMI) and over 8000 controls. These results are genome wide significant.

WO 2008/065682 PCT/IS2007/000020 87 Table 7. Association of rsl569699 and rs7756992 to Type 2 diabetes Iceland rs-Name Allele Chr Pos (B35) Aff.n Aff.frq Ctrl.n Ctrl.frq Rrisk Padj rsl 569699 2 chr6 20787289 1397 0.297 5264 0.256 1.224 0.000158 rs7756992 3 chr6 20787688 1398 0.270 5271 0.232 1.228 0.000204 Denmark (Steno) rs-Name Allele Chr Pos (B35) Aff.n Aff.frq Ctrl.n Ctrl.frq Rrisk P rsl 569699 2 chr6 20787289 1108 0.361 2346 0.321 1.200 0.00079 rs7756992 3 chr6 20787688 1131 0.320 2361 0.274 1.247 0.000078 Upenn rs-Name Allele Chr Pos (B35) Aff.n Aff.frq Ctrl.n Ctrl.frq Rrisk P rsl 569699 2 chr6 20787289 360 0.346 522 0.308 1.185 0.09944 rs7756992 3 chr6 20787688 392 0.293 690 0.261 1.176 0.103824 Combined replication cohorts rs-Name Allele Chr Pos (B35) Aff.n Aff.frq Ctrl.n Ctrl.frq Rrisk Pmh rsl 569699 2 chrf> 20787289 1468 1.195 0.00002 rs7756992 . 3 chr6 20787688 1523 3051 - 1.221 2.8E-06 Combined all cohorts rs-Name Allele Chr Pos (B35) Aff.n Aff.frq Ctrl.n Ctrl.frq Rrisk Pmh rsl 569699 2 chrf> 20787289 2865 1.207 1.1E-07 rs7756992 3 chr6 20787688 2921 - 8322 . 1.224 1.9E-09 These results show significant association to the 20634996-20836710 bp region (Build 34) on chromosome 6, between markers rs4429936 and rs6908425, in Type 2 diabetes. Values for relative risk (RR) are comparable in all three cohorts; the lack of significant association at the 0.05-level in the UPenn cohort is mainly due to lack of power compared with the other cohorts, although the RR value is slightly lower in this cohort as compared with Iceland (RR of 1.185 compared with 1.224 for rsl569699). Furthermore, RR-values for non-obese Type 2 diabetes patients in Iceland are even higher (RR = 1.33 for rsl569699).

Chromosome 10a23.33 locus Seven single markers and seven two marker haplotypes in a region on chromosome 10q23.33 were found to be associated with Type 2 diabetes (Table 1). Most of those markers are also associated to diabetes with elevated RR values when obese patients are analysed separately (Table 5). These markers are located within one LD block between positions 94192885and 94490091 (NCBI Build 35), corresponding to the genomic segment bridged by markers rs2798253 and rslll87152 (Figure 2). This LD block contains three genes, Insulin-degrading enzyme (IDE) 88 (NM_004969), Kinesin family member 11 (KIFll) (NM_004523) and Homeobox, hematopoietically expressed (HHEX) (NM_002729).

IDE may belong to a protease family responsible for intercellular peptide signalling. Though its role in the cellular processing of insulin has not yet been defined, insulin-degrading enzyme is thought to be involved in the termination of the insulin response (Fakhrai-Rad et al, Human Molecular Genetics 9:2149-2158, 2000). Genetic analysis of the diabetic GK rat has revealed 2 amino acid substitutions in the IDE gene (H18R and A890V) in the GK allele which reduced insulin-degrading activity by 31% in transfected cells. However, when the H18R and A890V variants were studied separately, no effects were observed, suggesting a synergistic effect of the 2 variants on insulin degradation. No effect on insulin degradation was observed in cell lysates, suggesting that the effect may be coupled to receptor-mediated internalization of insulin. Congenic rats with the IDE GK allele displayed postprandial hyperglycemia, reduced lipogenesis in fat cells, blunted insulin-stimulated glucose transmembrane uptake, and reduced insulin degradation in isolated muscle. Analysis of additional rat strains demonstrated that the dysfunctional IDE allele was unique to GK rats. The authors concluded that IDE plays an important role in the diabetic phenotype in GK rats. IDE has been studied as a candidate gene for Type 2 diabetes in humans with inconsistent results. Two large studies have recently analysed the association of IDE to Type 2 diabetes by mutation screening and haplotype analysis using tagging SNPs over the gene (Groves et al, Diabetes 52:1300-1305, 2003; Florez et al, Diabetes 55:128-135, 2006). Both studies conclude that common variants in IDE are unlikely to confer significant risk of Type 2 diabetes. These studies did however, not include the whole LD block as defined in figure 2 and at least some of the markers identified in our study as associated with Type 2 diabetes are outside the regions analysed in those previous studies. Based on the results reported here, markers in LD with IDE are associated with Type 2 diabetes, providing genetic evidence for the role of IDE in the etiology of Type 2 diabetes.

KIFll encodes a motor protein that belongs to the kinesin-like protein family. Members of this protein family are known to be involved in various kinds of spindle dynamics. The function of this gene product includes chromosome positioning, centrosome separation and establishing a bipolar spindle during cell mitosis. This gene is not a good functional candidate for diabetes but has to be considered as a positional candidate due to its location within the associated LD block.

HHEX encodes a member of the homeobox family of transcription factors, many of which are involved in developmental processes. Expression in specific hematopoietic lineages suggests that this protein may play a role in hematopoietic differentiation. HHEX is essential for pancreatic development; in HHEX negative mouse embryos there is a complete failure in ventral pancreatic specification (Bort et al, Development 131, 797-806, 2004). Other transcription factors involved in pancreatic development include the MODY genes as well as other factors that have been implicated in late onset diabetes. HHEX is also an essential effector of Wnt antagonist for heart induction (Foley and Mercola, GENES & DEVELOPMENT 19:387-396, 2005). This puts HHEX in the same pathway as the recently established Type 2 diabetes gene TCF7L2 and together these data make HHEX a functional as well as positional candidate for Type 2 diabetes. 89 To verify the association of rs2497304, rs947591, rsl0882091 and rs7914814 to Type 2 diabetes, the markers were genotyped in a Danish Type 2 diabetes case - control cohort and also in a US Caucasian cohort Type 2 diabetes cohort from the PENN CATH study (Table 8). The results show that the association is not replicated in either cohort independently. However, when the two cohorts are combined the association of rs947591 reaches significance at the 0.05 level, with a risk of 1.1 in the combined cohort. When all the cohorts are combined the risk is 1.15 for the rs947591 marker.

These results indicate that variants within the LD block on Chromosome 10 that includes IDE and HHEX are susceptibility variants for Type 2 diabetes. 90 Table 8. Association analysis of markers on Chromosome 10 to Type 2 diabetes in Iceland, Denmark, and the US.

Iceland rs-Name Allele Chr Pos (B35) Aff.n Aff.frq Ctrl.n Ctrl.frq Rrisk Padj rsl 0882091 2 chr10 94364357 1399 0.472 5275 0.415 1.257 0.0000023 rs7914814 4 chr10 94372930 1399 0.472 5275 0.416 1.256 0.0000024 rs2497304 1 chr10 94482696 1399 0.542 5275 0.485 1.257 0.0000019 rs947591 1 chr10 94485733 1399 0.526 5273 0.475 1.226 0.0000221 Denmark (Steno) rs-Name Allele Chr Pos (B35) Aff.n Aff.frq Ctrl.n Ctrl.frq Rrisk P rsl 0882091 2 chr10 94364357 1115 0.431 2341 0.413 1.077 0.15 rs7914814 4 chr10 94372930 1141 0.430 2360 0.410 1.088 0.10 rs2497304 1 chr10 94482696 1145 0.528 2348 0.509 1.079 0.14 rs947591 1 chr10 94485733 1140 0.502 2361 0.478 1.103 0.055 Upenn rs-Name Allele Chr Pos(B35) Aff.n Aff.frq Ctrl.n Ctrl.frq Rrisk P rsl 0882091 2 chr10 94364357 386 0.377 640 0.375 1.008 0.93 rs7914814 4 chr10 94372930 394 0.379 683 0.381 0.995 0.95 rs2497304 1 chr10 94482696 408 0.460 778 0.454 1.021 0.81 rs947591 1 chr10 94485733 393 0.480 687 0.459 1.089 0.34 Combined replication cohorts rs-Name Allele Chr Pos(B35) Aff.n Aff.frq Ctrl.n Ctrl.frq Rrisk Pmh rsl 0882091 2 chr10 94364357 1501 1.052 0.19 rs7914814 4 chr10 94372930 1535 1.053 0.16 rs2497304 1 chr10 94482696 1553 1.057 0.16 rs947591 1 chr10 94485733 1533 - 3048 ■ 1.098 0.032 Combined all cohorts rs-Name Allele Chr Pos(B35) Aff.n Aff.frq Ctrl.n Ctrl.frq Rrisk Pmh rsl 0882091 2 chr10 94364357 2900 1.136 0.000017 rs7914814 4 chr10 94372930 2934 1.137 0.000012 rs2497304 1 chr10 94482696 2952 1.139 0.000011 rs947591 1 chr10 94485733 2932 - 8321 . 1.152 9.7E-07 Chromosome 17a24.3 locus Five single markers and two two marker haplotypes in a region of chromosome 17q24.3 were found to be associated with Type 2 diabetes in non-obese patients (Table 3). Some of these markers show the strongest association reported in Table 3 and association to this region was also observed when all diabetics were analysed (Table 1). These markers are located within two adjacent LD blocks located between positions 66037656 and 66163076 (NCBI Build 35) on 91 chromosome 17, between markers rsll077501 and rs4793497 (Figure 3). The association is significant after correction for the number of tests performed in the single marker association analysis; i.e., the association is significant at the genome-wide level. No known genes are located within these LD blocks. However, it is possible that variants in this region affect genes in neighboring regions including KCNJ2 and KCNJ16. Alternatively these variants may affect unknown genes within these LD block regions. 92 Table 9. SNPs located within the CDKALl gene (Located between position 20,642,736 and 21,340,611 bp on Chromosome 6 in NCBI Build 35 and NCBI Build 36) Pos Build 35/36 Marker ID 20642787 rs41271303 20642953 rsl 1963450 20643397 rs981043 20643513 rs981042 20643675 rsl 6883895 20643753 rsl 7512225 20643840 rs35035071 20643949 rs6904566 20644073 rs6927356 20644093 rs35281412 20644313 rs35915788 20644314 rs34025398 20644319 rs34361235 20644335 rs6905138 20644499 rsl 3194858 20644717 rs2179551 20644727 rs2179550 20644787 rs9465794 20644787 rs9465795 20644848 rs7747962 20644858 rs6910725 20644918 rs965054 20644971 rs2143407 20645032 rsl 0619380 20645431 rs2328525 20645661 rsl 3199286 20645841 rs10611252 20645940 rs7753499 20646023 rs7753956 20646024 rs34811195 20646024 rs7753670 20646107 rs3060613 20646109 rsl 1277970 20646110 rsl 1280099 20646114 rs6149468 20646139 rsl 6883900 20646175 rs7774291 20646441 rs10612082 20646476 rs9368198 20646502 rsl 3203336 20646504 rsl 3203631 20646619 rs6456355 20646644 rsl 0484635 20647190 rsl 2204173 20647320 rsl 3207544 20647851 rsl 2198728 20647984 rs28396084 20648327 rsl 2199073 20648500 rs9465796 20648561 rsl 2212600 20648596 rsl 3212040 20648663 rs35291340 20648722 rsl 2199324 20649085 rsl 2200871 20649159 rs9348432 Pos Build 35/36 Marker ID 20649183 rsl 2200834 20649236 rs34860173 20649324 rsl 1754872 20649498 rs6456356 20649517 rs9368199 20649682 rs2143406 20650176 rsl 0484634 20650200 rs7758851 20650398 rs34677076 20651447 rs6928571 20651461 rsl 2192584 20651608 rs34856684 20652015 rs9350255 20652091 rs9368200 20652136 rs12214002 20652245 rs9465797 20652300 rs9465798 20652574 rs28699301 20652650 rsl 3215844 20652678 rs12214315 20652722 rsl 1759517 20652786 rs13218957 20652806 rsl 3218962 20653186 rsl 0543744 20653201 rsl 2216047 20653447 rs9366354 20653890 rs9358342 20654091 rs9368201 20654382 rs34206163 20654506 rs9465799 20654794 rs34187071 20654867 rs9465800 20654890 rs6908974 20654992 rsl 3197372 20655361 rs13214145 20655793 rsl 6883910 20655968 rsl 2194705 20656271 rs35080661 20656465 rs7753467 20656466 rs7773488 20656986 rs34182285 20657084 rs34242699 20657780 rs9348433 20657942 rs9460519 20658083 rsl 2198377 20658096 rs9465801 20658195 rs9465802 20658822 rs28458932 20658823 rs9465803 20658981 rs2103682 20659321 rs9465804 20659580 rs34611621 20660058 rsl 2055423 20660653 rs9465805 20660829 rsl 1365187 Pos Build Marker ID /36 20660836 rsl 1320714 20660918 rs9350256 20661764 rs7756211 20662069 rs9460520 20662498 rs34245467 20662930 rs9350257 20663855 rsl 1964554 20663990 rs9465806 20664109 rsl 1964635 20664190 rsl 3199421 20664314 rs6932320 20664570 rsl 2200078 20664659 rsl 3437555 20664884 rs9350258 20665256 rsl 2176441 20665260 rsl 2183826 20665264 rs9356738 20665272 rs9348434 20665343 rs9465807 20665804 rs4458667 20665995 rs7739402 20667590 rsl 6883914 20667591 rsl 6883916 20667900 rs9654584 20667999 rs9465808 20668414 rsl 7584626 20668565 rs7751682 20669667 rsl 1361279 20669681 rs34634263 20670059 rsl 2214549 20670364 rs7753519 20670575 rs28567007 20670597 rs7772137 20670719 rsl 2208597 20670998 rs9368202 20671877 rs2328526 20672452 rs34823358 20673287 rs28639914 20673363 rs34233572 20673415 rs4712506 20673935 rsl 3203450 20674280 rs9350259 20674435 rs6918457 20674595 rs35210537 20674749 rsl 1329887 20675016 rs9348435 20675068 rs35366106 20675342 rsl 6901563 20675352 rsl 2333229 20675520 rs9460521 20676092 rsl 0589899 20676351 rs2876573 20676957 rs6935461 20676963 rs6935465 20676968 rsl 0603174 Pos Build 35/36 Marker ID 20677060 rsl 2333291 20677967 rs2064321 20677985 rs35546893 20678018 rs4291090 20678121 rs2064320 20678268 rs9465810 20678275 rs9465811 20678423 rs9358344 20678756 rsl 0946390 20679114 rs6905281 20679339 rsl 6883932 20679612 rs34904067 20679660 rs7744002 20679763 rs35142564 20680095 rs9465812 20680678 rs7759094 20680784 . rs9460522 20681538 rs7764551 20681585 rsl 0541455 20682409 rsl 6883935 20682542 rs13215603 20682568 rs962576 20683235 rsl 474720 20683797 rsl 6883944 20684155 rs34538343 20684269 rs9350260 20684353 rsl 6883951 20684645 rs9358345 20684862 rs1012627 20684890 rs9368203 20684939 rs35894322 20684965 rs4710932 20684984 rs6909117 20685540 rs1012626 20685748 rs1012625 20685760 rs7752194 20685958 rs9465813 20686014 rsl 2207923 20686355 rsl 6883963 20686831 rsl 3205786 20686887 rs35205364 20687102 rsl 0456232 20687189 rs9465814 20687201 rs35571892 20687740 rs9465815 20687753 rs36119371 20687921 rs28621813 20687926 rs9350261 20687928 rs7341226 20688175 rs6927481 20688323 rs35313444 20688373 rs6928198 20688404 rs6907897 20688545 rs6928586 20688872 rs9368204 93 Pos Build Marker ID /36 20689021 rs9358346 20689589 rsl 1967546 20689593 rs34134803 20689772 rsl 0456233 20689807 rs7744833 20690122 rs9460523 20690123 rs9465816 20690432 rs6908077 20690630 rs9465817 20691069 rsl 1967445 20691263 rs34022950 20691793 rs9460524 20691994 rs34020592 20692003 rsl 1448102 20692339 rs9465818 20692402 rs9350262 20692513 rsl 3205241 20693000 rsl 2153939 20693100 rs6925593 20693119 rs4712507 20693225 rsl 0558806 20693267 rs35982532 20693276 rsl 1385529 20693360 rs9348436 20693416 rs9368206 20693438 rsl 3209542 20693452 rs9368207 20693630 rsl 3209907 20693635 rs6926658 20694018 rs12213132 20694182 rs4357125 20694554 rs6932944 20694607 rs6932962 20695026 rs9348437 20695332 rsl 2201857 20695356 rs9465819 20695447 rs6938955 20695539 rs9460525 20695827 rs9465820 20695964 rsl 0946391 20695968 rs9368208 20696003 rs9465821 20696183 rs6923790 20696399 rsl 0558139 20697309 rs6907459 20697320 rs6907767 20697321 rs9465822 20697349 rs6930283 20697706 rs6908042 20697741 rs6935317 20697761 rs35370102 20698266 rs9368209 20698366 rsl 3216746 20698367 rsl 3216747 20699007 rs35485532 20699747 rsl 3216324 20699817 rs4336434 20700046 rs4509107 20700428 rs9465823 20700465 rs6936705 Pos Build Marker ID /36 20700679 rs34023799 20700929 rs6942313 20701057 rs28869917 20701318 rs34982231 20701631 rs9358349 20701770 rs9460526 20701829 rs9366356 20702163 rs36120092 20702181 rs9465824 20702519 rs4712512 20702561 rs4712513 20702646 rs4710934 20702658 rs9348438 20702902 rs9460529 20703363 rsl 3199587 20703470 rsl 3199384 20703526 rsl 0223680 20703606 rs9350263 20703768 rs9465825 20703832 rsl 0223876 20704100 rs35702271 20704171 rs9358350 20704432 rsl 2208985 20704771 rsl 2210459 20704892 rs35431707 20705144 rs36039523 20705297 rsl 1758281 20705350 rs28893199 20705757 rs34256347 20706019 rsl 2192740 20706282 rs13212326 20706486 rs12199184 20706753 rsl 0456234 20707009 rs4712514 20707422 rs9465826 20707607 rs9366357 20707867 rs2294809 20708549 rs2294808 20708813 rs7762750. 20708976 rs4712515 20708998 rsl 0522824 20708999 rs35660518 20709002 rsl 0679950 20709003 rs34870864 20709022 rs4712516 20709145 rs4710935 20709386 rs9465827 20709388 rsl 2204865 20709672 rsl 0946393 20709764 rsl 2209806 20709894 rsl 0946394 20709921 rsl 997778 20709971 rs35878587 20710359 rsl 997777 20710378 rs2223622 20710776 rsl 1964057 20711246 rs9460530 20711344 rs9460531 20711376 rs34329159 20711640 rs7764558 Pos Build 35/36 Marker ID 20711804 rs4710936 20712056 rsl 2213940 20712228 rsl 3215038 20712739 rsl 0946395 20712832 rs6939917 20712975 rs9358351 20713800 rs6925097 20713924 rs9465828 20713955 rs9465829 20713961 rs6902661 20714057 rs34373680 20714281 rs35051096 20714508 rs932405 20714591 rs6926585 20714635 rs3938395 20715464 rsl 1964664 20715551 rs35964987 20715663 rsl 2206413 20715758 rs35990187 20715763 rs4991654 20715910 rs9460532 20715991 rsl 3328250 20716030 rsl 3328252 20716194 rs4712517 20716257 rs4712518 20717220 rs7758129 20717475 rsl 3206462 20717483 rsl 3192442 20717486 rsl 3206468 20717492 rsl 3192445 20717498 rsl 3192450 20717504 rsl 3206477 20717510 rsl 3206483 20717577 rs12179168 20717586 rsl 2180975 20717611 rs12179172 20717860 rsl 2179563 20718357 rsl 1355836 20718696 rs2328527 20718709 rsl 1452882 20718920 rs2876574 20719905 rs9465831 20720031 rs34877824 20720290 rs13212501 20720647 rs9358352 20720703 rs9358353 20720761 rs28756205 20720889 rs9350265 20720989 rs7750508 20721130 rs7771052 20721141 rs9460533 20721195 rsl 3200415 20721216 rsl 0550932 20721312 rs9465832 20721463 rs9368211 20721471 rs9350266 20721507 rsl 1752592 20721515 rs9350267 20721754 rs978988 20721898 rs978987 Pos Build 35/36 Marker ID 20721906 rs978986 20722036 rs5874773 20722196 rs5874774 20722500 rs7756788 20722659 rs9348439 20722661 rs9356739 20722693 rs9356740 20722738 rs7760894 20723021 rs2796913 20723046 rs2608613 20723121 rsl 0456710 20723139 rs9476286 20723140 rs28368538 20723140 rs9476287 20723141 rs28612622 20723142 rs9463660 20723146 rs9463661 20723162 rs9461022 20723193 rs9461021 20723235 rs34980442 20723239 rs34049080 20723258 rs35218684 20723260 rs12175876 20723270 rsl 0948323 20723287 rs34400313 20723292 rs36081550 20723304 rsl 2175878 20723305 rs34520184 20723305 rs34756989 20723322 rs4629736 20723322 rs9296917 20723324 rs28562027 20723333 rs9381823 20723346 rs34769771 20723346 rs34774640 20723346 rs36038896 20723365 rsl 3209195 20723369 rs12213541 20723369 rs34112320 20723371 rs34615869 20723379 rs35949519 20723381 rs9257498 20723383 rs34200576 20723393 rs4960519 20723396 rs9261905 20723402 rs9267103 20723404 rsl 7367677 20723416 rs9261906 20723421 rs9267104 20723424 rs9267105 20723434 rs28810763 20723438 rs12179121 20723438 rs4714959 20723439 rsl 0946636 20723439 rs28763327 20723439 rs28847950 20723439 rs3933247 20723449 rs28808723 20723451 rs9767082 20723452 rs35132675 94 Pos Build 35/36 Marker ID 20723452 rs35517166 20723452 rs4714297 20723456 rsl 2182737 20723456 rs36163804 20723460 rs35790973 20723464 rs35236694 20723469 rs35567559 20723469 rs9267106 20723471 rs9800557 20723484 rsl 2182463 20723489 rsl 0948322 20723489 rs34052284 20723489 rs9268999 20723490 rs9258377 20723495 rs9257499 20723498 rs9265816 20723500 rs28771402 20723501 rs28771401 20723502 rs12194731 20723502 rs4451188 20723502 rs9717323 20723502 rs9765920 20723503 rs9265815 20723504 rs28771400 20723506 rs12190813 20723506 rs12215416 20723507 rsl 2178527 20723510 rs35234761 20723510 rs35887156 20723512 rs28797321 20723515 rs28771399 20723522 rsl 3207682 20723522 rs36099432 20723531 rs28749543 20723535 rsl 3196506 20723535 rs35716308 20723536 rs28831180 20723536 rs34938144 20723537 rs36142967 20723541 rs35313792 20723542 rs9260904 20723543 rs34597832 20723545 rs9767740 20723546 rs28771398 20723550 rs34384951 20723554 rsl 2524128 20723554 rsl 2665124 20723554 rs34922643 20723555 rs9260903 20723557 rs28771397 20723557 rs6915279 20723559 rs9261907 20723559 rs9766798 20723559 rs9767242 20723560 rs6914835 20723560 rs9260902 20723560 rs9767101 20723562 rs9261908 20723563 rsl 2207064 20723563 rs12213193 Pos Build Marker ID /36 20723563 rs35750154 20723566 rs9260901 20723570 rs9269000 20723579 rsl 2178368 20723579 rs13197714 20723579 rs28771396 20723579 rs34443697 20723579 rs9267107 20723582 rs35113301 20723582 rs3933248 20723583 rs28819830 20723586 rsl 0947899 20723586 rs9260900 20723588 rsl 3204671 20723588 rs34094007 20723588 rs34963756 20723588 rs4304158 20723589 rs4298351 20723590 rsl 2182307 20723590 rsl 2201487 20723590 rs34097573 20723595 rs13219021 20723596 rs34456153 20723596 rs9767597 20723597 rs9767102 20723598 rs9269001 20723601 rsl 2180097 20723603 rsl 2178465 20723603 rs35128115 20723607 rs4273681 20723609 rsl 2193754 20723617 rs813814 20723617 rs9689672 20723619 rs36173068 20723623 rsl 2202172 20723623 rs28862376 20723625 rsl 2178884 20723625 rsl 2203117 20723625 rs34250588 20723626 rs12182581 20723632 rs34147797 20723635 rs9688484 20723636 rs9269002 20723636 rs9767733 20723637 rsl 0948989 20723637 rs34732676 20723637 rs9260899 20723638 rs35686233 20723639 rsl 1753098 20723639 rs35156647 20723646 rs34719653 20723646 rs35575623 20723648 rsl 2192046 20723649 rsl 1759854 20723649 rs28771395 20723649 rs35563402 20723649 rs36016334 20723649 rs4555911 20723653 rsl 1965757 20723654 rsl 0948990 Pos Build 35/36 Marker ID 20723654 rs28808296 20723654 rs34995142 20723654 rs809919 20723657 rsl 1571978 20723659 rsl 2208488 20723662 rsl 1751374 20723663 rs13217613 20723667 rsl 2528735 20723668 rs35160656 20723668 rs35322569 20723668 rs9766221 20723670 rs35120225 20723670 rs511868 20723674 rs9269003 20723675 rs34290316 20723675 rs35735496 20723675 rs9689102 20723676 rsl 0948991 20723676 rs9269004 20723677 rsl 3220607 20723677 rs34700647 20723677 rs9260898 20723678 rs9260897 20723684 rs28771394 20723686 rs12213200 20723687 rs9717987 20723688 rs28771393 20723688 rs9717716 20723689 rs28771392 20723690 rsl 1758009 20723690 rs34159662 20723690 rs34683172 20723690 rs9717331 20723691 rs9717853 20723692 rs9765875 20723696 rs12178974 20723696 rs36003577 20723698 rs9767747 20723700 rs28771391 20723704 rs13216352 20723707 rsl 2200762 20723707 rsl 2206373 20723707 rs34570202 20723707 rs36197940 20723707 rs9265814 20723714 rs34131282 20723717 rs12175478 20723720 rs28772692 20723722 rs35516674 20723722 rs35704013 20723727 rs34691406 20723728 rs28771390 20723728 rs4374863 20723730 rs34826149 20723734 rsl 2207894 20723734 rsl 2662476 20723736 rs9260896 20723739 rs28771389 20723740 rs28771388 20723741 rs9382592 Pos Build 35/36 Marker ID 20723745 rsl 2173375 20723745 rs9268072 20723745 rs9382110 20723746 rs4715211 20723747 rs35961188 20723747 rs34128950 20723747 rs4620119 20723749 rs9767236 20723752 rs34717143 20723755 rsl 3201202 20723756 rsl 3201503 20723762 rsl 3197088 20723762 rs35347849 20723766 rs35650828 20723766 rs34663083 20723767 rsl 3199241 20723767 rs34205031 20723768 rs34469031 20723768 rs28749541 20723768 rs9279137 20723769 rs9260895 20723770 rs35446958 20723770 rs12212483 20723775 rs28380829 20723777 rsl 2525384 20723777 rs34576984 20723782 rs283541 20723785 rs28380828 20723788 rsl 0948698 20723790 rs9265813 20723791 rs9689173 20723792 rs28380827 20723795 rs35399169 20723799 rs9260894 20723800 rsl 2173388 20723800 rs9269005 20723802 rs28359816 20723803 rs28380826 20723807 rs280297 20723807 rs34507582 20723807 rs9261623 20723810 rs12174621 20723813 rs28380825 20723815 rs35197377 20723816 rsl 7362870 20723816 rs35071522 20723816 rs34562190 20723816 rs35179751 20723816 rs4458721 20723817 rsl 2180385 20723817 rsl 2206581 20723817 rsl 2333308 20723817 rs9269006 20723821 rs9688475 20723829 rs9269007 20723832 rs9269008 20723832 rs9269009 20723834 rs35899754 20723836 rs13211190 20723837 rsl 2216274 95 Pos Build Marker ID /36 20723838 rs12191544 20723838 rs4337934 20723841 rs9279295 20723842 rsl 2178577 20723849 rsl 2215604 20723853 rs9395360 20723854 rs28749540 20723855 rs28895226 20723855 rs9260893 20723861 rs4365925 20723864 rs9261912 20723865 rs28895227 20723870 rs9261913 20723873 rsl 2183502 20723873 rs34332895 20723873 rs9472692 20723876 rs35640475 20723884 rs9269010 20723888 rs12192337 20723888 rs35349786 20723891 rs34978372 20723893 rs280296 20723894 rsl 1755576 20723903 rs35553517 20723903 rs28803616 20723904 rs4358654 20723910 rs9260892 20723914 rsl 3196941 20723914 rs9717238 20723915 rsl 2175553 20723915 rs12191408 20723915 rs4460210 20723915 rs9260891 20723918 rs9395361 20723920 rs9766917 20723926 rs35073779 20723931 rs9765884 20723931 rs9767229 20723932 rs35247846 20723932 rs9717328 20723936 rs28805674 20723936 rs9260890 20723938 rs34926348 20723938 rs9717233 20723945 rs35869128 20723946 rs12175941 20723951 rs9260889 20723952 rs9766686 20723956 rsl 0046203 20723957 rs9260888 20723958 rsl 2180540 20723961 rs9766115 20723968 rs6912019 20723969 rs9767458 20723976 rsl 3202161 20723989 rsl 3218048 20724000 rsl 3218040 20724001 rsl 3206557 20724002 rsl 3202152 20724013 rs12210049 Pos Build Marker ID /36 20724013 rs34552032 20724018 rs28890881 20724018 rs34478537 20724025 rs35191657 20724038 rs34450517 20724043 rs9689655 20724064 rs12180172 20724068 rs28865015 20724071 rs9717839 20724072 rs9717836 20724074 rs9885593 20724082 rs28887572 20724083 rs13216113 20724083 rs35254115 20724084 rsl 0949190 20724085 rs6923503 20724087 rsl 2214411 20724091 rs28747986 20724096 rsl 087363 20724096 rs1091092 20724104 rsl 2180759 20724107 rsl 1758052 20724112 rs9261321 20724113 rs28861738 20724113 rs36109104 20724123 rsl 3208115 20724129 rs9472693 20724130 rsl 2208570 20724130 rs28832660 20724131 rsl 3200482 20724131 rs9260886 20724131 rs9472694 20724159 rs9260885 20724172 rs280295 20724172 rs28749538 20724174 rsl 3201041 20724184 rsl 087362 20724187 rsl 2183850 20724190 rsl 2202552 20724208 rs9260884 20724210 rs9474341 20724211 rs9260883 20724222 rs34669820 20724225 rsl 2189886 20724234 rs12182114 20724266 rs9688643 20724272 rsl 2195237 20724281 rs35293595 20724281 rs9381428 20724306 rs34665644 20724309 rsl 2189599 20724311 rsl 2208503 20724312 rs9800791 20724330 rsl 2173681 20724337 rsl 2182094 20724343 rs12182119 20724352 rs12182102 20724392 rsl 2174506 20724393 rs9767809 20724394 rsl 2173703 Pos Build Marker ID /36 20724401 rsl 2202889 20724435 rs28840538 20724466 rs9473983 20724467 rs34220946 20724487 rs9261322 20724491 rs9261323 20724517 rs526092 20724564 rs9473982 20724566 rs34307764 20724626 rs34490559 20724665 rs4449621 20724685 rs4714818 20724698 rs4714817 20724722 rs682384 20724738 rs682051 20724753 rsl 2530056 20724756 rs35086683 20724888 rsl 2528468 20725092 rsl 0650195 20725092 rs35956126 20725109 rs6937578 20725159 rsl 2530107 20725173 rs720448 20725176 rs9368212 20725250 rs35481531 20725253 rs720449 20725262 rs10650196 20725495 rs2064 20725499 rs2065 20725638 rs9368213 20725732 rs41455744 20726077 rs34960654 20726154 rs6900954 20726168 rs6456359 20726176 rs7739405 20726601 rs7760508 20726684 rsl 0456007 20726987 rs9460534 20727168 rsl 1966749 20727353 rs9358354 20727809 rs9368214 20727982 rs9350268 20728095 rs2069013 20728160 rs2069014 20728290 rs2069015 20728292 rsl 1967475 20729096 rs10214549 20729217 rs2223621 20729281 rs9465835 20729984 rs35404829 20729995 rsl 0687080 20730233 rs6915936 20730331 rs9295472 20730732 rsl 569660 20730929 rs7455009 20730945 rsl 569659 20730946 rs5874775 20730948 rsl 0601252 20730983 rsl 569658 20731030 rs34142400 Pos Build Marker ID /36 20731063 rsl 6883996 20731181 rs35073110 20731184 rs5028948 20731263 rs34201758 20731371 rs6456360 20731373 rs6456361 20731380 rs6456362 20731584 rs6922571 20731925 rs35145358 20731950 rs9465836 20732013 rs7763304 20732158 rs9465837 20732218 rs7743314 20732337 rs714831 20732361 rs714830 20732484 rs7743789 20732584 rs5874776 20732589 rs5874777 20732965 rsl 6884003 20733079 rs9356741 20733080 rs9366358 20733246 rs9356742 20733430 rsl 1756987 20733470 rs9465838 20733613 rs2206579 20733920 rs35111339 20734361 rs6917583 20734388 rs6917599 20734630 rsl 3437429 20735418 rs34307011 20735420 rs4515379 20735756 rs2223620 20735870 rs9465839 20735993 rsl 2664972 20736790 rs28402356 20736798 rs6934727 20736873 rs35493429 20736881 rsl 1369825 20737261 rs4523079 20737470 rs7771213 20737568 rs9465840 20737687 rs9465841 20737767 rs9465842 20737837 rs9460535 20737992 rs34835908 20738060 rs9465843 20738139 rsl 3220465 20738159 rsl 3220352 20738321 rs4710937 20738375 rs9460536 20738376 rsl 3190734 20738451 rs9465844 20738712 rs35976895 20738713 rsl 1327958 20738932 rsl 3194407 20738990 rsl 0484633 20739524 rs2328528 20739789 rs35958155 20739809 rs4421185 20739932 rs2328529 96 Pos Build Marker ID /36 20740089 rs9460537 20740745 rsl 7224527 20740886 rs34166991 20741024 rsl 7823073 20741276 rsl 2183074 20741316 rs9465845 20741844 rs35148963 20741886 rs7768642 20742320 rs9465846 20742407 rs9465847 20742551 rsl 7823127 20742594 rsl 6884021 20742630 rs4533976 20742865 rs7755830 20743005 rs7756031 20743139 rs35650451 20743188 rs10561117 20743241 rs6940200 20743799 rs9465848 20743808 rs34351919 20745083 rs4712519 20745285 rs9368215 20745566 rsl 2206285 20745853 rs34049994 20745988 rs7751957 20746702 rs9465849 20746857 rs7341291 20746957 rs6921014 20747388 rs9465850 20747583 rs7758612 20747681 rs35602526 20748295 rs9465851 20748399 rs34257578 20748403 rsl 1339738 20748516 rs9460538 20748850 rs4712520 20748883 rs4710938 20749084 rs35889049 20749315 rs9348440 20749879 rs9465852 20750054 rsl 2196009 20750306 rsl 1968248 20750353 rs34797179 20750764 rs6925328 20750913 rs36073053 20751140 rs36224625 20751145 rs35462488 20751150 rs3060659 20751153 rs5874778 20751155 rsl 1267861 20751201 rs4235999 20751230 rsl 6884038 20751706 rs2328530 20751731 rs2328531 20751750 rs28360636 20752162 rs6932676 20752183 rs9460539 20752303 rs6932876 20752346 rs34929755 20752359 rs28733367 Pos Build 35/36 Marker ID 20752360 rsl 1348111 20752473 rs6933219 20752702 rs6933165 20752872 rs35255583 20752901 rs34332316 20752923 rs4710939 20753486 rsl 1970417 20753659 rsl 1963217 20753670 rsl 1965473 20753833 rs2876575 20754049 rs7739974 20754976 rs7745175 . 20755173 rs7765784 20755178 rs6907731 20755250 rs35057896 20755313 rs7746072 20755639 rsl 0484632 20755770 rs35444529 20755849 rsl 7823571 20755941 rsl 1965062 20755962 rs6936199 20755965 rs6913126 20756178 rs6913509 20756613 rs34638218 20756673 rs35746011 20756741 rs9460540 20757090 rs36045545 20757129 rs35392790 20757233 rs6456364 20757260 rs2179553 20757513 rs9350269 20757531 rs9465854 20757787 rs2179552 20757936 rs6925233 20758033 rs2328532 20758248 rs7743970 20758317 rsl 3209457 20758318 rs34641285 20758344 rsl 3209538 20758387 rs2876576 20758479 rsl 3209572 20758653 rs28783153 20758712 rs9969037 20758800 rs7766844 20758969 rs7767133 20759291 rs7749464 20760100 rs2050225 20760696 rs9295474 20760744 rs9295475 20761529 rs2328545 20761548 rs28846771 20761779 rs2876582 20761899 rsl 0223446 20762094 rsl 3219723 20762095 rsl 3203489 20762154 rsl 3203583 20762172 rsl 3203887 20762279 rs6456366 20762876 rs9358355 20763089 rs9368216 Pos Build Marker ID /36 20763375 rs9465855 20763384 rs9465856 20763463 rsl 6884070 20763482 rsl 6884072 20763647 rsl 3208604 20764169 rs9465857 20764307 rs9368217 20764559 rs9460541 20764746 rs9460542 20764765 rsl 1969955 20764779 rs4712522 20764924 rsl 6884074 20765172 rs34489684 20765324 rs2328546 20765543 rs4712523 20765844 rs4712524 20765898 rs35397753 20765991 rs4710940 20766197 rsl 3190727 20766215 rs35136485 20766311 rs35260725 20766335 rs35939620 20766566 rsl 7823996 20766713 rsl 6884082 20767438 rs6906327 20767566 rs6456367 20767785 rs6456368 20768202 rs7749083 20768344 rs6456369 20768669 rsl 0946396 20768672 rsl 0946397 20768710 rsl 1759505 20769000 rsl 3203361 20769013 rsl 0946398 20769122 rs7774594 20769229 rs7754840 20769249 rs9460543 20769508 rs9460544 20769529 rs9460545 20769711 rs2206740 20769806 rs5874779 20769807 rs33970890 20769815 rs5874780 20769816 rs35014292 20769816 rs35363501 20770092 rs6456370 20770102 rs979614 20770196 rs35456723 20770571 rs9368218 20770945 rs4712525 20771014 rs4712526 20771314 rs4712527 20771442 rs35191644 20771443 rs34470647 20771611 rs9460546 20771938 rs9465859 20772079 rs9465860 20772291 rs736425 20772508 rs3060776 20772509 rs34941928 Pos Build 35/36 Marker ID 20772512 rs5874781 20772761 rs35778487 20773060 rs742642 20773305 rs35248697 20773436 rsl1967127 20773528 rs7748382 20773547 rs9688549 20773548 rs9689351 20773570 rs28665000 20773886 rs7752236 20773925 rs7772603 20774001 rs7752780 20774034 rs7752906 20774160 rs34184260 20774223 rs2206739 20774225 rs2206738 20774250 rs2206737 20774436 rsl 1970425 20774484 rs36034806 20774899 rs35042364 20775218 rs35540121 20775361 rs9358356 20775667 rs9356743 20775778 rs9350270 20776366 rs34929853 20778035 rs34971765 20778443 rsl 1970596 20779261 rsl 2527373 20779367 rs35916847 20780262 rsl 1968224 20780271 rsl 1968225 20780276 rs9465861 20780296 rsl 1968264 20780406 rsl 2189849 20780413 rsl 2209627 20780432 rsl 2189895 20780855 rsl 1968848 20781135 rsl 1963945 20781601 rs35677128 20781859 rs7451008 20782670 rs9368219 20782790 rs1012636 20782945 rsl 3217846 20783274 rs1012635 20783700 rs35665197 20783771 rs35261542 20783828 rs28823314 20783899 rs28890810 20784051 rs28871991 20784393 rs34499031 20784650 rsl 3208763 20784747 rs28719685 20784789 rs28856096 20785042 rsl 1961863 20785211 rsl 7824302 20785289 rsl 2660618 20786302 rsl 1371206 20786303 rs34152621 20786409 rs4712528 20786463 rsl 3217082 97 Pos Build 35/36 Marker ID 20786470 rs13217085 20786481 rsl 3217090 20786483 rsl 3217091 20786523 rsl 3200946 20786772 rsl 1968032 20786954 rs9465863 20787289 rsl 569699 20787386 rs34168173 20787688 rs7756992 20788045 rs35312717 20788657 rs9348441 20788843 rs9368220 20788941 rs6931254 20789327 rs6911742 20790601 rs35612982 20791039 rs35816514 20791123 rs34612860 20791143 rs9350271 20791162 rs35657899 20791179 rsl 1364854 20791249 rs9460547 20791646 rsl 6884103 20791961 rs2206736 20793465 rs9356744 20794295 rs34987372 20794427 rs36005020 20794552 rs7766070 20794975 rs9368222 20795290 rs35566695 20795781 rsl 0440832 20796100 rsl 0440833 20796237 rs35747076 20796578 rs6900217 20797102 rs34433496 20797924 rs7748720 20797928 rs34175709 20798290 rs6911357 20800493 rsl 2200791 20800955 rs5874782 20800957 rs36119385 20801341 rs13219682 20802207 rs4710941 20802270 rs4620109 20802272 rs28459626 20802273 rs4712529 20802292 rsl 0577753 20802504 rs2223683 20802573 rs2206735 20802863 rs2206734 20802910 rs34530846 20803458 rsl 6884131 20804127 rsl 0806921 20805104 rsl 6884133 20805571 rsl 7824500 20805652 rsl 0946401 20806114 rsl 6884135 20806582 rs35711395 20807220 rsl 1969783 20807364 rsl 6884137 20808600 rsl 1970626 Pos Build 35/36 Marker ID 20809092 rs12190713 20809106 rsl 1398905 20809415 rsl 1961445 20809470 rs35982077 20809486 rsl 1305935 20810952 rs9356745 20811700 rs35043644 20811842 rsl 6884140 20811931 rs6931514 20812147 rs35443650 20813281 rs34671712 20813569 rsl 1753081 20814081 rs7739516 20814209 rs6901559 20815176 rsl 3196379 20815177 rsl 3212234 20816204 rsl 0536170 20817155 rs9465869 20817688 rs36070002 20818288 rsl 7226450 20818905 rsl 073247 20819131 rs9465870 20819386 rsl 7226492 20819433 rs13213613 20819567 rsl 6884146 20819958 rs2206733 20820440 rs3749925 20821121 rs9460548 20821619 rs9460549 20821685 rsl 040558 20821893 rs4712530 20822083 rs35629277 20822362 rs7451928 20822445 rs6456371 20822589 rsl 3220116 20822823 rs2206732 20823169 rs2179633 20823483 rsl 1963770 20823805 rsl 0946402 20823840 rs4712531 20824098 rs35738288 20824232 rs9295478 20824549 rs2328547 20824763 rs3060781 20824764 rs34686252 20824856 rsl 3215905 20824884 rs9368223 20824937 rs2328548 20825025 rsl 1427712 20825074 rs6935599 20825100 rs13216165 20825234 rs9465871 20825383 rsl 0946403 20826219 rs2328549 20826449 rsl 7226774 20827124 rs9358357 20827211 rs9368224 20827321 rsl 1756271 20827372 rs9358358 20827540 rs9460550 Pos Build 35/36 Marker ID 20827858 rsl 2110493 20827866 rs12193125 20828258 rs9356746 20828797 rs9350272 20829322 rsl 3219444 20829342 rs12111216 20829562 rs9350273 20829700 rs9368225 20830399 rsl 7825025 20831036 rs9368226 20832213 rs6903175 20832229 rs6903744 20832537 rs12111351 20832754 rs4712536 20832986 rs9356747 20833076 rs9356748 20833219 rs7767391 20833402 rs7747752 20833511 rs9350274 20833853 rs34170041 20833919 rs6915155 20834014 rs6914868 20834472 rs4538697 20835549 rs4712537 20836048 rs34097377 20836492 rs6928012 20836710 rs6908425 20837083 rs28713236 20837085 rs28570482 20837098 rs35373857 20837704 rs35980729 20838039 rs9465872 20838780 rs9942459 20838787 rs9942429 20838794 rsl 2197544 20839053 rs34407999 20839503 rs7741604 20840493 rs35573456 20840651 rs35633408 20841368 rs9465873 20841433 rsl 2211466 20842055 rs4712538 20842055 rs41413744 20842592 rsl 3213979 20842973 rs13217519 20843073 rs34169067 20843074 rs34773978 20843075 rs34104100 20843076 rs34790688 20843373 rsl 1753021 20843473 rsl 1753041 20843666 rs6938978 20844017 rs9295479 20844137 rsl 0484631 20844216 rs9358361 20844796 rs9688471 20844922 rs7744943 20844996 rs9295480 20845006 rs9368227 20845333 rs9465874 Pos Build Marker ID /36 20845619 rs9358362 20845736 rs9368228 20845737 rsl 7839864 20845816 rs34427164 20846388 rs9368229 20846555 rs9295481 20846750 rs9368230 20846907 rs9356750 20846992 rs9366359 20847710 rs41272361 20847886 rs4710942 20847986 rs9465875 20847998 rs4710943 20848275 rs9350276 20848458 rs9465876 20848854 rs34604097 20849362 rs9688952 20849423 rs34933309 20849720 rs9350277 20850306 rsl 3204257 20850665 rs35106298 20851446 rsl 3194434 20851931 rs9358363 20852254 rs34929383 20852706 rs4710944 20852720 rsl 2529627 20853053 rs4710945 20853694 rs9350278 20854215 rs7738382 20854499 rsl 474739 20854568 rs35432334 20854686 rsl 6884185 20855689 rs35345966 20856120 rs2745928 20856124 rs2745927 20856166 rs2473649 20856236 rs13215601 20856258 rs35386836 20856392 rs2819991 20856706 rs2819995 20856744 rsl 1752936 20856762 rsl 543364 20856765 rsl 3203288 20856879 rs2473648 20856966 rs2473647 20856967 rs2473646 20857002 rsl 543363 20857270 rsl 6884190 20857656 rs4644038 20858009 rs2819988 20858162 rs4475313 20858693 rs2745933 20858865 rs9460552 20859007 rs9460553 20859031 rs9350279 20859173 rsl 0568019 20859187 rsl 0598071 20859199 rs12199271 20859220 rs7765413 20859294 rs7747724 98 Pos Build 35/36 Marker ID 20859674 rsl 1756862 20859995 rs4712539 20860175 rs2819989 20860310 rs2819990 20860358 rs9465877 20860448 rs34996587 20860459 rs34744837 20861169 rs2819992 20861420 rsl 0946405 20861729 rs2745932 20861866 rs2819993 20861911 rs9465879 20861915 rs2819994 20861965 rs34164249 20862098 rs2493995 20862168 rs35908672 20862169 rs35525968 20862500 rs9358364 20862605 rs2745931 20862716 rs2745930 20862740 rs2745929 20863911 rs2819996 20864423 rs1012114 20864756 rs2473651 20864955 rsl 6901574 20865045 rs9358365 20865049 rs6913831 20865061 rsl 0652206 20865064 rsl 0652207 20865081 rsl 1281792 20865121 rs6934147 20865127 rsl 3200804 20865134 rs6934300 20865135 rs2473650 20865136 rs6913999 20865625 rs9465880 20866301 rs34767457 20866310 rs35499882 20866326 rs2819997 20866505 rs2819998 20866612 rs2819999 20866683 rs2820000 20866739 rsl 0946406 20866788 rs34291318 20866813 rs9465881 20866829 rs9465882 20866922 rs2820001 20867101 rs2820002 20867254 rs9350280 20867255 rs9356751 20868156 rs6909558 20868333 rsl 1415727 20868591 rs6910326 20869059 rsl 2664021 20869213 rs9295482 20869314 rs9465883 20869658 rs9465884 20870485 rs4437452 20871061 rs34235608 20871150 rs4712540 Pos Build Marker ID /36 20871244 rs35450702 20872229 rs4351239 20872296 rs12190376 20872578 rs4710946 20873095 rs9465885 20873251 rs12192328 20873365 rsl 0536083 20873375 rs36210777 20873677 rs6149469 20874082 rs4585542 20874261 rs7751154 20874410 rs9356752 20874676 rs4510656 20875450 rs7452218 20875680 rs4320364 20876442 rs9465886 20876454 rs6926436 20877469 rs34127549 20877508 rsl 3214325 20877580 rs7750031 20877596 rs34801493 20877974 rs7772390 20878762 rs6900375 20879028 rs4712541 20879194 rs4710947 20879323 rs34893361 20879617 rs35938647 20879690 rs9465887 20879842 rs9368232 20879939 rs9350281 20880120 rs4132894 20880272 rsl 2195490 20880344 rs9465888 20880553 rs6941727 20880797 rs4712542 20880982 rs6923622 20881085 rs4712543 20881539 rs9358366 20881700 rs12211178 20881731 rs7453352 20881858 rs6929760 20881957 rs6929918 20882292 rs9465889 20882389 rs4712545 20882575 rsl 2193239 20882738 rs9465890 20883200 rs6936300 20883430 rs6936840 20883639 rs4493738 20883701 rsl 1965197 20884250 rs6899514 20884329 rs6456372 20885570 rs34358176 20886538 rs9465891 20886687 rsl 0946407 20887060 rs35581397 20887457 rs9358367 20887829 rs4076137 20888220 rsl 3207747 20888221 rsl 3208059 Pos Build Marker ID /36 20888329 rs4074058 20888884 rs9350282 20888894 rs3193655 20888919 rsl 1545101 20888919 rs3193654 20889269 rsl 2199265 20889428 rs34113701 20889600 rs41272363 20890872 rs4478387 20891222 rsl 1752139 20891373 rs6910215 20891415 rsl 0690190 20891417 rsl 0647996 20891638 rsl 0946408 20892162 rs4710949 20892292 rs4712547 20892371 rs4712548 20892641 rsl 0550462 20892642 rs34372186 20893118 rs9368234 20893144 rs9348443 20893525 rs5874783 20893543 rsl 1344905 20893671 rsl 2210335 20893673 rsl 2210336 20893711 rs6902757 20893943 rs6456373 20894027 rs6927892 20894054 rsl 3210599 20894573 rs34563996 20895285 rs35066145 20897153 rsl 0498698 20898456 rsl 0806923 20898488 rsl 0806924 20898554 rs9368235 20898785 rs9368236 20898787 rs9368237 20899054 rs9356753 20899265 rs12111182 20899490 rsl 1752772 20899516 rsl 2661145 20899518 rsl 2665631 20899691 rsl 2208378 20900193 rs34964322 20901075 rs34430352 20901172 rs4299818 20901416 rs4495263 20901588 rs7773697 20901981 rsl 0684385 20901982 rs33967126 20902035 rs34171574 20902604 rs9460557 20902661 rs4492184 20902662 rs35025612 20903233 rsl 0946409 20903353 rs9295483 20903427 rs11751916 20904975 rs36025037 20905571 rs7738948 20905701 rs9465892 Pos Build Marker ID /36 20905830 rsl 2211211 20906051 rsl 1968853 20906198 rsl 0456236 20906864 rs4712549 20906867 rs36194803 20906929 rs4712550 20907200 rs12213259 20907404 rs4496779 20907564 rs34432145 20907866 rs9358368 20908149 rs9368238 20908386 rs4524599 20908448 rs9465893 20908614 rs12215519 20909486 rs5874784 20909709 rs34686362 20910367 rs9460558 20910522 rsl 2664231 20910525 rsl 0946410 20911078 rs4710950 20911442 rs9465894 20911666 rs6925153 20911791 rs6456374 20912542 rs9465895 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20922954 rs35040258 20922958 rs4710954 20923239 rsl 2661606 20923432 rsl 0946411 20923828 rs36037446 20924516 rs12212105 20925219 rsl 2213857 20925336 rsl 2213956 20925602 rsl 0946412 20925812 rsl 1759888 20925967 rs9366360 20926372 rsl 2665734 20926457 rs4712552 20926516 rs9465903 20926518 rs4712553 20927237 rsl 2190831 20927408 rs4334968 20927432 rs34237934 20927804 rsl 1961950 20927955 rsl 0806925 20929468 rs7753109 20929641 rs9465904 20929820 rs6931788 20929846 rsl 1304808 20930110 rs9465905 20930489 rs9465906 20930866 rs9465907 20931188 rs9465908 20931485 rs6938757 20931735 rs6923264 20931827 rs6900509 20932202 rs9460561 20932400 rsl 0946413 20932413 rs9465909 20932808 rs9460562 20932809 rs9465910 20932976 rsl 0806926 20932997 rs9460563 20933029 rs9465911 20933338 rsl 1404073 20933339 rs34199366 20933375 rs4712554 20933483 rs4712555 20933542 rs35893096 20933749 rs34260649 20933990 rs9465912 Pos Build Marker ID /36 20934012 rs9368240 20934024 rs9368241 20934147 rs9368242 20934260 rs4395717 20934729 rsl 2209113 20935051 rs4446563 20935807 rs9348447 20936313 rsl 0806927 20936483 rs35622501 20936512 rsl 2211426 20936992 rs9368243 20937713 rs7768091 20937751 rs9356755 20938085 rs6917412 20938283 rs12215186 20938644 rs9348448 20938681 rsl 0570889 20938807 rs34799469 20938927 rs12190001 20938932 rs9465913 20939133 rs35997536 20939251 rs6901110 20939636 rs35810189 20940144 rs9368244 20940807 rs9350288 20940851 rsl 2210496 20941839 rs4568440 20942876 rsl 1964964 20943072 rs28616599 20943192 rsl 2201027 20943239 rsl 2194825 20943369 rs34826961 20943724 rs5874788 20943727 rs34317828 20944192 rs9465914 20944328 rs9465915 20946192 rsl 0592623 20946236 rs7749282 20946253 rs7769205 20946255 rs7749021 20946263 rs7769209 20946275 rs7749034 20946424 rs9295484 20946948 rs6456377 20947467 rs34883184 20948065 rs9465917 20948650 rsl 2210803 20948719 rs4345385 20949055 rs7764980 20949271 rs7765060 20949459 rsl 1967047 20949540 rs35943413 20949572 rsl 1967068 20949779 rs9460564 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rs9350290 20963662 rsl 0558810 20963671 rsl 0608340 20963756 rs7761330 20963966 rsl 3209243 20964017 rs35463313 20964570 rsl 2211628 20964682 rs4712556 20965069 rs4710955 20965780 rs34481273 20965904 rsl 6884229 20966215 rsl 1965417 20966239 rs4712558 20966335 rs4712559 20966543 rs34865786 20966637 rsl 7826361 20966708 rs9366362 Pos Build Marker ID /36 20966831 rs9366363 20967583 rsl 1966194 20968463 rsl 2524318 20968532 rs28412953 20968698 rs9358374 20968821 rs9350291 20968927 rs9350292 20969034 rs9350293 20969131 rsl 6901585 20969205 rs5007237 20969579 rs4383807 20969839 rs4330531 20970113 rsl 2662176 20970590 rs9356757 20970850 rs34873202 20970884 rs9368245 20970889 rs34101377 20971175 rsl 2201353 20971267 rs12214755 20972435 rsl 1269210 20973576 rs9465922 20973608 rs12191898 20973841 rs35647500 20973851 rs5874790 20973852 rs35372258 20974027 rs7749397 20974223 rs7454011 20974715 rs35244703 20974836 rs9368246 20974986 rs34062103 20975000 rs35487666 20975596 rsl 6884250 20975795 rsl 0554344 20976043 rs4370355 20976276 rsl 0588127 20976276 rs34382383 20977459 rs7766346 20977678 rs7766681 20977795 rs7770607 20978072 rs9350294 20978617 rs9350295 20978719 rs9366364 20978768 rs34447575 20978882 rs9366365 20980033 rs35505816 20980715 rs34113324 20981367 rs10946414 20981827 rs4645410 20982392 rsl 6884254 20982541 rsl 3197235 20983561 rs9350296 20983706 rs9368247 20984381 rsl 2665789 20984489 rs4077403 20984592 rs4077404 20984662 rs4077405 20984894 rs4529295 20984917 rs35499986 20985132 rs4618519 20985379 rs36002274 100 Pos Build Marker ID /36 20985482 rs9368248 20985514 rs7742802 20985952 rs4236004 20986261 rs4712561 20986658 rs9358375 20986864 rsl 2194583 20986999 rs34923632 20987073 rs4537128 20987237 rs4626408 20987282 rs12194813 20987312 rs6915746 20988259 rs9350297 20988570 rs12210231 20988821 rsl 2198243 20989365 rsl 0946415 20989383 rs7763704 20989596 rsl 0589878 20990154 rs9465923 20990216 rs9465924 20990238 rs9460567 20990523 rs9465925 20990820 rs4612156 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rs34720816 21002625 rsl 2528945 21004281 rsl 2206985 21004330 rsl 1757050 21004330 rs34449480 21004372 rs9368253 21004532 rs9295486 21004540 rs9465930 21004836 rsl 2208719 21005635 rs6918643 21005875 rs4712562 21006091 rs6456380 21006119 rs7759877 21006228 rs9358376 21006412 rs35620702 21006800 rs28665148 21006801 rs28599540 21007273 rs35400949 21007751 rsl 2153898 21007819 rs12154181 21007863 rs12154184 21008099 rs9368254 21008207 rs9368255 21009058 rs35958016 21009211 rs6456381 21009246 rs7758467 21009290 rs6456382 21009421 rs12153811 21009654 rs7739013 21009711 rs6922768 21009716 rs13191241 21009909 rsl 0640864 21009910 rs34135721 21010295 rs34154507 21010566 rs35386545 21010568 rs9368256 21010964 rs7740094 21010972 rs7758155 21011220 rs9366368 21011950 rs9358377 21012344 rs6908429 21012629 rs4712563 21012910 rs4710957 21013210 rsl 2214079 21013433 rs9460572 21013812 rs2876583 21013840 rs9465931 21014102 rs34068097 21014657 rsl 0080699 Pos Build Marker ID /36 21014657 rs9460573 21014665 rs9460574 21014666 rs6920918 21015860 rs4413596 21016247 rs6909682 21016278 rs6910032 21016580 rsl 498427 21016869 rs34713988 21017395 rs9368257 21017439 rs6939006 21017512 rsl 7236121 21017740 rsl 1753331 21018757 rsl 2198263 21018818 rs35916632 21018915 rs9350298 21018982 rs4710958 21019053 rs35886192 21019304 rs6456385 21019380 rs7763674 21019654 rs7746308 21020651 rsl 2190631 21020765 rsl 498425 21021671 rs13197106 21022074 rs6913538 21022178 rs9460575 21022308 rs6914232 21022483 rs9460576 21022485 rs6914586 21022873 rs9465932 21022913 rs2030082 21022932 rs9350299 21023379 rsl 0536841 21023692 rs9465933 21024540 rs34537557 21025636 rs9368258 21026230 rs6938184 21026422 rs6938415 21026611 rs35678799 21028069 rs28440883 21028102 rs4712564 21028251 rs4712565 21028711 rs9366369 21028958 rs9465934 21029390 rs6913658 21030247 rs7765765 21030707 rsl 2662218 21030842 rs9460577 21030852 rs4712566 21030926 rs4712567 21030962 rs6936002 21031254 rs9460578 21031561 rs7771782 21032098 rs2328550 21032169 rs9465935 21033024 rs9460579 21033247 rs2328551 21033384 rs34787947 21033907 rs35164658 21034157 rs34463604 21034296 rsl 6884302 Pos Build Marker ID /36 21034654 rsl 3215945 21034664 rs13215949 21034748 rsl 3202822 21034750 rsl 3203127 21034760 rsl 3203130 21035097 rs35259543 21035108 rsl 0687937 21035135 rs9358378 21035148 rs9465936 21035989 rs6903176 21036896 rs34272344 21037020 rs9366370 21037483 rs7747830 21037954 rs35552655, 21038014 rsl 1970010 21038092 rsl 1970030 21038468 rs35341341 21038480 rs5874794 21038957 rs34094116 21039069 rs9366371 21039135 rs7775995 21040473 rs6916666 21041656 rsl 6884308 21042140 rsl 1395158 21042539 rs34100038 21042991 rs7768647 21043110 rs35030815 21043259 rs9350300 21044027 rsl 0946419 21044393 rsl 0946420 21044437 rs9465937 21044451 rs9368259 21044452 rs33911838 21044591 rs9358379 21044671 rs9460580 21044802 rs35523552 21044952 rs16884310 21046071 rs34741537 21046084 rsl 2526287 21046565 rs9465938 21046566 rs28734969 21046585 rs7747773 21046841 rs9465939 21046900 rs4144650 21047359 rs4712569 21047690 rs4712570 21047713 rs6939250 21047725 rs4710959 21047769 rs4710960 21047987 rs13191844 21048358 rsl 2196595 21048740 rs9350301 21049043 rs9350302 21049105 rsl 1964084 21049192 rs6927419 21049306 rs12198512 21049369 rsl 1450413 21049370 rsl 1409601 21049371 rs33942714 21050175 rs4307160 101 Pos Build Marker ID /36 21050624 rs4712571 21051211 rs9465941 21051466 rsl 0946423 21051483 rs9465942 21051538 rs34759060 21051555 rs9295487 21051560 rs5874795 21051561 rs9358380 21051563 rs12174149 21051568 rs9350303 21051569 rs9358381 21052585 rsl 1279071 21052648 rs9465943 21053046 rs9465944 21053295 rsl 0690950 21053629 rs34879403 21053757 rs7772447 21053935 rs7773189 21054476 rs34602677 21054784 rs6901153 21054804 rsl 1361870 21054805 rs35132815 21055236 rsl 2203876 21055710 rs35896536 21055853 rs34881630 21055870 rs9368260 21056065 rs9460581 21056280 rs6930879 21056288 rs6930887 21056329 rs6931047 21056472 rs9350305 21058200 rs9350306 21058970 rsl 2197923 21059112 rs9460582 21059179 rs5874796 21059866 rs6922187 21060142 rs9465945 21060180 rsl 0558500 21060186 rsl 1289942 21060212 rs9348451 21060247 rs6922914 21060361 rs9358382 21060639 rs35863080 21061204 rs4631270 21061590 rs2015426 21061898 rs7749498 21062676 rs9350307 21062805 rs1004172 21063311 rs7775523 21064970 rs12199174 21066160 rs9368261 21067118 rs7738201 21067314 rsl 7236645 21067986 rsl 6884319 21068463 rs9918311 21068617 rs34769285 21068702 rsl 2205321 21068911 rs6456388 21069040 rs4712572 21069650 rsl 2524678 Pos Build 35/36 Marker ID 21069850 rs13211056 21070260 rsl 7236694 21070934 rs35382761 21071276 rs28612346 21071587 rs6915209 21071832 rs35420176 21072294 rs6940952 21072419 rs35708433 21072662 rs6941808 21072828 rsl 1966306 21073181 rsl 6884325 21073468 rs7743030 21073553 rs28429494 21074417 rs4712573 21074865 rsl 1752712 21075695 rs9460583 21075964 rs9460584 21076612 rs34425275 21076615 rsl 112255 21076815 rsl 112256 21077529 rs9348452 21077563 rs34660637 21077716 rs7746754 21077794 rs9350308 21078333 rs34215872 21079005 rs2030081 21079247 rs6940649 21079554 rs6941043 21079964 rs6913817 21080948 rs201361 21081289 rs34479545 21081631 rsl 980458 21082363 rs13210151 21082946 rs34266759 21083025 rs34192233 21083039 rsl 1427521 21083189 rs35882882 21083211 rsl 1330322 21083279 rsl 997685 21083363 rsl 0498699 21083433 rs201360 21085426 rs201359 21085653 rs201358 21085834 rs34764914 21087560 rs201357 21088272 rs4712575 21088448 rs4712576 21088450 rs4712577 21088472 rs365001 21088891 rs35829025 21089414 rs383684 21089616 rs444005 21090258 rs35693086 21090584 rsl 1961135 21091067 rs201356 21091773 rs201355 21091799 rsl 2193382 21091799 rs34391804 21091914 rs35723307 21091926 rs35448639 Pos Build 35/36 Marker ID 21093023 rs35957348 21093317 rs201354 21093369 rs201353 21093439 rs9350309 21093650 rs201352 21094109 rs201351 21094143 rs35853352 21094861 rs5874797 21094872 rs5874798 21094931 rs201350 21095014 rsl 997684 21095425 rs4560627 21095482 rsl 0699637 21095654 rs7453577 21096171 rsl 1300877 21096223 rs201349 21096419 rsl 0694429 21096428 rs3223730 21096922 rs201348 21097026 rs35010661 21097035 rs201347 21097047 rs10701919 21097265 rs201346 21098132 rs6456389 21099063 rsl 2528036 21099645 rs201345 21099698 rsl 3199754 21099916 rs35504365 21100226 rs35586782 21100247 rs28418444 21100248 rsl 3196975 21100263 rs35586503 21100320 rs9356759 21100418 rs9366372 21100871 rsl 0946424 21100949 rs201344 21101200 rsl 1964880 21101281 rsl 1967584 21101513 rs201343 21102229 rs201342 21102283 rs9350310 21102377 rs9368262 21102486 rs9368263 21103236 rs35996844 21103858 rs201341 21103935 rsl 2660707 21104054 rs201340 21104291 rs201339 21105034 rs396308 21105044 rs4712578 21105348 rs449233 21107366 rs9358383 21107874 rs36078234 21108856 rs9368264 21109330 rs9368265 21109358 rs9368266 21109523 rs9368267 21109553 rs6940871 21109878 rs35240009 21110331 rs6914677 Pos Build Marker ID /36 21110432 rs9350311 21110750 rsl 2195827 21110788 rs9366373 21110864 rs34620040 21111239 rs9350312 21111513 rs2038066 21111536 rs13191651 21111581 rs13191676 21111601 rs2038065 21112269 rs7744303 21112288 rs7744317 21112352 rs7762669 21113187 rs6932336 21113252 rs34002111 21113325 rs6932393 21113687 rs2839854 21114641 rs9348453 21115599 rs9358384 21115719 rs9348454 21115720 rs2473089 21115866 rs2494728 21116011 rs9358385 21116132 rsl 498426 21116718 rsl 2192642 21116822 rsl 3200036 21116851 rs9368268 21116920 rs7750463 21116972 rs7750903 21117087 rs374654 21117572 rs6914615 21117867 rs9465946 21118124 rs364334 21118132 rs416688 21118300 rsl 1382802 21118547 rs1548145 21118567 rs201291 21119018 rs9465947 21119021 rsl 2197742 21119236 rs201292 21119698 rs35998561 21119973 rs201293 21120225 rs9358386 21120735 rs35254358 21120883 rs6905258 21121364 rs201294 21121603 rs201295 21121962 rs7748932 21121994 rs2494729 21122535 rs3966676 21122822 rs34834774 21122975 rsl 6884376 21123408 rs201308 21123602 rs8180606 21123934 rs201309 21123964 rs201310 21124001 rs6456390 21124511 rs201311 21124822 rs5874799 21124823 rs34733906 21124830 rs400514 102 Pos Build 35/36 Marker ID 21124882 rs3061573 21125298 rsl 6884385 21125848 rs34894804 21125898 rs9460586 21126295 rsl 6884389 21126495 rs35678732 21126634 rsl 0946425 21127516 rs6899729 21127744 rsl 6884394 21128114 rs36115181 21128124 rs5874800 21128307 rs34639729 21128419 rs35260082 21128533 rs7744010 21128746 rs201290 21129343 rs201289 21129647 rs34802324 21129981 rs201288 21130208 rs201287 21131340 rs34891710 21131348 rsl 1438527 21131431 rs34878496 21131727 rsl 6884396 21132081 rs9465948 21132220 rsl 6884399 21133062 rsl 1297091 21133400 rsl 69293 21133737 rs201307 21133815 rsl 2206158 21133964 rs34317920 21134374 rs34305502 21134401 rs35570989 21135019 rs13218003 21135740 rsl 2209877 21136038 rs6921781 21136172 rsl 6884406 21136940 rs201306 21136972 rs201305 21137253 rs201304 21137477 rs34243092 21137698 rs201303 21138072 rs201302 21138132 rs201301 21138504 rs35592283 21138790 rsl 0946426 21138980 rs6919322 21139058 rs4710961 21139068 rs9465949 21139350 rs398913 21139414 rs4710962 21139480 rsl 2526927 21139855 rs9460587 21140661 rs415446 21141104 rs35761643 21141617 rsl 1961096 21141944 rs201300 21142185 rs35161624 21142199 rs35206549 21142635 rsl 3210277 21142726 rs12198160 Pos Build Marker ID /36 21142744 rs7766970 21143715 rs201299 21143786 rs35061829 21144118 rs201298 21144658 rs201297 21145049 rs201296 21145549 rs34771308 21145593 rs9295488 21145919 rs989969 21146291 rs34874522 21146814 rs201312 21146901 rs201313 21147026 rs201314 21147263 rs9350314 21147738 rs6918555 21147791 rs6918751 21147930 rs9295489 21148244 rsl 3190826 21148269 rsl 3190835 21148356 rsl 7662372 21148684 rs201315 21148701 rsl 6884415 21150019 rsl 6884420 21150116 rsl 7730046 21150139 rs201316 21151059 rsl 6884425 21151118 rsl 555052 21151344 rsl 1753092 21151557 rs34254730 21151557 rs9465950 21151573 rs7756338 21151831 rs9348455 21151949 rs201317 21152589 rs6925617 21152677 rs201318 21152873 rs9460588 21152874 rs34536386 21152874 rs9460589 21152898 rs201319 21153050 rs201320 21153105 rs201321 21153294 rs201322 21153342 rs201323 21153387 rs201324 21153587 rs201325 21153907 rs9460590 21153987 rs201326 21154014 rs201327 21154069 rs201328 21154147 rs201329 21154297 rs201330 21154380 rsl 3217562 21154919 rs34472513 21154958 rs201331 21155233 rs201332 21155256 rs34312444 21155363 rs201333 21155639 rs201334 21155793 rs201335 21156103 rs201336 Pos Build Marker ID /36 21156840 rs201337 21156885 rs201338 21157007 rs34847494 21157597 rs9942509 21157604 rs34987941 21158291 rsl 0806930 21158841 rs4712579 21160395 rs7775602 21160650 rsl 1760181 21160654 rs2056951 21160683 rs7758243 21160934 rs9358387 21160973 rs6456391 21160974 rs9465951 21161031 rs6903997 21162291 rs6933211 21162635 rs7748652 21162661 rs6456392 21162711 rsl 3215037 21162805 rs7752701 21163066 rs6456393 21163111 rs2328567 21163129 rs6456394 21163541 rsl 2661235 21163651 rs7754018 21163696 rs9350315 21163923 rs9918435 21165424 rs9465953 21165665 rs35560899 21165892 rs34142046 21166104 rs9465954 21166730 rsl 2202256 21166802 rs2206014 21167015 rsl 3219721 21167016 rsl 3205176 21167182 rsl 3219752 21167200 rsl 3205420 21167401 rs9350316 21167460 rs9368270 21167796 rs9465955 21169768 rs28532482 21170022 rsl 7237178 21170224 rsl 3209905 21170225 rsl 3209787 21170236 rsl 3210005 21170269 rsl 3210023 21170287 rsl 3210027 21170376 rs7744921 21170433 rs9465956 21170545 rs9465957 21170553 rs9465958 21170579 rsl 6884466 21170710 rsl 1969047 21170765 rsl 6884468 21170846 rsl 1969587 21171228 rs9465959 21171401 rs34908981 21172309 rs9460591 21173104 rs35603774 21173126 rs9465960 Pos Build Marker ID /36 21173198 rs34559907 21173393 rs4710963 21173679 rs9465961 21173766 rs1001310 21173805 rs4712580 21174689 rs9460592 21174762 rs9460593 21176267 rsl 2209678 21177342 rs35738724 21177501 rs7762612 21177928 rs36174378 21177981 rsl 3199309 21178014 rs9295490 21178237 rsl 2660913 21178243 rsl 0946427 21178328 rsl 2199982 21178333 rs34600664 21178468 rs6932873 21178475 rs9356760 21178487 rs9465962 21178588 rs9356761 21178609 rsl 0650825 21179141 rs4382241 21179575 rs2013346 21179832 rsl 0498700 21180396 rs9350317 21180629 rsl 1757139 21180733 rsl 1757596 21181008 rsl 1757677 21181027 rs9465963 21181171 rsl 3203959 21181269 rs9366374 21181357 rsl 1968037 21181410 rs6918997 21181499 rs9368271 21181567 rs9460594 21181588 rs9460595 21182172 rs9295491 21182342 rs4283868 21182548 rs4413602 21183182 rsl 0541645 21183338 rsl 0541646 21183364 rsl 1407560 21183365 rs35953450 21183371 rs7766554 21183409 rs7766574 21183437 rsl 0541647 21183457 rs7766451 21183464 rs7766713 21183493 rs7766728 21183552 rs4280955 21183645 rs7767038 21183675 rs7766788 21183741 rs7770701 21184027 rsl 6884481 21184246 rs9295492 21184599 rs4367364 21184749 rs2068072 21184770 rs2068071 21185523 rsl 1963640 103 Pos Build 35/36 Marker ID 21185602 rsl 1961090 21185611 rsl 1963654 21185810 rs35119417 21186212 rs9358388 21186666 rs4599624 21187063 rsl 0080639 21187282 rs7749838 21187336 rsl 1967298 21187386 rs34700985 21187552 rs9366375 21187610 rs4310041 21187627 rs4496780 21187688 rs7750461 21187916 rs6917272 21188170 rs6917904 21188430 rs34700472 21188451 rs9350318 21189185 rs4323302 21189629 rs9366376 21189885 rsl 0456237 21189931 rsl 3219886 21190084 rs9368272 21190476 rs35189729 21191594 rs6904648 21191595 rsl 1751563 21191595 rs35898656 21192182 rs4593348 21192409 rs4421186 21192801 rs6915237 21193447 rs7773973 21193514 rsl 7834555 21193811 rs6901354 21194026 rs4130033 21194285 rs35287977 21194419 rsl 0806931 21194732 rsl 1964144 21194764 rsl 0946428 21196061 re12200487 21196232 rs4712581 21196650 rs6456395 21196835 rs6456396 21197051 rs9368273 21197394 rs4712582 21198212 rs34465715 21198601 rs6904348 21199015 rsl 1433815 21199016 rs36110847 21199138 rs9368274 21199756 rsl 2197841 21199815 rs12197853 21199817 rs12197854 21200342 rs7762660 21200361 rs7762670 21200554 rs7762964 21200605 rsl 3210302 21200944 rs34756370 21201333 rs7768086 21201341 rs13214341 21202104 rs33945169 21202717 rs6939622 Pos Build 35/36 Marker ID 21202933 rs4454125 21203121 rs4401656 21204432 rsl 1969472 21204602 rs9358389 21204788 rs4712583 21205444 rsl 1757261 21205844 rs34430280 21206360 rsl 1757901 21206756 rs34764667 21206833 rs35866346 21207116 rs9465965 21207331 rs7744319 21207645 rs9368275 21207687 rs9356762 21208023 rs9350319 21208328 rs9350320 21208606 rs9366377 21208909 rs5874801 21209654 rs9368276 21210536 rs4712584 21210553 rs34092761 21210726 rs9366378 21211436 rsl 1968036 21211664 rs9465966 21211803 rs4569951 21212138 rs4130302 21212414 rs35081613 21212547 rs9358390 21212715 rs6925464 21212715 rs9460596 21212847 rsl 7834987 21213142 rsl 2529531 21213851 rs36086759 21214087 rs6936205 21215067 rs4574622 21215086 rs9465967 21215088 rs9358391 21215150 rs35347692 21215159 rs5874802 21215207 rs4624863 21215258 rs9465968 21215359 rs4526186 21215371 rs34865903 21215437 rs7739050 21215448 rs4326226 21216093 rs4712585 21216145 rs9356763 21216170 rs4710964 21216871 rs9460597 21218688 rsl 1963150 21218907 rs6923546 21219519 rs6924221 21220306 rsl 0456238 21222458 rs34418857 21222459 rs34251532 21222460 rs34219362 21222644 rs35962170 21223003 rsl 6884514 21223188 rs7773318 21223279 rs4340995 Pos Build Marker ID /36 21223295 rs9356764 21224572 rs35468559 21224879 rs3935207 21224965 rs35629967 21225019^ rs6927498 21225119 rsl 0613278 21225499 rs35372171 21225513 rsl 0554335 21225585 rs7764365 21225685 rs35234206 21225694 rsl 1418036 21225734 rs7768536 21226218 rs4389757 21227109 rs6456397 21227703 rs35183051 21228007 rs7741436 21228269 rs9356765 21228407 rs9366379 21228562 rs6926818 21228614 rsl 6884524 21228619 rs34425854 21228733 rs4074910 21228748 rs4076112 21229002 rs35885025 21229134 rs6909332 21229654 rs4438948 21229845 rs6905660 21230834 rs9358392 21231054 rs9368279 21231899 rs4315997 21231967 rs4479917 21232500 rsl 0946430 21232701 rs34821627 21232763 rs13191691 21232779 rsl 3207763 21232796 rsl 3207766 21232816 rs13191830 21233338 rs34857211 21234866 rs7750839 21235291 rs7751485 21235577 rsl 1757294 21235798 rs34183889 21236043 rsl 2055489 21236223 rs28421119 21237436 rs9295493 21237650 rsl 2055790 21237696 rs35692444 21237763 rs7766575 21237890 rs9356766 21237892 rs34802727 21237915 rs35927368 21238432 rsl 0708944 21238635 rs6932722 21238849 rs6937439 21238961 rs9986401 21239004 rs9465969 21239122 rs9986662 21239291 rs9295494 21239512 rs35030599 21240132 rs9460598 Pos Build Marker ID /36 21240526 rs28403910 21241995 rs9465970 21242670 rs7760880 21242672 rs7761283 21242682 rsl 1463641 21242783 rs7765177 21242820 rs7765199 21242857 rs7764887 21243009 rs7765106 21243039 rs28610069 21243105 rs7765274 21243107 rs2446490 21243137 rs2493869 21243228 rs7765725 21243240 rs7765730 21243646 rsl 6884554 21243857 rs13216162 21244099 rs2446489 21244512 rs2446488 21244516 rs7771907 21245195 rs9350322 21245369 rs2446487 21246042 rs35201465 21246079 rs9358393 21246445 rs959712 21246447 rs35541643 21246451 rs34848377 21246456 rs5874803 21246457 rs33951051 21246458 rs5874804 21246459 rs35717786 21246466 rs5874805 21246467 rs35384149 21246474 rs959711 21246487 rs34589183 21246785 rs9688559 21246915 rs9689353 21246958 rs34154291 21246988 rs9688564 21246992 rs9688565 21247009 rs2446486 21247020 rs9688569 21247061 rs9688573 21247079 rs9295495 21247094 rs9465971 21247737 rs9460599 21247746 rs6916667 21247788 rs9465972 21248278 rs2446485 21248465 rs2446484 21249707 rs28665959 21249879 rs35583136 21249895 rs34896971 21249984 rs7746383 21250235 rs7746846 21250457 rs28360550 21250639 rs6932702 21251345 rs9348456 21251752 rs35724409 21251989 rs2328573 104 Pos Build 35/36 Marker ID 21252098 rsl 7835633 21252216 rs36008085 21252578 rsl 0498701 21252578 rs35938718 21252735 rs34957382 21253603 rsl 0708192 21254245 rsl 466340 21255061 rsl 0710231 21255726 rsl 466339 21255824 rs7740358 21256011 rsl 1405792 21256411 rs1471205 21256721 rs9368280 21257043 rs9295496 21257242 rsl 2206028 21257356 rs9368281 21258107 rs2168985 21258129 rsl 2207912 21258136 rs35882470 21258203 rs9368282 21258436 rs7752602 21258626 rs7752788 21258747 rs2446483 21258795 rs9356768 21258995 rs34495814 21259344 rs9350323 21259352 rs4530843 21259489 rs9460600 21259600 rs9460601 21260113 rsl 0946431 21260135 rs35088240 21260216 rsl 0946432 21260253 rsl 0946433 21260917 rsl 1961031 21261341 rs4144175 21261468 rsl 0604354 21261575 rsl 2203853 21261620 rs6901380 21261891 rs6906201 21262118 rs9460602 21262389 rs35396145 21262741 rs9350324 21262775 rs9295497 21262969 rs9366381 21263128 rs6456398 21263152 rs6456399 21263168 rs6456400 21263322 rs6456401 21263462 rsl 1456476 21263471 rs34116986 21263595 rs6913868 21263798 rs9366382 21263882 rs9348457 21264053 rs35931974 21264270 rs9366383 21264385 rs9366384 21264393 rs9356769 21264732 rs34306955 21264842 rs9350325 21264968 rs6924598 Pos Build 35/36 Marker ID 21265017 rs4712586 21265065 rs7761116 21265072 rs9358395 21265152 rs9368283 21265828 rs34689265 21266252 rs6931316 21267009 rs6916577 21267167 rs6937555 21267311 rsl 0645059 21267321 rsl 0652396 21267832 rsl 6884591 21268027 rsl 1442196 21268361 rs7739578 21268400 rs7739596 21268426 rs4527692 21268664 rs9295498 21268668 rs9295499 21268866 rsl 0080292 21268870 rs35915482 21268881 rs9465976 21268928 rs28581582 21268942 rs34844023 21269038 rs12179712 21269039 rs9465977 21269504 rs9465978 21271039 rs6929437 21271299 rs4995985 21271738 rs34031561 21271898 rs6914598 21272056 rs6935079 21272110 rs6935117 21272124 rs6935124 21272174 rs9368284 21272190 rs6915161 21272228 rs9356770 21272416 rs35558562 21272655 rs6916053 21272716 rs34191499 21273107 rs6941714 21273161 rs34326160 21273168 rs9460603 21273192 rs9348458 21273257 rs7776158 21273274 rsl 1965768 21274046 rs35674401 21274684 rs2125570 21275213 rs7768526 21275957 rs9368285 21276570 rs28360551 21277729 rs7763700 21277824 rs4425589 21277964 rs9348459 21278549 rsl 3197595 21278592 rs9460604 21278780 rs12180174 21278845 rs9465979 21279293 rs36058161 21279338 rsl 1969929 21279609 rsl 1965049 21279673 rs9295500 Pos Build 35/36 Marker ID 21279689 rs34012677 21279828 rs12178179 21279839 rs9465980 21280353 rs9358396 21281052 rsl 2194541 21281118 rs2061441 21281632 rs9460605 21281781 rsl 2525339 21282235 rs35462438 21282590 rs9465981 21282848 rs4637624 21282946 rs35969558 21283471 rsl 2525940 21283655 rs34603118 21283948 rsl 2528104 21284103 rsl 2526391 21284906 rs6939148 21284912 rs9460606 21285561 rsl 3219281 21285569 rs13219285 21285598 rs13219506 21285611 rs13219193 21285620 rs13219198 21285664 rsl 3219637 21285689 rsl 3205078 21285691 rsl 3205079 21285875 rsl 1308599 21286261 rs9465982 21288187 rsl 2214946 21288554 rs34495587 21289215 rsl 2523755 21289629 rs35642303 21290957 rs9295501 21291348 rs35815279 21291533 rsl 2527222 21291647 rs9465983 21291857 rs2493868 21291918 rs35979352 21292407 rs34248538 21292789 rsl 0946434 21292811 rs9465984 21293033 rs34599800 21293434 rs35442433 21293569 rs9465985 21294166 rs35712201 21294748 rs35539626 21294750 rs9465986 21294751 rs9465987 21294801 rsl 1961469 21295134 rs2446482 21295312 rs9465988 21295313 rs12191416 21295313 rs35985333 21295996 rs9465989 21296793 rs9350327 21297183 rs34750271 21297265 rs35013686 21297416 rsl 6884616 21297902 rs35898446 21297924 rsl 1751020 Pos Build Marker ID /36 21297967 rsl 0452581 21298562 rsl 3192000 21298563 rs13191669 21298583 rs13192011 21298617 rsl 3192029 21298629 rs13192143 21298630 rsl 3207866 21298671 rs13191819 21298690 rs13192164 21298721 rs13192173 21298723 rs13191845 21299659 rs9465990 21299810 rs9460607 21299907 rs9465991 21299909 rs9366386 21299971 rs35944981 21300001 rs9366387 21300046 rs9366388 21300106 rs9368287 21300203 rsl 3193222 21300325 rsl 0080974 21300381 rs9295502 21300388 rsl 2528974 21300395 rs7759646 21300433 rs9465992 21300768 rsl 1964193 21301021 rs34456723 21301080 rs34094109 21301834 rsl 1759448 21302380 rsl 1962770 21303198 rs9366389 21303687 rsl 1753415 21304730 rs4712587 21304976 rs7748091 21305299 rs28469715 21305355 rs7748766 21305591 rs35164470 21305660 rs2125571 21305669 rs9465993 21306062 rs3793090 21307994 rs1531303 21308261 rs2305955 21308369 rsl 459047 21309244 rs35662535 21309281 rs9767650 21309286 rs9767186 21309387 rs9460608 21309472 rs9465994 21310133 rs9465995 21310563 rs36067162 21310749 rsl 1965158 21311344 rs9350328 21311426 rs5874806 21311451 rsl 0616274 21311452 rs5874807 21311454 rsl 1288843 21311471 rs9350329 21311502 rsl 824330 21311620 rs9717950 21311710 rs3898487 105 Pos Build 35/36 Marker ID 21311900 rs9350330 21311902 rs9350331 21312023 rs35603064 21312085 rs35615714 21312109 rs36017220 21312120 rsl 2196363 21312143 rs35881379 21312153 rs35710688 21312177 rs35017881 21312188 rs12196418 21312191 rs12196419 21312206 rs35883368 21312223 rsl 2196423 21312231 rs34046809 21312253 rs34108390 21312453 rs6921264 21312671 rs6921652 21312775 rs6926388 21312801 rsl 2527588 21313200 rsl 0456240 21313329 rsl 0456241 21313367 rsl 0456242 21313458 rsl 0456243 21313856 rs34046046 21313879 rsl 3213969 21313886 rs6932316 21313910 rs6932752 21313958 rsl 3214311 21313963 rs6932914 21313998 rs6932635 21314018 rs6912407 21314041 rs34849597 21314107 rs9366390 21314243 rsl 0223539 21314298 rsl 0223540 21314473 rs6913302 21315081 rs9366391 21315139 rs9356771 21315390 rsl 2530254 21315432 rs34085972 Pos Build 35/36 Marker ID 21315529 rs4291091 21315727 rs6940465 21315763 rs6901748 21316195 rs6902505 21316396 rs898167 21316398 rs898166 21316408 rs898165 21316820 rs34797264 21317102 rs9368288 21317206 rs9358397 21317611 rs2168984 21317978 rsl 563728 21318135 rs4712588 21318266 rsl 1267610 21318399 rs4712589 21318666 rs6915037 21318882 rsl 2664336 21319431 rs9465998 21319494 rs10214790 21319776 rs12201217 21320060 rs9350332 21320905 rs9358398 21321149 rs9358399 21321286 rs9358400 21321533 rsl 0214694 21321733 rs10214716 21322176 rs9460609 21322179 rs6929219 21322517 rsl 2527686 21322561 rsl 2527673 21322733 rs9350333 21323322 rsl 0946436 21323380 rs6913136 21323400 rsl 3200114 21323464 rsl 3200422 21323815 rs2328572 21323949 rs9350334 21324672 rs34913347 21324713 rsl 0946437 21324725 rsl 0946438 Pos Build Marker ID /36 21325164 rs9358401 21325261 rs34055473 21325350 rs34921405 21325357 rs6904880 21325395 rs6456403 21325653 rs2085654 21325832 rs9466000 21325853 rs9466001 21326033 rs2100707 21326158 rs12111402 21326366 rs4712590 21326649 rs4710965 21327416 rs6937610 21327459 rsl 2110862 21327488 rs35624914 21327606 rsl 1349673 21327854 rsl 6884681 21327895 rs7738425 21328030 rsl 6884685 21328355 rsl 6884688 21328398 rs35663664 21328510 rsl 2203389 21328818 rs12191541 21328946 rs34618548 21330074 rsl 563726 21330730 rsl 6884693 21331119 rs2328574 21331209 rsl 6884699 21331264 rsl 6884705 21331267 rs6929141 21331293 rsl 6884709 21331392 rsl 6884713 21332034 rs9466002 21332081 rs9466003 21332103 rs9466004 21332139 rs9466005 21332272 rs9460610 21332409 rs7770316 21332488 rsl 1964983 21332496 rs7770752 Pos Build 35/36 Marker ID 21332625 rs7770637 21333229 rsl 870421 21333556 rs6942273 21333618 rs9466006 21333709 rs9466007 21334500 rs7763249 21335731 rs9368289 21335750 rs9368290 21335782 rsl 3202305 21335903 rs34362358 21335906 rsl 1415596 21336317 rs28484932 21336582 rs7754027 21336699 rs34022115 21336867 rs4710966 21337512 rsl 6884722 21338182 rs35571136 21338184 rs35739791 21338815 rs9460611 21338986 rs9460612 21339013 rsl 2200511 21339097 rs35791563 21339201 rs34084405 21339207 rs34158326 21339453 rsl 563727 21339524 rs3840416 21339530 rsl 1362523 21339688 rs7770664 21339861 rs35121088 21339935 rs4712591 21340199 rs35206923 21340202 rs28600127 21340213 rs4710967 21340214 rs4710968 21340218 rs13213171 21340219 rsl 3197226 21340225 rsl 2199601 21340594 rsl 137970 106 Table 10. SNPs within LD block C06 (SEQ ID NO:l) between positions 20,634,996 and 20,836,710 bp on Chromosome 6 in NCBI Build 35 and NCBI Build 36 Position in Build 35/36 Position in SEQ ID NO:1 Marker ID 20634996 1 rs4429936 20635028 33 rs9465780 20635060 65 rs7743222 20635066 71 rs7743223 20635241 246 rs4516938 20635285 290 rs4628090 20635339 344 rs9465781 20635349 354 rs28450063 20635350 355 rs9465782 20635834 839 rs4712503 20635845 850 rs9465783 20635860 865 rs4712504 20636037 1042 rsl 0946388 20636813 1818 rs9460517 20636939 1944 rs34086777 20637089 2094 rs9465785 20637215 2220 rs7754223 20637279 2284 rs34173688 20637287 2292 rsl 1459684 20637288 2293 rs35781726 20637303 2308 rs9460518 20637450 2455 rsl 1362835 20637521 2526 rs7772956 20637824 2829 rsl 883641 20637875 2880 rsl 883640 20637944 2949 rsl 1402844 20638219 3224 rs35198704 20638372 3377 rs6923683 20638762 3767 rs12181295 20638829 3834 rs9465788 20638961 3966 rs34578766 20639509 4514 rs2206578 20639662 4667 rs35530523 20639708 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Position in SEQ ID NO:1 Marker ID 20723951 88956 rs9260889 20723952 88957 rs9766686 20723956 88961 rsl 0046203 20723957 88962 rs9260888 20723958 88963 rsl 2180540 20723961 88966 rs9766115 20723968 88973 rs6912019 20723969 88974 rs9767458 20723976 88981 rsl 3202161 20723989 88994 rsl 3218048 20724000 89005 rsl 3218040 20724001 89006 rsl 3206557 20724002 89007 rsl 3202152 20724013 89018 rsl 2210049 20724013 89018 rs34552032 20724018 89023 rs28890881 20724018 89023 rs34478537 20724025 89030 rs35191657 20724038 89043 rs34450517 20724043 89048 rs9689655 20724064 89069 rs12180172 20724068 89073 rs28865015 20724071 89076 rs9717839 20724072 89077 rs9717836 20724074 89079 rs9885593 20724082 89087 rs28887572 20724083 89088 rs13216113 20724083 89088 rs35254115 20724084 89089 rsl 0949190 20724085 89090 rs6923503 20724087 89092 rs12214411 20724091 89096 rs28747986 20724096 89101 rsl 087363 20724096 89101 rs1091092 20724104 89109 rsl 2180759 20724107 89112 rsl 1758052 20724112 89117 rs9261321 20724113 89118 rs28861738 20724113 89118 rs36109104 20724123 89128 rsl 3208115 20724129 89134 rs9472693 20724130 89135 rsl 2208570 20724130 89135 rs28832660 20724131 89136 rsl 3200482 20724131 89136 rs9260886 20724131 89136 rs9472694 20724159 89164 rs9260885 20724172 89177 rs280295 20724172 89177 rs28749538 20724174 89179 rsl 3201041 20724184 89189 rsl 087362 20724187 89192 rsl 2183850 20724190 89195 rsl 2202552 20724208 89213 rs9260884 20724210 89215 rs9474341 20724211 89216 rs9260883 20724222 89227 rs34669820 20724225 89230 rsl 2189886 20724234 89239 rs12182114 Position in Build 35/36 Position in SEQ ID NO:1 Marker ID 20724266 89271 rs9688643 20724272 89277 rsl 2195237 20724281 89286 rs35293595 20724281 89286 rs9381428 20724306 89311 rs34665644 20724309 89314 rsl 2189599 20724311 89316 rsl 2208503 20724312 89317 rs9800791 20724330 89335 rsl 2173681 20724337 89342 rsl 2182094 20724343 89348 rs12182119 20724352 89357 rs12182102 20724392 89397 rsl 2174506 20724393 89398 rs9767809 20724394 89399 rs12173703 20724401 89406 rsl 2202889 20724435 89440 rs28840538 20724466 89471 rs9473983 20724467 89472 rs34220946 20724487 89492 rs9261322 20724491 89496 rs9261323 20724517 89522 rs526092 20724564 89569 rs9473982 20724566 89571 rs34307764 20724626 89631 rs34490559 20724665 89670 rs4449621 20724685 89690 rs4714818 20724698 89703 rs4714817 20724722 89727 rs682384 20724738 89743 rs682051 20724753 89758 rsl 2530056 20724756 89761 rs35086683 20724888 89893 rsl 2528468 20725092 90097 rs10650195 20725092 90097 rs35956126 20725109 90114 rs6937578 20725159 90164 rsl 2530107 20725173 90178 rs720448 20725176 90181 rs9368212 20725250 90255 rs35481531 20725253 90258 rs720449 20725262 90267 rsl 0650196 20725495 90500 rs2064 20725499 90504 rs2065 20725638 90643 rs9368213 20725732 90737 rs41455744 20726077 91082 rs34960654 20726154 91159 rs6900954 20726168 91173 rs6456359 20726176 91181 rs7739405 20726601 91606 rs7760508 20726684 91689 rsl 0456007 20726987 91992 rs9460534 20727168 92173 rsl 1966749 20727353 92358 rs9358354 20727809 92814 rs9368214 20727982 92987 rs9350268 20728095 93100 rs2069013 20728160 93165 rs2069014 114 Position in Build 35/36 Position in SEQ ID NO:1 Marker ID 20728290 93295 rs2069015 20728292 93297 rsl 1967475 20729096 94101 rs10214549 20729217 94222 rs2223621 20729281 94286 rs9465835 20729984 94989 rs35404829 20729995 95000 rsl 0687080 20730233 95238 rs6915936 20730331 95336 rs9295472 20730732 95737 rsl 569660 20730929 95934 rs7455009 20730945 95950 rsl 569659 20730946 95951 rs5874775 20730948 95953 rsl 0601252 20730983 95988 rsl 569658 20731030 96035 rs34142400 20731063 96068 rsl 6883996 20731181 96186 rs35073110 20731184 96189 rs5028948 20731263 96268 rs34201758 20731371 96376 rs6456360 20731373 96378 rs6456361 20731380 96385 rs6456362 20731584 96589 rs6922571 20731925 96930 rs35145358 20731950 96955 rs9465836 20732013 97018 rs7763304 20732158 97163 rs9465837 20732218 97223 rs7743314 20732337 97342 rs714831 20732361 97366 rs714830 20732484 97489 rs7743789 20732584 97589 rs5874776 20732589 97594 rs5874777 20732965 97970 rsl 6884003 20733079 98084 rs9356741 20733080 98085 rs9366358 20733246 98251 rs9356742 20733430 98435 rsl 1756987 20733470 98475 rs9465838 20733613 98618 rs2206579 20733920 98925 rs35111339 20734361 99366 rs6917583 20734388 99393 rs6917599 20734630 99635 rsl 3437429 20735418 100423 rs34307011 20735420 100425 rs4515379 20735756 100761 rs2223620 20735870 100875 rs9465839 20735993 100998 rsl 2664972 20736790 101795 rs28402356 20736798 101803 rs6934727 20736873 101878 rs35493429 20736881 101886 rsl 1369825 20737261 102266 rs4523079 20737470 102475 rs7771213 20737568 102573 rs9465840 20737687 102692 rs9465841 20737767 102772 rs9465842 Position in Build 35/36 Position in SEQ ID NO:1 Marker ID 20737837 102842 rs9460535 20737992 102997 rs34835908 20738060 103065 rs9465843 20738139 103144 rsl 3220465 20738159 103164 rsl 3220352 20738321 103326 rs4710937 20738375 103380 rs9460536 20738376 103381 rsl 3190734 20738451 103456 rs9465844 20738712 103717 rs35976895 20738713 103718 rsl 1327958 20738932 103937 rsl 3194407 20738990 103995 rsl 0484633 20739524 104529 rs2328528 20739789 104794 rs35958155 20739809 104814 rs4421185 20739932 104937 rs2328529 20740089 105094 rs9460537 20740745 105750 rsl 7224527 20740886 105891 rs34166991 20741024 106029 rsl 7823073 20741276 106281 rs12183074 20741316 106321 rs9465845 20741844 106849 rs35148963 20741886 106891 rs7768642 20742320 107325 rs9465846 20742407 107412 rs9465847 20742551 107556 rsl 7823127 20742594 107599 rsl 6884021 20742630 107635 rs4533976 20742865 107870 rs7755830 20743005 108010 rs7756031 20743139 108144 rs35650451 20743192 108197 rs10561117 20743241 108246 rs6940200 20743799 108804 rs9465848 20743808 108813 rs34351919 20745083 110088 rs4712519 20745285 110290 rs9368215 20745566 110571 rsl 2206285 20745853 110858 rs34049994 20745988 110993 rs7751957 20746702 111707 rs9465849 20746857 111862 rs7341291 20746957 111962 rs6921014 20747388 112393 rs9465850 20747583 112588 rs7758612 20747681 112686 rs35602526 20748295 113300 rs9465851 20748399 113404 rs34257578 20748403 113408 rsl 1339738 20748516 113521 rs9460538 20748850 113855 rs4712520 20748883 113888 rs4710938 20749084 114089 rs35889049 20749315 114320 rs9348440 20749879 114884 rs9465852 20750054 115059 rsl 2196009 20750306 115311 rsl 1968248 115 Position in Build 35/36 Position in SEQ ID NO:1 Marker ID 20750353 115358 rs34797179 20750764 115769 rs6925328 20750913 115918 rs36073053 20751137 116142 rs35462488 20751140 116145 rs36224625 20751150 116155 rs3060659 20751153 116158 rs5874778 20751155 116160 rsl 1267861 20751201 116206 rs4235999 20751230 116235 rsl 6884038 20751706 116711 rs2328530 20751731 116736 rs2328531 20751750 116755 rs28360636 20752162 117167 rs6932676 20752183 117188 rs9460539 20752303 117308 rs6932876 20752346 117351 rs34929755 20752359 117364 rs28733367 20752360 117365 rsl 1348111 20752473 117478 rs6933219 20752702 117707 rs6933165 20752872 117877 rs35255583 20752901 117906 rs34332316 20752923 117928 rs4710939 20753486 118491 rsl 1970417 20753659 118664 rsl 1963217 20753670 118675 rsl 1965473 20753833 118838 rs2876575 20754049 119054 rs7739974 20754976 119981 rs7745175 20755173 120178 rs7765784 20755178 120183 rs6907731 20755250 120255 rs35057896 20755313 120318 rs7746072 20755639 120644 rsl 0484632 20755770 120775 rs35444529 20755849 120854 rsl 7823571 20755941 120946 rsl 1965062 20755962 120967 rs6936199 20755965 120970 rs6913126 20756178 121183 rs6913509 20756613 121618 rs34638218 20756673 121678 rs35746011 20756741 121746 rs9460540 20757090 122095 rs36045545 20757129 122134 rs35392790 20757233 122238 rs6456364 20757260 122265 rs2179553 20757513 122518 rs9350269 20757531 122536 rs9465854 20757787 122792 rs2179552 20757936 122941 rs6925233 20758033 123038 rs2328532 20758248 123253 rs7743970 20758317 123322 rsl 3209457 20758318 123323 rs34641285 20758344 123349 rsl 3209538 20758387 123392 rs2876576 20758479 123484 rsl 3209572 Position in Build 35/36 Position in SEQ ID NO:1 Marker ID 20758653 123658 rs28783153 20758712 123717 rs9969037 20758800 123805 rs7766844 20758969 123974 rs7767133 20759291 124296 rs7749464 20760100 125105 rs2050225 20760696 125701 rs9295474 20760744 125749 rs9295475 20761529 126534 rs2328545 20761548 126553 rs28846771 20761779 126784 rs2876582 20761899 126904 rsl 0223446 20762094 127099 rsl 3219723 20762095 127100 rsl 3203489 20762154 127159 rsl 3203583 20762172 127177 rsl 3203887 20762279 127284 rs6456366 20762876 127881 rs9358355 20763089 128094 rs9368216 20763375 128380 rs9465855 20763384 128389 rs9465856 20763463 128468 rsl 6884070 20763482 128487 rsl 6884072 20763647 128652 rsl 3208604 20764169 129174 rs9465857 20764307 129312 rs9368217 20764559 129564 rs9460541 20764746 129751 rs9460542 20764765 129770 rsl 1969955 20764779 129784 rs4712522 20764924 129929 rsl 6884074 20765172 130177 rs34489684 20765324 130329 rs2328546 20765543 130548 rs4712523 20765844 130849 rs4712524 20765898 130903 rs35397753 20765991 130996 rs4710940 20766197 131202 rsl 3190727 20766215 131220 rs35136485 20766311 131316 rs35260725 20766335 131340 rs35939620 20766566 131571 rsl 7823996 20766713 131718 rsl 6884082 20767438 132443 rs6906327 20767566 132571 rs6456367 20767785 132790 rs6456368 20768202 133207 rs7749083 20768344 133349 rs6456369 20768669 133674 rsl 0946396 20768672 133677 rsl 0946397 20768710 133715 rsl 1759505 20769000 134005 rsl 3203361 20769013 134018 rsl 0946398 20769122 134127 rs7774594 20769229 134234 rs7754840 20769249 134254 rs9460543 20769508 134513 rs9460544 20769529 134534 rs9460545 20769711 134716 rs2206740 116 Position in Build 35/36 Position in SEQ ID NO:1 Marker ID 20769806 134811 rs5874779 20769807 134812 rs33970890 20769815 134820 rs5874780 20769816 134821 rs35014292 20769816 134821 rs35363501 20770092 135097 rs6456370 20770102 135107 rs979614 20770196 135201 rs35456723 20770571 135576 rs9368218 20770945 135950 rs4712525 20771014 136019 rs4712526 20771314 136319 rs4712527 20771442 136447 rs35191644 20771442 136447 rs34470647 20771611 136616 rs9460546 20771938 136943 rs9465859 20772079 137084 rs9465860 20772291 137296 rs736425 20772508 137513 rs3060776 20772509 137514 rs34941928 20772512 137517 rs5874781 20772761 137766 rs35778487 20773060 138065 rs742642 20773305 138310 rs35248697 20773436 138441 rsl 1967127 20773528 138533 rs7748382 20773547 138552 rs9688549 20773548 138553 rs9689351 20773570 138575 rs28665000 20773886 138891 rs7752236 20773925 138930 rs7772603 20774001 139006 rs7752780 20774034 139039 rs7752906 20774160 139165 rs34184260 20774223 139228 rs2206739 20774225 139230 rs2206738 20774250 139255 rs2206737 20774436 139441 rsl 1970425 20774484 139489 rs36034806 20774899 139904 rs35042364 20775218 140223 rs35540121 20775361 140366 rs9358356 20775667 140672 rs9356743 20775778 140783 rs9350270 20776366 141371 rs34929853 20778035 143040 rs34971765 20778443 143448 rsl 1970596 20779261 144266 rsl 2527373 20779367 144372 rs35916847 20780262 145267 rsl 1968224 20780271 145276 rsl 1968225 20780276 145281 rs9465861 20780296 145301 rsl 1968264 20780406 145411 rsl 2189849 20780413 145418 rsl 2209627 20780432 145437 rsl 2189895 20780855 145860 rsl 1968848 20781135 146140 rsl 1963945 20781601 146606 rs35677128 Position in Build 35/36 Position in SEQ ID NO:1 Marker ID 20781859 146864 rs7451008 20782670 147675 rs9368219 20782790 147795 rs1012636 20782945 147950 rs13217846 20783274 148279 rs1012635 20783700 148705 rs35665197 20783771 148776 rs35261542 20783828 148833 rs28823314 20783899 148904 rs28890810 20784051 149056 rs28871991 20784393 149398 rs34499031 20784650 149655 rsl 3208763 20784747 149752 rs28719685 20784789 149794 rs28856096 20785042 150047 rsl 1961863 20785211 150216 rsl 7824302 20785289 150294 rsl 2660618 20786302 151307 rsl 1371206 20786303 151308 rs34152621 20786409 151414 rs4712528 20786463 151468 rs13217082 20786470 151475 rsl 3217085 20786481 151486 rsl 3217090 20786483 151488 rsl 3217091 20786523 151528 rsl 3200946 20786772 151777 rsl 1968032 20786954 151959 rs9465863 20787289 152294 rsl 569699 20787386 152391 rs34168173 20787688 152693 rs7756992 20788045 153050 rs35312717 20788657 153662 rs9348441 20788843 153848 rs9368220 20788941 153946 rs6931254 20789327 154332 rs6911742 20790601 155606 rs35612982 20791039 156044 rs35816514 20791123 156128 rs34612860 20791143 156148 rs9350271 20791162 156167 rs35657899 20791179 156184 rsl 1364854 20791249 156254 rs9460547 20791646 156651 rsl 6884103 20791961 156966 rs2206736 20793465 158470 rs9356744 20794295 159300 rs34987372 20794427 159432 rs36005020 20794552 159557 rs7766070 20794975 159980 rs9368222 20795290 160295 rs35566695 20795781 160786 rsl 0440832 20796100 161105 rsl 0440833 20796237 161242 rs35747076 20796578 161583 rs6900217 20797104 162109 rs34433496 20797924 162929 rs7748720 20797928 162933 rs34175709 20798290 163295 rs6911357 20800493 165498 rsl 2200791 117 Position in Build 35/36 Position in SEQ ID NO:1 Marker ID 20800955 165960 rs5874782 20800957 165962 rs36119385 20801341 166346 rsl 3219682 20802207 167212 rs4710941 20802270 167275 rs4620109 20802272 167277 rs28459626 20802273 167278 rs4712529 20802294 167299 rsl 0577753 20802504 167509 rs2223683 20802573 167578 rs2206735 20802863 167868 rs2206734 20802910 167915 rs34530846 20803458 168463 rsl 6884131 20804127 169132 rsl 0806921 20805104 170109 rsl 6884133 20805571 170576 rsl 7824500 20805652 170657 rsl 0946401 20806114 171119 rsl 6884135 20806582 171587 rs35711395 20807220 172225 rsl 1969783 20807364 172369 rsl 6884137 20808600 173605 rsl 1970626 20809092 174097 rs12190713 20809106 174111 rsl 1398905 20809415 174420 rsl 1961445 20809470 174475 rs35982077 20809486 174491 rsl 1305935 20810952 175957 rs9356745 20811700 176705 rs35043644 20811842 176847 rsl 6884140 20811931 176936 rs6931514 20812147 177152 rs35443650 20813281 178286 rs34671712 20813569 178574 rsl 1753081 20814081 179086 rs7739516 20814209 179214 rs6901559 20815176 180181 rsl 3196379 20815177 180182 rs13212234 20816204 181209 rs10536170 20817155 182160 rs9465869 20817688 182693 rs36070002 20818288 183293 rsl 7226450 20818905 183910 rsl 073247 20819131 184136 rs9465870 20819386 184391 rsl 7226492 20819433 184438 rs13213613 20819567 184572 rsl 6884146 20819958 184963 rs2206733 20820440 185445 rs3749925 20821121 186126 rs9460548 20821619 186624 rs9460549 20821685 186690 rsl 040558 20821893 186898 rs4712530 20822083 187088 rs35629277 20822362 187367 rs7451928 20822445 187450 rs6456371 20822589 187594 rsl 3220116 20822823 187828 rs2206732 20823169 188174 rs2179633 Position in Build 35/36 Position in SEQ ID NO:1 Marker ID 20823483 188488 rsl 1963770 20823805 188810 rsl 0946402 20823840 188845 rs4712531 20824098 189103 rs35738288 20824232 189237 rs9295478 20824549 189554 rs2328547 20824763 189768 rs3060781 20824764 189769 rs34686252 20824856 189861 rs13215905 20824884 189889 rs9368223 20824937 189942 rs2328548 20825025 190030 rsl 1427712 20825074 190079 rs6935599 20825100 190105 rs13216165 20825234 190239 rs9465871 20825383 190388 rsl 0946403 20826219 191224 rs2328549 20826449 191454 rsl 7226774 20827124 192129 rs9358357 20827211 192216 rs9368224 20827321 192326 rsl 1756271 20827372 192377 rs9358358 20827540 192545 rs9460550 20827858 192863 rsl 2110493 20827866 192871 rs12193125 20828258 193263 rs9356746 20828797 193802 rs9350272 20829322 194327 rs13219444 20829342 194347 rs12111216 -20829562 194567 rs9350273 20829700 194705 rs9368225 20830399 195404 rsl 7825025 20831036 196041 rs9368226 20832213 197218 rs6903175 20832229 197234 rs6903744 20832537 197542 rs12111351 20832754 197759 rs4712536 20832986 197991 rs9356747 20833076 198081 rs9356748 20833219 198224 rs7767391 20833402 198407 rs7747752 20833511 198516 rs9350274 20833853 198858 rs34170041 20833919 198924 rs6915155 20834014 199019 rs6914868 20834472 199477 rs4538697 20835549 200554 rs4712537 20836048 201053 rs34097377 20836492 201497 rs6928012 20836710 201715 rs6908425 118 Table 11. SNPs within LD block CIO (SEQ ID NO:2) between positions 94,192,885 and 94,490,091 bp on Chromosome 10 in NCBI Build 35 and NCBI Build 36 Position in Build 35/36 Position in SEQ ID NO:2 Marker ID 94192885 1 rs2798253 94193597 713 rs36087110 94193803 919 rs35771118 94193950 1066 rsl 2359552 94193961 1077 rsl 1186999 94194166 1282 rs7916460 94194775 1891 rsl 0882065 94195841 2957 rsl 1187000 94196162 3278 rs4933231 94196306 3422 rsl 1187001 94196353 3469 rs4933725 94196465 3581 rsl 1187002 94196477 3593 rs4933726 94196509 3625 rs4933232 94196716 3832 rsl 1187003 94196844 3960 rs34115369 94197028 4144 rsl 0786047 94197152 4268 rsl 1814521 94197347 4463 rsl 1814555 94198457 5573 rs7476275 94198727 5843 rs3118967 94199011 6127 rsl 1187004 94199856 6972 rs7910977 94199919 7035 rs6583813 94199932 7048 rs511985 94200269 7385 rs7911558 94200789 7905 rsl 2415807 94201174 8290 rs35125831 94201284 8400 rs2251101 94201876 8992 rs7896688 94202516 9632 rs5786996 94202722 9838 rs913648 94203071 10187 rs5786997 94203072 10188 rs35771235 94203255 10371 rs34872659 94203768 10884 rs34266748 94204339 11455 rs4646958 94204560 11676 rsl 1187007 94205437 12553 rsl 1459510 94205449 12565 rs35832015 94206153 13269 rsl 2356364 94206407 13523 rsl 1593933 94206490 13606 rs3781241 94206524 13640 rs3781240 94206594 13710 rsl 0562725 94206599 13715 rsl 0617641 94206609 13725 rs28641489 94207018 14134 rsl 1187009 94207224 14340 rs36119168 94207391 14507 rsl 1594562 94207777 14893 rs3781239 94208177 15293 rs3824738 94208228 15344 rsl 2782629 94208261 , 15377 rsl 2261501 94208278 15394 rsl 2781670 94208383 15499 rs568657 Position in Build 35/36 Position in SEQ ID NO:2 Marker ID 94208423 15539 rs509954 94209484 16600 rs489517 94209509 16625 rs9420586 94209578 16694 rsl 1187010 94209597 16713 rs2247348 94209748 16864 rs307638 94210585 17701 rs35118791 94210625 17741 rs520711 94211102 18218 rs7098739 94211382 18498 rs7081224 94211591 18707 rs7093437 94212604 19720 rs551266 94213696 20812 rsl 042444 94213766 20882 rs7087334 94214145 21261 rsl 887922 94214615 21731 rs7898862 94214726 21842 rsl 0882066 94214869 21985 rsl 1187011 94214932 22048 rs7916011 94214997 22113 rs7899603 94215212 22328 rs34934289 94215235 22351 rsl 2242504 94215277 22393 rs2275218 94215373 22489 rs538469 94215528 22644 rs35640611 94215823 22939 rsl 1187012 94216140 23256 rsl 1187013 94216829 23945 rs7893352 94217818 24934 rsl 1187014 94218798 25914 rs544537 94218805 25921 rsl 2243622 94219607 26723 rsl 1187015 94219726 26842 rs7920976 94219892 27008 rs4646957 94220409 27525 rsl 1187016 94221786 28902 rs2250090 94222227 29343 rs2149632 94222398 29514 rs35959170 94222860 29976 rs35551274 94222881 29997 rs7087153 94222964 30080 rsl 2762802 94223038 30154 rsl 2763971 94223085 30201 rsl 1187017 94223100 30216 rs2249960 94223275 30391 rsl 2262931 94223719 30835 rsl 1187018 94223794 30910 rsl 1323400 94223971 31087 rs7092468 94224735 31851 rsl 2245118 94224789 31905 rs35223317 94226905 34021 rs35637537 94227236 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94385728 192844 rs7900689 94386335 193451 rsl 1812813 94386492 193608 rs4933732 94386500 193616 rsl 1594678 94386540 193656 rsl 1813238 94386568 193684 rsl 972360 94386594 193710 rsl 1816962 94386703 193819 rs4558084 94386890 194006 rs34948996 94387372 194488 rs1547818 94387496 194612 rs34497717 94387741 194857 rs7069680 94387964 195080 rs7085790 94388094 195210 rs36015190 94388098 195214 rs6583830 94388569 195685 rs7090402 94388954 196070 rsl 1187109 94389669 196785 rs35137137 94389736 196852 rs35494689 94390313 197429 rs6583831 94390339 197455 rsl 1187110 94390489 197605 rsl 1187111 124 Position in Build 35/36 Position in SEQ ID NO:2 Marker ID 94390602 197718 rs4933733 94390673 197789 rs34848251 94390842 197958 rs7922902 94391081 198197 rsl 1282830 94391082 198198 rs35084253 94391352 198468 rs6583832 94391366 198482 rsl 0882096 94391873 198989 rs7079583 94391950 199066 rs7079602 94391966 199082 rsl 1187112 94392278 199394 rsl 2244429 94393212 200328 rs35312216 94393281 200397 rs28576319 94393578 200694 rs7088685 94394524 201640 rsl 7107776 94394677 201793 rs7902436 94394804 201920 rs7917359 94395324 202440 rs36070037 94395344 202460 rs34647366 94395706 202822 rs33915127 94396217 203333 rsl 1187114 94396832 203948 rs7069619 94397097 204213 rs34629164 94397263 204379 rsl 1187115 94397647 204763 rs7073957 94397851 204967 rsl 0686721 94397859 204975 rs34357393 94397981 205097 rs36046902 94398388 205504 rsl 2264712 94398585 205701 rs34132402 94398837 205953 rsl 2358273 94398866 205982 rs35625726 94398869 205985 rsl 1285704 94399729 206845 rs7067733 94399780 206896 rs6583833 94399806 206922 rs35230377 94400137 207253 rsl 0430651 94400806 207922 rsl 2262781 94400870 207986 rsl 2359115 94401006 208122 rsl 2359131 94401155 208271 rs7898318 94401180 208296 rsl 2359158 94401236 208352 rsl 2359159 94401240 208356 rsl 2764793 94401245 208361 rsl 2764800 94401246 208362 rsl 2241432 94401250 208366 rsl 1383128 94401253 208369 rs7898430 94401708 208824 rs35738968 94401710 208826 rsl 0537782 94401720 208836 rs36000362 94401732 208848 rs7893798 94402105 209221 rsl 1187116 94402138 209254 rsl 1187117 94402166 209282 rsl 1187118 94402579 209695 rsl 2411448 94402726 209842 rs35910196 94402828 209944 rs34963356 94403360 210476 rsl 7875344 Position in Build 35/36 Position in SEQ ID NO:2 Marker ID 94403488 210604 rs34417963 94403643 210759 rs41290170 94403647 210763 rsl 7875345 94403675 210791 rs41290172 94403774 210890 rs41290174 94403917 211033 rs1044146 94403990 211106 rsl 7875346 94404243 211359 rs7078243 94404370 211486 rsl 1187119 94404390 211506 rs36107638 94404547 211663 rs4933734 94404618 211734 rsl 7875347 94405058 212174 rs1044153 94405646 212762 rsl 1187120 94405813 212929 rs35698103 94406209 213325 rs7071912 94406381 213497 rsl 1597699 94406501 213617 rsl 1598250 94406519 213635 rs35135018 94406834 213950 rsl 2242617 94407185 214301 rsl 2264496 94407201 214317 rsl 1814562 94407283 214399 rs7916594 94407322 214438 rs7093043 94407327 214443 rs7092669 94407904 215020 rsl 2244738 94408110 215226 rsl 2573394 94408195 215311 rs34223527 94408405 215521 rs7921040 94408480 215596 rs35583259 94408734 215850 rs2901599 94409046 216162 rsl 1187122 94409276 216392 rs6583834 94410546 217662 rs7076842 94411653 218769 rs9804194 94411998 219114 rs7914504 94412220 219336 rs35580348 94412694 219810 rs7079361 94412743 219859 rs7095377 94413406 220522 rs7096187 94413485 220601 rs6583835 94413764 220880 rs6583836 94413791 220907 rs7100344 94414053 221169 rs2153827 94414178 221294 rs6583837 94414402 221518 rs35978445 94414724 221840 rs2497321 94414758 221874 rs2497320 94415097 222213 rsl 1187124 94415101 222217 rs7913315 94415116 222232 rs2497319 94415147 222263 rs7071919 94416183 223299 rs2488058 94416216 223332 rs2488057 94417125 224241 rs34940159 94417197 224313 rsl 2776166 94417669 224785 rsl 1187125 94418089 225205 rs7910187 94418694 225810 rs7914114 125 Position in Build 35/36 Position in SEQ ID NO:2 Marker ID 94418703 225819 rsl 1554568 94418859 225975 rs7914143 94418888 226004 rsl 832887 94418890 226006 rs1418391 94418990 226106 rs7914507 94419062 226178 rsl 7875348 94419074 226190 rs7899695 94419424 226540 rs12414381 94419447 226563 rs7918084 94419491 226607 rs7903302 94419506 226622 rsl 1187126 94419569 226685 rsl 1187127 94419688 226804 rsl 1187128 94419689 226805 rsl 2772782 94419887 227003 rsl 1187129 94420477 227593 rs2185756 94420505 227621 rs9419741 94420766 227882 rs34709928 94420766 227882 rs34848369 94420877 227993 rs35250649 94421300 228416 rs9419742 94421540 228656 rsl 1594482 94421980 229096 rs2497318 94422308 229424 rs2488055 94422330 229446 rs6583838 94422446 229562 rs2488054 94423353 230469 rs7909334 94423442 230558 rs35288203 94423443 230559 rs7897560 94423460 230576 rs35413668 94423462 230578 rs7897565 94423473 230589 rsl 2761997 94423750 230866 rs34831256 94424074 231190 rs4421685 94425223 232339 rs28514404 94425223 232339 rs28591207 94425307 232423 rs35885794 94425468 232584 rs7098199 94425577 232693 rs34985734 94425653 232769 rs35906730 94425663 232779 rs4933735 94425739 232855 rs7098638 94426831 233947 rs7911264 94427225 234341 rsl 1187131 94427575 234691 rsl 1187132 94428318 235434 rsl 1448446 94428319 235435 rs34215006 94428322 235438 rsl 1439271 94428328 235444 rs35808040 94429339 236455 rs34911167 94429434 236550 rsl 1599074 94429447 236563 rsl 2774356 94429484 236600 rsl 2779070 94430250 237366 rs28757342 94430530 237646 rs35299744 94431405 238521 rs7089358 94431962 239078 rs35828108 94432143 239259 rs34615602 94432674 239790 rs7914280 Position in Build 35/36 Position in SEQ ID NO:2 Marker ID 94432723 239839 rsl 7875349 94432994 240110 rs34669790 94434773 241889 rsl 0882098 94434827 241943 rsl 2778051 94434836 241952 rsl 1187133 94434881 241997 rsl 1187134 94435923 243039 rs2497317 94436021 243137 rs2488087 94436103 243219 rsl 2262390 94436615 243731 rsl 0786052 94437076 244192 rsl 0522178 94437120 244236 rsl 0531158 94437559 244675 rsl 2251379 94437891 245007 rs949579 94438736 245852 rsl 1187135 94438875 245991 rs34593856 94439140 246256 rs12781513 94439449 246565 rs7475059 94439530 246646 rs4075563 94439906 247022 rs34266926 94439912 247028 rs2229328 94439992 247108 rs1418387 94440106 247222 rs2901618 94440107 247223 rs2901619 94440209 247325 rs34372348 94440213 247329 rs9420589 94441710 248826 rs41290176 94442254 249370 rsl 7851141 94442322 249438 rs2275730 94442410 249526 rs2275729 94443456 250572 rsl 1319879 94443457 250573 rs34616944 94444237 251353 rs34433040 94445202 252318 rs35423905 94445857 252973 rs34619410 94448868 255984 rs3076219 94449333 256449 rs34231544 94449598 256714 rs35657492 94450261 257377 rsl 1187138 94450630 257746 rsl 0882099 94450667 257783 rs10882100 94451033 258149 rs7100035 94451324 258440 rs7100357 94451790 258906 rsl 2263166 94451929 259045 rsl 2263147 94451954 259070 rsl 2218257 94451963 259079 rs2488085 94451965 259081 rs2497316 94452407 259523 rs10882101 94452569 259685 rs5787008 94452862 259978 rs1111875 94453437 260553 rs7921459 94453671 260787 rs35245232 94453759 260875 rsl 977832 94453925 261041 rsl 977833 94453943 261059 rs35396842 94453943 261059 rsl 1309330 94453950 261066 rs34470242 94454287 261403 rsl 2778642 126 Position in Build 35/36 Position in SEQ ID NO:2 Marker ID 94454556 261672 rs7911447 94454563 261679 rs7894796 94454564 261680 rs7911455 94454571 261687 rs7895123 94455183 262299 rs4933234 94455211 262327 rs34991559 94455539 262655 rs5015480 94456086 263202 rs2497315 94456407 263523 rsl 1187139 94456419 263535 rs12219514 94456475 263591 rsl 0882102 94456646 263762 rsl 2572190 94456890 264006 rsl 1187140 94456999 264115 rs7904159 94457006 264122 rs7904279 94457011 264127 rs7904508 94457018 264134 rs7904513 94457029 264145 rs7904292 94457125 264241 rsl 1187141 94457267 264383 rs34744311 94458157 265273 rs9419743 94458159 265275 rsl 2254229 94458272 265388 rsl 2246641 94458305 265421 rsl 2246541 94458432 265548 rsl 1813799 94458665 265781 rsl 1187142 94458914 266030 rsl 1187143 94459172 266288 rs28590736 94459519 266635 rs28428943 94459960 267076 rsl 1187144 94460495 267611 rsl 0882104 94460975 268091 rs34859807 94460979 268095 rs2497314 94461575 268691 rs4933736 94462185 269301 rs34966020 94462949 270065 rs34290965 94463018 270134 rsl 1817277 94463116 270232 rs34600815 94463139 270255 rs34793711 94463609 270725 rs7087591 94464077 271193 rsl 0786053 94464091 271207 rs10882105 94464476 271592 rsl 578672 94465084 272200 rs35705157 94465091 272207 rs2901609 94465573 272689 rs34405337 94465640 272756 rs4545448 94466041 273157 rs4504977 94466253 273369 rs4262638 94466275 273391 rsl 2777206 94466575 273691 rsl 2782663 94466582 273698 rsl 2782667 94466623 273739 rsl 2781544 94467199 274315 rsl 0748582 94467336 274452 rsl 1378649 94467337 274453 rs33926570 94467472 274588 rs2488082 94467519 274635 rsl 832886 94467850 274966 rs7898054 Position in Build 35/36 Position in SEQ ID NO:2 Marker ID 94468084 275200 rsl 1187145 94468335 275451 rsl 1187146 94468644 275760 rs2488081 94468673 275789 rs2488080 94469087 276203 rsl 112718 94469812 276928 rsl 2260097 94469857 276973 rs34383024 94470058 277174 rs35816895 94470314 277430 rs10882106 94470371 277487 rs2497313 94470482 277598 rs7086841 94470666 277782 rs2497312 94471062 278178 rs9420591 94471614 278730 rs4933235 94471897 279013 rs7923837 94471924 279040 rsl 0673051 94471925 279041 rs35275238 94471968 279084 rs35606816 94471975 279091 rs2497311 94472056 279172 rs7923866 94472115 279231 rsl 2780253 94472584 279700 rs35282244 94473140 280256 rs36026029 94473357 280473 rsl 1187147 94473463 280579 rs2488079 94473656 280772 rsl 0529320 94473689 280805 rs2497310 94473690 280806 rs2488078 94473695 280811 rs3221117 94473956 281072 rs2497309 94474172 281288 rs870786 94474324 281440 rs2497308 94474328 281444 rs2488077 94474418 281534 rs5787009 94474440 281556 rs5787010 94474442 281558 rs5787011 94474472 281588 rsl 1187148 94474486 281602 rs1418390 94474604 281720 rs2497307 94474750 281866 rs7081035 94474783 281899 rs7081294 94474989 282105 rs7081351 94475058 282174 rs7081745 94475060 282176 rsl 0568596 94475063 282179 rs7099393 94475082 282198 rsl 0665748 94475086 282202 rs34350311 94475191 282307 rs2497306 94475601 282717 rs2497305 94475656 282772 rs34372918 94475743 282859 rsl 1187149 94476016 283132 rsl 1597458 94476061 283177 rs2488076 94476146 283262 rsl 1593164 94476357 283473 rs34848929 94476358 283474 rsl 1597547 94476822 283938 rsl 1187150 94477781 284897 rs1544210 94478596 285712 rs35619602 127 Position in Build 35/36 Position in SEQ ID NO:2 Marker ID 94479180 286296 rsl 0630735 94479181 286297 rs35097519 94479192 286308 rs34237492 94479194 286310 rsl 1309242 94480154 287270 rs2488075 94480323 287439 rsl 2762754 94480347 287463 rsl 1593631 94480992 288108 rs9730884 94481595 288711 rsl 1379031 94481781 288897 rs10615317 94481897 289013 rs35598412 94482696 289812 rs2497304 94482730 289846 rs9419745 94482914 290030 rs35849687 94483045 290161 rs34009238 94483719 290835 rs2488074 94484440 291556 rsl 1187151 94484498 291614 rs35406218 94485046 292162 rs34249712 94485097 292213 rs2497303 Position in Build 35/36 Position in SEQ ID NO:2 Marker iD 94485259 292375 rs4933738 94485733 292849 rs947591 94485978 293094 rs7916355 94486361 293477 rs2051004 94488416 295532 rs4933236 94488811 295927 rsl 7107841 94488843 295959 rs33985961 94488845 295961 rsl 0578040 94488955 296071 rs2488073 94489325 296441 rs2488072 94489493 296609 rs34209030 94489557 296673 rs2488071 94489846 296962 rs7917254 94490010 297126 rsl 1318190 94490015 297131 rs34994435 94490015 297131 rsl 0588167 94490091 297207 rsl 1187152 128 Table 12. SNPs within LD block C17 between positions 66,037,656 and 66,163,076 bp on Chromosome 17 in NCBI build 35 and NCBI Build 36.) Position in Build 35/36 Position in SEQ ID NO:3 Marker ID 66037656 1 rsl 1077501 66038245 590 rsl 0445229 66038446 791 rs8067115 66038456 801 rsl 0445230 66038691 1036 rsl 0445231 •66039757 2102 rs28569992 66039800 2145 rs4606755 66039816 2161 rs4435300 66039936 2281 rs35154837 66039942 2287 rs9630701 66040960 3305 rsl 2165045 66040982 3327 rs7359539 66041088 3433 rs7359543 66042479 4824 rs365813 66043002 5347 rs4261590 66043301 5646 rs7223187 66043481 5826 rs6146132 66043562 5907 rs721249 66043745 6090 rs5821786 66043746 6091 rs33957619 66043759 6104 rs5821787 66043760 6105 rs33961999 66043764 6109 rsl 2950870 66044207 6552 rs350605 66044302 6647 rsl 0559381 66044390 6735 rsl 1650835 66044411 6756 rs7209364 66044489 6834 rs350604 66044496 6841 rsl 1657696 66044614 6959 rsl 1651554 66044626 6971 rsl 1657734 66045245 7590 rs350603 66045317 7662 rs2307760 66045722 8067 rsl 1653245 66045948 8293 rsl 1653355 66047524 9869 rs34832542 66047547 9892 rs2567294 66047580 9925 rsl 1655558 66047597 9942 rsl 84783 66047621 9966 rs353452 66047646 9991 rs9897791 66047700 10045 rsl 1655611 66047739 10084 rsl 825672 66047807 10152 rs35941755 66047887 10232 rs9896649 66048278 10623 rs34984463 66048288 10633 rsl 1374691 66048300 10645 rsl 1868103 66048450 10795 rs7220610 66048799 11144 rs7216368 66048942 11287 rs16913 66049292 11637 rs34941209 66049692 12037 rs8069108 66049716 12061 rs420762 66050080 12425 rs2630640 66050452 12797 rs34793380 Position in Build 35/36 Position in SEQ ID NO:3 Marker ID 66050707 13052 rs1817630 66050903 13248 rsl 1077502 66050915 13260 rs7218450 66051172 13517 rs411602 66051859 14204 rsl 6975882 66051914 14259 rs41450951 66052282 14627 rsl 7780198 66052347 14692 rsl 0512540 66052398 14743 rs2630639 66052474 14819 rs4793432 66052546 14891 rs34696190 66052699 15044 rsl 2952273 66053325 15670 rs350612 66053541 15886 rsl 284043 66053695 16040 rs1298182 66053988 16333 rsl 092528 66054007 16352 rs1091892 66054019 16364 rsl 092390 66054025 16370 rsl 092391 66054076 16421 rs276805 66054488 16833 rsl 64784 66055098 17443 rsl 64785 66056158 18503 rs350611 66057036 19381 rs9736449 66057065 19410 rsl 161565 66057065 19410 rs350610 66057184 19529 rs36160618 66057341 19686 rs28835946 66057721 20066 rs350609 66057907 20252 rs36143257 66058061 20406 rsl 64786 66058223 20568 rs4506943 66058544 20889 rsl 64787 66058598 20943 rs35063328 66058616 20961 rs35629111 66058724 21069 rs35654390 66058733 21078 rs350608 66058804 21149 rs589894 66059113 21458 rs512280 66059121 21466 rs512274 66059131 21476 rs512241 66059267 21612 rs35813361 66059431 21776 rs34292805 66060049 22394 rs671190 66060102 22447 rs671117 66060111 22456 rs35419562 66060172 22517 rs8080393 66060192 22537 rs509784 66060244 22589 rs509924 66060364 22709 rs510865 66060367 22712 rs669895 66060401 22746 rs8075249 66060403 22748 rs8080759 66060407 22752 rs511552 66060416 22761 rs511578 66060618 22963 rsl 1326414 129 Position in Build 35/36 Position in SEQ ID NO:3 Marker ID 66061168 23513 rs350607 66061287 23632 rs8081864 66061435 23780 rs8066762 66063324 25669 rsl 0048191 66063794 26139 rs34162560 66063983 26328 rs350606 66064178 26523 rs8078924 66065291 27636 rs4793451 66065798 28143 rs350613 66066258 28603 rsl 0432003 66066436 28781 rs350614 66066465 28810 rs34703743 66066481 28826 rs35908278 66066608 28953 rsl 1654062 66067303 29648 rs350615 66067453 29798 rsl 6975891 66067482 29827 rsl 7823280 66067699 30044 rs350616 66068320 30665 rs350617 66068798 31143 rs1991680 66069274 31619 rs9896037 66069554 31899 rsl 6975893 66069880 32225 rs8081551 66070068 32413 rsl 1654475 66071319 33664 rsl 1651609 66071575 33920 rs34132957 66071603 33948 rsl 2603169 66071721 34066 rs8073324 66072276 34621 rs1431455 66072384 34729 rsl 7763769 66073012 35357 rs350618 66073300 35645 rs1991679 66073592 35937 rs34134043 66073862 36207 rs7208933 66074000 36345 rsl 1655478 66074367 36712 rs35062489 66074796 37141 rs9900305 66075575 37920 rsl 6975908 66076138 38483 rs7224554 66076400 38745 rs35795750 66076402 38747 rs5821788 66076579 38924 rs350619 66076797 39142 rs34028570 66076805 39150 rs5821789 66076806 39151 rs35251724 66077103 39448 rs7210525 66077477 39822 rs2567296 66077488 39833 rsl 843621 66077930 40275 rs34077265 66077984 40329 rs528669 66078111 40456 rs8067160 66078127 40472 rs350620 66078527 40872 rs191621 66079419 41764 rs350621 66079437 41782 rs350622 66079660 42005 rsl 2452538 66079935 42280 rsl 7176093 66079969 42314 rs350623 66079990 42335 rsl 1077503 Position in Build 35/36 Position in SEQ ID NO:3 Marker ID 66080024 42369 rsl 1077504 66080067 42412 rs350624 66080672 43017 rs35072892 66080920 43265 rsl 1657749 66080984 43329 rsl 6975914 66081110 43455 rs34693986 66081370 43715 rs350625 66081556 43901 rs818765 66081568 43913 rs415298 66081576 43921 rs376750 66081612 43957 rsl 0652573 66081700 44045 rs350626 66082086 44431 rs28590672 66083526 45871 rsl 6975922 66083670 46015 rs481417 66083783 46128 rs191622 66083825 46170 rs482515 66083858 46203 rs367218 66083931 46276 rs402214 66084484 46829 rs483543 66084515 46860 rs484253 66084734 47079 rs486202 66084769 47114 rs610662 66084772 47117 rsl 1310950 66084781 47126 rsl 2936985 66084782 47127 rsl 2945927 66084808 47153 rs610730 66084932 47277 rsl 825669 66084935 47280 rsl 825670 66084954 47299 rsl 825671 66085342 47687 rs8077690 66085473 47818 rsl 2602288 66086152 48497 rsl 6975937 66086744 49089 rs28694321 66087301 49646 rs35353185 66087527 49872 rs41486747 66087994 50339 rs718950 66088026 50371 rs718951 66089255 51600 rsl 1654235 66089418 51763 rsl 1077506 66090535 52880 rs1431454 66090620 52965 rs5821790 66090782 53127 rsl 367748 66090958 53303 rsl 2603995 66091042 53387 rsl 6975939 66091117 53462 rsl 1434683 66091324 53669 rs8081186 66091594 53939 rsl 49309 66091687 54032 rsl 84806 66091693 54038 rsl 49380 66091704 54049 rs151727 66091719 54064 rsl 89541 66091741 54086 rsl 1651021 66091844 54189 rs416121 66091912 54257 rs9302918 66092080 54425 rs9302919 66092700 55045 rs35618929 66092813 55158 rs35870620 66092904 55249 rsl 1652089 130 Position in Build 35/36 Position in SEQ ID NO:3 Marker ID 66093601 55946 rsl 2938026 66093669 56014 rsl 2948379 66094196 56541 rs9911671 66094376 56721 rsl 6975941 66094422 56767 rs7220885 66094832 57177 rs601297 66094858 57203 rs601615 66094862 57207 rs601617 66094892 57237 rs601656 66095313 57658 rs418402 66096181 58526 rs35417478 66097168 59513 rsl 6975944 66097631 59976 rs34913709 66097633 59978 rs9894781 66097634 59979 rs9914075 66097640 59985 rsl 1658937 66097733 60078 rs8078784 66097760 60105 rs9915992 66098070 60415 rsl 0634138 66098071 60416 rs34728014 66098073 60418 rs34864826 66098076 60421 rsl 0551730 66098084 60429 rs5821791 66098085 60430 rs34310496 66098092 60437 rs34563419 66098173 60518 rs7503632 66098597 60942 rs9902449 66098928 61273 rs9894881 66098930 61275 rs9894882 66098976 61321 rsl 1656877 66099163 61508 rs5821792 66099494 61839 rsl 6975946 66099600 61945 rsl 7779190 66099816 62161 rsl 1650015 66100055 62400 rsl 0607347 66100062 62407 rsl 1372958 66100081 62426 rs34073356 66100089 62434 rs36104345 66100401 62746 rs2109051 66100605 62950 rs2159312 66101242 63587 rs990043 66101267 63612 rs576754 66101396 63741 rs2035582 66101665 64010 rs9905624 66101895 64240 rs693914 66102064 64409 rs558507 66102168 64513 rs35142117 66102168 64513 rsl 0596869 66102213 64558 rs560206 66102221 64566 rsl 2949221 66102269 64614 rs560368 66102315 64660 rs1911969 66102441 64786 rs35550717 66102450 64795 rs34779818 66102555 64900 rs9892329 66102591 64936 rsl 1658215 66102896 65241 rs35815207 66103027 65372 rs9914225 66103236 65581 rs9894021 Position in Build 35/36 Position in SEQ ID NO:3 Marker ID 66103495 65840 rs9891523 66103561 65906 rs720877 66103923 66268 rs720876 66103928 66273 rs35174251 66104116 66461 rs9892968 66104437 66782 rsl 7779357 66104493 66838 rs34287249 66105315 67660 rs3042758 66105827 68172 rsl 872599 66106415 68760 rs7218838 66106622 68967 rs7209535 66106911 69256 rs9896809 66107082 69427 rs28507887 66107150 69495 rs8067542 66107151 69496 rsl 0641487 66107152 69497 rs33989506 66107167 69512 rs8081487 66108291 70636 rs4793495 66108545 70890 rs8073162 66108565 70910 rs8072591 66108901 71246 rs9905537 66108905 71250 rs8073114 66108924 71269 rs8072003 66108980 71325 rs35155940 66108991 71336 rsl 1459300 66108997 71342 rs36029337 66109457 71802 rsl 1656223 66110309 72654 rs6501400 66110507 72852 rs8074266 66110586 72931 rs388304 66110881 73226 rs4544280 66111138 73483 rsl 2601471 66111335 73680 rsl 2603574 66111468 73813 rsl 1077507 66111545 73890 rsl 1077508 66111926 74271 rs28546453 66112148 74493 rs412877 66112202 74547 rs391223 66112205 74550 rs7224183 66112227 74572 rs173318 66112234 74579 rs192147 66112749 75094 rs34361437 66113023 75368 rsl 2449913 66114764 77109 rs28496807 66114858 77203 rs7220084 66114926 77271 rs7224857 66115366 77711 rs7221542 66115371 77716 rs7221545 66115377 77722 rs34466876 66115416 77761 rsl 0610236 66115835 78180 rsl 979538 66116621 78966 rs8067103 66116703 79048 rs7216053 66116880 79225 rsl 2949351 66117903 80248 rs9913650 66117911 80256 rs1860316 66118086 80431 rs9914115 66118200 80545 rs9908443 66118485 80830 rs8079029 131 Position in Build 35/36 Position in SEQ ID NO:3 Marker ID 66118495 80840 rsl 2601922 66118737 81082 rsl 0545098 66118737 81082 rsl 2603987 66119589 81934 rs9897225 66119616 81961 rs35975623 66119642 81987 rs9895773 66119822 82167 rs9898518 66119823 82168 rs28422091 66119823 82168 rs36094553 66119863 82208 rs3220372 66119992 82337 rs41408048 66120631 82976 rs28373290 66120827 83172 rs41459950 66121181 83526 rs36013413 66121413 83758 rsl 0564191 66121468 83813 rs7221715 66121873 84218 rsl 2940023 66122077 84422 rs4019476 66122410 84755 rs7222670 66122508 84853 rs7211934 66122635 84980 rs7212243 66122801 85146 rsl 1655139 66123046 85391 rs4793317 66123283 85628 rsl 71384 66123342 85687 rs4793496 66123566 85911 rs507683 66123595 85940 rs507607 66123682 86027 rs41528454 66123714 86059 rs41381246 66123879 86224 rs192146 66123955 86300 rs34149626 66123959 86304 rs35260054 66125089 87434 rs9908077 66125154 87499 rsl 1077509 66125233 87578 rs35234488 66125360 87705 rsl 1871352 66125993 88338 rs7209850 66126471 88816 rs421333 66126699 89044 rs413073 66126766 89111 rs2035581 66126795 89140 rs392974 66126799 89144 rs28532132 66126840 89185 rs3931227 66126841 89186 rsl 6975961 66126875 89220 rs532348 66127256 89601 rsl 1867791 66127283 89628 rsl 1871014 66127312 89657 rs34866225 66127313 89658 rs35958830 66128191 90536 rs9904090 66128304 90649 rsl 6975968 66129127 91472 rs9911708 66129806 92151 rs34448828 66129814 92159 rsl 1398461 66130210 92555 rs9907685 66130284 92629 rs9914666 66130455 92800 rsl 7717654 66131911 94256 rsl 6975970 66131995 94340 rs1981646 Position in Build 35/36 Position in SEQ ID NO:3 Marker ID 66132156 94501 rsl 1656723 66132225 94570 rsl 6975976 66132788 95133 rs1981647 66133032 95377 rsl 6975979 66133370 95715 rsl 6975981 66134231 96576 rs9909661 66134831 97176 rs9890554 66135283 97628 rsl 1077510 66135627 97972 rs9302920 66135758 98103 rs34975186 66136201 98546 rsl 1870545 66136484 98829 rs9906234 66136910 99255 rsl 0621796 66136920 99265 rsl 1328278 66136922 99267 rsl 1328279 66137329 99674 rs35402203 66137331 99676 rs6501401 66137347 99692 rsl 0596163 66137437 99782 rs35029611 66137784 100129 rs35985303 66137798 100143 rsl 0595957 66137965 100310 rsl 0221271 66138452 100797 rsl 0221225 66138713 101058 rs34005576 66139441 101786 rs9913463 66139476 101821 rs9915148 66139800 102145 rsl 1650683 66140108 102453 rs34335723 66140414 r 102759 rsl 1654495 66141319 103664 rs35607820 66141543 103888 rsl 2601304 66141933 104278 rs1486290 66142011 104356 rsl 2452862 66142106 104451 rs35317540 66142226 104571 rsl 1077511 66142325 104670 rs35278774 66142329 104674 rs7216457 66142581 104926 rsl 1077512 66142607 104952 rs35634443 66142648 104993 rsl 1454851 66142729 105074 rsl 1654670 66142794 105139 rs34926966 66143200 105545 rs8078302 66143897 106242 rs562472 66144028 106373 rs28420303 66144129 106474 rs28542473 66144170 106515 rs28526433 66144232 106577 rsl 2185220 66144972 107317 rs7350903 66145018 107363 rs7350904 66145022 107367 rs7350905 66145067 107412 rs35353467 66145660 108005 rsl 6975985 66145765 108110 rsl 6975987 66145912 108257 rs412981 66145914 108259 rs412980 66145925 108270 rs9907746 66146236 108581 rs432688 66146640 108985 rs540331 132 Position in Build 35/36 Position in SEQ ID NO:3 Marker ID 66146722 109067 rs473792 66146816 109161 rs2630644 66146912 109257 rsl 2949591 66146954 109299 rs2109053 66147095 109440 rs35296857 66147167 109512 rsl 7791270 66147246 109591 rsl 6975989 66147343 109688 rsl 7791282 66147436 109781 rs17718124 66147660 110005 rsl 6975993 66147678 110023 rs35106633 66147754 110099 rs34429407 66147913 110258 rs2240749 66147960 110305 rsl 6975998 66148045 110390 rs3217050 66148046 110391 rs2240750 66148178 110523 rsl 6976000 66148512 110857 rsl 6976002 66148962 111307 rsl 89580 66149102 111447 rsl 843622 66149149 111494 rs543765 66149213 111558 rs434729 66149222 111567 rs375709 66149257 111602 rsl 1656782 66149348 111693 rsl 1653519 66149386 111731 rsl 90256 66149859 112204 rs4584866 66150283 112628 rsl 6976008 66150360 112705 rsl 6976009 66150511 112856 rsl 6976011 66150609 112954 rsl 7718380 66150898 113243 rsl 1652208 66150909 113254 rsl 1652209 66151294 113639 rsl 0491179 66151858 114203 rsl 6976019 66152747 115092 rs35499697 66152804 115149 rsl 7791650 66152863 115208 rsl 6976023 66152963 115308 rsl 6976024 66152998 115343 j rs9891997 66153185 115530 rsl 2942978 66153557 115902 rsl 6976027 66153631 115976 rsl 7718538 66154056 116401 rsl 6976031 66155045 117390 rs34736208 66155048 117393 rsl 2952540 66155070 117415 rs34389302 66155101 117446 rsl 89581 66155303 117648 rs9910837 66155784 118129 rsl 7718586 66156561 118906 rs544680 66156593 118938 rs8066818 66157022 119367 rs408448 66157073 119418 rsl 1650843 Position in Build 35/36 Position in SEQ ID NO:3 Marker ID 66157111 119456 rs367742 66157179 119524 rs550945 66157197 119542 rsl 83590 66157224 119569 rs551058 66157327 119672 rs34098284 66157893 120238 rsl 83591 66157917 120262 rsl 83059 66157976 120321 rs404774 66158027 120372 rsl 1657329 66158091 120436 rs405068 66158109 120454 rs35166389 66158247 120592 rsl 6976038 66158414 120759 rsl 83592 66159001 121346 rs34458687 66159262 121607 rs35760966 66159416 121761 rs2191113 66159464 121809 rs5821793 66159546 121891 rs5821794 66159547 121892 rs35222039 66159556 121901 rsl 0648023 66159562 121907 rs3048626 66159637 121982 rs8072436 66159764 122109 rs2215270 66159891 122236 rsl 6976043 66160076 122421 rs8074760 66160292 122637 rsl 1657599 66160331 122676 rs34281212 66160370 122715 rs36074213 66160438 122783 rs171385 66160451 122796 rs412353 66160480 122825 rs422923 66160492 122837 rsl 1654012 66160668 123013 rs35429609 66160721 123066 rs2367004 66161977 124322 rs35222003 66161994 124339 rsl 1867678 66162691 125036 rsl 2953137 66162852 125197 rsl 0642929 66162854 125199 rs34937331 66162869 125214 rsl 0585639 66163076 125421 rs4793497 66037656 1 rsl 1077501 66038245 590 rsl 0445229 66038446 791 rs8067115 66038456 801 rsl 0445230 66038691 1036 rsl 0445231 66039757 2102 rs28569992 66039800 2145 rs4606755 66039816 2161 rs4435300 66039936 2281 rs35154837 WO 2008/065682 PCT/IS2007/000020 133 Table 13. Key to Sequence listing provided herein.

SEQ ID NO Name 1 LD block C06 2 LD block C10 3 LD block C17 4 rsl 0882091 rsl 111875 6 rsl 569699 7 rsl7763769 8 rsl7763811 9 rsl843622 rsl860316 11 rsl981647 12 rsl999763 13 rs2191113 14 rs2275729 rs2421943 16 rs2497304 17 rs3829170 18 rs4712527 19 rs6583826 rs6583830 21 rs7756992 22 rs7758851 SEQ ID NO Name 23 rs7908111 24 rs7914814 rs7915186 26 rs7917359 27 rs7922112 28 rs7923837 29 rs9295478 rs947591 31 rs9890889 32 rs7752906 33 rs9350271 34 rs9356744 rs9368222 36 rsl0440833 37 rs6931514 38 rs2009802 39 rsl7718938 40 rsl7223216 41 rs2109050 42 rs 1962801 43 rs7086285 44 rsl7234378 134 EXAMPLE 2 VARIANTS IN THE CDKALl GENE INFLUENCE INSULIN RESPONSE AND THE RISK OF TYPE 2 DIABETES We have recently described a variant in TCF7L2 associated to T2D (Grant, S.F. et al. Nat Genet 38, 320-3 (2006); Helgason, A. et al. Nat Genet (2007)). In the following, we describe a genome-wide association study on Icelandic T2D patients, using the Illumina Hap300 chip. We individually tested 313,179 SNPs for association to T2D in a sample of 1399 T2D patients and 5275 controls. We further tested 339,846 two-marker haplotypes identified as efficient surrogates (r2 > 0.8) for a set of SNPs which were not included on the Hap300 chip but were typed in the HapMap project (Pe'er, I. et al. Nat Genet 38, 663-7 (2006)). In addition to analyzing the entire group of T2D patients we separately tested 700 non-obese T2D patients and 531 obese T2D patients for association. Overall, a total of 1,959,075 (653,025 variants x 3 phenotypes) tests were performed. The results were adjusted for relatedness between individuals and potential population stratification by genomic control (Devlin, B. & Roeder, K. Biometrics 55, 997-1004 (1999)) (see Methods). Specifically, the (unadjusted) chi-square statistics were divided by 1.287, 1.204 and 1.184 respectively for the analyses of all, non-obese and obese T2D cases. A previously identified SNP rs7903146 in the TCF7L2 gene gave the most significant results with OR = 1.38 and P = 1.82xlO"10 in all T2D patients. Although no other SNP or haplotype was significant after adjustment for the number of tests performed, more borderline significant signals were observed than expected by chance alone (Fig. 4). Hence we decided to further pursue the top signals.

METHODS Icelandic study population The Icelandic T2D group has been described previously (Reynisdottir, I. et al. Am 3 Hum Genet 73, 323-35 (2003)). A total of 1500 T2D patients were recruited for this genome-wide association study, using the Infinium II assay method and the Sentrix HumanHap300 BeadChip (Illumina, San Diego, CA, USA). Thereof, 1399 were successfully genotyped according to our quality control criteria (see Supplementary Methods) and used in the present case control-analysis; 531 of the genotyped cases were obese (BMI > 30). The controls used in this study consisted of 599 controls randomly selected from the Icelandic genealogical database and 4676 individuals from other ongoing genome-wide association studies at deCODE. The study was approved by the Data Protection Commission of Iceland and the National Bioethics Committee of Iceland. Written informed consent was obtained from all cases and controls. 135 Other study populations The Danish female study group of 282 cases and 629 controls, herein termed Denmark A, was selected from the Prospective Epidemiological Risk Factor (PERF) study in Denmark (Tanko, L.B., et al. Bone 32, 8-14 (2003)). This is a group of postmenopausal women who took part in various screening placebo-controlled clinical trials and epidemiological studies performed at the Center for Clinical and Basic Research. At a follow-up examination of 5847 women in 2000-2001 medical history including diabetes type I and type II, family history, and current or previous long-term use of drugs were gathered during personal interviews using a preformed questionnaire. If subject was diagnosed as diabetes of either type I or type II, the time of diagnosis or treatment was also collected. The study was approved by the Ethical Committee of Copenhagen County and was in accordance with the principles of the Helsinki Declaration.

The second Danish study population of 1359 T2D cases and 4858 control individuals with normal glucose tolerance was from the Steno Diabetes Center in Copenhagen and from the Inter99 population-based sample of 30- to 60-year-old individuals living in the greater Copenhagen area and sampled at Research Centre for Prevention and Health (Jorgensen, T. et al. Eur J Cardiovasc Prev Rehabil 10, 377-86 (2003)). This dataset is referred to in the text as Denmark B. Diabetes and pre-diabetes categories were diagnosed according to the 1999 World Health Organization (WHO) criteria. An oral glucose tolerance test was performed on participants in the Inter99 study as described (Jorgensen, T. et al. Eur J Cardiovasc Prev Rehabil 10, 377-86 (2003)). Informed written consent was obtained from all subjects before participation. The study was approved by the Ethical Committee of Copenhagen County and was in accordance with the principles of the Helsinki Declaration.

The Philadelphia study population consisted of 468 T2D cases and 1024 control individuals. The study population was selected from the PENN CATH study, a cross-sectional study of the association of biochemical and genetic factors to coronary atherosclerosis in a study population of consecutive individuals undergoing cardiac catheterization at the University of Pennsylvania Medical Center. T2D was defined as a history of fasting blood glucose > 126 mg dl"1, 2 h postprandial glucose > 200 mg dl"1, use of oral hypoglycemic agents, or use of insulin and oral hypoglycemic in a subject older than age 40. The University of Pennsylvania Institutional Review Board approved the study protocol, and all subjects gave written informed consent. All cases and controls were of European ancestry. Ethnicity was determined through self-report.

The Dutch Breda study population consisted of 370 T2D cases and 916 control individuals. The cases were recruited in 1998-1999 in collaboration with the Diabetes Service Breda and 80 general practitioners from the region around Breda. All patients are diagnosed according to WHO criteria (plasma glucose levels >11.1 mmol/l or a fasting plasma glucose level > 7.0 mmol/l), and undergo clinical and laboratory evaluations for their diabetes at regular 3-month intervals. The 136 Medical Ethics Committee of the University Medical Centre in Utrecht approved the study protocol. All probands filled out an informed consent and a questionnaire on clinical data, including their diabetes related medication, height and weight at present and at the age of 20 year. The controls are Dutch blood bank donors with an average age of 48.

The Scottish study population consisted of type 2 diabetic cases and non-diabetic controls from the Wellcome Trust UK T2D case-control collection (Go-DARTS2) which is a sub-study of Diabetes Audit and Research Tayside (DARTS) (Morris, A.D. eta/. BMJ 315, 524-8 (1997)). All T2D patients were physician-diagnosed T2D cases recruited at primary or secondary care diabetes clinics, or invited to participate from primary care registers and have not been characterized for GAD anti-bodies or MODY gene mutations. The controls were invited to participate through the primary care physicians or through their workplace occupational health departments. Controls did not have a previous diagnosis of diabetes, but the glucose tolerance status of the controls is unknown. All individuals in this ongoing study were recruited in Tayside between October 2004 and July 2006. This study was approved by the Tayside Medical Ethics Committee and informed consent was obtained from all subjects.

All subjects in the Hong Kong study population were of southern Han Chinese ancestry residing in Hong Kong. The cases consisted of 1500 individuals with T2D selected from the Prince of Wales Hospital Diabetes Registry. Of these, 682 patients had young-onset diabetes (age-at-diagnosis < 40 years) with positive family history. An additional 818 cases were randomly selected from the same registry. The controls consisted of 1000 subjects with normal glucose tolerance (fasting plasma glucose < 6.1 mmol/l). Of these, 617 were recruited from the general population participating in a community-based cardiovascular risk screening program as well as hospital staff. In addition, 383 subjects were recruited from a cardiovascular risk screening program for adolescents. Informed consent was obtained for each participating subject. This study was approved by the Clinical Research Ethics Committee of the Chinese University of Hong Kong.

The African study population comes from the Africa America Diabetes Mellitus study, which was originally designed as an affected sibling pair study with enrollment of available spouses as controls. It has since been expanded to include other family members of the affected pairs and population controls. Recruitment strategies and eligibility criteria for the families enrolled in this report have been described previously (Rotimi, C.N. etal. Ann Epidemiol 11, 51-8 (2001)). This West African case-control series consisted of individuals from the Yoruba (233 affected individuals, 432 controls) and Igbo (237 affected individuals, 276 controls) groups from Nigeria and the Akan (257 affected individuals, 248 controls), Ewe (22 affected individuals, 30 controls) and Gaa-Adangbe (123 affected individuals, 141 controls) groups from Ghana. 137 With the exception of the Scottish Go-DARTS study population the DNA used for genotyping in all replication study populations was the product of whole-genome amplification (GenomiPhi Amplification kit, Amersham) of DNA isolated from the peripheral blood.

Statistical analysis Illumina Genome-Wide Genotyping. All Icelandic case- and control-samples were assayed with the Infinium HumanHap300 SNP chips (Illumina, SanDiego, CA, USA), containing 317,503 haplotype tagging SNPs derived from phase I of the International HapMap project. Of the SNPs assayed on the chip, 4,324 SNPs were excluded as the had (a) yield lower than 95% in cases or controls; (b) minor allele frequency less than 1% in the population; or (c) showed significant distortion from Hardy-Weinberg equilibrium in the controls (P-value < 0.001). Any samples with a call rate below 98% were excluded from the analysis. Thus, the final analyses presented in the text utilizes 313,179 SNPs.

Single SNP genotyping. Single SNP genotyping for all population studied, except for the Scottish Go-DARTS population, was carried out at deCODE Genetics in Reykjavik, Iceland by the Centaurus (Nanogen) platform (Kutyavin, I.V. et al. Nucleic Acids Res 34, el28 (2006)). The quality of each Centaurus SNP assay was evaluated by genotyping each assay in the CEU and/or YRI HapMap samples and comparing the results with the HapMap data. Assays with >1.5% mismatch rate were not used and a linkage disequilibrium (LD) test was used for markers known to be in LD. Single SNP genotyping for the Scottish population was carried out at the Biomedical Research Centre, Ninewells Hospital and Medical School, Dundee, Scotland, by the TaqMan® method.

Association analysis. For association analysis we utilized a standard likelihood ratio statistics, implemented in the NEMO software (Gretarsdottir, S. et al. Nat Genet 35, 131-8 (2003)) to calculate two-sided p-values and allele specific OR for each individual allele, assuming a multiplicative model for risk, i.e., that the risks of the two alleles a person carries multiply. Allelic frequencies, rather than carrier frequencies are presented for the markers, and p-values are given after adjustment for the relatedness of the subjects. When estimating genotype specific OR (Table 19) genotype frequencies in the population were estimated assuming HWE.

In general, allele/haplotype frequencies are estimated by maximum likelihood and tests of differences between cases and controls are performed using a generalized likelihood ratio test (Rice, J.A. Mathematical Statistics and Data Analysis, (Wadsworth Inc., Belmont, CA, 1995)). This method is particularly useful in situations where there are some missing genotypes for the marker of interest and genotypes of another marker, which is in strong LD with the marker of interest, are used to provide some partial information. This was used in the association tests presented in Table 138 17 to ensure that the comparison of the highly correlated markers was done using the same number of individuals. To handle uncertainties with phase and missing genotypes, maximum likelihood estimates, likelihood ratios and p-values are computed directly for the observed data, and hence the loss of information due to uncertainty in phase and missing genotypes is automatically captured by the likelihood ratios.

Results from multiple case-control groups were combined using a Mantel-Haenszel model (Mantel, N. & Haenszel, W. J Natl Cancer Inst 22, 719-48 (1959)) in which the groups were allowed to have different population frequencies for alleles, and genotypes but were assumed to have common relative risks.

Correction for relatedness of the subjects and Genomic Control. Some of the individuals in both the Icelandic patient and control groups are related to each other, causing the chi-square test statistic to have a mean >1 and median >0.6752. We estimated the inflation factor by calculating the average of the 653,025 chi-square statistics, which was a method of genomic control4 to adjust for both relatedness and potential population stratification. The inflation factor was estimated as 1.287, 1.204 and 1.184, for the analysis of all, non-obese and obese T2D cases, respectively. The results presented are based on adjusting the chi-square statistics by dividing each of them by the corresponding inflation factor.

Quantitative analysis. Data from oral glucose tolerance test on individuals from the Danish Inter99 study were used to calculate insulin secretion as corrected insulin response (CIR) using the following equation: (100 x insulin at 30 minutes) 4- [glucose at 30 minutes x(glucose at 30 minutes - 3.89 mmol)]. Insulin sensitivity was estimated as the reciprocal of the insulin resistance according to the homeostasis model assessment (HOMA): 22.5 / [fasting insulin x fasting glucose] (Matthews, D.R. eta/. Diabetologia 28, 412-9 (1985)). The association between CIR (HOMA) and genotype status was tested using a multiple regression where the log-transformed CIR (HOMA) where taken as the response variable and the explanatory variable was either the number of copies of risk allele an individual carries (an additive model) or an indicator variable for homozygous carriers of the risk allele (a recessive model). Adjustment for sex, age and affection status was done by including the appropriate terms as explanatory variables. For comparison insulin secretion was also calculated as (insulin at 30 minutes - insulin at 0 minutes) -f- (glucose at 30 minutes -glucose at 0 minutes), yielding comparable results. 139 Cell lines. The INS1 cells were provided by Hoffmann-LaRoche. They were grown in RPMI1640 (Invitrogen) supplemented with 10% fetal bovine serum (Invitrogen), 50 pg/ml penicillin-streptomycin (Invitrogen), 50 nM 2-mercaptoethanol (SIGMA), 1 mM MEM sodium pyruvate (Invitrogen) and 10 mM Hepes buffer solution (Invitrogen). They were split 1:2 twice per week by washing once in IX Hanks Balanced Salt Solution (Invitrogen) and then trypsinized (trypsin-EDTA; Invitrogen).

Preparation of RNA and cDNA amplification. INS1 cells were incubated for 48h in normal growth medium containing 10 mM glucose. At the time of harvest there were 2xl07 cells, which were used for the preparation of total RNA. RNA was extracted using RNeasy Midi Kit (Quiagen). cDNA was prepared using High-Capacity cDNA Archive Kit (Applied Biosystems). CDKALl cDNA was amplified using two different primer pairs between exons 2 and 8 (forward: 5'- GGGGCTGCTCACATAATAATTCA-3'; reverse: 5'-TGTGCCAATGTCTCTGCCATA-3') and between exons 7 and 13 (forward: 5'-ACCTGGCCAGCTATCCCATT-3'; reverse: 5 '-CC ATTTTT CCC AT G AAT G C AG - 3'). Primers from beta-actin served as positive controls (forward 5'-ATCTGGCACCACACCTCCTACAATGAGCTGC-3'; reverse: 5'-CGTCATACTCCTGCTTGCTGATCCACATCTGC-3').

RESULTS AND DISCUSSION For each phenotype tested we selected all single SNPs and two marker haplotypes with P < 0.00005 for replication in a case-control sample from Denmark (Denmark B). After eliminating redundant markers a total of 46 SNPs were taken further for the attempt at replication (Table 14). In addition, we included the five most significant non-synonymous SNPs present on the Illumina Hap300 chip. Out of those 51 SNPs, 47 were successfully genotyped in 1110 Danish T2D cases and 2272 controls. In the Danish group SNPs rs7756992 and rsl3266634 stood out and were significantly replicated with P= 0.00013 and OR = 1.24 and P = 0.0012 and OR = 1.20, respectively, in the Danish group of all T2D patients (Table 15). This is compared to P = 0.00021 and OR = 1.23 and P = 0.000061 and OR = 1.19, respectively in the initial Icelandic study. All of the other SNPs genotyped had P > 0.01 in the Danish group and were not pursued further. The first SNP, rs7756992, is located in intron 5 of the CDK5 regulatory subunit associated protein 1-like 1 (CDKALl) gene on 6p22.3. It resides in a large LD block of 201.7 kb that includes exons 1-5 of the CDKALl gene as well as the minimal promoter region but no other known genes (Figure 5). The second SNP, rsl3266634, is a non-synonymous SNP causing an arginine 325 to tryptophan change in the last exon of the solute carrier family 30 (zinc transporter), member 8 (SLC30A8) gene on 8q24. The gene product of SLC30A8 is specific to the pancreas and it is expressed in beta 140 cells where it facilitates the accumulation of zinc from the cytoplasm into intracellular vesicles (Chimienti, F., eta/. Diabetes 53, 2330-7 (2004)). The risk allele of rsl3266634 on 8q24 has recently been found to confer risk of T2D in a genome wide association study of French T2D cases and controls (Sladek, R. eta/. Nature 445, 881-5 (2007)). Of other significantly associated SNPs in that study, we also replicated, in the initial Icelandic samples, association to two SNPs close to the HHEX gene (Table 16). However, we did not replicate the reported association to markers in the LOC387761 and EXT2 genes also described in that study.

We typed the SNPs rs7756992 and rsl3266634 in four other T2D case-control groups of European ancestry from Denmark (Denmark A), Scotland, the Netherlands and Philadelphia, US as well as case-control groups from Hong Kong and West Africa. Furthermore, the size of the Denmark B study group was expanded mostly by increasing the number of genotyped controls. The association of the G allele of rs7756992 was replicated with significance in the Scottish (OR = 1.11; P = 0.0042) and the Hong Kong (OR = 1.25; P = 0.00018) case-control groups (Table 17). Association in other study groups was not individually significant, but all were in the same direction. The observed association from combining all eight case-control groups gave an OR of 1.15 with a corresponding P of 9.0x10 12 (Table 17). Given that approximately 2 million tests were performed in the initial genome-scan, this association remained highly significant with Bonferonni adjustment Cadj = 1-8 xlO"5) (Skol, A.D., et ai. Nat Genet 38, 209-13 (2006)). Attempts at refining the association observed with rs7756992 by genotyping additional markers that correlate with the original signal in the HapMap CEPH (CEU) dataset, did not yield more significant results (Table 18). As could be expected the linkage disequilibrium observed for the West African population was considerably less than that seen for the Icelandic and Hong Kong groups (Table 19). Further work is needed to determine if an associated variant with a higher OR than observed for rs7756992 can be identified in the West African group. Likewise, for allele C of the non-synonymous SNP rsl3266634 the association to T2D was replicated with significance in three of the six additional groups (from Scotland, Philadelphia and Hong Kong) (Table 17). Even though the OR for Denmark B decreased with the larger sample size and the estimated effect was in the opposite direction (only slightly and non-significant) for Denmark A, the combined results from all study group yielded a genome-wide significant P of 2.5x10'" and an OR of 1.16 (Table 17).

In the Icelandic study the association to rs7756992 was more significant in non-obese T2D patients (OR = 1.37; P = 9.0xi0"6) than in the group of all patients (OR = 1.23; P = 0.00021) (Table 14 and Table 17). A higher OR in non-obese than in obese T2D patients was also observed for this variant in the other populations studied. For the combined populations of European origin the OR was 1.19; P = 7.29xi0"9 for the non-obese T2D patients compared to OR = 1.12; P = 0.00017 for the obese group. An even stronger effect was seen in the Hong Kong non-obese T2D group (OR = 1.36; P = 7.48xl0"6), compared to the obese group (OR = 1.13; P = 0.094), where obesity was defined as BMI > 25. When the results for all groups were combined, relative to 141 controls, OR = 1.19; P = 1.93xl0"n and OR = 1.13; P = 2.68xl0"5 was obtained for the non-obese and obese T2D patient groups, respectively. These results indicate that this variant does not confer increased risk of T2D through increased BMI.

Genotype odds ratio was estimated for each of the two loci (Table 20). Based on the results for the combined Caucasian study populations rs7756992 deviates significantly from the multiplicative model with OR for the heterozygote = 1.09 compared to OR = 1.45 for the homozygote, supporting a nearly recessive mode of inheritance. The same trend, although nonsignificant, was seen for the Hong Kong samples with heterozygote OR = 1.13 and OR = 1.55 for the homozygote. Conversely, a multiplicative model for the genotype relative risk provided an adequate fit for rsl3266634.

The function of the gene product of CDKALl is not known. However, as implied in the gene name the protein product is similar to another protein, CDK5 regulatory subunit associated protein 1 (CDK5RAP1). CDK5RAP1 is expressed in neuronal tissues where it inhibits cyclin dependent kinase 5 (CDK5) activity by binding to the CDK5 regulatory subunit p35 (Ching, Y.P., et al. J Biol Chem 277, 15237-40 (2002)). In pancreatic beta cells, CDK5 has been shown to play a role in the loss of beta cell function under glucotoxic conditions (Wei, F.Y. et al. Nat Med 11, 1104-8 (2005)). Furthermore, inhibition of the CDK5/p35 complex prevents decrease of insulin gene expression that results from glucotoxicity (Ubeda, M., et al. J Biol Chem 281, 28858-64 (2006)). It is tempting to speculate that CDKALl might play a role in the inhibition of CDK5/p35 in pancreatic beta cells similar to that of CDK5RAP1 in neuronal tissue. Reduced expression of CDKALl or reduced inhibitory function thus could lead to an impaired response to glucotoxicity. In this study we showed that CDKALl is expressed in the rat pancreatic beta cell line INS-1 (Figure 6). Further studies are needed to determine if the effect of CDKALl on increasing the risk of T2D is exerted through this pathway.

Based on the predicted function of CDKALl and known function of SLC30A8 we would expect both rs7756992 and rsl3266634 to affect insulin secretion. To evaluate the effects of the two SNPs on insulin secretion we analyzed the effect of genotype status on corrected insulin response (CIR) in a set of individuals from the Inter99 study (part of Denmark B) that had undergone an oral glucose tolerance test (OGTT). For rs7756992, we demonstrated that the homozygote carriers of the risk allele had an estimated 24% less CIR than the heterozygote carriers or non-carriers (P < 0.00001, Fig. 7). This observation is consistent with the variant's nearly recessive mode of inheritance with respect to disease risk. Furthermore, the effect observed on CIR is present in both males and females (Figure 8) and in T2D patients as well as controls, and adjusting for BMI status did not affect the results (Table 21). The effect of rsl3266634 on insulin response was smaller but significant and for this risk variant the reduction in CIR was consistent with an additive effect. No effect on insulin sensitivity was observed for either variant (Table 21). 142 The identification of CDKALl as a susceptibility gene for T2D adds a new piece to the puzzle of how genetic factors may predispose to T2D. Although the function of this gene remains to be elucidated we have shown that it is expressed in pancreatic beta cells and that a variant within the gene is correlated with insulin secretion. The similarity to CDK5RAP1 further indicates that CDKALl may facilitate insulin production under glucotoxic conditions through interaction with CDK5. In conclusion, we have identified a variant in the CDKALl gene that in a nearly recessive manner blunts the insulin response and predisposes to T2D.

Table 14. Association to T2D in the Icelandic discovery group.

The upper table includes association results for all SNPs or two-marker haplotypes that have an adjusted P value less than 10"5 for either all T2D cases, non-obese T2D cases or obese T2D cases. Included in the table is the chromosome, the position of the markers (or the midpoint for two-marker haplotypes) in NCBI Build 34, the markers and alleles tested, the corresponding surrogate SNP for two-markers haplotypes selected for replication, the frequency in controls and the frequency in cases, the odds ratio (OR) and adjusted P-value for the three case groups tested. The number of T2D cases in each of the three groups is included in parenthesis and the same set of 5275 controls is used in all tests. Note that information on BMI is missing for 168 of the cases. The lower table includes the corresponding values for the five most significant non-synonymous SNPs selected for replication. Included in column five are the corresponding genes and the codon changes. In both tables markers selected for further testing in the first replication group (Denmark B) are indicated with bold typesetting. Other markers / haplotypes were excluded from the replication study as they were a) highly correlated with another marker selected for replication, or b) belong to the TCF7L2 locus that has been studied previously.

All T2D cases (1399) NonObese T2D cases (700) Obese T2D cases (531) Chr Position Markers Allele Surrogate3 (/*) Con.frq Case.frq OR P" Case.frq OR P" Case.frq OR P" C01 29602516 rs4949283 rs502545 TC rsl 0798895 G (1) 0.149 0.117 0.76 0.00016 0.104 0.66 0.000033 0.133 0.88 0.21 C01 104461151 rs7553985 C - 0.394 0.430 1.16 0.0023 0.419 1.11 0.11 0.466 1.34 0.000027 C01 104467009 rs2166890 T - 0.393 0.430 1.16 0.0018 0.419 1.11 0.091 0.466 1.35 0.000024 C01 104468502 rs7552405 T - 0.317 0.355 1.19 0.00078 0.346 1.14 0.047 0.386 1.35 0.000030 C01 151915609 rs3738028 G - 0.360 0.407 1.22 0.000046 0.417 1.27 0.00016 0.409 1.23 0.0038 C02 40632580 rsl 3414307 rsl 990609 AG - 0.517 0.571 1.24 0.0000089 0.568 1.23 0.0011 0.582 1.30 0.00026 C02 40623619 rsl3414307 A - 0.543 0.593 1.22 0.000033 0.589 1.21 0.0028 0.603 1.28 0.00056 . C02 55036788 rs930493 rs10173697 GT - 0.281 0.335 1.29 0.0000017 0.325 1.23 0.0024 0.333 1.27 0.0016 C02 55040844 rsl 0173697 T - 0.503 0.553 1.22 0.000040 0.545 1.18 0.0086 0.560 1.25 0.0014 C03 89162181 rsl2486049 T - 0.872 0.904 1.38 0.000035 0.907 1.43 0.00043 0.901 1.34 0.0095 C03 146863467 rs7630694 G - 0.060 0.070 1.20 0.065 0.056 0.93 0.60 0.097 1.70 . 0.000033 C03 196904151 rs9858622 A - 0.668 0.701 1.17 0.0028 0.682 1.07 0.34 0.737 1.40 0.000016 C04 140508134 rsl 3116075 rs6824182 AA rs10033117 C (1) 0.741 0.763 1.13 0.036 0.734 0.96 0.60 0.804 1.43 0.000024 C04 140604420 rs2292837rs11725721 TC - 0.254 0.232 0.89 0.038 0.259 1.03 0.69 0.194 0.71 0.000047 C04 140621178 rs3762864rs11725721 GC - 0.254 0.233 0.89 0.042 0.262 1.04 0.60 0.194 0.70 0.000038 C05 76637396 rs832785 rs2859576 AA - 0.510 0.470 C05 76635083 rs4704400 T - 0.490 0.530 C05 C06 87882885 6967990 rsl 0505855 rsl 2514611 rs490213 rs814174 GC AG rsl 0452479 G (0.94) rs12201780 A (1) 0.188 0.044 0.224 0.072 C06 9509965 rs214447 T - 0.424 0.449 C06 20779501 rs4712527 rs7756992 AG - 0.232 0.270 C06 20805960 rs7756992 rs9295478 AG - 0.743 0.701 C06 20787688 rs7756992 G - 0.232 0.270 C06 31552682 rs2516424 C - 0.325 0.372 C06 31592562 rs2516424 rs4947324 CC - 0.320 0.368 C06 41130207 rsl0456499 A - 0.563 0.597 C06 132387934 rs9483377 rs997607 GC - 0.234 0.278 C06 132379686 rs9483377 rs7745875 GG - 0.233 0.276 C06 132361238 rs9483377 G - 0.307 0.356 C06 150399255 rsl1155700 A - 0.749 0.794 C06 150399954 rs12213837 C - 0.749 0.794 C06 164421443 rs206732 rs933251 TC rsl 0085202 A (1) 0.531 0.479 C08 124084183 rs952656 G - 0.673 0.721 C08 124092339 rsl 3252935 rs7824293 TG - 0.143 0.108 C08 128249239 rs283710 rs412835 CC - 0.254 0.222 C08 128250055 rsl85852 G - 0.755 0.791 C08 128265112 rs283718 rs283720 CA - 0.255 0.223 C09 88426790 rsl0993008 A - 0.154 0.192 C09 C09 93768899 93802193 rs10818991 rs10990303 rs10990568 rs4743148 CC GG rsl0985640 A (0.85) 0.537 0.263 0.490 0.309 C09 93810412 rs4743148 G - 0.315 0.365 C09 124790974 rs3814120 T - 0.093 0.113 C10 52735263 rs7915186 rs3829170 TT - 0.328 0.377 C10 52746400 rs3829170 rs7922112 TG rs12247188T (0.9) 0.336 0.386 C10 93976392 rs2421943 G - 0.555 0.614 C10 94022896 rs2421943 rs7917359 GC - 0.521 0.585 C10 94068337 rs7908111 rs2497304 GG - 0.499 0.443 0.85 0.00082 0.489 0.92 0.18 0.438 0.75 0.000043 1.18 0.0008 0.511 1.09 0.18 0.562 1.33 0.000043 1.25 0.00023 0.244 1.39 0.000015 0.200 1.08 0.38 1.71 0.000016 0.080 1.89 0.000037 0.063 1.48 0.033 1.11 0.034 0.416 0.97 0.61 0.495 1.34 0.000035 1.23 0.00021 0.292 1.37 0.0000090 0.250 1.11 0.21 0.81 0.000089 0.682 0.74 0.000013 0.718 0.88 0.11 1.23 0.00021 0.292 1.37 0.0000090 0.250 1.11 0.20 1.23 0.000039 0.375 1.25 0.00080 0.376 1.25 0.0020 1.24 0.000027 0.370 1.25 0.00074 0.373 1.26 0.0016 1.15 0.0040 0.575 1.05 0.43 0.637 1.36 0.000018 1.26 0.000040 0.272 1.22 0.0067 0.276 1.25 0.0065 1.25 0.000048 0.271 1.22 0.0052 0.273 1.23 0.0087 1.25 0.000013 0.348 1.20 0.0052 0.354 1.24 0.0040 1.29 0.0000095 0.786 1.23 0.0049 0.801 1.35 0.00039 1.29 0.0000097 0.786 1.23 0.0049 0.801 1.35 0.00040 0.81 0.000037 0.469 0.78 0.00015 0.497 0.87 0.058 1.25 0.000019 0.706 1.17 0.021 0.725 1.28 0.0012 0.72 0.000010 0.116 0.78 0.0099 0.104 0.69 0.00067 0.84 0.0024 0.245 0.95 0.51 0.190 0.69 0.000025 1.22 0.00050 0.764 1.05 0.49 0.822 1.49 0.0000046 0.84 0.0026 0.256 1.01 0.94 0.189 0.68 0.0000092 1.30 0.000027 0.181 1.21 0.019 0.194 1.32 0.0020 0.83 0.00019 0.469 0.76 0.000037 0.513 0.91 0.18 1.25 0.000032 0.314 1.28 0.00038 0.306 1.23 0.0076 1.25 0.000010 0.371 1.28 0.00013 0.358 1.21 0.0092 1.25 0.0046 0.094 1.01 0.91 0.140 1.59 0.000014 1.24 0.000021 0.374 1.22 0.0021 0.375 1.23 0.0049 1.24 0.000021 0.381 1.22 0.0027 0.387 1.24 0.0027 1.28 9.1 *10"7 0.600 1.20 0.0043 0.621 1.31 0.00017 1.30 1.3x10"® 0.565 1.19 0.0052 0.602 1.39 0.0000041 0.80 0.0000034 0.456 0.84 0.0072 0.427 0.75 0.000039 C10 94011761 rsl 999763 rsl 0882091 GT - 0.517 0.455 C10 94023632 rsl 999763 rs6583830 GG - 0.517 0.455 C10 94012407 rs6583826 G - 0.467 0.518 C10 94025680 rs6583826 rsl 0882091 GC - 0.393 0.449 C10 94092724 rs10882091 rs7923837 CG - 0.410 0.466 C10 94038954 rsl 0882091 C - 0.415 0.472 C10 94047527 rs7914814 T - 0.416 0.472 C10 94062695 rs6583830 A - 0.415 0.472 C10 94122233 rs2275729 rsl 111875 AG - 0.470 0.527 C10 94157293 rs2497304 A - 0.530 0.473 C10 94160330 rs947591 A - 0.475 0.526 C10 114441018 rs7895307 rsl 2255372 GT - 0.257 0.308 C10 114422936 rs7903146 T - 0.300 0.372 C10 114434905 rs7903146 rsl 1196192 TT - 0.220 0.282 C10 114438514 rs7904519 G - 0.480 0.522 C10 114455586 rs7904519 rsl 0885409 GC - 0.474 0.516 C10 114455586 rs7904519 rs10885409 AT - 0.510 0.471 C10 114472659 rsl 0885409 C - 0.484 0.523 C10 114473489 rs 12255372 T - 0.294 0.351 C10 118261345 rsl681748 rs2170862 TT - 0.238 0.265 C10 118285583 rs2170862 T - 0.256 0.281 C10 118555280 rsl0787760 G - 0.278 0.300 C11 23946882 rsl879230 T - 0.088 0.111 C11 106474406 rsl455593 T - 0.097 0.114 C12 30390375 rsl429622 rsl506382 AG rs794598 C (0.9) 0.368 0.321 C12 33373479 rsl 905421 T - 0.082 0.110 C13 25558690 rs565707 rs6491198 AA - 0.281 0.249 C13 25478564 rs565707 C - 0.700 0.734 C13 25535031 rs7984685 C - 0.540 0.582 C13 25537643 rs7998347 C - 0.540 0.582 C13 25715179 rs 1333350 rs7987436 GT - 0.254 0.216 C14 80759910 rs799099 rs4899801 AG - 0.365 0.390 0.78 2.9x10'7 0.472 0.83 0.0038 0.442 0.74 0.000019 0.78 2.9x10"' 0.472 0.83 0.0038 0.442 0.74 0.000019 1.23 0.000020 0.508 1.18 0.0080 0.527 1.28 0.00048 1.26 0.0000021 0.435 1.19 0.0062 0.469 1.36 0.000012 1.26 0.0000022 0.452 1.19 0.0063 0.486 1.36 0.000011 1.26 0.0000024 0.456 1.18 0.0079 0.491 1.36 0.000014 1.26 0.0000025 0.456 1.18 0.0081 0.491 1.35 0.000014 1.26 0.0000024 0.456 1.18 0.0079 0.491 1.36 0.000014 1.26 0.0000023 0.519 1.22 0.0018 0.534 1.29 0.00025 0.80 0.0000 0.481 0.82 0.00 0.466 0.77 0.000251 1.23 0.000023 0.521 1.21 0.0028 0.545 1.33 0.000053 1.29 0.0000049 0.330 1.42 4.5x10"' 0.269 1.06 . 0.45 1.38 1.9x10"10 0.396 1.53 2.4x10"11 0.342 1.21 0.010 1.39 3.4x10"9 0.298 1.51 9.4x10"9 0.263 1.27 0.0042 1.18 0.00045 0.553 1.34 0.0000026 0.483 1.01 0.84 1.18 0.00055 0.549 1.35 0.0000018 0.476 1.01 0.90 0.86 0.0013 0.441 0.76 0.000011 0.510 1.00 0.99 1.17 0.0014 0.555 1.33 0.0000060 0.483 0.99 0.94 1.29 4.9x10"7 0.371 1.41 1.6x10"' 0.317 1.11 0.15 1.15 0.013 0.245 1.04 0.59 0.302 1.38 0.000041 1.13 0.020 0.259 1.02 0.82 0.320 1.37 0.000043 1.12 0.037 0.269 0.96 0.53 0.347 1.38 0.000017 1.30 0.00097 0.128 1.53 0.000021 0.093 1.07 0.57 1.20 0.021 0.087 0.89 0.29 0.142 1.54 0.000040 0.82 0.000083 0.341 0.89 0.092 0.296 0.72 0.000023 1.39 0.000044 0.116 1.47 0.00020 0.107 1.35 0.011 0.85 0.0039 0.220 0.72 0.000016 0.274 0.97 0.69 1.19 0.0016 0.763 1.38 0.0000073 0.710 1.05 0.53 1.19 0.00043 0.606 1.31 0.000022 0.568 1.12 0.11 1.19 0.00046 0.606 1.31 0.000024 0.568 1.12 0.11 0.81 0.00030 0.195 0.71 0.000010 0.251 0.98 0.82 1.11 0.037 0.359 0.97 0.64 0.439 1.36 0.000022 C14 80763881 rs2066041 G - 0.367 0.394 C14 80820260 rsl 0483957 A - 0.459 0.493 C15 98094991 rs9920347 rsl 1635811 AG rs2045107 C (0.9) 0.521 0.469 C16 12811478 rs6498353 rs9941146 CG - 0.105 0.080 C16 22764405 rs724466 T - 0.738 0.781 C16 24353768 rsl 1074618 rs985729 AC rsl 1644596 G (1) 0.299 0.342 C16 73296557 rs1862773 rs825842 CT - 0.059 0.038 C16 73311680 rs2432543 rs4887826 TG - 0.069 0.043 C17 69180675 rsl 7763769 rsl 860316 GA - 0.511 0.564 C17 69203439 rs1860316 A - 0.653 0.707 C17 69242752 rs1860316 rs17763811 GC - 0.335 0.282 C17 69218316 rs1981647 C - 0.513 0.563 C17 69234630 rs1843622 T - 0.615 0.665 C17 69244944 rs2191113 A - 0.696 0.744 C17 69259003 rs9890889 A - 0.839 0.869 C18 41051796 rsl0502860 G - 0.167 0.194 C18 63451377 rs764133 rs7237209 TT - 0.167 0.132 C18 63463071 rs7237209 C - 0.819 0.852 C19 3316583 rs3810420 A - 0.176 0.189 C20 37651862 rs4592915 rs2232580 GC rs6127771 C (1) 0.495 0.550 C21 13769165 rs468601 A - 0.888 0.908 C21 33296778 rs2834061 G - 0.249 0.291 C21 39373432 rs369906 T - 0.566 0.613 Gene C03 69453958 rsl0510980 A ENST00000343145 (K211R) 0.808 0.840 C08 118141371 rsl3266634 C SLC30A8 (R325W) 0.646 0.685 C10 124472418 rs2495774 G LOC390009 (Q27H) 0.547 0.594 C11 3624302 rs2271586 T ART5 (T284K) 0.176 0.208 C19 8669900 rsl0410943 G MGC33407 (A51V) 0.674 0.714 aA surrogate of the corresponding two marker haplotype with a correlation coefficient control (see Methods). 1.12 0.021 0.368 1.01 0.92 0.437 1.34 0.000038 1.15 0.0042 0.476 1.07 0.28 0.530 1.33 0.000042 0.81 0.000044 0.475 0.84 0.0056 0.468 0.81 0.0041 0.74 0.00054 0.068 0.62 0.000047 0.082 0.75 0.026 1.26 0.000038 0.781 1.27 0.0012 0.783 1.29 0.0025 1.21 0.00044 0.332 1.16 0.040 0.372 1.39 0.000032 0.63 0.000048 0.041 0.67 0.0075 0.039 0.64 0.0072 0.61 0.000010 0.042 0.60 0.00046 0.049 0.69 0.019 1.24 0.000013 0.585 1.35 0.0000023 0.543 1.14 0.069 1.28 0.0000020 0.734 1.46 3.2x10"® 0.687 1.17 0.039 0.78 0.0000028 0.254 0.68 2.6x10"® 0.301 0.86 0.039 1.23 0.000026 0.583 1.33 0.0000065 0.544 1.14 0.071 1.24 0.000021 0.684 1.35 0.0000043 0.640 1.11 0.14 1.27 0.000013 0.771 1.47 9.5x10"® 0.713 1.08 0.30 1.27 0.00053 0.885 1.47 0.000032 0.857 1.14 0.17 1.20 0.0035 0.218 1.39 0.000028 0.174 1.05 0.61 0.76 0.00010 0.121 0.69 0.000048 0.135 0.78 0.014 1.27 0.00028 0.867 1.44 0.000029 0.847 1.22 0.037 1.09 0.16 0.227 1.37 0.000045 0.146 0.80 0.021 1.25 0.0000048 0.558 1.29 0.000051 0.543 1.21 0.0060 1.25 0.0054 0.927 1.60 0.000026 0.895 1.08 0.48 1.24 0.000076 0.311 1.36 0.0000094 0.271 1.12 0.15 1.21 0.00010 0.631 1.31 0.000028 0.587 1.09 0.24 1.25 0.00065 0.836 1.22 0.019 0.845 1.30 0.0061 1.19 0.00060 0.678 1.16 0.030 0.697 1.26 0.0020 1.21 0.00011 0.592 1.20 0.0039 0.597 1.22 0.0043 1.23 0.00059 0.212 1.26 0.0033 0.203 1.20 0.042 1.20 0.00043 0.713 1.20 0.0076 0.708 1.17 0.035 °P values adjusted for relatedness and population stratification using genomic Table 15. Association to T2D in the primary replication group (Denmark B).

Association results for the 47 SNPs tested in the primary replication cohort (Denmark B), consisting of 1110 T2D cases and 2272 controls. Included in the table is the chromosome, the position of the SNPs in NCBI Build 34, the marker and allele tested, frequency in controls and the frequency in cases, odds ratio (OR) and P value in all T2D cases, non-obese T2D cases and obese T2D cases, respectively. For all three groups of cases, the same group of controls is used and the number of cases is included in the parentheses. The two SNPs selected for replication in additional T2D case-control groups are highlighted with bold typesetting.

All T2D cases (1110) NonObese T2D cases (640) Obese T2D cases (470) Chr Position Marker Allele Con.frq Case.frq OR P Case.frq OR P Case.frq OR P C01 29589307 rsl 0798895 A 0.832 0.828 0.97 0.68 0.831 0.99 0.94 0.824 0.94 0.55 C01 104461151 rs7553985 C 0.367 0.379 1.05 0.34 0.375 1.03 0.62 0.385 1.08 0.30 C01 151915609 rs3738028 G 0.385 0.410 1.11 0.050 0.419 1.15 0.029 0.397 1.05 0.47 C02 40623619 rsl 3414307 A 0.537 0.540 1.01 0.84 0.544 1.03 0.67 0.534 0.99 0.86 C03 69453958 rsl 0510980 A 0.826 0.833 1.05 0.50 0.835 1.06 0.50 0.831 1.03 0.74 C03 89162181 rsl 2486049 T 0.878 0.872 0.94 0.47 0.871 0.93 0.49 0.873 0.96 0.70 C03 146863467 rs7630694 G 0.053 0.054 1.02 0.85 0.051 0.95 0.72 0.059 1.12 0.46 C03 196904151 rs9858622 A 0.656 0.667 1.05 0.39 0.662 1.02 0.73 0.674 1.08 0.29 C04 140660180 rsl 0033117 C 0.740 0.746 1.03 0.65 0.747 1.04 0.65 0.744 1.02 0.81 C05 76635083 rs4704400 T 0.472 0.456 0.94 0.23 0.452 0.92 0.22 0.461 0.96 0.55 C05 87825021 rs10452479 G 0.229 0.238 1.05 0.43 0.240 1.06 0.43 0.235 1.04 0.68 C06 6971276 rs12201780 A 0.043 0.048 1.12 0.36 0.049 1.16 0.32 0.045 1.07 0.71 C06 9509965 rs214447 T 0.418 0.427 1.03 0.52 0.432 1.06 0.39 0.419 1.00 0.95 C06 20787688 rs7756992 G 0.276 0.322 1.24 0.00013 0.321 1.24 0.0021 0.323 1.25 0.0044 C06 31552682 rs2516424 C 0.363 0.380 1.07 0.19 0.374 1.05 0.48 0.387 1.11 0.18 C06 41130207 rsl 0456499 A 0.581 0.579 0.99 0.92 0.576 0.98 0.78 0.583 1.01 0.87 C06 132361238 rs9483377 G 0.306 0.331 1.12 0.039 0.334 1.14 0.061 0.327 1.10 0.20 C06 150399255 rsl 1155700 A 0.758 0.734 0.88 0.043 0.737 0.90 0.14 0.731 0.87 0.089 C06 164425224 rsl 0085202 G 0.430 0.426 0.99 0.78 0.424 ■ 0.98 0.73 0.428 0.99 0.94 C08 118141371 rsl3266634 C 0.664 0.704 1.20 0.0012 0.701 1.19 0.013 0.707 1.22 0.012 C08 124084183 rs952656 G 0.672 0.672 1.00 0.98 0.680 1.04 0.56 0.660 0.95 0.51 C08 128250055 rs185852 G 0.796 0.797 1.01 0.92 0.794 0.99 0.88 0.801 1.03 0.72 C09 88426790 rsl 0993008 A 0.146 0.150 1.03 0.66 C09 93745181 rsl 0985640 G 0.430 0.434 1.01 0.78 C09 93810412 rs4743148 G 0.382 0.381 1.00 0.94 C09 124790974 rs3814120 T 0.089 0.090 1.02 0.84 C10 52758344 rsl 2247188 T 0.331 0.315 0.93 0.19 C10 94047527 rs7914814 T 0.413 0.432 1.08 0.14 C10 118555280 rs 10787760 G 0.294 0.276 0.91 0.15 C10 124472418 rs2495774 G 0.524 0.540 1.07 0.22 C11 23946882 rsl 879230 T 0.127 0.115 0.89 0.13 C11 3624302 rs2271586 T 0.190 0.201 1.07 0.28 C11 106474406 rs 1455593 T 0.081 0.080 0.98 0.81 C12 30434349 rs794598 T 0.623 0.600 0.91 0.063 C12 33373479 rs1905421 T 0.099 0.097 0.98 0.79 C14 80763881 rs2066041 G 0.427 0.415 0.95 0.35 C15 98060278 rs2045107 G 0.524 0.527 1.01 0.78 C16 12756032 rs6498353 C 0.136 0.134 0.98 0.80 C16 22764405 rs724466 T 0.695 0.715 1.10 0.085 C16 24356412 rsl 1644596 G 0.324 0.323 1.00 0.94 C16 73314817 rs4887826 G 0.064 0.052 0.82 0.068 C17 69203439 rs 1860316 A 0.679 0.682 1.01 0.82 C18 41051796 rs 10502860 G 0.222 0.197 0.86 0.044 C18 63463071 rs7237209 C 0.861 0.852 0.92 0.29 C19 3316583 rs3810420 A 0.181 0.191 1.07 0.30 C20 37645161 rs6127771 C 0.447 0.451 1.02 0.77 C21 33296778 rs2834061 G 0.250 0.255 1.03 0.66 3 o K) 0.151 1.04 0.64 0.149 1.02 0.84 0.421 0.96 0.57 0.451 1.09 0.25 © o 00 0.370 0.95 0.41 0.398 1.07 0.39 o 0.076 0.85 0.16 0.109 1.27 0.052 •Jl 00 K) 0.312 0.92 0.22 0.318 0.94 0.45 0.434 1.09 0.18 0.429 1.07 0.35 0.268 0.88 0.080 0.288 0.97 0.73 0.542 1.07 0.27 0.538 1.06 0.46 0.118 0.91 0.36 0.110 0.85 0.14 0.194 1.02 0.77 0.211 1.14 0.13 0.081 0.99 0.92 0.078 0.96 0.77 0.594 0.88 0.058 0.608 0.94 0.37 0.086 0.85 0.17 0.113 1.16 0.24 0.427 1.00 1.00 0.398 0.89 0.11 0.522 0.99 0.92 0.534 1.04 0.55 148 0.140 1.04 0.68 0.124 0.90 0.35 0.719 1.12 0.10 0.710 1.08 0.34 0.336 1.06 0.43 0.305 0.92 0.27 0.054 0.84 0.21 0.050 0.78 0.11 0.684 1.02 0.74 0.679 1.00 1.00 0.198 0.87 0.12 0.196 0.86 0.13 0.848 0.89 0.22 0.857 0.97 0.74 0.188 1.05 0.54 0.195 1.10 0.30 0.442 0.98 0.77 0.462 1.06 0.39 0.267 1.09 0.23 0.239 0.94 0.48 ^5 n <z> In) o o © o o o In) o Table 16. Association results for SNPs with reported association to T2D in Sladek et al.

Shown are association results for T2D in the Icelandic study group for the eight SNPs identified by Sladek et al (Nature 445, 881-5 (2007)) to associate with T2D. For the Icelandic group the table includes the frequency in cases and controls, odds ratio (OR) and adjusted P value for five of the eight SNP's. Corresponding values are shown for the replication cohort used in Sladek et al. Three of the markers, rslll3132, rsll037909 and rs3740878, are not on the Illumina 300K chip; however, a surrogate SNP rs729287 which has a correlation r2 = 1 to rsll037909 and rs3740878 (based on HapMap CEU data) has been typed in the Icelandic study group and results for this marker are included in the table.

Icelandic study group Sladek et al Chr Position Marker Allele Controls Cases OR P Controls Cases ORa P" Nearest gene C08 118141371 rsl 3266634 C 0.646 0.685 1.19 0.00060 0.699 0.746 1.26 .0*10"7 ' SLC30A8 C10 94127459 rs1111875 G 0.550 0.588 1.17 0.0014 0.598 0.642 1.21 9.1x10"® HHEX C10 94146494 rs7923837 G 0.583 0.624 1.19 0.00058 0.623 0.665 1.20 2.2X10"5 HHEX C10 114422936 rs7903146 T 0.300 0.372 1.38 1.9x10"10 0.293 0.406 1.65 <1.0*10~7 TCF7L2 C11 42211027 rs7480010 G 0.273 0.271 0.95 0.33 0.301 0.336 1.18 2.9*10^ LOC387761 C11 44207712 rs1113132 C - - - - 0.733 0.763 1.17 8.1x10^ EXT2 C11 44219923 rsl 1037909 T - - - - 0.729 0.760 1.18 4.5X10"4 EXT2 C11 44222111 rs3740878 A - - ' - - 0.728 0.760 1.18 2.8x10^ EXT2 C11 44244399 rs729287 C 0.748 0.759 1.06 0.33 - - - - EXT2 a Allelic OR calculated from frequency information provided in Table 1 of Sladek et al. b P value (based on permutation) for Stage 2 in Table 1 in Sladek et al. 150 Table 17. Association results for the SNPs rs7756992 and rsl3266634 in six Caucasian T2D case-control groups and in case-control groups from Hong Kong and from West-Africa.

Study population (n//n) Frequency Variant (allele) Controls Cases OR (95% CI) P value Iceland (1399/5275) rs7756992 (G) 0.232 0.270 1.23(1.10-1.37) 0.00021 rsl 3266634 (C) 0.646 0.685 1.19(1.08-1.31) 0.0006 Denmark A (263/597) rs7756992 (G) 0.297 0.331 1.17(0.93-1.47) 0.18 rsl 3266634 (C) 0.686 0.672 0.94(0.75-1.17) 0.58 Denmark B (1359/4825) rs7756992 (G) 0.279 0.320 1.21 (1.10-1.33) 0.000054 rsl 3266634 (C) 0.673 0.692 1.09 (0.99-1.19) 0.073 Philadelphia (447/950) rs7756992 (G) 0.262 0.295 1.18(0.98-1.42) 0.073 rsl 3266634 (C) 0.678 0.760 1.51 (1.25-1.81) 1,5*10"5 Scotland (3742/3718) rs7756992 (G) 0.267 0.288 1.11 (1.03-1.19) 0.0042 rsl 3266634 (C) 0.682 0.710 1.14(1.06-1.22) 0.00025 The Netherlands (368/915) rs7756992 (G) 0.270 0.280 1.05 (0.86-1.27) 0.64 rsl 3266634 (C) 0.717 0.736 1.10(0.91-1.33) 0.33 Caucasian combined3 (7578/16280) rs7756992 (G) 0.264 0.293 1.16(1.09-1.22) 3.9x10"10 rsl3266634 (C) 0.675 0.700 1.15(1.10-1.20) 3.3x10"9 Hong Kong(1457/986) rs7756992 (G) 0.462 0.517 1.25(1.11-1.40) 0.00018 rsl3266634 (C) 0.523 0.566 1.19(1.06-1.33) 0.0035 West Africa3 (865/1106) rs7756992 (G) 0.612 0.625 1.02 (0.92-1.14) 0.72 rsl 3266634 (C) 0.962 0.971 1.26 (0.88-1.81) 0.21 All groups combined (9900/18372) rs7756992 (G) 1.15(1.11-1.20) 9..0*10"12 rsl 3266634 (C) 1.16(1.11-1.21) 2.5x10"11 Shown are the number of T2D cases and controls (nlm), the allelic frequency in the affected and control individuals, the allelic odds-ratio (OR) with 95 confidence intervals (CI 95%) and two-sided P values based on the multiplicative model. ''When combining results for the Caucasian groups and for the five West-African groups, OR's and P values are combined using a Mantel-Haenzsel model, while the frequency in cases and controls is estimated as a weighted average over the different study groups.

Table 18. Association of eight SNP's in CDKALl to T2D in Iceland, Hong Kong and West-Africa.

Association to T2D for eight SNP's in the CDKALl gene for three of the eight study groups; from Iceland, Hong Kong and West-Africa. The seven additional SNP's are all highly correlated to rs7756992.

Combined3 Iceland Hong Kong West-Africa0 SNP Allele Positionb OR (95% CI) P Con.frq Case.frq OR P Con.frq Case.frq OR P Con.frq Case.frq OR P rs7752906 A 20774034 1.19(1.11-1.28) 6.5*10'7 0.296 0.338 1.22 0.00076 0.362 0.422 1.29 3.2x10"5 0.654 0.674 1.06 0.43 rsl 569699 C 20787289 1.19 (1.12-1.27) 1.4x10"7 0.257 0.297 1.22 0.00018 0.463 0.519 1.25 0.00019 0.627 0.656 1.10 0.17 rs7756992 G 20787688 1.17 (1.09-1.25) 3.1x10"® 0.232 0.270 1.23 0.00023 0.462 0.517 1.25 0.00018 0.612 0.625 1.02 0.72 rs9350271.

A 20791143 1.18(1.11-1.26) 9.6x10"7 0.257 0.298 1.23 0.00016 0.356 0.406 1.23 0.00055 0.695 0.712 1.07 0.38 rs9356744 C 20793465 1.18 (1.11-1.26) 7.9x10"7 0.256 0.297 1.23 0.00014 0.357 0.407 1.24 0.00045 0.696 0.713 1.06 0.39 rs9368222 A 20794975 1.20(1.12-1.28) 4.8x10"7 0.231 0.269 1.22 0.00029 0.355 0.405 1.24 0.00041 0.184 0.203 1.10 0.27 rsl0440833 A 20796100 1.18(1.11-1.27) 1.4X10"6 0.233 0.269 1.22 0.00046 0.354 0.407 1.25 0.00024 0.213 0.226 1.06 0.48 rs6931514 G 20811931 1.19 (1.11-1.27) 7.8x10 7 0.231 0.267 1.22 0.00047 0.464 0.520 1.25 0.00015 0.231 0.249 1.07 0.41 aResults for the three groups were combined using a Mantel-Haenszel model. "Basepair position in NCBI Build 34. cResults for the five West-African groups were combined using Mantel-Haenszel model and the allele frequencies shown are a weighted average of the frequency for the five groups. 152 Table 19. Pair-wise correlation for SNP's typed in CDKALl.

Pair-wise correlation, D' (lower left corner) and r2 (upper right corner), for the eight SNP's in CDKALl that were tested for association to T2D. The correlation is estimated for control individuals from the Icelandic, Hong Kong and West-African study groups, respectively. rs7752906 rsi 569699 CM O) h* J CM CM CO o CO rs6931514 D'\ <0 ■n t-. £ o in CO O) e CO in CO o> 2 CO CO n o> £ o o e Iceland ! rs7752906 - 0.55 0.66 0.56 0.56 0.67 0.66 0.65 rsl 569699 0.83 - 0.87 0.99 0.98 0.85 0.83 0.83 rs7756992 0.98 1.00 - 0.86 0.86 0.99 0.97 0.96 rs9350271 0.84 1.00 1.00 - 1.00 0.86 0.85 0.84 rs9356744 0.84 1.00 1.00 1.00 - 0.87 0.86 0.85 rs9368222 0.99 1.00 1.00 1.00 1.00 - 0.98 0.97 rsl 0440833 0.96 0.97 1.00 0.98 0.99 1.00 - 0.99 rs6931514 0.96 0.97 0.99 0.98 0.99 0.99 1.00 - Hong Kong rs7752906 - 0.45 0.46 0.77 0.76 0.77 0.77 0.46 rsl 569699 0.84 - 0.99 0.63 0.63 0.62 0.62 0.98 rs7756992 0.84 1.00 - 0.63 0.62 0.64 0.64 0.99 rs9350271 0.89 1.00 0.99 - 1.00 0.99 0.99 0.62 rs9356744 0.88 0.99 0.99 1.00 - 0.99 0.99 0.62 rs9368222 0.89 0.99 1.00 1.00 1.00 - 1.00 0.63 rsl 0440833 0.89 1.00 1.00 1.00 1.00 1.00 - 0.63 rs6931514 0.84 0.99 1.00 0.99 0.99 1.00 1.00 - West-Africa rs7752906 - 0.16 0.32 0.13 0.14 0.12 0.07 0.08 rsl 569699 0.42 - 0.61 0.72 0.72 0.12 0.07 0.09 rs7756992 0.62 0.84 - 0.67 0.67 0.14 0.08 0.10 rs9350271 0.40 0.96 0.99 - 0.99 0.10 0.04 0.05 rs9356744 0.41 0.96 1.00 1.00 - 0.10 0.04 0.06 rs9368222 1.00 0.96 0.95 1.00 1.00 - 0.86 0.76 rsl 0440833 0.68 0.68 0.68 0.59 0.60 . 1.00 - 0.87 rs6931514 0.73 0.72 0.73 0.63 0.65 0.99 1.00 - 153 Table 20. Genotype specific odds ratio for rs7756992 and rsl3266634.

Study population Allelic Genotype odds ratio3 Variant (allele) OR (95% CI) 00 OX (95% CI) XX (95% CI) P" Caucasian rs7756992 (G) 1.16(1.09-1.22) 1 1.09(1.03-1.16) 1.45(1.31-1.61) 0.00052 rsl 3266634 (C) 1.15(1.11-1.20) 1 1.12(1.03-1.23) 1.30(1.18-1.43) 0.63 Hong Kong rs7756992 (G) 1.25(1.11-1.40) 1 1.13(0.97-1.31) 1.55(1.23-1.95) 0.071 rsl 3266634 (C) 1.19(1.06-1.33) 1 1.13(0.96-1.34) 1.40(1.11-1.76) 0.43 aGenotype odds ratio for heterozygous (OX) and homozygous carrier (XX) compared with non-carriers (00). Test of the multiplicative model (the null hypotheses) versus the full model, one degree of freedom.

Table 21. Association to insulin secretion and insulin sensitivity.

Association of the risk variants rs7756992 (G) and rsl3266634 (C) to insulin secretion, estimated by corrected insulin response (CIR), and insulin sensitivity estimated the reciprocal of HOMA (homeostasis model assessment). The table includes number of T2D cases (n) and controls (m) used, the estimated effect and standard error and the P value obtained by regressing the log-transformed trait values on age, sex and either the number of risk alleles an individual carries (additive model) or an indicator variable for homozygous carriers of the risk allele (recessive model). When controls and T2D cases are analysed together an indicator variable for the affection status is included in the analysis. Also shown, for the combined group, is the corresponding P value obtained by adjusting for BMI status of the individuals in the analysis.

Analysis Combined group Controls T2D Trait Group (n/m) Effect (se) P P* Effect (se) P Effect (se) P rs7756992 (add) All (3715/223) -0.083 (0.018) 4.0E-06 9.1 E-06 -0.080 (0.018) 1.3E-05 -0.142 (0.095) 0.14 t? O a> (0 c Males (1742/139) -0.056 (0.025) 0.025 0.042 -0.058 (0.025) 0.021 -0.028 (0.119) 0.82 Females (1973/84) -0.100 (0.025) 6.8E-05 0.00012 -0.088 (0.025) 0.00049 -0.342 (0.144) 0.02 rs7756992 (rec) o Q.

All (3715/223) -0.243(0.041) 3.3E-09 4.9E-09 -0.230 (0.042) 3.7E-08 -0.417(0.199) 0.037 (A © Males (1742/139) -0.225 (0.055) 4.9E-05 0.00014 -0.222 (0.056) 7.5E-05 -0.250 (0.250) 0.32 0£ {2 Females (1973/84) -0.232 (0.059) 7.5E-05 7.6E-05 -0.204 (0.060) 0.00063 -0.696 (0.301) 0,023 "3 rsl 3266634 (add) to c All (3698/228) -0.061 (0.017) 0.0005 0.00056 -0.059 (0.018) 0.00075 -0.083 (0.094) 0.38 Males (1736/143) -0.079 (0.024) 0.0011 0.00091 -0.062 (0.024) 0.011 -0.262 (0.109) 0.017 Females (1962/85) -0.048 (0.024) 0.047 0.052 -0.058 (0.024) 0.016 0.233 (0.166) 0.16 < 2 rs7756992 (add) All (4430/1164) -0.013(0.013) 0.33 0.7 0.002 (0.013) 0.85 -0.065 (0.038) 0.082 O x Males (2062/691) -0.002 (0.019) 0.94 0.51 0.022 (0.020) 0.26 -0.070 (0.049) 0.15 Females (2368/473) -0.026 (0.018) 0.14 0.22 -0.018(0.018) 0.31 -0.061 (0.059) 0.3 rsl 3266634 (add) All (4411/1166) -0.015(0.013) 0.24 0.19 -0.013(0.013) 0.31 -0.024(0.039) 0.55 Males (2058/697) -0.003(0.019) 0.88 0.81 -0.010(0.019) 0.61 0.019(0.050) 0.7 Females (2353/469) -0.028(0.017) 0.11 0.087 -0.016(0.017) 0.34 -0.092(0.063) 0.14 ' P value after adjusting for BMI by including a log(BMI) term among the explanatory variables. 156 Table 22. Surrogate markers for marker rs7756992 on chromosome 6. The table shows markers with values for r2 of greater than 0.2 in the HapMap Caucasian CEPH samples. The search was performed over a 2Mb region flanking rs77566992 (1Mb upstream and 5 1Mb downstream).

Surrogates for rs7756992 on chromosome 6 SNP D* R2 Pos B36 Pos SEQ ID NO:l rs9460517 0.82 0.30 20636813 1818 rs7772956 0.72 0.29 20637521 2526 rs6904566 0.73 0.32 20643949 8954 rs6927356 0.73 0.32 20644073 9078 rs6905138 0.73 0.32 20644335 9340 rsl3194858 0.73 0.32 20644499 9504 rs6456356 1.00 0.22 20649498 14503 rs9366354 0.84 0.40 20653447 18452 rs9368201 0.84 0.41 20654091 19096 rs9348433 0.84 0.40 20657780 22785 rsl3203450 0.73 0.32 20673935 38940 rsl012626 0.82 0.39 20685540 50545 rs9460523 0.55 0.23 20690122 55127 rs9350262 0.55 0.23 20692402 57407 rs4712507 0.56 0.24 20693119 58124 rs9366357 0.56 0.23 20707607 72612 rsl997777 1.00 0.22 20710359 75364 rsl1964057 0.56 0.23 20710776 75781 rsl2206413 1.00 0.22 20715663 80668 rs4515379 0.66 0.20 20735420 100425 rs9465841 0.66 0.20 20737687 102692 rsl3190734 0.62 0.31 20738376 103381 rs2328528 0.67 0.21 20739524 104529 rs2328529 0.67 0.21 20739932 104937 rs7768642 0.67 0.21 20741886 106891 rs9465846 0.67 0.21 20742320 107325 rs9465847 0.67 0.21 20742407 107412 rs7755830 1.00 0.32 20742865 107870 rs6940200 0.67 0.21 20743241 108246 rs9465850 0.67 0.22 20747388 112393 rs4710938 1.00 0.34 20748883 113888 rs9348440 0.79 0.23 20749315 114320 rs4235999 1.00 0.33 20751201 116206 rs4710939 1.00 0.35 20752923 117928 rsl 1965062 1.00 0.33 20755941 120946 rs9460540 1.00 0.33 20756741 121746 rs6456364 0.79 0.23 20757233 122238 rs9295474 0.95 0.68 20760696 125701 rs2328545 0.79. 0.23 20761529 126534 rs9368216 0.79 0.23 20763089 128094 rsl6884072 0.66 0.33 20763482 128487 rs9460541 0.66 0.33 20764559 129564 rs9460542 0.66 0.33 20764746 129751 rs4712522 0.95 0.68 20764779 129784 rsl6884074 0.66 0.32 20764924 129929 157 rs4712523 0.95 0.68 20765543 130548 rs4710940 0.95 0.52 20765991 130996 rsl3190727 0.66 0.33 20766197 131202 rs6906327 0.95 0.52 20767438 132443 rs6456367 0.95 0.68 20767566 132571 rs6456368 0.95 0.67 20767785 132790 rs7749083 0.66 0.33 20768202 133207 rs6456369 0.95 0.52 20768344 133349 rsl3203361 0.66 0.33 20769000 134005 rsl0946398 0.95 0.68 20769013 134018 rs7774594 0.95 0.67 20769122 134127 rs7754840 0.95 0.68 20769229 134234 rs9460544 0.95 0.68 20769508 134513 rs9460545 0.95 0.68 20769529 134534 rs979614 1.00 0.34 20770102 135107 rs4712525 0.95 0.68 20770945 135950 rs4712526 0.95 0.68 20771014 136019 rs9460546 0.95 0.68 20771611 136616 rs736425 0.66 0.33 20772291 137296 rs742642 0.79 0.23 20773060 138065 rs7748382 0.95 0.68 20773528 138533 rs7772603 0.95 0.68 20773925 138930 rs7752780 0.95 0.68 20774001 139006 rs7752906 0.95 0.70 20774034 139039 rsl 1970425 0.66 0.33 20774436 139441 rs9358356 0.95 0.67 20775361 140366 rs9356743 0.79 0.23 20775667 140672 rs9368219 1.00 0.53 20782670 147675 rsl012635 1.00 0.42 20783274 148279 rsl 569699 1.00 0.72 20787289 152294 rs9350271 1.00 0.78 20791143 156148 rs9356744 1.00 0.75 20793465 158470 rs7766070 1.00 1.00 20794552 159557 rs9368222 1.00 1.00 20794975 159980 rsl0440833 1.00 1.00 20796100 161105 rs2206734 1.00 0.53 20802863 167868 rs6931514 1.00 1.00 20811931 176936 rsll753081 1.00 0.53 20813569 178574 rsl040558 1.00 0.53 20821685 186690 rs9295478 0.62 0.30 20824232 189237 rs2328548 1.00 0.53 20824937 189942 rs6935599 1.00 0.53 20825074 190079 rs9465871 1.00 0.53 20825234 190239 rsl0946403 1.00 0.53 20825383 190388 rs2328549 1.00 0.30 20826219 191224 rs9358357 1.00 0.53 20827124 192129 rs9368224 1.00 0.53 20827211 192216 rs9358358 1.00 0.30 20827372 192377 rs9460550 1.00 0.53 20827540 192545 rs9356746 1.00 0.30 20828258 193263 rs9368226 1.00 0.50 20831036 196041 rsl2111351 0.61 0.29 20832537 197542 rs9356747 0.60 0.29 20832986 197991 rs9356748 1.00 0.30 20833076 198081 rs7767391 1.00 0.50 20833219 198224 rs7747752 0.62 0.30 20833402 198407 rsl7234378 0.80 0.24 20952720 158 Table 23. Surrogate markers for marker rsl0882091 on chromosome 10. The table shows markers with values for r2 of greater than 0.2 in the HapMap Caucasian CEPH samples. The search was performed over a 2Mb region flanking rsl0882091 (1Mb upstream and 1Mb downstream).

Surrogates for rsl0882091 on chromosome 10 SNP D' R2 Pos B36 Pos SEQ ID NO:2 rs7086285 0.71 0.23 94166068 rs2798253 0.93 0.32 94192885 1 rs6583813 1.00 0.33 94199919 7035 rsl1187007 1.00 0.35 94204560 11676 rs2149632 1.00 0.35 94222227 29343 rslll87025 0.95 0.48 94247956 55072 rslll87033 1.00 0.35 94252339 59455 rsl0509645 1.00 0.35 94267846 74962 rs7078413 0.49 0.23 94280464 87580 rs4646955 0.75 0.37 94284271 91387 rsl7445328 0.68 0.32 94295169 102285 rsl1187064 0.68 0.31 94298233 105349 rs2421943 1.00 0.45 94301795 108911 rsl1187065 0.95 0.48 94301904 109020 rsl1187078 1.00 0.35 94330685 137801 rs6583823 1.00 0.52 94334395 141511 rs2421941 0.96 0.93 94335889 143005 rs6583826 0.95 0.57 94337810 144926 rs3824735 1.00 0.36 94344184 151300 rsl0786050 1.00 1.00 94357210 164326 rsl1187094 1.00 0.21 94358158 165274 rsl1187096 1.00 0.35 94359568 166684 rs7914814 1.00 1.00 94372930 180046 rsl2772554 1.00 0.23 94373838 180954 rsl0882094 1.00 1.00 94377656 184772 rsl0882095 1.00 0.37 94384382 191498 rsl0736069 1.00 1.00 94385373 192489 rs7900689 1.00 1.00 94385728 192844 rs6583830 1.00 1.00 94388098 195214 rsl0882096 1.00 0.35 94391366 198482 rsl 1187114 1.00 0.36 94396217 203333 rs6583833 1.00 0.76 94399780 206896 rs7078243 1.00 0.78 94404243 211359 rs4933734 1.00 1.00 94404547 211663 rs7911264 1.00 0.73 94426831 233947 rs2488087 1.00 0.74 94436021 243137 rsl0882100 1.00 0.74 94450667 257783 rsl 111875 1.00 0.51 94452862 259978 rsl2778642 1.00 0.55 94454287 261403 rs5015480 1.00 0.51 94455539 262655 rsl0882102 1.00 0.52 94456475 263591 rsl 1187144 1.00 0.40 94459960 267076 rs7087591 1.00 0.39 94463609 270725 rsl0748582 1.00 0.39 94467199 274315 rs7923837 1.00 0.39 94471897 279013 rs7923866 1.00 0.39 94472056 279172 rs2497306 1.00 0.58 94475191 282307 rs2488075 1.00 0.60 94480154 287270 rs2497304 0.96 0.63 94482696 289812 159 rs947591 0.81 0.57 94485733 292849 rs2488071 0.62 0.24 94489557 296673 Table 24. Surrogate markers for marker rs2191113 on chromosome 17. The table shows markers with values for r2 of greater than 0.2 in the HapMap Caucasian CEPH 5 samples. The search was performed over a 2Mb region flanking rs2191113 (1Mb upstream and 1Mb downstream).

Surrogates for rs2191113 on chromosome 17 SNP D' R2 Pos B36 POS SEQ ID NO:3 rs350605 0.82 0.54 66044207 6552 rs350603 0.80 0.22 66045245 7590 rs420762 0.80 0.24 66049716 12061 rs350615 0.86 0.58 66067303 29648 rs350616 0.81 0.25 66067699 30044 rs350621 0.86 0.58 66079419 41764 rs350624 0.86 0.58 66080067 42412 rsl2602288 1.00 0.36 66085473 47818 rsl431454 0.82 0.26 66090535 52880 rs9302918 1.00 0.23 66091912 54257 rs9302919 0.81 0.26 66092080 54425 rs9911671 0.86 0.61 66094196 56541 rsl911969 0.86 0.60 66102315 64660 rs9894021 1.00 0.21 66103236 65581 rs720877 1.00 0.23 66103561 65906 rs720876 1.00 0.23 66103923 66268 rs7218838 0.86 0.61 66106415 68760 rs9896809 1.00 0.21 66106911 69256 rs7220084 0.82 0.26 66114858 77203 rsl860316 0.86 0.61 66117911 80256 rs8079029 0.90 0.62 66118485 80830 rs4019476 0.87 0.63 66122077 84422 rsl981647 0.82 0.26 66132788 95133 rs9890554 0.80 0.21 66134831 97176 rsl0221225 0.80 0.22 66138452 100797 rsl1650683 0.84 0.22 66139800 102145 rsl486290 0.82 0.27 66141933 104278 rs8078302 0.85 0.23 66143200 105545 rsl2949591 1.00 0.20 66146912 109257 rsl843622 1.00 0.61 66149102 111447 rs9891997 1.00 0.28 66152998 115343 rs9910837 1.00 0.28 66155303 117648 rs4793497 0.94 0.58 66163076 125421 rs9890889 0.89 0.24 66173475 rs2009802 0.71 0.23 66178475 rsl7718938 1.00 0.28 66184700 rsl7223216 0.89 0.24 66207685 rs2109050 0.89 0.24 66228633 rsl962801 1.00 0.31 66236090 160

Claims (27)

1. A method of determining a susceptibility to Type 2 diabetes in a human individual, comprising determining the presence or absence of at least one allele of at least one polymorphic marker in a nucleic acid sample obtained from the individual, or in a genotype dataset derived from the individual, wherein the at least one polymorphic marker is selected from rs7756992, and markers in linkage disequilibrium therewith, and wherein determination of the presence or absence of the at least one allele is indicative of a susceptibility to Type 2 diabetes.

2. The method of Claim 1, wherein the at least one polymorphic marker is present within SEQ ID NO: 1.

3. The method of any of the preceding Claims, wherein said markers in linkage disequilibrium are defined by numeric values for |D'| of greater than 0.8 and/or r2 of greater than 0.2.

4. The method of any of claim 1 or 2, wherein the presence of at least one at-risk allele of at least one polymorphic marker is indicative of an increased susceptibility to Type 2 diabetes, and wherein the absence of the at least one at-risk allele is indicative of a decreased susceptibility of Type 2 diabetes.

5. The method of claim 4, wherein the increased susceptibility is characterized by a relative risk (RR) or odds ratio (OR) of at least 1.15.

6. The method of Claim 4 or 5, wherein the increased susceptibility is characterized by a relative risk (RR) or odds ratio (OR) of at least 1.20.

7. The method of Claim 4, wherein the at least one at-risk allele is rs7756992 allele G.

8. The method of any of the claims 1-3, wherein the presence of at least one protective allele in a nucleic acid sample from the individual is indicative of a decreased susceptibility of Type 2 diabetes.

9. The method of any of the claims 1-3, wherein the absence of at least one at-risk allele in a nucleic acid sample from the individual is indicative of a decreased susceptibility of Type 2 diabetes. 161

10. The method of any of Claims 1 to 9, further, comprising screening the nucleic acid or the genotype dataset for the presence or absence of at least one at-risk allele of at least one at-risk marker for Type 2 diabetes in the TCF7L2 gene, wherein determination of the presence of the at least one at-risk allele is indicative of increased susceptibility of Type 2 diabetes.

11. The method of Claim 10, wherein the at least one at-risk marker in the TCF7L2 gene is selected from marker DG10S478, rsl2255372, rs7895340, rslll96205, rs7901695, rs7903146, rsl2243326 and rs4506565, and markers in linkage disequilibrium therewith.

12. A method of identification of a marker for use in assessing susceptibility to Type 2 diabetes in human individuals, the method comprising a. identifying at least one polymorphic marker within SEQ ID NO: 1, or at least one polymorphic marker in linkage disequilibrium therewith; b. determining the genotype status of a sample of individuals diagnosed with, or having a susceptibility to, Type 2 diabetes; and c. determining the genotype status of a sample of control individuals; wherein a significant difference in frequency of at least one allele in at least one marker in individuals diagnosed with, or having a susceptibility to, Type 2 diabetes, as compared with the frequency of the at least one allele in the control sample is indicative of the at least one marker being useful for assessing susceptibility to Type 2 diabetes.

13. The method of Claim 12, wherein linkage disequilibrium is characterized by numerical values of r2 of greater than 0.2 and/or |D'| of greater than 0.8.

14. The method of Claim 13, wherein an increase in frequency of the at least one allele in the at least one marker in individuals diagnosed with, or having a susceptibility to, Type 2 diabetes, as compared with the frequency of the at least one allele in the control sample, is indicative of the at least one marker being useful for assessing increased susceptibility to Type 2 diabetes, and wherein a decrease in frequency of the at least one allele in the at least one marker in individuals diagnosed with, or having a susceptibility to, Type 2 diabetes, as compared with the frequency of the at least one allele in the control sample is indicative of the at least one marker being useful for assessing decreased susceptibility to, or protection against, Type 2 diabetes. 162

15. A method of assessing an individual for probability of response to a therapeutic agent for preventing and/or ameliorating symptoms associated with Type 2 diabetes, comprising: determining the presence or absence of at least one allele of at least one polymorphic marker in a nucleic acid sample obtained from the individual, wherein the at least one polymorphic marker is selected from rs7756992 (SEQ ID NO:21), and markers in linkage disequilibrium therewith, wherein determination of the presence of the at least one allele of the at least one marker is indicative of a probability of a positive response to the Type 2 diabetes therapeutic agent.

16. The method of Claim 15, wherein the Type 2 diabetes therapeutic agent is selected from the agents set forth in Agent Table 1 and Agent Table 2.

17. A method of predicting prognosis of an individual diagnosed with, Type 2 diabetes, the method comprising determining the presence or absence of at least one allele of at least one polymorphic marker in a nucleic acid sample obtained from the individual, wherein the at least one polymorphic marker is selected from the group consisting of rs7756992 (SEQ ID NO:21), and markers in linkage disequilibrium therewith, wherein determination of the presence of the at least one allele is indicative of a worse prognosis of the Type 2 diabetes in the individual.

18. A method of monitoring progress of a treatment of an individual undergoing treatment for Type 2 diabetes, the method comprising determining the presence or absence of at least one allele of at least one polymorphic marker in a nucleic acid sample obtained from the individual, wherein the at least one polymorphic marker is selected from the group consisting of rs7756992 (SEQ ID NO: 21), and markers in linkage disequilibrium therewith, wherein determination of the presence of the at least one allele is indicative of the treatment outcome of the individual.

19. The method of any of the Claims-17-18, wherein linkage disequilibrium is defined by numerical values of r2 of at least 0.2 and/or values of |D'| of at least 0.8

20. The method of any of the preceding Claims, further comprising assessing at least one biomarker in a sample from the individual.

21. The method of any of the preceding Claims, further comprising analyzing non-genetic information to make risk assessment, diagnosis, or prognosis of the individual.

22. The method of Claim 21, wherein the non-genetic information is selected from age, gender, ethnicity, socioeconomic status, previous disease diagnosis, medical history of received 17 may 2012. 163 subject, family history of Type 2 diabetes, biochemical measurements, and clinical measurements.

23. The method of any of the Claims -20-22, further comprising calculating overall risk.

24. Use of an oligonucleotide probe in the manufacture of a diagnostic reagent for diagnosing and/or assessing susceptibility to Type 2 diabetes in a human individual, wherein the probe hybridizes to a segment of a nucleic acid whose nucleotide sequence is given by SEQ ID NO: 1 that comprises at least one polymorphic site, wherein the fragment is 15-500 nucleotides in length.

25. The use according to Claim 24, wherein the polymorphic site is selected from the polymorphic markers rs7756992 (SEQ ID NO:21), and polymorphisms in linkage disequilibrium therewith.

26. A computer program when used to determine a genetic indicator for Type 2 diabetes in a human individual: wherein the computer program is adapted to be executed on a processor to analyze marker and/or haplotype information for at least one human individual with respect to at least one polymorphic marker selected from the markers rs7756992 (SEQ ID NO:21), and markers in linkage disequilibrium therewith, as defined by numerical values of r2 of at least 0.2 and/or values of |D'| of at least 0.8, and generate an output based on the marker or haplotype information, wherein the output comprises a risk measure of the at least one marker or haplotype as a genetic indicator of Type 2 diabetes for the human individual.

27. The method of any of the Claims 1-6 and 10-23, wherein the at least one polymorphic marker is selected from the markers set forth in Table 22. 28 A method according to any one of claims 1, 12 or 15-18, substantially as herein described with reference to any one of the accompanying Examples and Figures thereof. 29 Use according to claim 24, substantially as herein described with reference to any one of the accompanying Examples and Figures thereof. 30 A computer program according to claim 26, substantially as herein described with reference to any one of the accompanying Examples and Figures thereof.