WO2002018414A2 - Haplotypes du gène bf - Google Patents

Haplotypes du gène bf Download PDF

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Publication number
WO2002018414A2
WO2002018414A2 PCT/US2001/027098 US0127098W WO0218414A2 WO 2002018414 A2 WO2002018414 A2 WO 2002018414A2 US 0127098 W US0127098 W US 0127098W WO 0218414 A2 WO0218414 A2 WO 0218414A2
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Prior art keywords
seq
haplotype
nucleotide
gene
thymine
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PCT/US2001/027098
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WO2002018414A3 (fr
Inventor
Alison E. Anastasio
Kevin Finkel
Amir Kazemi
Beena Koshy
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Genaissance Pharmaceuticals, Inc.
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Priority to AU2001286949A priority Critical patent/AU2001286949A1/en
Publication of WO2002018414A2 publication Critical patent/WO2002018414A2/fr
Publication of WO2002018414A3 publication Critical patent/WO2002018414A3/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/78—Connective tissue peptides, e.g. collagen, elastin, laminin, fibronectin, vitronectin, cold insoluble globulin [CIG]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/172—Haplotypes

Definitions

  • This invention relates to variation in genes that encode pharmaceutically-important proteins.
  • this invention provides genetic, variants of the human B-factor, properdin (BF) gene and methods for identifying which variant(s) of this gene is/are possessed by an individual.
  • BF properdin
  • haplotype is the ordered combination of polymorphisms in the sequence of each form of a gene that exists in the population. Because haplotypes represent the variation across each form of a gene, they provide a more accurate and reliable measurement of genetic variation than individual polymorphisms. For example, while specific variations in gene sequences have been associated with a particular phenotype such as disease susceptibility (Roses AD supra; Ulbrecht M et al. 2000 Am JRespir Crit Care Med 161: 469-74) and drug response (Wolfe CR et al.
  • BF B-factor, properdin
  • GCG glycine-rich beta-glycoprotein
  • the complement system is comprised of two pathways, classical and alternative, which act to amplify the action of antibodies on target cells, with the ultimate consequence being the assembly of membrane attack complexes which destroy microorganisms (Albert et al., 1994; Molecular Biology of the Cell, 3rd ed). For both pathways, complement activation can be subdivided into early and late stages.
  • BF forms a complex with C3b (a cleavage product of C3).
  • C3b a cleavage product of C3
  • C3 convertase undergoes additional cleavage and binding steps to produce C5 convertases.
  • the C5 covertaseses in both the classical and alternative pathways, initiate the formation of the membrane attack complexes which participate in a range of cellular processes including cell lysis (Makrides, Pharmacol Rev
  • BF Another BF allele (SO.7), occurred with greater frequency in the diabetic subjects (8.85%) versus controls (3.57%).
  • BF may be involved in the etiology of type I diabetes.
  • IC immue complex
  • SLE systemic lupus erythamotosis
  • BF represents a potential therapeutic target for treating some forms of this disease.
  • the B-factor, properdin gene is located on chromosome 6p21.3, within the class IH region of major histocompatibility complex (Meijia et al., Hum Immunol 1994 Jan;39(l):49-53), and contains 18 exons that encode a 764 amino acid protein.
  • a reference sequence for the BF gene is shown in the contiguous lines of Figure 1 (Genaissance Reference No. 1621934; SEQ ID NO: 1).
  • Reference sequences for the coding sequence (GenBank Accession No. NM_001710.1) and protein are shown in Figures 2 (SEQ ID NO: 2) and 3 (SEQ ID NO: 3), respectively.
  • Single nucleotide polymorphisms have been detected in the BF gene.
  • the following SNPs have been deposited into the NCBI SNP database: cytosine or thymine at a position corresponding to nucleotide 6976 (rs541862), and a SNP of cytosine or thymine corresponding to nucleotide 9944 in Figure 1 (rs522162).
  • polymorphic sites correspond to the following nucleotide positions in Figure 1 : 3834 (PSl), 4049 (PS2), 4204 (PS3), 4331 (PS4), 4438 (PS5), 4915 (PS6), 4960 (PS7), 5028 (PS8), 5169 (PS9), 5557 (PS10), 5639 (PS11), 5844 (PS12), 5971 (PS13), 6038 (PS14), 6087 (PS15), 6709 (PS16), 6732 (PS17), 6941 (PS18), 7010 (PS20), 7316 (PS21), 7565 (PS22), 7836 (PS23), 8107 (PS24), 8181 (PS25), 8887 (PS26), 8930 (PS27), 9045 (PS28) and 9857 (PS29).
  • PS polymorphic sites
  • the polymorphisms at these sites are cytosine or thymine at PSl, thymine or adenine at PS2, cytosine or thymine at PS3, guanine or adenine at PS4, cytosine or thymine at PS5, cytosine or thymine at PS6, guanine or adenine at PS7, thymine or guanine at PS8, guanine or adenine at PS9, cytosine or thymine at PS 10, guanine or adenine at PSl 1, cytosine or thymine at PS12, cytosine or thymine at PS13, thymine or cytosine at PS 14, guanine or adenine at PS 15, guanine or adenine at PS 16, cytosine or thymine at PS 17, adenine or guanine at PS18, thymine or adenine at PS20, cytosine or thy
  • the inventors have determined the identity of the alleles at these sites, as well as at the previously identified sites at nucleotide positions 6976 (PS19) and 9944 (PS30), in a human reference population of 79 unrelated individuals self-identified as belonging to one of four major population groups: African descent, Asian, Caucasian and Hispanic/Latino. From this information, the inventors deduced a set of haplotypes and haplotype pairs for PS1-PS30 in the BF gene, which are shown below in Tables 4 and 3, respectively. Each of these BF haplotypes constitutes a code that defines the variant nucleotides that exist in the human population at this set of polymorphic sites in the BF gene.
  • each BF haplotype also represents a naturally-occurring isoform (also referred to herein as an "isogene") of the BF gene.
  • the frequency of each haplotype and haplotype pair within the total reference population and within each of the four major population groups included in the reference population was also determined.
  • the invention provides a method, composition and kit for genotyping the BF gene in an individual.
  • the genotyping method comprises identifying the nucleotide pair that is present at one or more polymorphic sites selected from the group consisting of PSl, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10, PS11, PS12, PS13, PS14, PS15, PS16, PS17, PS18, PS20, PS21, PS22, PS23, PS24, PS25, PS26, PS27, PS28 and PS29 in both copies of the BF gene from the individual.
  • a genotyping composition of the invention comprises an oligonucleotide probe or primer which is designed to specifically hybridize to a target region containing, or adjacent to, one of these novel BF polymorphic sites.
  • a genotyping kit of the invention comprises a set of oligonucleotides designed to genotype each of these novel BF polymorphic sites.
  • the genotyping kit comprises a set of oligonucleotides designed to genotype each of PS1-PS30. The genotyping method, composition, and kit are useful in determining whether an individual has one of the haplotypes in Table 4 below or has one of the haplotype pairs in Table 3 below.
  • the invention also provides a method for haplotyping the BF gene in an individual.
  • the haplotyping method comprises determining, for one copy of the BF gene, the identity of the nucleotide at one or more polymorphic sites selected from the group consisting of PSl, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10, PS11, PS12, PS13, PS14, PS15, PS16, PS17, PS18, PS20, PS21, PS22, PS23, PS24, PS25, PS26, PS27, PS28 andPS29.
  • the haplotyping method comprises determining whether one copy of the individual's BF gene is defined by one of the BF haplotypes shown in Table 4, below, or a sub-haplotype thereof. In a preferred embodiment, the haplotyping method comprises determining whether both copies of the individual's BF gene are defined by one of the BF haplotype pairs shown in Table 3 below, or a sub-haplotype pair thereof. Establishing the BF haplotype or haplotype pair of an individual is useful for improving the efficiency and reliability of several steps in the discovery and development of drugs for treating diseases associated with BF activity, e.g., diabetes and systemic lupus erythamotosis.
  • diseases associated with BF activity e.g., diabetes and systemic lupus erythamotosis.
  • the haplotyping method can be used by the pharmaceutical research scientist to validate BF as a candidate target for treating a specific condition or disease predicted to be associated with BF activity. Determining for a particular population the frequency of one or more of the individual BF haplotypes or haplotype pairs described herein will facilitate a decision on whether to pursue BF as a target for treating the specific disease of interest. In particular, if variable BF activity is associated with the disease, then one or more BF haplotypes or haplotype pairs will be found at a higher frequency in disease cohorts than in appropriately genetically matched controls.
  • variable BF activity has little, if any, involvement with that disease.
  • the pharmaceutical research scientist can, without a priori knowledge as to the phenotypic effect of any BF haplotype or haplotype pair, apply the information derived from detecting BF haplotypes in an individual to decide whether modulating BF activity would be useful in treating the disease.
  • the claimed invention is also useful in screening for compounds targeting BF to treat a specific condition or disease predicted to be associated with BF activity.
  • detecting which of the BF haplotypes or haplotype pairs disclosed herein are present in individual members of a population with the specific disease of interest enables the pharmaceutical scientist to screen for a compound(s) that displays the highest desired agonist or antagonist activity for each of the BF isoforms present in the disease population, or for only the most frequent BF isoforms present in the disease population.
  • the claimed haplotyping method provides the scientist with a tool to identify lead compounds that are more likely to show efficacy in clinical trials.
  • Haplotyping the BF gene in an individual is also useful in the design of clinical trials of candidate drugs for treating a specific condition or disease predicted to be associated with BF activity. For example, instead of randomly assigning patients with the disease of interest to the treatment or control group as is typically done now, determining which of the BF haplotype(s) disclosed herein are present in individual patients enables the pharmaceutical scientist to distribute BF haplotypes and/or haplotype pairs evenly to treatment and control groups, thereby reducing the potential for bias in the results that could be introduced by a larger frequency of a BF haplotype or haplotype pair that is associated with response to the drug being studied in the trial, even if this association was previously unknown. Thus, by practicing the claimed invention, the scientist can more confidently rely on the information learned from the trial, without first determining the phenotypic effect of any BF haplotype or haplotype pair.
  • the invention provides a method for identifying an association between a trait and a BF genotype, haplotype, or haplotype pair for one or more of the novel polymorphic sites described herein.
  • the method comprises comparing the frequency of the BF genotype, haplotype, or haplotype pair in a population exhibiting the trait with the frequency of the BF genotype or haplotype in a reference population.
  • a higher frequency of the BF genotype, haplotype, or haplotype pair in the trait population than in the reference population indicates the.trait is associated with the BF genotype, haplotype, or haplotype pair.
  • the trait is susceptibility to a disease, severity of a disease, the staging of a disease or response to a drug.
  • the BF haplotype is selected from the haplotypes shown in Table 4, or a sub-haplotype thereof.
  • Such methods have applicability in developing diagnostic tests and therapeutic treatments for diabetes and systemic lupus erythamotosis.
  • the invention provides an isolated polynucleotide comprising a nucleotide sequence which is a polymorphic variant of a reference sequence for the BF gene or a fragment thereof.
  • the reference sequence comprises the contiguous sequences shown in Figure 1 and the polymorphic variant comprises at least one polymorphism selected from the group consisting of thymine at PSl, adenine at PS2, thymine at PS3, adenine at PS4, thymine at PS5, thymine at PS6, adenine at PS7, guanine at PS8, adenine at PS9, thymine at PS10, adenine at PSl 1, thymine at PS12, thymine at PS13, cytosine at PS14, adenine at PS15, adenine at PS16, thymine at PS17, guanine at
  • the polymorphic variant comprises one or more additional polymorphisms selected from the group consisting of thymine at PS 19 and thymine at PS30.
  • a particularly preferred polymorphic variant is an isogene of the BF gene.
  • a BF isogene of the invention comprises cytosine or thymine at PSl, thymine or adenine at PS2, cytosine or thymine at PS3, guanine or adenine at PS4, cytosine or thymine at PS5, cytosine or thymine at PS6, guanine or ⁇ adenine at PS7, thymine or guanine at PS8, guanine or adenine at PS9, cytosine or thymine at PS 10, guanine or adenine at PS 11 , cytosine or thymine at PS 12, cytosine or thymine at PS 13 , thymine or cytosine at PS 14, guanine or adenine at PS 15, guanine or adenine at PS 16, cytosine or thymine at PS 17, adenine or guanine at PS
  • the invention provides a polynucleotide comprising a polymorphic variant of a reference sequence for a BF cDNA or a fragment thereof.
  • the reference sequence comprises SEQ ID NO:2 (Fig.2) and the polymorphic cDNA comprises at least one polymorphism selected from the group consisting of adenine at a position corresponding to nucleotide 26, thymine at a position corresponding to nucleotide 94, adenine at a position corresponding to nucleotide 221, thymine at a position corresponding to nucleotide 405, adenine at a position corresponding to nucleotide 450, adenine at a position corresponding to nucleotide 504, thymine at a position corresponding to nucleotide 672, adenine at a position corresponding to nucleotide 754, thymine at a position corresponding to nucleotide 858, adenine at a position corresponding to
  • Polynucleotides complementary to these BF genomic and cDNA variants are also provided by the invention. It is believed that polymorphic variants of the BF gene will be useful in studying the expression and function of BF, and in expressing BF protein for use in screening for candidate drugs to treat diseases related to BF activity.
  • the invention provides a recombinant expression vector comprising one of the polymorphic genomic and cDNA variants operably linked to expression regulatory elements as well as a recombinant host cell transformed or transfected with the expression vector.
  • the recombinant vector and host cell may be used to express BF for protein structure analysis and drug binding studies.
  • the invention provides a polypeptide comprising a polymorphic variant of a reference amino acid sequence for the BF protein.
  • the reference amino acid sequence comprises SEQ ID NO:3 (Fig.3) and the polymorphic variant comprises at least one variant amino acid selected from the group consisting of histidine at a position corresponding to amino acid position 9, histidine at a position corresponding to amino acid position 74, serine at a position corresponding to amino acid position 252, isoleucine at a position corresponding to amino acid position 372, arginine at a position corresponding to amino acid position 533 and glutamic acid at a position corresponding to amino acid position 651 and/or the protein truncates prematurely at amino acid 31 due to the termination signal at codon 32 in the coding sequence.
  • a polymorphic variant of BF is useful in studying the effect of the variation on the biological activity of BF as well as on the binding affinity of candidate drugs targeting BF for the treatment of diabetes and systemic lupus eryfhamotosis.
  • the present invention also provides antibodies that recognize and bind to the above polymorphic BF protein variant. Such antibodies can be utilized in a variety of diagnostic and prognostic formats and therapeutic methods.
  • the present invention also provides nonhuman transgenic animals comprising one or more of the BF polymorphic genomic variants described herein and methods for producing such animals.
  • the transgenic animals are useful for studying expression of the BF isogenes in vivo, for in vivo screening and testing of drugs targeted against BF protein, and for testing the efficacy of therapeutic agents and compounds for diabetes and systemic lupus erythamotosis in a biological system.
  • the present invention also provides a computer system for storing and displaying polymorphism data determined for the BF gene.
  • the computer system comprises a computer processing unit; a display; and a database containing the polymorphism data.
  • the polymorphism data includes one or more of the following: the polymorphisms, the genotypes, the haplotypes, and the haplotype pairs identified for the BF gene in a reference population.
  • the computer system is capable of producing a display showing BF haplotypes organized according to their evolutionary relationships.
  • Figure 1 illustrates a reference sequence for the BF gene (Genaissance Reference No. 1621934; contiguous lines), with the start and stop positions of each region of coding sequence indicated with a bracket ([ or ]) and the numerical position below the sequence and the polymorphic site(s) and polymorphism(s) identified by Applicants in a reference population indicated by the variant nucleotide positioned below the polymorphic site in the sequence.
  • SEQ ID NO: 144 is a modified version of SEQ ID NO: 1 that shows the context sequence of each polymorphic site, PS1-PS30, in a uniform format to facilitate electronic searching.
  • SEQ ID NO: 144 contains a block of 60 bases of the nucleotide sequence encompassing the centrally-located polymorphic site at the 30 th position, followed by 60 bases of unspecified sequence to represent that each PS is separated by genomic sequence whose composition is defined elsewhere herein.
  • Figure 2 illustrates a reference sequence for the BF coding sequence (contiguous lines; SEQ ID NO:2), with the polymorphic site(s) and polymorphism(s) identified by Applicants in a reference population indicated by the variant nucleotide positioned below the polymorphic site in the sequence.
  • Figure 3 illustrates a reference sequence for the BF protein (contiguous lines; SEQ ID NO:3), with the variant amino acid(s) caused by the polymorphism(s) of Figure 2 positioned below the polymorphic site in the sequence. Any exclamation points (!) presented below the reference sequence represent a termination codon introduced by a polymorphism of Figure 2.
  • the present invention is based on the discovery of novel variants of the BF gene.
  • the inventors herein discovered 31 isogenes of the BF gene by characterizing the BF gene found in genomic DNAs isolated from an Index Repository that contains immortalized cell lines from one chimpanzee and 93 human individuals.
  • the human individuals included a reference population of 79 unrelated individuals self-identified as belonging to one of four major population groups: Caucasian (21 individuals), African descent (20 individuals), Asian (20 individuals), or Hispanic/Latino (18 individuals). To the extent possible, the members of this reference population were organized into population subgroups by their self-identified ethnogeographic origin as shown in Table 1 below.
  • the Index Repository contains three unrelated indigenous American Indians (one from each of North, Central and South America), one three-generation Caucasian family (from the CEPH Utah cohort) and one two-generation African- American family.
  • the BF isogenes present in the human reference population are defined by haplotypes for 30 polymorphic sites in the BF gene, 28 of which are believed to be novel.
  • the BF polymorphic sites identified by the inventors are referred to as PS1-PS30 to designate the order in which they are located in the gene (see Table 2 below), with the novel polymorphic sites referred to as PSl, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10, PS11, PS12, PS13, PS14, PS15, PS16, PS17, PS18, PS20, PS21, PS22, PS23, PS24, PS25, PS26, PS27, PS28 and PS29.
  • the inventors herein Using the genotypes identified in the Index Repository for PS1-PS30 and the methodology described in the Examples below, the inventors herein also determined the pair of haplotypes for the BF gene present in individual human members of this repository.
  • the human genotypes and haplotypes found in the repository for the BF gene include those shown in Tables 3 and 4, respectively.
  • the polymorphism and haplotype data disclosed herein are useful for validating whether BF is a suitable target for drugs to treat diabetes and systemic lupus erythamotosis, screening for such drugs and reducing bias in clinical trials of such drugs.
  • Candidate Gene - A gene which is hypothesized to be responsible for a disease, condition, or the response to a treatment, or to be correlated with one of these.
  • Genotype An unphased 5 ' to 3 ' sequence of nucleotide pair(s) found at one or more polymorphic sites in a locus on a pair of homologous chromosomes in an individual.
  • genotype includes a full-genotype and/or a sub-genotype as described below.
  • Full-genotype The unphased 5 ' to 3 ' sequence of nucleotide pairs found at all polymorphic sites examined herein in a locus on a pair of homologous chromosomes in a single individual.
  • Sub-genotype The unphased 5' to 3' sequence of nucleotides seen at a subset of the polymorphic sites examined herein in a locus on a pair of homologous chromosomes in a single individual.
  • Genotyping A process for determining a genotype of an individual.
  • Haplotype A 5' to 3' sequence of nucleotides found at one or more polymorphic sites in a locus on a single chromosome from a single individual.
  • haplotype includes a fiill- haplotype and/or a sub-haplotype as described below.
  • Full-haplotype The 5 ' to 3 ' sequence of nucleotides found at all polymorphic sites examined herein in a locus on a single chromosome from a single individual.
  • Sub-haplotype The 5' to 3' sequence of nucleotides seen at a subset of the polymorphic sites examined herein in a locus on a single chromosome from a single individual.
  • Haplotype pair The two haplotypes found for a locus in a single individual.
  • Haplotyping A process for determining one or more haplotypes in an individual and includes use of family pedigrees, molecular techniques and/or statistical inference.
  • Haplotype data Information concerning one or more of the following for a specific gene: a listing of the haplotype pairs in each individual in a population; a listing of the different haplotypes in a population; frequency of each haplotype in that or other populations, and any known associations between one or more haplotypes and a trait.
  • Isoform - A particular form of a gene, mRNA, cDNA or the protein encoded thereby, distinguished from other forms by its particular sequence and/or structure.
  • Isogene - One of the isoforms (e.g., alleles) of a gene found in a population.
  • An isogene (or allele) contains all of the polymorphisms present in the particular isoform of the gene.
  • Isolated - As applied to a biological molecule such as RNA, DNA, oligonucleotide, or protein, isolated means the molecule is substantially free of other biological molecules such as nucleic acids, proteins, lipids, carbohydrates, or other material such as cellular debris and growth media. Generally, the term “isolated” is not intended to refer to a. complete absence of such material or to absence of water, buffers, or salts, unless they are present in amounts that substantially interfere with the methods of the present invention.
  • Locus - A location on a chromosome or DNA molecule corresponding to a gene or a physical or phenotypic feature, where physical features include polymorphic sites.
  • Naturally-occurring - A term used to designate that the object it is applied to, e.g., naturally- occurring polynucleotide or polypeptide, can be isolated from a source in nature and which has not been intentionally modified by man.
  • Nucleotide pair The nucleotides found at a polymorphic site on the two copies of a chromosome from an individual.
  • Phased As applied to a sequence of nucleotide pairs for two or more polymorphic sites in a locus, phased means the combination of nucleotides present at those polymorphic sites on a single copy of the locus is known.
  • Polymorphism The sequence variation observed in an individual at a polymorphic site. Polymorphisms include nucleotide substitutions, insertions, deletions and microsatellites and may, but need not, result in detectable differences in gene expression or protein function.
  • Polymorphism data Information concerning one or more of the following for a specific gene: location of polymorphic sites; sequence variation at those sites; frequency of polymorphisms in one or more populations; the different genotypes and/or haplotypes determined for the gene; frequency of one or more of these genotypes and/or haplotypes in one or more populations; any known associations) between a trait and a genotype or a haplotype for the gene.
  • Polymorphism Database A collection of polymorphism data arranged in a systematic or methodical way and capable of being individually accessed by electronic or other means.
  • Polynucleotide A nucleic acid molecule comprised of single-stranded RNA or DNA or comprised of complementary, double-stranded DNA.
  • Population Group A group of individuals sharing a common ethnogeographic origin.
  • Reference Population A group of subjects or individuals who are predicted to be representative of the genetic variation found in the general population. Typically, the reference population represents the genetic variation in the population at a certainty level of at least 85%, preferably at least 90%, more preferably at least 95% and even more preferably at least 99%.
  • Single Nucleotide Polymorphism SNP
  • SNP Single Nucleotide Polymorphism
  • Subject A human individual whose genotypes or haplotypes or response to treatment or disease state are to be determined.
  • Treatment A stimulus administered internally or externally to a subject.
  • Unphased As applied to a sequence of nucleotide pairs for two or more polymorphic sites in a locus, unphased means the combination of nucleotides present at those polymorphic sites on a single copy of the locus is not known.
  • the invention also provides compositions and methods for detecting the novel BF polymorphisms, haplotypes and haplotype pairs identified herein.
  • compositions comprise at least one oligonucleotide for detecting the variant nucleotide or nucleotide pair located at a novel BF polymorphic site in one copy or two copies of the BF gene.
  • oligonucleotides are referred to herein as BF haplotyping oligonucleotides or genotyping oligonucleotides, respectively, and collectively as BF oligonucleotides.
  • a BF haplotyping or genotyping oligonucleotide is a probe or primer capable o hybridizing to a target region that contains, or that is located close to, one of the novel polymorphic sites described herein.
  • oligonucleotide refers to a polynucleotide molecule having less than about 100 nucleotides.
  • a preferred oligonucleotide of the invention is 10 to 35 nucleotides long. More preferably, the oligonucleotide is between 15 and 30, and most preferably, between 20 and 25 nucleotides in length. The exact length of the oligonucleotide will depend on many factors that are routinely considered and practiced by the skilled artisan.
  • oligonucleotide may be comprised of any phosphorylation state of ribonucleotides, deoxyribonucleotides, and acyclic nucleotide derivatives, and other functionally equivalent derivatives.
  • oligonucleotides may have a phosphate- free backbone, which may be comprised of linkages such as carboxymethyl, acetamidate, carbamate, polyamide (peptide nucleic acid (PNA)) and the like (Varma, R. in Molecular Biology and
  • Oligonucleotides of the invention may be prepared by chemical synthesis using any suitable methodology known in the art, or may be derived from a biological sample, for example, by restriction digestion.
  • the oligonucleotides may be labeled, according to any technique known in the art, including use of radiolabels, fluorescent labels, enzymatic labels, proteins, haptens, antibodies, sequence tags and the like.
  • Haplotyping or genotyping oligonucleotides of the invention must be capable of specifically hybridizing to a target region of a BF polynucleotide.
  • the target region is located in a BF isogene.
  • specific hybridization means the oligonucleotide forms an anti-parallel double-stranded structure with the target region under certain hybridizing conditions, while failing to form such a structure when incubated with another region in the BF polynucleotide or with a non-BF polynucleotide under the same hybridizing conditions.
  • the oligonucleotide specifically hybridizes to the target region under conventional high stringency conditions.
  • a nucleic acid molecule such as an oligonucleotide or polynucleotide is said to be a "perfect” or “complete” complement of another nucleic acid molecule if every nucleotide of one of the molecules is complementary to the nucleotide at the corresponding position of the other molecule.
  • a nucleic acid molecule is "substantially complementary” to another molecule if it hybridizes to that molecule with sufficient stability to remain in a duplex form under conventional low-stringency conditions.
  • an oligonucleotide primer may have a non-complementary fragment at its 5' end, with the remainder of. the primer being complementary to the target region.
  • non-complementary nucleotides may be interspersed into the probe or primer as long as the resulting probe or primer is still capable of specifically hybridizing to the target region.
  • Preferred haplotyping or genotyping oligonucleotides of the invention are allele-specific oligonucleotides.
  • ASO allele-specific oligonucleotide means an oligonucleotide that is able, under sufficiently stringent conditions, to hybridize specifically to one allele of a gene, or other locus, at a target region containing a polymorphic site while not hybridizing to the corresponding region in another allele(s).
  • allele-specif ⁇ city will depend upon a variety of readily optimized stringency conditions, including salt and formamide concentrations, as well as temperatures for both the hybridization and washing steps.
  • stringency conditions including salt and formamide concentrations, as well as temperatures for both the hybridization and washing steps.
  • Examples of hybridization and washing conditions typically used for ASO probes are found in Kogan et al., "Genetic Prediction of Hemophilia A” in PCR Protocols, A Guide to Methods and Applications, Academic Press, 1990 and Ruano et al., 87 Proc. Natl. Acad. Sci. USA 6296-6300, 1990.
  • an ASO will be perfectly complementary to one allele while containing a single mismatch for another allele.
  • Allele-specific oligonucleotides of the invention include ASO probes and ASO primers.
  • ASO probes which usually provide good discrimination between different alleles are those in which a central position of the oligonucleotide probe aligns with the polymorphic site in the target region (e.g., approximately the 7 th or 8 th position in a 15mer, the 8 th or 9 th position in a 16mer, and the 10 th or 11 m position in a 20mer).
  • An ASO primer of the invention has a 3 ' terminal nucleotide, or preferably a 3 ' penultimate nucleotide, that is complementary to only one nucleotide of a particular SNP, thereby acting as a primer for polymerase-mediated extension only if the allele containing that nucleotide is present.
  • ASO probes and primers hybridizing to either the coding or noncoding strand are contemplated by the invention.
  • a preferred ASO probe for detecting BF gene polymorphisms comprises a nucleotide sequence, listed 5' to 3', selected from the group consisting of:
  • CAGACACRTACCTGC (SEQ ID NO 7) and its complement
  • CAGTGGCYTAAGGCA (SEQ ID NO 8) and its complement
  • CTCTGAAYAACAGGG SEQ ID NO 16 and its complement
  • TACTGAGRGCCTCCC (SEQ ID NO 18 and its complement
  • AGATGACRTCCCTCC (SEQ ID NO 19 and its complement,
  • ATCAACTRTCTCTAA SEQ ID NO 21 and its complement
  • TCTTCCTWATCTCCT SEQ ID NO 22 and its complement
  • TCAGCACRTTCTCCT (SEQ ID NO 25 and its complement
  • a preferred ASO primer for detecting BF gene polymorphisms comprises a nucleotide sequence, listed 5' to 3', selected from the group consisting of:
  • ATGTGTTCAAAGTYA SEQ ID NO- 7.0
  • TTTCCATATCCTTRA SEQ ID NO 71
  • GAGTTTTCAGCACRT SEQ ID .NO: 74 CAGAGAAGGAGAAYG SEQ ID NO 75)
  • TCTACTGAGTGACRA SEQ ID NO 80 TCCCCATTGCCTTYG SEQ ID NO ⁇ 81)
  • oligonucleotides of the invention hybridize to a target region located one to several . nucleotides downstream of one of the novel polymo ⁇ hic sites identified herein. Such oligonucleotides are useful in polymerase-mediated primer extension methods for detecting one of the novel polymo ⁇ hisms described herein and therefore such oligonucleotides are referred to herein as "primer- extension oligonucleotides".
  • the 3 '-terminus of a primer-extension oligonucleotide is a deoxynucleotide complementary to the nucleotide located immediately adjacent to the polymo ⁇ hic site.
  • a particularly preferred oligonucleotide primer for detecting BF gene polymo ⁇ hisms by primer extension terminates in a nucleotide sequence, listed 5 ' to 3 ', selected from the group consisting of:
  • GTAGGACAGG (SEQ ID NO:88); GGCTCGCCCC (SEQ ID NO 89);
  • AGCCCCCAAC (SEQ ID NO: 90 CATCAGGCAG (SEQ ID NO: 91);
  • GGGCAGTGGC SEQ ID NO: 96
  • TTCTGCCTTA SEQ ID NO 97
  • ATGACGGTTA SEQ ID NO: 98
  • CCCGGAGAGT SEQ ID NO 99
  • TGAATGGCCG SEQ ID NO: 100
  • GCCCACTCCA SEQ ID NO 101
  • GCTCCAACCC (SEQ ID NO: 104) TGGGGATGCC (SEQ ID NO: 105) ;
  • CCTTCATGTA (SEQ ID NO: 106) GAGGGGTGTC (SEQ ID NO 107); GGATGGGCAC (SEQ ID NO: 108) AAACCTGGGC (SEQ ID NO 109);
  • AAGCAGTTTC (SEQ ID NO: 114) TTACCAGTCA (SEQ ID, NO. 115);
  • TCTTACTGAG (SEQ ID NO: 116) ACAGGGAGGC (SEQ ID NO: 117); GCCAGATGAC (SEQ ID NO: 118) TCAGGAGGGA (SEQ ID NO: 119) ;
  • GTGATCAACT (SEQ ID NO: 122)
  • GGGTTAGAGA (SEQ ID NO 123);
  • TTATCTTCCT (SEQ ID NO: 124) GGTAGGAGAT (SEQ ID NO 125);
  • TGTTCAAAGT SEQ ID NO: 126) CCATATCCTT (SEQ ID NO 127).
  • GATCTTTCTA SEQ ID NO: 128) ATGTAGGACT (SEQ ID NO 129) ;
  • TTTTCAGCAC AGAAGGAGAA (SEQ ID NO 131) ; CAAAGGGACA (SEQ ID NO 132) TACAGCTCTC (SEQ ID NO: 133)
  • TGGACAGGGG SEQ ID NO- 142
  • TCAATCCCAC SEQ ID NO: 143
  • a composition contains two or more differently labeled BF oligonucleotides for simultaneously probing the identity of nucleotides or nucleotide pairs at two or more polymo ⁇ hic sites. It is also contemplated that primer compositions may contain two or more sets of allele-specific primer pairs to allow simultaneous targeting and amplification of two or more regions containing a polymo ⁇ hic site.
  • BF oligonucleotides of the invention may also be immobilized on or synthesized on a solid surface such as a microchip, bead, or glass slide (see, e.g., WO 98/20020 and WO 98/20019).
  • Such immobilized oligonucleotides may be used in a variety of polymo ⁇ hism detection assays, including but not limited to probe hybridization and polymerase extension assays.
  • Immobilized BF oligonucleotides of the invention may comprise an ordered array of oligonucleotides designed to rapidly screen a DNA sample for polymo ⁇ hisms in multiple genes at the same time.
  • the invention provides a kit comprising at least two BF oligonucleotides packaged in separate containers.
  • the kit may also contain other components such as hybridization buffer (where the oligonucleotides are to be used as a probe) packaged in a separate container.
  • the kit may contain, packaged in separate containers, a polymerase and a reaction buffer optimized for primer extension mediated by the polymerase, such as PCR.
  • the additional polymorphic sites may be currently known polymo ⁇ hic sites or sites that are subsequently discovered.
  • One embodiment of a genotyping method of the invention involves isolating from the individual a nucleic acid sample comprising the two copies of the BF gene, mRNA transcripts thereof or cDNA copies thereof, or a fragment of any of the foregoing, that are present in the individual, and determining the identity of the nucleotide pair at one or more polymo ⁇ hic sites selected from the group consisting of PSl, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10, PS11, PS12, PS13, PS14, PS15, PS16, PS17, PS18, PS20, PS21, PS22, PS23, PS24, PS25, PS26, PS27, PS28 and PS29 in the two copies to assign a BF genotype to the individual.
  • the two "copies" of a gene, mRNA or cDNA (or fragment of such BF molecules) in an individual may be the same allele or may be different alleles.
  • the identity of the nucleotide pair at one or more of the polymorphic sites selected from the group consisting of PS 19 and PS30 is also determined.
  • a genotyping method of the invention comprises determining the identity of the nucleotide pair at each of PS1-PS30.
  • the nucleic acid sample is isolated from a biological sample taken from the individual, such as a blood sample or tissue sample.
  • tissue samples include whole blood, semen, saliva, tears, urine, fecal material, sweat, buccal, skin and hair.
  • the nucleic acid sample may be comprised of genomic DNA, mRNA, or cDNA and, in the latter two cases, the biological sample must be obtained from a tissue in which the BF gene is expressed.
  • mRNA or cDNA preparations would not be used to detect polymo ⁇ hisms located in introns or in 5 ' and 3 ' untranslated regions if not present in the mRNA or cDNA. If a BF gene fragment is isolated, it must contain the polymo ⁇ hic site(s) to be genotyped.
  • One embodiment of a haplotyping method of the invention comprises isolating from the individual a nucleic acid sample containing only one of the two copies of the BF gene, mRNA or cDNA, or a fragment of such BF molecules, that is present in the individual and determining in that copy the identity of the nucleotide at one or more polymo ⁇ hic sites selected from the group consisting of PSl, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10, PS11, PS12, PS13, PS14, PS15, PS16, PS17, PS 18, PS20, PS21, PS22, PS23, PS24, -PS25, PS26, PS27, PS28 and PS29 in that copy to assign a BF haplotype to the individual.
  • the nucleic acid used in the above haplotyping methods of the invention may be isolated using any method capable of separating the two copies of the BF gene or fragment such as one of the methods described above for preparing BF isogenes, with targeted in vivo cloning being the preferred approach.
  • any individual clone will typically only provide haplotype information on one of the two BF gene copies present in an individual. If haplotype information is desired for the individual's other copy, additional BF clones will usually need to be examined. Typically, at least five clones should be examined to have more than a 90% probability of haplotyping both copies of the BF gene in an individual.
  • the haplotype for the other allele may be inferred if the individual has a known genotype for the polymo ⁇ hic sites of interest or if the haplotype frequency or haplotype pair frequency for the individual's population group is known.
  • the BF haplotype is assigned to the individual by also identifying the nucleotide at one or more polymo ⁇ hic sites selected from the group consisting of PS 19 and PS30.
  • the nucleotide at each of PS 1-PS30 is identified.
  • the haplotyping method comprises determining whether an individual has one or more of the BF haplotypes shown in Table 4.
  • Two sites are said to be. in linkage disequilibrium if the presence of a particular variant at one site enhances the predictability of another variant at the second site (Stephens, JC 1999, Mol. Diag. 4:309-317).
  • Techniques for determining whether any two polymo ⁇ hic sites are in linkage disequilibrium are well-known in the art (Weir B.S. 1996 Genetic Data Analysis II, Sinauer
  • a BF haplotype pair is determined for an individual by identifying the phased sequence of nucleotides at one or more polymo ⁇ hic sites selected from the group consisting of PSl, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10, PS11, PS12, PS13, PS14, PS15, PS16, PS17, PS18, PS20, PS21, PS22, PS23, PS24, PS25,
  • the haplotyping method comprises identifying the phased sequence of nucleotides at each of PS1-PS30 in each copy of the BF gene.
  • the identifying step is preferably performed with each copy of the gene being placed in separate containers. However, it is also envisioned that if the
  • first and second copies of the gene are labeled with different first and second fluorescent dyes, respectively, and an allele-specific oligonucleotide labeled with yet a third different fluorescent dye is used to assay the polymo ⁇ hic site(s), then detecting a combination of the first and third dyes would identify the 25 polymo ⁇ hism in the first gene copy while detecting a combination of the second and third dyes would identify the polymo ⁇ hism in the second gene copy.
  • the identity of a nucleotide (or nucleotide pair) at a polymo ⁇ hic site(s) may be determined by amplifying a target region(s) containing the polymo ⁇ hic site(s) directly from one or both copies of the.BF gene, or a fragment thereof, and the
  • sequence of the amplified region(s) determined by conventional methods. It will be readily appreciated by the skilled artisan that only one nucleotide will be detected at a polymo ⁇ hic site in individuals who are homozygous at that site, while two different nucleotides will be detected if the individual is heterozygous for that site.
  • the polymo ⁇ hism may be identified directly, known as positive-type identification, or by inference, referred to as negative-type identification. For example,
  • a site may be positively determined to be either guanine or cytosine for an individual homozygous at that site, or both guanine and cytosine, if the individual is heterozygous at that site.
  • the site may be negatively determined to be not guanine (and thus cytosine/cytosine) or not cytosine (and thus guanine/guanine).
  • the target region(s) may be amplified using any oligonucleotide-directed amplification method, including but not limited to polymerase chain reaction (PCR) (U.S. Patent No. 4,965,188), ligase chain reaction (LCR) (Barany et al., Proc. Natl. Acad. Sci. USA 88: 189-193, 1991; WO90/01069), and oligonucleotide ligation assay (OLA) (Landegren et al., Science 241: 1077-1080, 1988).
  • PCR polymerase chain reaction
  • LCR ligase chain reaction
  • OLA oligonucleotide ligation assay
  • Other known nucleic acid amplification procedures may be used to amplify the target region including transcription-based amplification systems (U.S. Patent No.
  • a polymo ⁇ hism in the target region may also be assayed before or after amplification using one of several hybridization-based methods known in the art.
  • allele-specific oligonucleotides are utilized in performing such methods.
  • the allele-specific oligonucleotides may be used as differently labeled probe pairs, with one member of the pair showing a perfect match to one variant of a target sequence and the other member showing a perfect match to a different variant.
  • more than one polymo ⁇ hic site may be detected at once using a set of allele- specific oligonucleotides or oligonucleotide pairs.
  • the members of the set have melting temperatures within 5°C, and more preferably within 2°C, of each other when hybridizing to each of the polymo ⁇ hic sites being detected.
  • Hybridization of an allele-specific oligonucleotide to a target polynucleotide may be performed with both entities in solution, or such hybridization may be performed when either the oligonucleotide or the target polynucleotide is covalently or noncovalently affixed to a solid support. Attachment may be mediated, for example, by antibody-antigen interactions, poly-L-Lys, streptavidin or avidin-biotin, salt bridges, hydrophobic interactions, chemical linkages, UV cross-linking baking, etc. Allele- specific oligonucleotides may be synthesized directly on the solid support or attached to the solid support subsequent to synthesis.
  • Solid-supports suitable for use in detection methods of the invention include substrates made of silicon, glass, plastic, paper and the like, which may be formed, for example, into wells (as in 96-well plates), slides, sheets, membranes, fibers, chips, dishes, and beads.
  • the solid support may be treated, coated or derivatized to facilitate the immobilization of the allele- specific oligonucleotide or target nucleic acid.
  • the genotype or haplotype for the BF gene of an individual may also be determined by hybridization of a nucleic acid sample containing one or both copies of the gene, mRNA, cDNA or fragments) thereof, to nucleic acid arrays and subarrays such as described in WO 95/11995.
  • the arrays would contain a battery of allele-specific oligonucleotides representing each of the polymo ⁇ hic sites to be included in the genotype or haplotype.
  • the identity of polymo ⁇ hisms may also be determined using a mismatch detection technique, including but not limited to the RNase protection method using riboprobes (Winter et al., Proc. Natl. Acad. Sci. USA 82:7575, 1985; Meyers et al., Science 230:1242, 1985) and proteins which recognize nucleotide mismatches, such as the E. coli mutS protein (Modrich, P. Ann. Rev. Genet. 25:229-253, 1991).
  • variant alleles can be identified by single strand conformation polymo ⁇ hism (SSCP) analysis (Orita et al., Genomics 5:874-879, 1989; Humphries et al., in Molecular Diagnosis of Genetic Diseases, R. Elles, ed., pp. 321-340, 1996) or denaturing gradient gel electrophoresis (DGGE) (Wartell et al, Nucl. Acids Res. 18:2699-2706, 1990; Sheffield et al, Proc. Natl. Acad. Sci. USA 86:232-236, 1989).
  • SSCP single strand conformation polymo ⁇ hism
  • DGGE denaturing gradient gel electrophoresis
  • a polymerase-mediated primer extension method may also be used to identify the polymo ⁇ hism(s).
  • Several such methods have been described in the patent and scientific literature and , include the "Genetic Bit Analysis” method (W092/15712) and the ligase/polymerase mediated genetic bit analysis (U.S. Patent 5,679,524.
  • Related methods are disclosed in WO91/02087, WO90/09455, WO95/17676, U.S. Patent Nos. 5,302,509, and 5,945,233.
  • Extended primers containing a polymo ⁇ hism may be detected by mass spectrometry as described in U.S. Patent No. 5,605,798.
  • Another primer extension method is allele-specific PCR (Ruano et al, Nucl. Acids Res. 17:8392, 1989; Ruano et al, Nucl. Acids Res. 19, 6877-6882, 1991; WO 93/22456; Turki et al, J. Clin. Invest. 95:1635-1641, 1995).
  • multiple polymo ⁇ hic sites may be investigated by simultaneously amplifying multiple regions of the nucleic acid using sets of allele-specific primers as described in Wallace et al. (WO89/10414).
  • the identity of the allele(s) present at any of the novel polymo ⁇ hic sites described herein may be indirectly determined by haplotyping or genotyping another polymo ⁇ hic site that is in linkage disequilibrium with the polymo ⁇ hic site that is of interest.
  • Polymo ⁇ hic sites in linkage disequilibrium with the presently disclosed polymo ⁇ hic sites may be located in regions of the gene or in other genomic regions not examined herein.
  • Detection of the allele(s) present at a polymo ⁇ hic site in linkage disequilibrium with the novel polymo ⁇ hic sites described herein may be performed by, but is not limited to, any of the above-mentioned methods for detecting the identity of the allele at a polymo ⁇ hic site.
  • an individual's BF haplotype pair is predicted from its BF genotype using information on haplotype pairs known to exist in a reference population.
  • the haplotyping prediction method comprises identifying a BF genotype for the . individual at two or more BF polymo ⁇ hic sites described herein, accessing data containing BF haplotype pairs identified in a reference population, and assigning a haplotype pair to the individual that is consistent with the genotype data.
  • the reference haplotype pairs include the BF haplotype pairs shown in Table 3.
  • the BF haplotype pair can be assigned by comparing the individual's genotype with the genotypes corresponding to the haplotype pairs known to exist in the general population or in a specific population group, and determining which haplotype pair is consistent with the genotype of the individual.
  • comparison of the genotype of the individual to the haplotype pairs identified in a reference population and determination of which haplotype pair is consistent with the genotype of the individual may be performed by visual inspection (for example, by consulting Table 3).
  • haplotype pair frequency data (such as that presented in Table 6) may be used to determine which of these haplotype pairs is most likely to be present in the ' individual.
  • This determination may also be performed in some embodiments by visual inspection upon consulting Table 6. If a particular BF haplotype pair consistent with the genotype of the individual is more frequent in the reference population than others consistent with the genotype, then that haplotype pair with the highest frequency is the most likely to be present in the individual. In other embodiments, the comparison may be made by a computer-implemented algorithm with the genotype of the individual and the reference haplotype data stored in computer-readable formats.
  • one computer-implemented algorithm to perform this comparison entails enumerating all possible haplotype pairs which are consistent with the genotype, accessing data containing BF haplotype pairs frequency data determined in a reference population to determine a probability that the individual has a possible haplotype pair, and analyzing the determined probabilities to assign a haplotype pair to the individual.
  • the reference population should be composed of randomly-selected individuals representing the major ethnogeographic groups of the world.
  • a preferred reference population allows the detection of any haplotype whose frequency is at least 10% with about 99% certainty and comprises about 20 unrelated individuals from each of the four population groups named above.
  • a particularly preferred reference population includes a 3-generation family representing one or more of the four population groups to serve as controls for checking quality of haplotyping procedures.
  • the haplotype frequency data for each ethnogeographic group is examined to determine whether it is consistent with Hardy- Weinberg equilibrium.
  • Hardy- Weinberg equilibrium D.L. Hartl et al. Principles of Population Genomics, Sinauer Associates (Sunderland, MA), 3 rd Ed, 1997) postulates that the frequency of finding the haplotype pair H x I H 2 is equal to
  • the assigning step involves performing the following analysis.
  • each of the possible haplotype pairs is compared to the haplotype pairs in the reference population.
  • the haplotype pairs in the reference population matches a possible haplotype pair and that pair is assigned to the individual.
  • only one haplotype represented in the reference haplotype pairs is consistent with a possible haplotype pair for an individual, and in such cases the individual is assigned a haplotype pair containing this known haplotype and a new haplotype derived by subtracting the known haplotype from the possible haplotype pair.
  • the haplotype pair in an individual may be predicted from the individual's genotype for that gene using reported methods (e.g., Clark et al.
  • the individual is preferably haplotyped using a direct molecular haplotyping method such as, for example, CLASPER SystemTM technology (U.S. Patent No. 5,866,404), SMD, or allele-specific long-range PCR (Michalotos-Beloin et al, supra).
  • a direct molecular haplotyping method such as, for example, CLASPER SystemTM technology (U.S. Patent No. 5,866,404), SMD, or allele-specific long-range PCR (Michalotos-Beloin et al, supra).
  • the invention also provides a method for determining the frequency of a BF genotype, haplotype, or haplotype pair in a population.
  • the method comprises, for each member of the population, determining the genotype or the haplotype pair for the novel BF polymo ⁇ hic sites described herein, and calculating the frequency any particular genotype, haplotype, or haplotype pair is found in the population.
  • the population may be e.g., a reference population, a family population; a same gender population, a population group, or a trait population (e.g., a group of individuals exhibiting a trait of interest such as a medical condition or response to a therapeutic treatment).
  • frequency data for BF genotypes, haplotypes, and/or haplotype pairs are determined in a reference population and used in a method for identifying an association between a trait and a BF genotype, haplotype, or haplotype pair.
  • the trait may be any detectable phenotype, including but not limited to susceptibility to a disease or response to a treatment.
  • the method involves obtaining data on the frequency of the genotype(s), haplotype(s), or haplotype pair(s) of interest in a reference population as well as in a population exhibiting the trait.
  • Frequency data for one or both of the reference and trait populations may be obtained by genotyping or haplotyping each individual in the populations using one or more of the methods' described above.
  • the haplotypes for the trait population may be determined directly or, alternatively, by a predictive genotype to haplotype approach as described above.
  • the frequency data for the reference and/or trait populations is obtained by accessing previously determined frequency data, which may be in written or electronic form.
  • the frequency data may be present in a database that is accessible by a computer. Once the frequency data is obtained, the frequencies of the genotype(s), haplotype(s), or haplotype pair(s) of interest in the reference and trait populations are compared.
  • the frequencies of all genotypes, haplotypes, and/or haplotype pairs observed in the populations are compared. If a particular BF genotype, haplotype, or haplotype pair is more frequent in the trait population than in the reference population at a statistically significant amount, then the trait is predicted to be associated with that BF genotype, haplotype or haplotype pair.
  • the BF genotype, haplotype, or haplotype pair being compared in the trait and reference populations is selected from the full- genotypes and full-haplotypes shown in Tables 3 and 4, or from sub-genotypes and sub-haplotypes derived from these genotypes and haplotypes.
  • Sub-genotypes useful in the invention preferably do not include sub-genotypes solely for any one of PS 19 and PS30 or for any combination thereof.
  • the trait of interest is a clinical response exhibited by a patient to some therapeutic treatment, for example, response to a drug targeting BF or response to a therapeutic treatment for a medical condition.
  • medical condition includes but is not limited to any condition or disease manifested as one or more physical and/or psychological symptoms for which treatment is desirable, and includes previously and newly identified diseases and other disorders.
  • clinical response means any or all of the following: a quantitative measure of the response, no response, and/or adverse response (i.e, side effects).
  • clinical population In order to deduce a correlation between clinical response to a treatment and a BF genotype, haplotype, or haplotype pair, it is necessary to obtain data on the clinical responses exhibited by a population of individuals who received the treatment, hereinafter the "clinical population".
  • This clinical data may be obtained by analyzing the results of a clinical trial that has already been run and/or the clinical data may be obtained by designing and carrying out one or more new clinical trials.
  • the term "clinical trial” means any research study designed to collect clinical data on responses to a particular treatment, and includes but is not limited to phase I, phase II and phase IH clinical trials. Standard methods are used to define the patient population and to enroll subjects.
  • the individuals included in the clinical population have been graded for the existence of the medical condition of interest. This is important in cases where the symptom(s) being presented by the patients can be caused by more than one underlying condition, and where treatment of the underlying conditions are not the same. An example of this would be where patients experience ⁇ . breathing difficulties that are due to either asthma or respiratory infections. If both sets were treated with an asthma medication, there would be a spurious group of apparent non-responders that did not actually have asthma. These people would affect the ability to detect any co ⁇ relation between haplotype and treatment outcome. This grading of potential patients could employ a standard physical exam or one or more lab tests. Alternatively, grading of patients could use haplotyping for situations where there is a strong correlation between haplotype pair and disease susceptibility or severity.
  • the therapeutic treatment of interest is administered to each individual in the trial population and each individual's response to the treatment is measured using one or more predetermined criteria. It is contemplated that in many cases, the trial population will exhibit a range of responses and that the investigator will choose the number of responder groups (e.g., low, medium, high) made up by the various responses.
  • the BF gene for each individual in the trial population is genotyped and/or haplotyped, which may be done before or after administering the treatment.
  • correlations between individual response and BF genotype or haplotype content are created. Correlations may be produced in several ways. In one method, individuals are grouped by their BF genotype or haplotype (or haplotype pair) (also referred to as a polymo ⁇ hism group), and then the averages and standard deviations of clinical responses exhibited by the members of each polymo ⁇ hism group are calculated.
  • the correlation is found using a genetic algorithm approach as described in WO 01/01218. Correlations may also be analyzed using analysis of variation (ANOVA) techniques to determine how much of the variation in the clinical data is explained by different subsets of the polymo ⁇ hic sites in the BF gene. As described in WO 01/01218, ANOVA is used to test hypotheses about whether a response variable is caused by or correlated with one or more traits or variables that can be measured (Fisher and vanBelle, supra, Ch. 10).
  • ANOVA analysis of variation
  • a mathematical model may be readily constructed by the skilled artisan that predicts clinical response as a function of BF genotype or haplotype content.
  • the model is validated in one or more follow-up clinical trials designed to test the model.
  • the identification of an association between a clinical response and a genotype or haplotype (or haplotype pair) for the BF gene may be the basis for designing a diagnostic method to determine those individuals who will or will not respond to the treatment, or alternatively, will respond at a lower level and thus may require more treatment, i.e, a greater dose of a drug.
  • the diagnostic method may take one of several forms: for example, a direct DNA test (i.e, genotyping or haplotyping one or more of the polymo ⁇ hic sites in the BF gene), a serological test, or a physical exam measurement.
  • a direct DNA test i.e, genotyping or haplotyping one or more of the polymo ⁇ hic sites in the BF gene
  • serological test i.e, genotyping or haplotyping one or more of the polymo ⁇ hic sites in the BF gene
  • a physical exam measurement i.e, genotyping or haplotyping one or more of the polymo ⁇ hic sites in the BF gene
  • this diagnostic method uses the predictive haplotyping method described above.
  • the invention provides an isolated polynucleotide comprising a polymo ⁇ hic variant of the BF gene or a fragment of the gene which contains at least one of the novel polymo ⁇ hic sites described herein.
  • nucleotide sequence of a variant BF gene is identical to the reference genomic sequence for those portions of the gene examined, as described in the Examples below, except that it comprises a different nucleotide at one or more of the novel polymo ⁇ hic sites PSl, PS2, PS3, PS4, PS5, PS6, PS7, PS8,PS9, PS10, PS11, PS12, PS13, PS14, PS15, PS16, PS17,
  • PS18, PS20, PS21, PS22, PS23, PS24, PS25, PS26, PS27, PS28 and PS29 and may also comprise one or more additional polymo ⁇ hisms selected from the group consisting of thymine at PS 19 and thymine at PS30.
  • nucleotide sequence of a variant fragment of the BF gene is identical to the corresponding portion of the reference sequence except for having a different nucleotide at one or more of the novel polymo ⁇ hic sites described herein.
  • the invention specifically does not include polynucleotides comprising a nucleotide sequence identical to the reference sequence of the BF gene, which is defined by haplotype 19, (or other reported BF sequences) or to portions of the reference sequence (or other reported BF sequences), except for the haplotyping and genotyping oligonucleotides described above.
  • the location of a polymo ⁇ hism in a variant BF gene or fragment is preferably identified by aligning its sequence against SEQ ID NO:l.
  • the polymo ⁇ hism is selected from the group consisting of thymine at PSl, adenine at PS2, thymine at PS3, adenine at PS4, thymine at PS5, thymine at PS6, adenine at PS7, guanine at PS8, adenine at PS9, thymine at PS10, adenine at PSl 1, thymine at PS12, thymine at PS13, cytosine at PS14, adenine at PS15, adenine at PS16, thymine at PS17, guanine at PS18, adenine at PS20, thymine at PS21, cytosine at PS22, guanine at PS23, thymine at PS24, guanine at PS25, guanine at PS26, thymine at PS27, guanine at PS28 and thymine at PS29.
  • the polymo ⁇ hic variant comprises a naturally-occurring
  • Polymo ⁇ hic variants of the invention may be prepared by isolating a clone containing the BF gene from a human genomic library.
  • the clone may be sequenced to determine the identity of the nucleotides at the novel polymo ⁇ hic sites described herein.
  • Any particular variant or fragment thereof, that is claimed herein could be prepared from this clone by performing in vitro mutagenesis using procedures well-known in the art.
  • Any particular BF variant or fragment thereof may also be prepared using synthetic or semi-synthetic methods known in the art.
  • BF isogenes, or fragments thereof may be isolated using any method that allows separation of the two "copies" of the BF gene present in an individual, which, as readily understood by the skilled artisan, may be the same allele or different alleles. Separation methods include targeted in vivo cloning (TIVC) in yeast as described in WO 98/01573, U.S. Patent No. 5,866,404, and U.S. Patent No. 5,972,614. Another method, which is described in U.S. Patent No. 5,972,614, uses an allele specific . oligonucleotide in combination with primer extension and exonuclease degradation to generate hemizygous DNA targets.
  • TIVC targeted in vivo cloning
  • Another method which is described in U.S. Patent No. 5,972,614, uses an allele specific . oligonucleotide in combination with primer extension and exonuclease degradation to generate hemizygous DNA targets.
  • the invention also provides BF genome anthologies, which are collections of at least two BF isogenes found in a given population.
  • the population may be any group of at least two individuals, including but not limited to a reference population, a population group, a family population, a clinical population, and a same gender population.
  • a BF genome anthology may comprise individual BF isogenes stored in separate containers such as microtest tubes, separate wells of a microtitre plate and the like. Alternatively, two or more groups of the BF isogenes in the anthology may be stored in separate containers.
  • a preferred BF genome anthology of the invention comprises a set of isogenes defined by the haplotypes shown in Table 4 below.
  • a BF genome anthology is useful in providing control nucleic acids for kits of the invention.
  • An isolated polynucleotide containing a polymo ⁇ hic variant nucleotide sequence of the invention may be operably linked to one or more expression regulatory elements in a recombinant expression vector capable of being propagated and expressing the encoded BF protein in a prokaryotic or a eukaryotic host cell.
  • expression regulatory elements which may be used include, but are not limited to, the lac system, operator and promoter regions of phage lambda, yeast promoters, and promoters derived from vaccinia virus, adenovirus, retroviruses, or SV40.
  • regulatory elements include, but are not limited to, appropriate leader sequences, termination codons, polyadenylation signals, and other sequences required for the appropriate transcription and subsequent translation of the nucleic acid sequence in a given host cell.
  • the expression vector contains any additional elements necessary for its transfer to and subsequent replication in the host cell. Examples of such elements include, but are not limited to, origins of replication and selectable markers.
  • Such expression vectors are commercially available or are readily constructed using methods known to those in the art (e.g., F. Ausubel et al, 1987, in "Current Protocols in Molecular Biology", John Wiley and Sons, New York, New York).
  • Host cells which may be used to express the variant BF sequences of the invention include, but are not limited to, eukaryotic and mammalian cells, such as animal, plant, insect and yeast cells, and prokaryotic cells, such as E. coli, or algal cells as known in the art.
  • the recombinant expression vector may be introduced into the host cell using any method known to those in the art including, but not limited to, microinjection, electroporation, particle bombardment, transduction, and transfection using DEAE-dextran, lipofection, or calcium phosphate (see e.g., Sambrook et al. (1989) in "Molecular Cloning. A Laboratory Manual", Cold Spring Harbor Press, Plainview, New York).
  • eukaryotic expression vectors that function in eukaryotic cells, and preferably mammalian cells, are used.
  • Non-limiting examples of such vectors include vaccinia virus vectors, adenovirus vectors, he ⁇ es virus vectors, and baculovirus transfer vectors.
  • Preferred eukaryotic cell lines include COS cells, CHO cells, HeLa cells, NIH/3T3 cells, and embryonic stem cells (Thomson, J. A. et al, 1998 Science 282: 1145-1147).
  • Particularly preferred host cells are mammalian cells.
  • polymo ⁇ hic variants of the BF gene will produce BF mRNAs varying from each other at any polymo ⁇ hic site retained in the spliced and processed mRNA molecules.
  • These mRNAs can be used for the preparation of a BF cDNA comprising a nucleotide sequence which is a polymo ⁇ hic variant of the BF reference coding sequence shown in Figure 2.
  • the invention also provides BF mRNAs and corresponding cDNAs which comprise a nucleotide sequence that is identical to SEQ ID NO:2 (Fig.
  • RNA sequence for those regions of SEQ ID NO:2 that correspond to the examined portions of the BF gene (as described in the Examples below), except for having one or more polymo ⁇ hisms selected from the group consisting of adenine at a position corresponding to nucleotide 26, thymine at a position corresponding to nucleotide 94, adenine at a position corresponding to. nucleotide 221, thymine at a position corresponding to nucleotide 405, adenine at a position corresponding to .
  • nucleotide 450 adenine at a position corresponding to nucleotide 504, thymine at a position corresponding to nucleotide 672, adenine at a position corresponding to nucleotide 754, thymine at a position corresponding to nucleotide 858, adenine at a position corresponding to nucleotide 1114, thymine at a position corresponding to nucleotide 1137, thymine at a position corresponding to nucleotide 1365, thymine at a position corresponding to nucleotide 1524, guanine at a position corresponding to nucleotide 1598 and guanine at a position corresponding to nucleotide 1953.
  • a particularly preferred polymo ⁇ hic cDNA variant comprises the coding sequence of a BF isogene defined by any one of haplotypes 1-7, 10, 12, 13, 18, 21, 22, and 24-31. Fragments of these variant mRNAs and cDNAs are included in the scope of the invention, provided they contain one or more of the novel polymo ⁇ hisms described herein.
  • the invention specifically excludes polynucleotides identical to previously identified and characterized BF mRNAs, cDNAs or fragments thereof. Polynucleotides comprising a variant BF RNA or DNA sequence may be isolated from a biological sample using well-known molecular biological procedures or may be chemically synthesized.
  • a polymo ⁇ hic variant of a BF gene, mRNA or cDNA fragment comprises at least one novel polymo ⁇ hism identified herein and has a length of at least 10 nucleotides and may range up to the full length of the gene.
  • such fragments are between 100 and 3000 nucleotides in length, and more preferably between 200 and 2000 nucleotides in length, and most preferably between 500 and 1000 nucleotides in length.
  • nucleic acid molecules containing the BF gene or cDNA may be complementary double stranded molecules and thus reference to a particular site on the sense strand refers as well to the corresponding site on the complementary antisense strand.
  • reference may be made to the same polymo ⁇ hic site on either strand and an oligonucleotide may be designed to hybridize specifically to either strand at a target region containing the polymo ⁇ hic site.
  • the invention also includes single-stranded polynucleotides which are complementary to the sense strand of the BF genomic, mRNA and cDNA variants described herein.
  • Polynucleotides comprising a polymo ⁇ hic gene variant or fragment of the invention may be useful for therapeutic pu ⁇ oses.
  • an expression vector encoding the isoform may be administered to the patient.
  • the patient may be one who lacks the BF isogene encoding that isoform or may already have -at least one copy of that isogene.
  • a BF isogene may be turned off by transforming a targeted organ, tissue or cell population with an expression vector that expresses high levels of untranslatable mRNA or antisense RNA for the isogene or fragment thereof.
  • oligonucleotides directed against the regulatory regions (e.g., promoter, introns, enhancers, 3' untranslated region) of the isogene may block transcription. Oligonucleotides targeting the transcription initiation site, e.g., between positions -10 and +10 from the start site are preferred.
  • inhibition of transcription can be achieved using oligonucleotides that base-pair with region(s) of the isogene DNA to form triplex DNA (see e.g., Gee et al. in Huber, B.E. and B.I. Carr, Molecular and Immunologic Approaches, Futura Publishing Co, Mt. Kisco, N.Y, 1994).
  • Antisense oligonucleotides may also be designed to block translation of BF mRNA transcribed from a particular isogene. It is also contemplated that ribozymes may be designed that can catalyze the specific cleavage of BF mRNA transcribed from a particular isogene.
  • the untranslated mRNA, antisense RNA ot antisense oligonucleotides may be delivered to a target cell or tissue by expression from a vector introduced into the cell or tissue in vivo or ex vivo. Alternatively, such molecules may be formulated as a pharmaceutical composition for administration to the patient. Oligoriboriucleotides and/or oligodeoxynucleotides intended for use as antisense oligonucleotides may be modified to increase stability and half-life.
  • Possible modifications include, but are not limited to phosphorothioate or 2' O-methyl linkages, and the inclusion of nontraditional bases such as inosine and queosine, as well as acetyl-, methyl-, thio-, and similarly modified forms of adenine, cytosine, guanine, thymine, and uracil which are not as easily recognized by endogenous nucleases.
  • the invention also provides an isolated polypeptide comprising a polymo ⁇ hic variant of (a) the reference BF amino acid sequence shown in Figure 3 or (b) a fragment of this reference sequence.
  • the location of a variant amino acid in a BF polypeptide or fragment of the invention is identified by aligning its sequence against SEQ ID NO:3 (Fig. 3).
  • a BF protein variant of the invention comprises an amino acid sequence identical to SEQ ID NO:3 for those regions of SEQ ID NO:3 that are encoded by examined portions of the BF gene (as described in the Examples below), except for having one or more variant amino acids selected from the group consisting ofhistidine at a position corresponding to amino acid position 9, histidine at a position corresponding to amino acid position 74, serine at a position corresponding to amino acid position 252, isoleucine at a position corresponding to amino acid position 372, arginine at a position corresponding to amino acid position 533 and glutamic acid at a position corresponding to amino acid position 651 and/or the protein truncates prematurely at amino acid 31 due to the termination signal at codon 32 in the coding sequence.
  • a BF fragment of the invention is any fragment of a BF protein variant that contains one or more of the amino acid variations described herein.
  • the invention specifically excludes amino acid sequences identical to those previously identified for BF, including SEQ ID NO:3, and previously described fragments thereof.
  • BF protein variants included within the invention comprise all amino acid sequences based on SEQ ID NO:3 and having any combination of amino acid variations described herein.
  • a BF protein variant of the invention is encoded by an isogene defined by one of the observed haplotypes, 1-7, 10, 12, 13, 18, 21, 22, and 24- 31 , shown in Table 4.
  • a BF peptide variant of the invention is at least 6 amino acids in length and is preferably any number between 6 and 30 amino acids long, more preferably between 10 and 25, and most preferably between 15 and 20 amino acids long.
  • Such BF peptide variants may be useful as antigens to generate antibodies specific for one of the above BF isoforms.
  • the BF peptide variants may be useful in drug screening assays.
  • a BF variant protein or peptide of the invention may be prepared by chemical synthesis or by expressing an appropriate variant BF genomic or cDNA sequence described above.
  • the ' BF protein variant may be isolated from a biological sample of an individual having a BF isogene which encodes the variant protein.
  • a particular BF isoform of the invention can be isolated by immunoaffinity chromatography using an antibody which specifically binds to that particular BF isoform but does not bind to the other BF isoform.
  • the expressed- or isolated BF protein or peptide may be detected by methods known in the art, including Coomassie blue staining, silver staining, and Western blot analysis using antibodies specific for the isoform of the BF protein or peptide as discussed further below.
  • BF variant proteins and peptides can be purified by standard protein purification procedures known in the art, including differential precipitation, molecular sieve chromatography, ion-exchange chromatography, isoelectric focusing, gel electrophoresis, affinity and immunoaffinity chromatography and the like. (Ausubel et. al, 1987, In Current Protocols in Molecular Biology John Wiley and Sons, New York, New York). In the case of immunoaffinity chromatography, antibodies specific for a particular polymo ⁇ hic variant may be used.
  • a polymo ⁇ hic variant BF gene of the invention may also be fused in frame with a heterologous sequence to encode a chimeric BF protein.
  • the non-BF portion of the chimeric protein may be recognized by a commercially available antibody.
  • the chimeric protein may also be engineered to contain a cleavage site located between the BF and non-BF portions so that the BF protein may be cleaved and purified away from the non-BF portion.
  • An additional embodiment of the invention relates to using a novel BF protein isoform, or a fragment thereof, in any of a variety of drug screening assays.
  • screening assays may be performed to identify agents that bind specifically to all known BF protein isoforms or to only a subset of one or more of these isoforms.
  • the agents may be from chemical compound libraries, peptide libraries and the like.
  • the BF protein or peptide variant may be free in solution or affixed to a solid support.
  • high throughput screening of compounds for binding to a BF variant may be accomplished using the method described in PCT application WO84/03565, in which large numbers of test compounds are synthesized on a solid substrate, such as plastic pins or some other surface, contacted with the BF protein(s) of interest and then washed. Bound BF protein(s) are then detected using methods well-known in the art.
  • a novel BF protein isoform may be used in assays to measure the binding affinities of one or more candidate drugs targeting the BF protein.
  • a particular BF haplotype or group of BF haplotypes encodes a BF protein variant with an amino acid sequence distinct from that of BF protein isoforms encoded by other BF haplotypes
  • detection of that particular BF haplotype or group of BF haplotypes may be accomplished by detecting expression of the encoded BF protein variant using any of the methods described herein or otherwise commonly known to the skilled artisan.
  • the invention provides antibodies specific for and immunoreactive with one or more of the novel BF variant proteins described herein.
  • the antibodies may be either monoclonal or polyclonal in origin.
  • the BF protein or peptide variant used to generate the antibodies may be from natural or recombinant sources or produced by chemical synthesis using synthesis techniques known in the art. If the BF protein variant is of insufficient size to be antigenic, it may be conjugated, complexed, or otherwise covalently linked to a carrier molecule to enhance the antigenicity of the peptide.
  • carrier molecules include, but are not limited to, albumins (e.g., human, bovine, fish, ovine), and keyhole limpet hemocyanin (Basic and Clinical Immunology, 1991, Eds.
  • an antibody specifically immunoreactive with one of the novel protein isoforms described herein is administered to an individual to neutralize activity of the BF isoform expressed by that individual.
  • the antibody may be formulated as a pharmaceutical composition which includes a pharmaceutically acceptable carrier.
  • Antibodies specific for and immunoreactive with one of the novel protein isoforms described herein may be used to immunoprecipitate the BF protein variant from solution as well as react with BF protein isoforms on Western or immunoblots of polyacrylamide gels on membrane supports or substrates.
  • the antibodies will detect BF protein isoforms in paraffin or frozen tissue sections, or in cells which have been fixed or unfixed and prepared on slides, coverslips, or the like, for use in immunocytochemical, immunohistochemical, and immunofluorescence techniques.
  • an antibody specifically immunoreactive with one of the novel BF protein variants described herein is used in immunoassays to detect this variant in biological samples.
  • an antibody of the present invention is contacted with a biological sample and the formation of a complex between the BF protein variant and the antibody is detected.
  • suitable immunoassays include radioimmunoassay, Western blot assay, immunofluorescent assay, enzyme linked immunoassay (ELISA), chemiluminescent assay, immunohistochemical assay, immunocytochemical assay, and the like (see, e.g., Principles and Practice of Immunoassay, 1991, Eds. Christopher P. Price and David J. Neoman, Stockton Press, New York, New York; Current Protocols in Molecular Biology, 1987, Eds. Ausubel et al,. John Wiley and Sons, New York, New York).
  • Proteins may be isolated from test specimens and biological samples by conventional methods, as described in Current Protocols in Molecular Biology, supra.
  • Exemplary antibody molecules for use in the detection and therapy methods of the present invention are intact immunoglobulin molecules, substantially intact immunoglobulin molecules, or those portions of immunoglobulin molecules that contain the antigen binding site.
  • Polyclonal or monoclonal antibodies may be produced by methods conventionally known in the art (e.g., Kohler and Milstein, 1975, Nature, 256:495-497; Campbell Monoclonal Antibody Technology, the Production and Characterization of Rodent and Human Hybridomas, 1985, In: Laboratory Techniques in Biochemistry and Molecular Biology, Eds. Burdon et al. Volume 13, Elsevier Science Publishers, Amsterdam).
  • the antibodies or antigen binding fragments thereof may also be produced by genetic engineering.
  • the technology for expression of both heavy and light chain genes in E. coli is the subject of PCT patent applications, publication number WO 901443, WO 901443 and WO 9014424 and in Huse et al, 1989,, Science, 246:1275-1281.
  • the antibodies may also be humanized (e.g., Queen, C. et al. 1989 Proc. Natl. Acad. Sci.USA 86; 10029).
  • Effect(s) of the polymo ⁇ hisms identified herein on expression of BF may be investigated by preparing recombinant cells and/or nonhuman recombinant organisms, preferably recombinant animals, containing a polymo ⁇ hic variant of the BF gene.
  • expression includes but is not limited to one or more of the following: transcription of the gene into precursor mRNA; splicing and other processing of the precursor mRNA to produce mature mRNA; mRNA stability; translation of the mature mRNA into BF protein (including codon usage and tRNA availability); and glycosylation and/or other modifications of the translation product, if required for proper expression and function.
  • the desired BF isogene may be introduced into the cell in a vector such that the isogene remains extrachromosomal. In such a situation, the gene will be expressed by the cell from the extrachromosomal location.
  • the BF isogene is introduced into a cell in such a way that it recombines with the endogenous BF gene present in the cell. Such recombination requires the occurrence of a double recombination event, thereby resulting in the desired BF gene polymo ⁇ hism.
  • Vectors for the introduction of genes both for recombination and for extrachromosomal maintenance are known in the art, and any suitable vector or vector construct may be used in the invention.
  • BF isogene examples include, but are not limited to, continuous culture cells, such as COS, NIH/3T3, arid primary or culture cells of the relevant tissue type, i.e, they express the BF isogene.
  • continuous culture cells such as COS, NIH/3T3, arid primary or culture cells of the relevant tissue type, i.e, they express the BF isogene.
  • recombinant cells can be used to compare the biological activities of the different protein variants.
  • Recombinant nonhuman organisms, i.e, transgenic animals, expressing a variant BF gene are prepared using standard procedures known in the art.
  • a construct comprising the variant gene is introduced into a nonhuman animal or an ancestor of the animal at an embryonic stage, i.e., the one-cell stage, or generally not later than about the eight-cell stage.
  • Transgenic animals carrying the constructs of the invention can be made by several methods known to those having skill in the art.
  • One method involves transfecting into the embryo a retrovirus constructed to contain one or more insulator elements, a gene or genes of interest, and other components known to those skilled in the art to provide a complete shuttle vector harboring the insulated gene(s) as a transgene, see e.g., U.S. Patent No. 5,610,053.
  • Another method involves directly injecting a transgene into the embryo.
  • a third method involves the use of embryonic stem cells.
  • animals into which the BF isogenes may be introduced include, but are not limited to, mice, rats, other rodents, and nonhuman primates (see “The Introduction of Foreign Genes into Mice” and the cited references therein, In: Recombinant DNA, Eds. J.D. Watson, M. Gilman, J. Wifkowski, and M. Zoller; W.H. Freeman and Company, New York, pages 254-272).
  • Transgenic animals stably expressing a human BF isogene and producing the encoded human BF protein can be used as biological models for studying diseases related to abnormal BF expression and/or activity, and for screening and assaying various candidate drugs, compounds, and treatment regimens to reduce the symptoms or effects of these diseases.
  • An additional embodiment of the invention relates to pharmaceutical compositions for treating disorders affected by expression or function of a novel BF isogene described herein.
  • the pharmaceutical composition may comprise any of the following active ingredients: a polynucleotide comprising one of these novel BF isogenes; an antisense oligonucleotide directed against one of the novel BF isogenes, a polynucleotide encoding such an antisense oligonucleotide, or another compound which inhibits expression of a novel BF isogene described herein.
  • the composition contains the active ingredient in a therapeutically effective amount.
  • therapeutically effective amount is meant that one or more of the symptoms relating to disorders affected by expression or function of a novel BF isogene is reduced and/or eliminated.
  • the composition also comprises a pharmaceutically acceptable carrier, examples of which include, but are not limited to, saline, buffered saline, dextrose, and water.
  • a pharmaceutically acceptable carrier examples of which include, but are not limited to, saline, buffered saline, dextrose, and water.
  • Those skilled in the art may employ a formulation most suitable for the active ingredient, whether it is a polynucleotide, oligonucleotide, protein, peptide or small molecule antagonist.
  • the pharmaceutical composition may be administered alone or in combination with at least one other agent, such as a stabilizing compound.
  • Administration of the pharmaceutical composition may be by any number of routes including, but not limited to oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, intradermal, transdermal, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, or rectal. Further details on techniques for formulation and administration may be found in the latest edition of Remington's Pharmaceutical Sciences (Maack Publishing Co, Easton, PA).
  • the dose can be estimated initially either in cell culture assays or in animal models.
  • the animal model may also be used to determine the appropriate concentration range and route of administration.
  • Such information can then be used to determine useful doses and routes for administration in humans.
  • the exact dosage will be determined by the practitioner, in light of factors relating to the patient requiring treatment, including but not limited to severity of the disease state, general health, age, weight and gender of the patient, diet, time and frequency of administration, other drugs being taken by the patient, and tolerance/response to the treatment.
  • any or all analytical and mathematical operations involved in practicing the methods of the present invention may be implemented by a computer.
  • the computer may execute a program that generates views (or screens) displayed on a display device and with which the user can interact to view and analyze large amounts of information relating to the BF gene and its genomic variation, including chromosome location, gene structure, and gene family, gene expression data, polymo ⁇ hism data, genetic sequence data, and clinical data population data (e.g., data on ethnogeographic origin, clinical responses, genotypes, and haplotypes for one or more populations).
  • the BF polymo ⁇ hism data described herein may be stored as part of a relational database (e.g., an instance of an Oracle database or a set of ASCII flat files).
  • polymo ⁇ hism data may be stored on the computer's hard drive or may, for example, be stored on a CD-ROM or on one or more other storage devices accessible by the computer.
  • the data may be stored on one or more databases in communication with the computer via a network.
  • EXAMPLE 1 This example illustrates examination of various regions of the BF gene for polymo ⁇ hic sites.
  • the following target regions of the BF gene were amplified using PCR primer pairs.
  • the primers used for each region are represented below by providing the nucleotide positions of their initial and final nucleotides, which correspond to positions in SEQ ID NO: 1 ( Figure 1).
  • Fragment 12 7081-7101 complement of 7609 - 7587 529 nt
  • Fragment 15 8380-8399 ' complement of 8942 - 8920 563 nt
  • Fragment 16 8716-8738 complement of 9272 - 9250 557 nt
  • Fragment 17 9043-9065 complement of 9615 - 9592 573 nt
  • Fragment 18 9616-9637 complement of 10103 - 10081 488 nt
  • Amplification profile 97°C - 2 min. 1 cycle
  • the PCR products were purified using a Whatman/Polyfiltronics 100 ⁇ l 384 well unifilter plate essentially according to the manufacturers protocol.
  • the purified DNA was eluted in 50 ⁇ l of distilled water.
  • Sequencing reactions were set up using Applied Biosystems Big Dye Terminator chemistry essentially according to the manufacturers protocol.
  • the purified PCR products were sequenced in both directions using the primer sets described previously or those represented below by the nucleotide positions of their initial and final nucleotides, which correspond to positions in SEQ ID NO:l ( Figure 1). Reaction products were purified by isopropanol precipitation, and run on an Applied Biosystems 3700 DNA Analyzer. Sequencing Primer Pairs
  • PS30 R 1621986 9944 C T a PolyId is a unique identifier assigned to each PS by Genaissance Pharmaceuticals, Inc.
  • This example illustrates analysis of the BF polymo ⁇ hisms identified in the Index Repository for human genotypes and haplotypes.
  • the different genotypes containing these polymo ⁇ hisms that were observed in unrelated members of the reference population are shown in Table 3 below, with the haplotype pair indicating the combination of haplotypes determined for the individual using the haplotype derivation protocol described below.
  • Table 3 homozygous positions are indicated by one nucleotide and heterozygous positions are indicated by two nucleotides. Missing nucleotides in any given genotype in Table 3 were inferred based on linkage disequilibrium and/or Mendelian inheritance.
  • haplotype pairs shown in Table 3 were estimated from the unphased genotypes using a computer-implemented extension of Clark's algorithm (Clark, A.G.1990 Mol Bio Evol 7, 111-122) for assigning haplotypes to unrelated individuals in a population sample, as described in PCT/US01/12831, filed April 18, 2001.
  • haplotypes are assigned directly from individuals who are homozygous at all sites or heterozygous at no more than one of the variable sites.
  • This list of haplotypes is then used to deconvolute the unphased genotypes in the remaining (multiply heterozygous) individuals.
  • the list of haplotypes was augmented with haplotypes obtained from two families (one three-generation Caucasian family and one two-generation African- American family).
  • a BF isogene defined by a full-haplotype shown in Table 4 below comprises the regions of the SEQ ID NOS indicated in Table 4, with their corresponding set of polymo ⁇ hic locations and identities, which are also set forth in Table 4.
  • a A ' T T T T T T T T T 2 4049/150 1/144 3199-4516
  • G G G G A A G G G G G 7 4960/750 1/144 4666-8356
  • Region examined represents the nucleotide positions defining the start and stop positions within the 1 st SEQ ID NO of the sequenced region.
  • SEQ ID NO: 1 refers to Figure 1 , with the two alternative allelic variants of each polymo ⁇ hic site indicated by the appropriate nucleotide symbol.
  • SEQ ID NO: 144 is a modified version of SEQ ID NO:l that shows the context sequence of each of PS1-PS30 in a uniform format to facilitate electronic searching of the BF haplotypes.
  • SEQ ID NO: 144 contains a block of 60 bases of the nucleotide sequence encompassing the centrally-located polymo ⁇ hic site at the 30 th position, followed by 60 bases of unspecified sequence to represent that each polymo ⁇ hic site is separated by genomic sequence whose composition is defined elsewhere herein.
  • Table 5 shows the percent of chromosomes characterized by a given BF haplotype for all umelated individuals in the Index Repository for which haplotype data was obtained. The percent of these umelated individuals who have a given BF haplotype pair is shown in Table 6.
  • the "Total" column shows this frequency data for all of these unrelated individuals, while the other columns show the frequency data for these umelated individuals categorized according to their self-identified ethnogeographic origin.
  • HAP1 HAP2 Total CA AF AS HL AM
  • the size and composition of the Index Repository were chosen to represent the genetic diversity across and within four major population groups comprising the general United States population.
  • this repository contains approximately equal sample sizes of African-descent, Asian- American, European- American, and Hispanic-Latino population groups. Almost all individuals representing each group had all four grandparents with the same ethnogeographic background.
  • the number of unrelated individuals in the Index Repository provides a sample size that is sufficient to detect SNPs and haplotypes that occur in the general population with high statistical certainty. For instance, a haplotype that occurs with a frequency of 5% in the general population has a probability higher than 99.9% of being observed in a sample of 80 individuals from the general population.
  • a haplotype that occurs with a frequency of 10% in a specific population group has a 99% probability of being observed in a sample of 20 individuals from that population group.
  • the size and composition of the Index Repository means that the relative frequencies determined therein for the haplotypes and haplotype pairs of the BF gene are likely to be similar to the relative frequencies of these BF haplotypes and haplotype pairs in the general U.S. population and in the .four population groups represented in the Index Repository. The genetic diversity observed for the three Native Americans is presented because it is of scientific interest, but due to the small sample size it lacks statistical significance.

Abstract

L'invention a trait à de nouvelles variantes génétiques du Facteur-B, le gène BF (properdine). Plusieurs génotypes, haplotypes et paires d'haplotypes existant dans la population des Etats-Unis sont également présentés pour le gène BF. L'invention concerne également des compositions et des méthodes destinées à l'haplotypage et/ou au génotypage du gène BF chez un individu. Elle se rapporte en outre à des polynucléotides définis par la séquence des haplotypes susmentionnés.
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US9063139B2 (en) 2006-02-13 2015-06-23 The Trustees Of Columbia University In The City Of New York Variants in complement regulatory genes predict age-related macular degeneration
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JP2022002539A (ja) * 2013-10-15 2022-01-11 コネクシオ ゲノミクス ピーティーワイ リミテッド 主要組織適合遺伝子複合体一塩基多型
US11279976B2 (en) 2013-10-15 2022-03-22 Illumina, Inc. Major histocompatibility complex single nucleotide polymorphisms
JP7297840B2 (ja) 2013-10-15 2023-06-26 イルミナ インコーポレイテッド 主要組織適合遺伝子複合体一塩基多型

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