WO2006063703A2 - Polymorphisme a simple nucleotide (snp) - Google Patents

Polymorphisme a simple nucleotide (snp) Download PDF

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Publication number
WO2006063703A2
WO2006063703A2 PCT/EP2005/012986 EP2005012986W WO2006063703A2 WO 2006063703 A2 WO2006063703 A2 WO 2006063703A2 EP 2005012986 W EP2005012986 W EP 2005012986W WO 2006063703 A2 WO2006063703 A2 WO 2006063703A2
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Prior art keywords
seq
snp
polynucleotide
nos
complement
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PCT/EP2005/012986
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WO2006063703A8 (fr
WO2006063703A3 (fr
Inventor
Malek Faham
Soren Germer
Hywel Bowden Jones
Mitchell Lee Martin
Martin Emilio Moorhead
Erik Roy Rasmussen
James Andrew Rosinski
Delphine Lagarde
Brian Kent Rhees
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F.Hoffmann-La Roche Ag
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Priority to CA002589037A priority Critical patent/CA2589037A1/fr
Priority to JP2007544791A priority patent/JP2008522597A/ja
Priority to EP05823148A priority patent/EP1828417A2/fr
Publication of WO2006063703A2 publication Critical patent/WO2006063703A2/fr
Publication of WO2006063703A3 publication Critical patent/WO2006063703A3/fr
Publication of WO2006063703A8 publication Critical patent/WO2006063703A8/fr

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    • 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
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P3/00—Drugs for disorders of the metabolism
    • A61P3/08—Drugs for disorders of the metabolism for glucose homeostasis
    • A61P3/10—Drugs for disorders of the metabolism for glucose homeostasis for hyperglycaemia, e.g. antidiabetics
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6893—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids related to diseases not provided for elsewhere
    • 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
    • C12Q2600/158—Expression 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/04—Endocrine or metabolic disorders
    • G01N2800/042—Disorders of carbohydrate metabolism, e.g. diabetes, glucose metabolism

Definitions

  • SNP Single Nucleotide Polymorphism
  • Diabetes mellitus a metabolic disease in which carbohydrate utilization is reduced and lipid and protein utilization is enhanced, is caused by an absolute or relative deficiency of insulin.
  • diabetes is characterized by chronic hyperglycemia, glycosuria, water and electrolyte loss, ketoacidosis and coma.
  • Long term complications include development of neuropathy, retinopathy, nephropathy, geneneralized degenerative changes in large and small blood vessels and increased susceptibility to infection.
  • the most common form of diabetes is Type 2, non-insulin-dependent diabetes that is characterized by hyperglycemia due to impaired insulin secretion and insulin resistance in target tissues. Both genetic and environmental factors contribute to the disease. For example, obesity plays a major role in the development of the disease.
  • Type 2 diabetes is often a mild form of diabetes mellitus of gradual onset.
  • Type 2 diabetes The health implications of Type 2 diabetes are enormous. In 1995, there were 135 million adults with diabetes worldwide. It is estimated that close to 300 million will have diabetes in the year 2025. (King H., et al, Diabetes Care, 21(9): 1414-1431 (1998)).
  • Type 2 diabetes has been shown to have a strong familial transmission: 40% of monozygotic twin pairs with Type 2 diabetes also have one or several first degree relatives affected with the disease. Barnett et al. 20 Diabetologia 87-93 (1981). In the Pima Indians, the relative risk of becoming diabetic is increased twofold for a child born to one parent who is diabetic, and sixfold when both parents are affected Knowler, W. C, et al. Genetic Susceptibility to Environmental Factors. A Challenge for Public Intervention 67-74 (Almquist & Wiksele International: Sweden, 1988). Concordance of monozygotic twins for Type 2 diabetes has been observed to be over 90%, compared with approximately 50% for monozygotic twins affected with Type I diabetes.
  • a nucleic acid sequence at which more than one sequence is possible in a population is referred to herein as a "polymorphic site.”
  • Polymorphic sites can allow for differences in sequences based on substitutions, insertions, or deletions. Such substitutions, insertions, or deletions can result in frame shifts, the generation of premature stop codons, the deletion or addition of one or more amino acids encoded by a polynucleotide, alter splice sites, and affect the stability or transport of mRNA.
  • a polymorphic site is a single nucleotide in length, the site is referred to as a single nucleotide polymorphism ("SNP").
  • SNPs are the most common form of genetic variation responsible for differences in disease susceptibility and drug response. SNPs can directly contribute to or, more commonly, serve as markers for many phenotypic endpoints such as disease risk or the drug response differences between patients.
  • the instant invention concerns the identification of genetic factors that predispose individuals to diabetes, with a focus on candidate genes and specifically, nucleic acid fragments of genes having single nucleotide polymorphisms ("SNPs”) which are amenable to diagnostic and therapeutic intervention.
  • SNPs single nucleotide polymorphisms
  • the invention provides isolated polynucleotides containing SNPs located within sequences selected from the group consisting of sequences identified by Sequence Identification Numbers ("SEQ. ID. NOS.") 1-92 and the complements of the sequences identified by SEQ. ID. NOS.: 1-92 as well as vectors, recombinant host cells, transgenic animals, and compositions containing such polynucleotides.
  • the invention also provides methods of diagnosing a susceptibility to Type 2 diabetes in an individual, by detecting one or more at- risk alleles of SNPs associated with Type 2 diabetes.
  • the invention provides methods of diagnosing a susceptibilityjto Type 2 diabetes in an individual by detecting one or more haplotypes associated with Type 2 diabetes.
  • Also contemplated by the invention are methods of identifying agents which can alter the course of the disease as well as the agents themselves and pharmaceutical compositions comprising these agents.
  • Figures 1A-1F (collectively referred to herein as " Figure 1") show SEQ. ID. NOS.: 1-92 with SNPs indicated by brackets within each sequence. The allele of each SNP that is associated with Type 2 diabetes is shown in a separate column.
  • Figures 2A- 2ICK (collectively referred to herein as " Figure 2") show haplotypes associated with Type 2 diabetes.
  • Figures 3A-3B (collectively referred to herein as " Figure 3") show how much each at-risk allele identified for each SNP in Figure 1 is associated with Type 2 diabetes (significance at p ⁇ 0.05) based upon the allelic chi-square association test.
  • Figure 4 shows how much each at-risk allele identified for each SNP in Figure 1 is associated with Type 2 diabetes (significance at p ⁇ 0.05) based upon the genotypic chi- square association test.
  • Figure 5 shows how much each at-risk allele identified for each SNP in Figure 1 is associated with Type 2 diabetes (significance at p ⁇ 0.05) based upon the chi-square test for recessive effects.
  • Figures 6A-6B provide a summary of the SNPs found to be associated with Type 2 diabetes using allelic association, genotypic association and/or the chi-square test for recessive effects.
  • Single nucleotide polymorphisms the most frequent DNA sequence variations in the human genome, gain more and more importance for a wide range of biological and biomedical applications.
  • SNPs are used to explore the evolutionary history of human populations and to analyze forensic samples. SNPs also play a major role in genetic analysis.
  • pharmacogenetics utilizes these DNA variations to elucidate genetic factors that underlie different drug efficacies or adverse events.
  • SNPs are thought to help identify genes that are involved in complex diseases.
  • the present invention relates to the identification of specific loci or single nucleotide polymorphisms (SNPs) that are specifically identified to be phenotypically associated with Type 2 diabetes.
  • SNPs single nucleotide polymorphisms
  • intervention can be prescribed to such individuals before symptoms of the disease present, e.g., dietary changes, exercise and/or medication.
  • Identification of genes implicated in Type 2 diabetes locus can pave the way for a better understanding of the disease process, which in turn can lead to improved diagnostics and therapeutics.
  • SNPs thought to be implicated in Type 2 diabetes were analyzed to identify SNPs. Nucleic acid sequences containing the SNPs were then genotyped in diabetic cases and matched controls. Statistical analysis was then performed to find association with Type 2 diabetes in analysis of control and diabetic populations. After the analysis of 1,769 SNPs in 186 genes, certain SNPs were found to be statistically associated with Type 2 diabetes ( ⁇ 0.05).
  • SNP refers to a single nucleotide polymorphism at a particular position in the human genome that varies among a population of individuals.
  • a SNP maybe identified by its name or by location within a particular sequence.
  • the SNPs identified in the SEQ. ID. NOS. of Figure 1 are indicated by brackets.
  • the SNP "[G/A]" in SEQ. ID. NO.: 1 of Figure 1 indicates that the nucleotide base (or the allele) at that position in the sequence may be either guanine or adenine.
  • the allele associated with Type 2 diabetes in Figure 1 (e.g., a guanine in SEQ. ID. NO.: 1) is indicated in a separate column.
  • nucleotides flanking the SNP for each SEQ. ID. NO. in Figure 1 are the flanking sequences which are used to identify the location of the SNP in the genome.
  • nucleotide sequences disclosed by the SEQ. ID. NOS. of the present invention encompass the complements of said nucleotide sequences.
  • SNP encompasses any allele among a set of alleles.
  • allele refers to a specific nucleotide among a selection of nucleotides defining a SNP.
  • minor allele refers to an allele of a SNP that occurs less frequently within a population of individuals than the major allele.
  • major allele refers to an allele of a SNP that occurs more frequently within a population of individuals than the minor allele.
  • At- risk allele refers to an allele that is associated with Type 2 diabetes.
  • Figure 1 and Figures 3-5 show a number of at-risk alleles of the present invention.
  • haplotype refers to a combination of particular alleles from two or more SNPs.
  • At-risk haplotype refers to a haplotype that is associated with Type 2 diabetes.
  • Figure 2 shows a number of at-risk haplotypes of the present invention.
  • polynucleotide refers to polymeric forms of nucleotides of any length.
  • the polynucleotides may contain deoxyribonucleotides, ribonucleotides, and/or their analogs.
  • Polynucleotides may have any three-dimensional structure including single-stranded, double-stranded and triple helical molecular structures, and may perform any function, known or unknown.
  • polynucleotides a gene or gene fragment, exons, introns, mRNA, tRNA, rRNA, short interfering nucleic acid molecules (siNA), ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers.
  • a polynucleotide may also comprise modified nucleic acid molecules, such as methylated nucleic acid molecules and nucleic acid molecule analogs.
  • a “substantially isolated” or “isolated” polynucleotide is one that is substantially free of the sequences with which it is associated in nature. By substantially free is meant at least 50%, at least 70%, at least 80%, or at least 90% free of the materials with which it is associated in nature.
  • An “isolated polynucleotide” also includes recombinant polynucleotides, which, by virtue of origin or manipulation: (1) are not associated with all or a portion of a polynucleotide with which it is associated in nature, (2) are linked to a polynucleotide other than that to which it is linked in nature, or (3) does not occur in nature.
  • hybridizes under stringent conditions is intended to describe conditions for hybridization and washing under which nucleotide sequences at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98% identical to each other typically remain hybridized to- each other.
  • stringent conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y (1989), 6.3.1- 6.3.6.
  • a non-limiting example of stringent hybridization conditions are hybridization in 6x sodium chloride/sodium citrate (SSC) at about 45 0 C, followed by one or more washes in 0.2. x SSC, 0.1% SDS at 50-65 0 C.
  • vector refers to a DNA molecule that can carry inserted DNA and be perpetuated in a host cell.
  • Vectors are also known as cloning vectors, cloning vehicles or vehicles.
  • vector includes vectors that function primarily for insertion of a nucleic acid molecule into a cell, replication vectors that function primarily for the replication of nucleic acids, and expression vectors that function for transcription and/or translation of the DNA or RNA. Also included are vectors that provide more than one of the above functions.
  • a "host cell” includes an individual cell or cell culture which can be or has been a recipient for vector(s) or for incorporation of nucleic acid molecules and/or proteins.
  • Host cells include progeny of a single host cell, and the progeny may not necessarily be completely identical (in morphology or in total DNA complement) to the original parent due to natural, accidental, or deliberate mutation.
  • a host cell includes cells transfected with the polynucleotides of the present invention.
  • An "isolated host cell” is one which has been physically dissociated from the organism from which it was derived. '
  • the terms "individual,” “host,” and “subject” are used interchangeably herein to refer to a vertebrate, preferably a mammal, more preferably a human.
  • transformation transformation
  • transduction transformation
  • CaPU 4 precipitation DEAE-dextran
  • particle bombardment etc.
  • the exogenous polynucleotide may be maintained as a non-integrated vector, for example, a plasmid, or alternatively, may be integrated into the host cell genome.
  • the genetic transformation may be transient or stable.
  • the present invention employs, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry and immunology, which are within the skill of the art.
  • the present invention provides isolated polynucleotides comprising a SNP located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS.:l-92; wherein the presence of a particular allele of a SNP (a particular nucleotide base) is indicative of a propensity to develop Type 2 diabetes or otherwise may be used to identify a Type 2 diabetic.
  • the polynucleotide is selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS.: 1-92.
  • the polynucleotide comprises at least a portion of a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS.:l-92.
  • the present invention also relates to isolated polynucleotides comprising a SNP located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS.:l-92, which hybridize, are complementary, or are partially complementary to a nucleotide sequence present in a test sample.
  • an isolated polynucleotide is selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS.:l-92, which hybridizes, is complementary, or is partially complementary to a nucleotide sequence present in a test sample.
  • an isolated polynucleotide comprises at least a portion of a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS.:l-92, which hybridizes, is complementary, or is partially complementary to a nucleotide sequence present in a test sample.
  • the present invention also provides isolated polynucleotides comprising one or more haplotypes selected from the group consisting of the haplotypes identified in Figure 2 which are indicative of a propensity to develop Type 2 diabetes.
  • a polynucleotide of the present invention can be isolated using standard molecular biology techniques and the sequence information provided herein. Using all or a portion of a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS.:1- 92, polynucleotides can be isolated using standard hybridization and cloning techniques (e.g., as described in Sambrook et al., eds., Molecular Cloning: A Laboratory Manual, 2 nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y, 1989).
  • a polynucleotide can be amplified using cDNA, mRNA or genomic DNA as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques.
  • the polynucleotide so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis.
  • oligonucleotides corresponding to all or a portion of a polynucleotide can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer.
  • Probes based on the sequence of a polynucleotide of the invention can be used to detect transcripts or genomic sequences.
  • a probe may comprise a label group attached thereto, e.g., a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor.
  • Such probes can be used as part of a diagnostic test kit for identifying cells or tissues which miss-express the protein, such as by measuring levels of a nucleic acid molecule encoding a protein in a sample of cells from a subject, e.g., detecting mRNA levels or determining whether a gene encoding a protein has been mutated or deleted.
  • the invention also provides polypeptides encoded by a polynucleotide, wherein the polynucleotide comprises a SNP located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS. 1-92 and the complements of sequences identified by SEQ. ID. NOS. 1-92.
  • a polypeptide is encoded by a polynucleotide, wherein the polynucleotide is selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS.:l-92.
  • a polypeptide is encoded by a polynucleotide, wherein the polynucleotide comprises at least a portion of the sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS.:l-92. Also contemplated are antibodies that bind such polypeptides.
  • the present invention also provides polypeptides encoded by a polynucleotide, wherein the polynucleotide comprises a haplotype selected from the group consisting of the haplotypes identified in Figure 2.
  • the invention also provides a vector comprising a haplotype identified in Figure 2 or a SNP located within a sequence selected from the group consisting of the sequences identified by SEQ. ID. NOS. 1-92 and the complements of sequences identified by SEQ. ID. NOS. 1-92; operably linked to a regulatory sequence.
  • a vector comprises a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.: 1-92 and the complements of sequences identified by SEQ. ID. NOS.:l-92; operably linked to a regulatory sequence.
  • a vector comprises at least a portion of a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS.: 1-92; operably linked to a regulatory sequence.
  • the invention also provides recombinant host ' cells comprising such vectors.
  • the invention also provides a method for producing a polypeptide encoded by a polynucleotide, wherein the polynucleotide comprises a haplotype identified in Figure 2 or a SNP located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS. 1-92 and the complements of sequences identified by SEQ. ID. NOS. 1-92, comprising culturing a recombinant host cell containing such a polynucleotide under conditions suitable for expression.
  • a polypeptide is produced by culturing a recombinant host cell containing a polynucleotide under conditions for expression, wherein the polynucleotide comprises a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS/.1-92.
  • a polypeptide is produced by culturing a recombinant host cell containing a polynucleotide under conditions for expression, wherein the polynucleotide comprises a portion of a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS.:l-92.
  • transgenic animal containing a polynucleotide comprising a haplotype identified in Figure 2 or a SNP located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS. 1-92 and the complements of sequences identified by SEQ. ID. NOS. 1-92.
  • a transgenic animal contains a polynucleotide comprising a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS.:l-92.
  • a transgenic animal contains a polynucleotide comprising at least a portion of a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.: 1-92 and the complements of sequences identified by SEQ. ID. NOS.:l-92.
  • compositions and kits are contemplated which contain the polynucleotides, proteins, antibodies, vectors, and/or host cells of the present invention.
  • One application of the current invention involves prediction of those at 1 higher risk of developing Type 2 diabetes. Diagnostic tests that define genetic factors contributing to Type 2 diabetes maybe used together with, or independent of, the known clinical risk factors to define an individual's risk relative to the general population. Means for identifying those individuals at risk for Type 2 diabetes should lead to better prophylactic and treatment regimens, including more aggressive management of the, current clinical risk factors.
  • the present invention includes methods of diagnosing a susceptibility to Type 2 diabetes in an individual, comprising detecting polymorphisms in nucleic acids of specific genes or gene segments, wherein the presence of the polymorphism in the nucleic acid is indicative of a susceptibility to Type 2 diabetes.
  • the present invention includes methods of diagnosing Type 2 diabetes or a susceptibility to Type 2 diabetes in an individual, comprising determining the presence or absence of particular alleles of SNPs contained in SEQ. ID. NOS. 1-92 and shown in Figure 1.
  • methods comprise screening for one of the at-risk alleles associated with Type 2 diabetes shown in Figure 1.
  • the present invention provides methods of diagnosing or determining a susceptibility to Type 2 diabetes in an individual, or methods of screening for individuals which are susceptible to Type 2 diabetes, comprising detecting an at-risk allele of a SNP associated with Type 2 diabetes, wherein the SNP is located within a sequence selected from the group consisting of sequences identified by SEQ ID.
  • the SNP is located within SEQ ID NO: 23 or the complement of SEQ ID NO: 23. In certain embodiments, the SNP is located within SEQ ID NO: 32 or the complement of SEQ ID NO: 32. In certain embodiments, the SNP is located within SEQ ID NO: 35 or the complement of SEQ ID NO: 35. In certain embodiments, the SNP is located within SEQ ID NO: 40 or the complement of SEQ ID NO: 40. In certain embodiments, the SNP is located within SEQ ID NO: 41 or the complement of SEQ ID NO: 41.
  • the SNP is located within SEQ ID NO: 17 or the complement of SEQ ID NO: 17. In certain embodiments, the SNP is located within SEQ ID NO: 36 or the complement of SEQ ID NO: 36. In certain embodiments, the SNP is located within SEQ ID NO: 74 or the complement of SEQ ID NO: 74. In certain embodiments, the SNP is located within SEQ ID NO: 62 or the complement of SEQ ID NO: 62. In certain embodiments, the SNP is located within SEQ ID NO: 10 or the complement of SEQ ID NO: 10. In certain embodiments, the SNP is located within SEQ ID NO: 11 or the complement of SEQ ID NO: 11.
  • the SNP is located within SEQ ID NO: 8 or the complement of SEQ ID NO: 8. In certain embodiments, the SNP is located within SEQ ID NO: 54 or the complement of SEQ ID NO: 54. In certain embodiments, the SNP is located within SEQ ID NO: 65 or the complement of SEQ ID NO: 65. In certain embodiments, the SNP is located within SEQ ID NO: 9 or the complement of SEQ ID NO: 9. In certain embodiments, the s SNP is located within SEQ ID NO:67 or the complement of SEQ ID NO: 67. In certain embodiments, the SNP is located within SEQ ID NO: 4 or the complement of SEQ ID NO: 4.
  • the SNP is located within SEQ ID NO: 91 or the complement of SEQ ID NO: 91. In certain embodiments, the SNP is located within SEQ ID NO: 92 or the complement of SEQ ID NO: 92. In certain embodiments, the SNP is located within SEQ ID NO: 68 or the complement of SEQ ID NO: 68. In certain embodiments, the SNP is located within SEQ ID NO: 69 or the complement of SEQ ID NO: 69. In certain embodiments, the SNP is located within SEQ ID NO: 7 or the complement of SEQ ID NO: 7. In certain embodiments, the SNP is located within SEQ ID NO: 20 or the complement of SEQ ID NO: 20.
  • the SNP is located within SEQ ID NO: 16 or the complement of SEQ ID NO: 16. In certain embodiments, the SNP is located within SEQ ID NO: 31 or the complement of SEQ ID NO: 31. In certain embodiments, the SNP is located within SEQ ID NO: 42 or the complement of SEQ ID NO: 42. In certain embodiments, the SNP is located within SEQ ID NO: 39 or the complement of SEQ ID NO: 39. In certain embodiments, the SNP is located within SEQ ID NO: 53 or the complement of SEQ ID NO: 53. In certain embodiments, the SNP is located within SEQ ID NO: 38 or the complement of SEQ ID NO: 38.
  • the invention provides a method of detecting the presence of a polynucleotide in a sample containing a SNP located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS. 1-92 and the complements of sequences identified by SEQ. ID. NOS. 1-92, wherein the method comprises contacting the sample with an isolated polynucleotide comprising a sequence (or a portion of a sequence) selected from the group consisting of sequences identified by SEQ. ID. NOS.: 1- 92 and the complements of sequences identified by SEQ. ID.
  • the isolated polynucleotide is completely complementary to the polynucleotide present in the sample. In other embodiments of the above method, the isolated polynucleotide is partially complementary to the polynucleotide present in the sample.
  • the isolated polynucleotide is at least 80% identical to the polynucleotide pjresent in the sample and capable of selectively hybridizing to said polynucleotide. If desired, amplification of the polynucleotide present in the sample can be performed using known methods in the art.
  • the present invention further provides a method for assaying a sample for the presence of a first polynucleotide which is at least partially complementary to a part of a second polynucleotide wherein the second polynucleotide comprises a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.:l-92 and the complements of sequences identified by SEQ. ID. NOS.:l-92 comprising: a) contacting said sample with said second polynucleotide under conditions appropriate for hybridization, and b) assessing whether hybridization has occurred between said first and said second polynucleotide, wherein if hybridization has occurred, said first polynucleotide is present in said sample.
  • the presence of said first polynucleotide is indicative of Type 2 diabetes or the propensity to develop Type 2 diabetes.
  • said second polynucleotide is completely complementary to a part of the sequence of said first polynucleotide.
  • said method further comprises amplification of at least part of said first polynucleotide.
  • said second polynucleotide is 99 or fewer nucleotides in length and is either: (a) at least 80 % identical to a contiguous sequence of nucleotides in said first polynucleotide or (b) capable of selectively hybridizing to said first polynucleotide.
  • Also contemplated by the invention is a method of assaying a sample for the presence of a polypeptide associated with Type 2 diabetes encoded by a polynucleotide, wherein the polynucleotide comprises an allele of a SNP associated with Type 2 diabetes located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS. 1-92 and the complements of sequences identified by SEQ. ID. NOS. 1-92, the method comprising contacting the sample with an antibody that specifically binds to said polypeptide.
  • the presence of a polypeptide associated with Type 2 diabetes in a sample encoded by a polynucleotide comprising a sequence selected from the group consisting of sequences identified by SEQ.
  • a polypeptide associated with Type 2 diabetes in a sample encoded by a polynucleotide (comprising at least a portion of a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.: 1-92 and the complements of sequences identified by SEQ. ID. NOS.: 1-92) is assayed by contacting the sample with an antibody that specifically binds to said polypeptide.
  • a polypeptide associated with Type 2 diabetes in a sample encoded by a polynucleotide (comprising at least a portion of a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.: 1-92 and the complements of sequences identified by SEQ. ID. NOS.: 1-92) is assayed by contacting the sample with an antibody that specifically binds to said polypeptide.
  • the present invention also includes a reagent for assaying a sample for the presence of a first polynucleotide comprising a SNP located within a sequence selected from the group consisting of sequences identified by SEQ ID. NOs.: 1-92 and the complements of sequences identified by SEQ ID. NOs.: 1-92, said reagent comprising a second polynucleotide comprising a contiguous nucleotide sequence which is at least partially complementary to a part of the first polynucleotide.
  • said second polynucleotide is completely complementary to a part of the first polynucleotide.
  • the present invention also encompasses a reagent kit for assaying a sample for the presence of a first polynucleotide comprising a SNP located within a sequence selected from the group consisting of sequences identified by SEQ ID. NOs.: 1-92 and the complements of sequences identified by SEQ ID. NOs: 1-92, comprising in separate containers: a) one or more labeled second polynucleotides comprising a sequence selected from thr group consisting of the sequences identified by SEQ ID. NOs.: 1-92 and the complements of sequences identified by SEQ ID. NOs.: 1-92; and b) reagents for detection of said label.
  • kits are contemplated containing polynucleotides which can be used to assay samples for the presence of polynucleotides containing an allele of a SNP associated (or not associated) with Type 2 diabetes located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS. 1-92 and the complements of sequences identified by SEQ. ID. NOS. 1-92. Kits are also contemplated which contain antibodies which can be used to assay samples for the presence of proteins associated (or not associated) with Type 2 diabetes that are encoded by the polynucleotides containing an allele of a SNP associated (or not associated) with Type 2 diabetes.
  • Other methods of diagnosing a susceptibility to Type 2 diabetes in an individual comprise determining the expression or composition of a polypeptide in a control sample encoded by a polynucleotide containing an allele of a SNP not associated with Type 2 diabetes and comparing it with the expression or composition of a polypeptide in a test sample encoded by the same polynucleotide except containing an allele of a SNP associated with Type 2 diabetes, wherein the presence of an alteration in expression or composition of the polypeptide in the test sample compared to the control sample is indicative of a susceptibility to Type 2 diabetes.
  • the invention also relates to a method of diagnosing Type 2 diabetes or a susceptibility to Type 2 diabetes in an individual, comprising determining the presence or absence in the individual of certain haplo types.
  • methods comprise screening for one of the at-risk haplotypes shown in Figure 2.
  • the present invention encompasses a method for diagnosing a susceptibility to Type 2 diabetes in an individual, or a method of screening for individuals with a susceptibility to Type 2 diabetes, comprising detecting a haplotype associated with Type 2 diabetes selected from the group consisting of the haplotypes shown in Figure 2.
  • the presence or absence of the haplotype may be determined by various methods, including, for example, using enzymatic amplification of nucleic acid from the individual, electrophoretic analysis, restriction fragment length polymorphism analysis and/or sequence analysis.
  • a method of diagnosing a susceptibility to Type 2 diabetes in an individual, or for screening individuals for a susceptibility to Type 2 diabetes comprising: a) obtaining a polynucleotide sample from said individual; and b) analyzing the polynucleotide sample for the presence or absence of a haplotype, comprising a haplotype shown in Figure 2, wherein the presence of the haplotype corresponds to a susceptibility to Type 2 diabetes.
  • a method of determining or diagnosing the susceptibility to Type 2 diabetes in an individual comprising detecting multiple SNPs identified in Figures 1 or 2.
  • the method of determining the susceptibility to Type 2 diabetes in an individual comprises detecting multiple SNPs identified in SEQ. ID. NOS.: 23, 32, 35, 40, 41, 17, and/or 36.
  • the method of determining the susceptibility to Type 2 diabetes in an individual comprises detecting multiple SNPs identified in SEQ. ID. NOS.: 74, 62, 10, 11, 8, and/or 54.
  • the method of determining the susceptibility to Type 2 diabetes in an individual comprises detecting multiple SNPs identified in SEQ. ID.
  • the method of determining the susceptibility to Type 2 diabetes in an individual comprises detecting multiple SNPs identified in SEQ. ID. NOS.: 7, 20, 16, 31, 42, 39, 53 and/or 38.
  • the presence of a first polynucleotide in a sample containing one or more at-risk alleles in Figure 1 is assayed for by contacting the sample with probe polynucleotides that are complementary to said first polynucleotide.
  • At least one SNP is located within SEQ ID NO: 23 or the complement of SEQ ID NO: 23. In certain embodiments, at least one SNP is located within SEQ ID NO: 32 or the complement of SEQ ID NO: 32. In certain embodiments, at least one SNP is located within SEQ ID NO: 35 or the complement of SEQ ID NO: 35. In certain embodiments, at least one SNP is located within SEQ ID NO: 40 or the complement of SEQ ID NO: 40. In certain embodiments, at least one SNP is located within SEQ ID NO: 41 or the complement of SEQ ID NO: 41. In certain embodiments, at least one SNP is located within SEQ ID NO: 17 or the complement of SEQ ID NO: 17.
  • At least one SNP is located within SEQ ID NO: 36 or the complement of SEQ ID NO: 36. In certain embodiments, at least one SNP is located within SEQ ID NO: 74 or the complement of SEQ ID NO: 74. In certain embodiments, at least one SNP is located within SEQ ID NO: 62 or the complement of SEQ ID NO: 62. In certain embodiments, at least one SNP is located within SEQ ID NO: 10 or the complement of SEQ ID NO: 10. In certain embodiments, at least one SNP is located within SEQ ID NO: 11 or the complement of SEQ ID NO: 11. In certain embodiments, at least one SNP is located within SEQ ID NO: 8 or the complement of SEQ ID NO: 8.
  • At least one SNP is located within SEQ ID NO: 54 or the complement of SEQ ID NO: 54. In certain embodiments, at least one SNP is located within SEQ ID NO: 65 or the complement of SEQ ID NO: 65. In certain embodiments, at least one SNP is located within SEQ ID NO: 9 or the complement of SEQ ID NO: 9. In certain embodiments, at least one SNP is located within SEQ ID NO:67 or the complement of SEQ ID NO: 67. In certain embodiments, at least one SNP is located within SEQ ID NO: 4 or the complement of SEQ ID NO: 4. In certain embodiments, at least one SNP is located within SEQ ID NO: 91 or the complement of SEQ ID NO: 91.
  • At least one SNP is located within SEQ ID NO: 92 or the complement of SEQ ID NO: 92. In certain embodiments, at least one SNP is located within SEQ ID NO: 68 or the complement of SEQ ID NO: 68. In certain embodiments, at least one SNP is located within SEQ ID NO: 69 or the complement of SEQ ID NO: 69. In certain embodiments, at least one SNP is located within SEQ ID NO: 7 or the complement of SEQ ID NO: 7. In certain embodiments, at least one SNP is located within SEQ ID NO: 20 or the complement of SEQ ID NO: 20. In certain embodiments, at least one SNP is located within SEQ ID NO: 16 or the complement of SEQ ID NO: 16.
  • At least one SNP is located within SEQ ID NO: 31 or the complement of SEQ ID NO: 31. In certain embodiments, at least one SNP is located within SEQ ID NO: 42 or the complement of SEQ ID NO: 42. In certain embodiments, at least one SNP is located within SEQ ID NO: 39 or the complement of SEQ ID NO: 39. In certain embodiments, at least one SNP is located within SEQ ID NO: 53 or the complement of SEQ ID NO: 53. In certain embodiments, at least one SNP is located within SEQ ID NO: 38 or the complement of SEQ ID NO: 38.
  • a Type 2 diabetes therapeutic agent is contemplated.
  • the Type 2 diabetes therapeutic agent can be an agent that alters (e.g., enhances or inhibits) polypeptide activity and/or expression of a polynucleotide comprising a haplotype identified in Figure 2 or a SNP located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.: 1-92 and the complements of sequences identified by SEQ. ID. NOS.: 1-92.
  • Such agents include polynucleotides, polypeptides, receptors, binding agents, peptidomimetics, fusion proteins, prodrugs, antibodies, agents that alter polynucleotide expression, agents that alter activity of a polypeptide encoded by a gene or polynucleotide of the invention, agents that alter post- transcriptional processing of a polypeptide encoded by a gene or polynucleotide of the invention, agents that alter interaction of a polypeptide with a binding agent or receptor, agents that alter transcription of splicing variants encoded by a gene or polynucleotide, and ribosomes.
  • the invention also relates to pharmaceutical compositions comprising at least one of the Type 2 diabetes therapeutic agents as described herein.
  • Type 2 diabetes therapeutic agents can alter polypeptide activity or expression of a polynucleotide by a variety of means, such as, for example, by up-regulating the transcription or translation of the polynucleotide encoding the polypeptide, by altering posttranslational processing of the polypeptide, by altering transcription of splicing variants, or by interfering with polypeptide activity (e.g., by binding to the polypeptide, or by binding to another polypeptide that interacts with the polypeptide of interest) by down-regulating the expression, transcription or translation of a polynucleotide encoding the polypeptide, or by altering interaction among the polypeptide of interest and a polypeptide binding agent.
  • means such as, for example, by up-regulating the transcription or translation of the polynucleotide encoding the polypeptide, by altering posttranslational processing of the polypeptide, by altering transcription of splicing variants, or by interfering with polypeptide activity (e.g.
  • the invention also pertains to a method of treating an individual suffering from Type 2 diabetes by administering a Type 2 diabetes therapeutic agent to the individual in a therapeutically effective amount.
  • the Type 2 diabetes therapeutic agent is an agonist and, in other embodiments, the Type 2 diabetes therapeutic agent is an antagonist.
  • the invention additionally pertains to the use of a Type 2 diabetes therapeutic agent for the manufacture of a medicament for use in the treatment of Type 2 diabetes.
  • the therapeutic agents as described herein can be delivered in a composition or alone. They can be administered systemically, or can be targeted to a particular tissue.
  • the therapeutic agents can be produced by a variety of means, including chemical synthesis; recombinant production and in vivo production (e.g.-, a transgenic animal, see U.S. Patent No: 4,873,316 to Meade et ah, incorporated herein by reference in its entirety), and can be isolated using standard methods known in the art.
  • a combination of any of the above methods of treatment e.g., administration of a polypeptide in conjunction with antisense therapy targeting mRNA; administration of a first splicing variant in conjunction with antisense therapy targeting a second splicing variant
  • administration of a polypeptide in conjunction with antisense therapy targeting mRNA e.g., administration of a polypeptide in conjunction with antisense therapy targeting mRNA; administration of a first splicing variant in conjunction with antisense therapy targeting a second splicing variant
  • the current invention also encompasses methods of monitoring the effectiveness of therapeutic agents of the invention on the treatment of Type 2 diabetes using methods known in the art.
  • Another application of the current invention is its use to predict an individual's response to a particular therapeutic agent.
  • SNPs or haplotypes may be used as a pharmacogenomic diagnostic to predict drug response and guide the choice of therapeutic agent in a given individual.
  • the invention pertains to a method of identifying an agent that alters expression of a polynucleotide containing an allele of a SNP associated with Type 2 diabetes comprising: (a) contacting a polynucleotide with an agent to be tested under conditions for expression, wherein the polynucleotide comprises, (1) an allele of a SNP associated with Type 2 diabetes located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS. 1-92 and the complements of sequences identified by SEQ. ID. NOS.
  • step (b) assessing the level of expression of the reporter gene in the presence of the agent; (c) assessing the level of expression of the reporter gene in the absence of the agent; and (d) comparing the level of expression in step (b) with the level of expression in step (c) for differences indicating that expression was altered by the agent.
  • the invention pertains to a method of identifying an agent suitable for treating Type 2 diabetes comprising: (a) contacting a polynucleotide with an agent to be tested, wherein the polynucleotide contains a haplotype identified in Figure 2 or a SNP located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS. 1-92 and the complements of sequences identified by SEQ. ID. NOS. 1-92; and (b) determining whether said agent binds to, alters, or affects the polynucleotide in a manner which would be useful for treating Type 2 diabetes.
  • the expression of the polynucleotide in the presence of the agent comprises expression of one or more splicing variant(s) that differ in kind or in quantity from the expression of one or more splicing variant(s) in the absence of the agent.
  • the invention pertains to a method of identifying an agent suitable for treating Type 2 diabetes comprising: (a) contacting a polypeptide with an agent to be tested, wherein the polypeptide is encoded by a polynucleotide containing a haplotype identified in Figure 2 or a SNP located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS. 1-92 and the complements of sequences identified by SEQ. ID. NOS. 1-92; and (b) determining whether said agent binds to, alters, or affects the polypeptide in a manner which would be useful for treating Type 2 diabetes.
  • Agents identified by the above methods are also contemplated as well as pharmaceutical compositions containing such agents.
  • a polynucleotide comprising a haplotype identified in Figure 2 or a SNP located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.: 1-92 and the complements of sequences identified by SEQ. ID. NOS.: 1-92 is used in "antisense" therapy in which the polynucleotide is administered or generated in situ and specifically hybridizes to mRNA and/or genomic DNA.
  • the antisense polynucleotide that specifically hybridizes to the mRNA and/or DNA inhibits expression of the polypeptide encoded by that mRNA and/or DNA, e.g., by inhibiting translation and/or transcription. Binding of the antisense polynucleotide can be by- conventional base pair complementarity, or, for example, in the case of binding to DNA duplexes, through specific interaction in the major groove of the double helix.
  • an antisense construct can be delivered, for example, as an expression plasmid.
  • the plasmid When the plasmid is transcribed in the cell, it produces RNA that is complementary to a portion of the mRNA and/or DNA that encodes a polypeptide.
  • the antisense construct can be a polynucleotide probe that is generated ex vivo and introduced into cells; it then inhibits expression by hybridizing with the mRNA and/or genomic DNA encoding the polypeptide.
  • the polynucleotide probes are modified oligonucleotides that are resistant to endogenous nucleases, e.g., exonucleases and/or endonucleases, thereby rendering them stable in vivo.
  • nucleic acid molecules for use as antisense oligonucleotides are phosphoramidate, phosphothioate and methylphosphonate analogs of DNA (see also U.S. Patent Nos. 5,176,996, 5,264,564, and 5,256,775, all of which are incorporated herein by reference in their entirety).
  • oligodeoxyribonucleotides derived from the translation initiation site may be used.
  • oligonucleotides are designed that are complementary to mRNA encoding a polypeptide.
  • the antisense oligonucleotides bind to mRNA transcripts and prevent translation. Absolute complementarity, is not required as along as the oligonucleotides have sufficient complementarity to be able to hybridize with the RNA, forming a stable duplex.
  • the ability to hybridize will depend on both the degree of complementarity and the length of the antisense oligonucleotides. Generally, the longer the hybridizing oligonucleotides, the more base mismatches with RNA they may contain and still form a stable duplex (or triplex, as the case may be).
  • One skilled in the art can ascertain a tolerable degree of mismatch by the use of standard procedures.
  • the oligonucleotides used in antisense therapy can be DNA, RNA, or chimeric mixtures or derivatives or modified versions thereof, single-stranded or double-stranded.
  • the oligonucleotides can be modified at the base moiety, sugar moiety, or phosphate backbone, for example, to improve stability of the molecule, hybridization, etc.
  • the oligonucleotid.es can include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger et al, Proc. Natl. Acad.
  • the oligonucleotide maybe conjugated to another molecule (e.g., a peptide, hybridization triggered cross-linking agent, transport agent, hybridization-triggered cleavage agent).
  • the antisense molecules are delivered to cells that express polypeptides implicated in Type 2 diabetes in vivo.
  • a number of methods can be used for delivering antisense DNA or RNA to cells; e.g., antisense molecules can be injected directly into the tissue site, or modified antisense molecules, designed to target the desired cells (e.g., antisense linked to peptides or antibodies that specifically bind receptors or antigens expressed on the target cell surface) can be administered systematically.
  • a recombinant DNA construct is utilized in which the antisense oligonucleotide is placed under the control of a strong promoter (e.g., pol III or pol II).
  • a vector can be introduced in vivo such that it is taken up by a cell and directs the transcription of an antisense RNA.
  • a vector can remain episomal or become chromosomally integrated, as long as it can be transcribed to produce the desired antisense RNA.
  • Such vectors can be constructed by recombinant DNA technology and methods standard in the art.
  • a plasmid, cosmid or viral vector can be used to prepare the recombinant DNA construct that can be introduced directly into the tissue site.
  • RNA interference small double-stranded interfering RNA
  • RNAi is a post-transcription process, in which double-stranded RNA is introduced, and sequence- specific gene silencing results, though catalytic degradation of the targeted mRNA. See, e.g., Elbashir, S.M. et al, Nature 411:494-498 (2001); Lee, N.S., Nature Biotech. 19:500- 505 (2002); Lee, S-K. et al, Nature Medicine 8(7):681-686 (2002); the entire teachings of which are incorporated herein by reference in their entirety.
  • the invention comprises a short interfering nucleic acid (“siNA”) molecule comprising a double-stranded RNA polynucleotide that down-regulates expression of a polynucleotide containing a haplotype identified in Figure 2 or a SNP identified in a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS.: 1-92 and the complements of sequences identified by SEQ. ID. NOS.: 1- 92.
  • the invention comprises polynucleotides, compositions, and methods used in RNA interference (as described in U.S.
  • Endogenous expression of a gene product can also be reduced by inactivating or "knocking out" the gene or its promoter using targeted homologous recombination.
  • an altered, non-functional gene or a completely unrelated DNA sequence flanked by DNA homologous to the endogenous gene (either the coding regions or regulatory regions of the gene) can be used, with or without a selectable marker and/or a negative selectable marker, to transfect cells that express the gene in vivo. Insertion of the DNA construct, via targeted homologous recombination, results in inactivation of the gene.
  • the recombinant DNA constructs can be directly administered or targeted to the required site in vivo using appropriate vectors, as described above.
  • targeted homologous recombination can be used to insert a DNA construct comprising a non- altered functional gene, or the complement thereof, or a portion thereof, in place of a gene in the cell, as described above.
  • targeted homologous recombination can be used to insert a DNA construct comprising a polynucleotide that encodes a polypeptide variant that differs from that present in the cell.
  • endogenous expression of a gene product can be reduced by targeting deoxyribonucleotide sequences complementary to the regulatory region (i.e., the promoter and/or enhancers) to form triple helical structures that prevent transcription of the gene in target cells in the body.
  • deoxyribonucleotide sequences complementary to the regulatory region i.e., the promoter and/or enhancers
  • triple helical structures that prevent transcription of the gene in target cells in the body.
  • the antisense constructs described herein can be used in the manipulation of tissue by antagonizing the normal biological activity of the gene product, e.g., tissue differentiation, both in vivo and for ex vivo tissue cultures.
  • the anti-sense techniques e.g., microinjection of antisense molecules, or transection with plasmids whose transcripts are anti-sense with regard to RNA or nucleic acid sequences
  • Such techniques can be utilized in cell culture, but can also be used in the creation of transgenic animals.
  • compositions suitable for administration can be incorporated into pharmaceutical compositions suitable for administration.
  • Such compositions typically comprise polynucleotides, proteins, and/or therapeutic agents and a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration.
  • the use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.
  • a pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration.
  • routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration.
  • Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerin, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
  • the parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
  • compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions.
  • suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF; Parsippany, NJ.) or phosphate buffered saline (PBS).
  • the composition is sterile and should be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof.
  • the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in the composition.
  • Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
  • Sterile injectable solutions can be prepared by incorporating the active compound (e.g., a polynucleotide, polypeptide or antibody) in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • the active compound e.g., a polynucleotide, polypeptide or antibody
  • dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • some methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • Oral compositions generally include an inert diluent or an edible carrier.
  • compositions can also, be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed.
  • Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition.
  • the tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid or corn starch; a lubricant such as magnesium stearate; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.
  • a binder such as microcrystalline cellulose, gum tragacanth or gelatin
  • an excipient such as starch or lactose, a disintegrating agent such as alginic acid or corn starch
  • a lubricant such as magnesium stearate
  • a glidant such as colloidal silicon dioxide
  • a sweetening agent such as sucrose or saccharin
  • a flavoring agent such as
  • the compounds are delivered in the form of an aerosol spray from a pressurized container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.
  • a suitable propellant e.g., a gas such as carbon dioxide, or a nebulizer.
  • Systemic administration can also be by transmucosal or transdermal means.
  • penetrants appropriate to the barrier to be permeated are used in the formulation.
  • penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives.
  • Transmucosal administration can be accomplished through the use of nasal sprays or suppositories.
  • the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.
  • the compounds can also be prepared in the form of suppositories (e.g., with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.
  • suppositories e.g., with conventional suppository bases such as cocoa butter and other glycerides
  • retention enemas for rectal delivery.
  • the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems.
  • a controlled release formulation including implants and microencapsulated delivery systems.
  • Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc.
  • Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Patent No. 4,522,811.
  • Dosage unit form refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
  • the specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic effect to the achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals.
  • the nucleic acid molecules of the invention can be inserted into vectors and used as gene therapy vectors.
  • Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (see U.S. Patent No. 5,328,470) or by stereotactic injection (see, e.g., Chen et al. (1994) Proc. Natl Acad. Sci. USA 91:3054- 3057).
  • the pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded.
  • the pharmaceutical preparation can include one or more cells which produce the gene delivery system.
  • kits are contemplated which contain the therapeutic agents of the invention.
  • Another embodiment of the invention is its use to predict an individual's response to a particular drug to treat Type II diabetes. It is a well-known phenomenon that in general, patients do not respond equally to the same drug. Much of the differences in drug response to a given drug are thought to be based on genetic and protein differences among individuals in certain genes and their corresponding pathways.
  • the present invention defines particular SNPs, haplotypes, and genes that are associated with Type 2 diabetes.
  • Some current or future therapeutic agents may be able to affect pathways that are related to such SNPs, haplotypes, and/or genes directly or indirectly and therefore, be effective in those patients whose Type II diabetes risk is in part determined by such SNPs, haplotypes, and/or genes.
  • those same drugs may be less effective or ineffective in those patients who do not have particular alleles of said SNPs and/or haplotypes. Therefore, the SNPs and/or haplotypes of the present invention may be used as a pharmacogenomic diagnostic to predict drug response and guide choice of therapeutic agent in a given individual.
  • a method for monitoring the effectiveness of a drug on the treatment of Type 2 diabetes comprises, monitoring the level of expression of a gene associated with Type 2 diabetes containing one or more SNPs selected from the group of SNPs consisting of the SNPs identified in Figure 1 before treatment with a drug, monitoring the expression of said gene after treatment with said drug, and comparing the level of expression of said gene before said treatment and after said treatment.
  • a method for predicting the effectiveness of a given therapeutic agent in the treatment of Type 2 diabetes comprises screening for the presence or absence of one or more SNPs located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS. 1-92 and the complements of sequences identified by SEQ. ID. NOS. 1-92.
  • a method for predicting the effectiveness of a given therapeutic agent in the treatment of Type 2 diabetes comprises screening for the presence or absence of one or more haplotypes identified in Figure 2.
  • Another application of the current invention is the specific identification of a rate- limiting pathway involved in Type 2 diabetes.
  • a disease gene with genetic variation that is significantly more common in diabetic patients as compared to controls represents a specifically validated causative step in the pathogenesis of Type 2 diabetes. That is, the uncertainty about whether a gene is causative or simply reactive to the disease process is eliminated.
  • the protein encoded by the disease gene defines a rate-limiting molecular pathway involved in the biological process of Type 2 diabetes predisposition.
  • the proteins encoded by such Type 2 genes or its interacting proteins in its molecular pathway may represent drug targets that may be selectively modulated by small molecule, protein, antibody, or nucleic acid therapies. Such specific information is greatly needed since the population affected with Type 2 diabetes is growing.
  • Genes not known previously to be implicated with Type 2 diabetes by SNP based association but which were discovered to be implicated with Type 2 diabetes by SNP based association in the present invention include the following:
  • the invention pertains to a method of identifying a gene associated with Type 2 diabetes comprising: (a) identifying a gene containing a SNP that is located within a sequence selected from the group consisting of sequences identified by SEQ. ID. NOS. 1-92 and the complements of sequences identified by SEQ. ID. NOS. 1-92; and (b) comparing the expression of said gene in an individual having the at-risk allele with the expression of said gene in an individual having the non-risk allele for differences indicating that the gene is associated with Type 2 diabetes.
  • the invention pertains to a method of identifying a gene associated with Type 2 diabetes comprising: (a) identifying a gene containing an at-risk haplotype identified in Figure 2; and (b) comparing the expression of said gene in an individual having the at-risk haplotype with the expression of said gene in an individual not having the at-risk haplotype for differences indicating that the gene is associated with Type 2 diabetes.
  • Tab e 2 Summary of case and contro samples used in this stu y.
  • the phenotype was simply "diabetes".
  • Other sub- phenotypes could be included in the analysis including BMI, haemoglobin AIC, heart disease (MI etc), nephropathy etc.
  • the samples were collected by Genomics
  • CGI Collaborative Inc.
  • the population contained roughly equal numbers of males and females (274 males and 326 females). Samples were also well matched with identical numbers of males (163 cases and 163 controls) and females (137 cases and 137 controls) in the diabetic and unaffected groups.
  • case and control populations should be genetically identical across the genome, with the exception of regions containing genes that predispose to the phenotype being studied. That is, a random set of markers should show broadly similar allele frequencies in the case and control populations.
  • Population stratification was unlikely to be present in this study as the patients and controls were not only matched for sex and ethnicity, but were selected from the same country (Poland). However, to test for population stratification, the data was analyzed using the software program STRUCTURE 2.0 by Falush et al.
  • STRUCTURE implements a model-based clustering method as described in Pritchard et al., Association mapping in structured population,. AM. J. HUM. GENET. 671:170-81 (2000); incorporated herein by reference in its entirety. The program was allowed to sort the data into pre-specified numbers of clusters without any intervention.
  • the data sets consisted of 150 markers which were chosen based on three criteria. First, the minor allele had to have frequency >5% in the total population. Second, at least 80% of the individuals were required to have genotypes and third, the markers could not be closer than 100kb to any other marker in the set.
  • MRD detects variants or SNPs utilizing the mismatch repair system of Escherichia coli Modrich, P., Mechanisms and biological effects of mismatch repair, ANN REV. GENET, 25: 2259-53 (1991), incorporated herein by reference in its entirety.
  • a specific strain is engineered to sort a pool of transformed fragments into two pools: those carrying a variation and those that do not.
  • MRD has been described before as a method for multiplex variation scanning Faham.
  • MRD is used in combination with standard dideoxy terminator sequencing to discover common variant alleles in two different populations.
  • Individual PCR reactions using pooled genomic DNA from a population as a template are mixed with PCR fragments from a single haploid individual.
  • Sanger sequencing does not have sufficient sensitivity to detect rare alleles from genomic pools in which the pooled population is sequenced directly. Instead, many PCR reactions are pooled and one MRD reaction is done to produce a pool of colonies enriched for variant alleles compared to the haploid standard.
  • One amplication reaction from the variant-enriched pool is done for each amplicon followed by a sequencing reaction to identify common and rare variations in the population examined.
  • MRD based SNP discovery is limited by backgrounds caused by MRD enrichment of non-genomic DNA mismatches. These can occur in two ways: oligonucleotide mutations and PCR error. Both oligo error in the PCR primers and PCR errors introduce a set of fragments which contain mutations in the absence of any actual DNA variation. These fragments will be enriched along with the actual variations meaning that it is impossible to enrich a mutation that occurs at a frequency lower than the background level. Oligos having low rates of mutation and PCR using high fidelity polymerases are used in order to minimize these problems. Control experiments were performed using patients with variation in the BRCAl gene. These patients were sequenced to identify mutations in the BRCAl exons.
  • the first of these is that multiple SNPs can occur on a particular sequencing fragment. If this occurs with the two SNPs having very different frequencies, the SNP with the higher frequency will tend to dominate the enriched pool, suppressing the signal of the rarer SNP. This effect can be mitigated in several ways. The first is to use fairly small PCR fragments to minimize the chances of multiple SNPs occurring within a single fragment (typically fragments of ⁇ 300bp are used). Secondly, in cases when common SNPs are known to occur, PCR primers can be designed to exclude these SNPs. These limitations are to be weighed against the prohibitive costs of sequencing and analysis of many individuals in the typical manner. Reducing the number of individuals sequenced in the classical manner reduces coverage by introducing Poisson noise in the choice of a small population.
  • MIP Molecular Inversion Probes
  • SNPs were chosen to provide information on 186 genes which may play a role in susceptibility to diabetes. These genes are located across the genome with at least one gene from every chromosome with the exception of 21 and the Y chromosome. The genes varied in size from 0 to 992kb. Note that the length of the gene was measured by size of the region between the most widely spaced SNPs in each gene, hence genes with only one SNP were recorded as having size Okb.
  • the oligonucleotide probes in this process undergo a unimolecular rearrangement from a molecule that cannot be amplified, into a molecule that can be amplified.
  • This rearrangement is mediated by genomic DNA and an enzymatic "gap fill" process that occurs in an allele-specific manner.
  • the gap-fill process results in an important intermediate state in which the probes are circularized. This state allows a selection for the unimolecular interactions through exonuclease treatment that will degrade all cross- reacted and un-reacted probes.
  • the probes are amplified using generic PCR primers that are fluorescently labeled. See Hardenbol et al., Multiplexed genotyping with sequence tagged molecular inversion probes, 21 NAT. BlOTECHNOL. (6):673-7 ⁇ (June, 2003), incorporated herein by reference in its entirety.
  • each of four multiplexed reactions scores a different SNP allele by using a single nucleotide species (A,C,G or T).
  • PCR is carried out with a common primer pair such that all probes that have undergone inversion will be amplified in each reaction.
  • the SNP allele can be inferred by identifying which labels are present on the MIP probe amplicon that results from the four separate reactions.
  • the four reactions are hybridized to universal oligonucleotide arrays.
  • the relative base incorporation is measured by the fluorescent signal at the corresponding complementary tag site on the DNA array.
  • Four intensity values for each probe are generated.
  • the two values for the expected allele bases are compared to determine whether the SNP is homozygous or heterozygous for the given individual, and the two non-allele bases are compared to the allele bases to measure the signal to noise for the probe as a quality control check.
  • the genotype test also includes a test for a dominance. However, both the genotype and allele tests do not address recessive allelic effects and if present, they would be missed. To address this problem another series of chi-square tests were run where the minor allele of each SNP was modeled as a recessive effect (2x2, 1 d.f). Several SNPs were significant by the recessive test (see Figure 5), some of which were already implicated by the allele test. Figure 6 provides a summary of the SNPs found to be associated with Type 2 diabetes using allelic association, genotypic association and the chi-square test for recessive effects.
  • Example 8 Assessment For At- Risk Haplotypes
  • haplotypes described herein are found more frequently in individuals with Type 2 diabetes than in individuals without Type 2 diabetes. Accordingly, these haplotypes have predictive value for detecting Type 2 diabetes or a susceptibility to Type 2 diabetes in an individual.
  • an individual who is at risk for Type 2 diabetes is an individual in whom an at-risk haplotype is identified.
  • the at-risk haplotype is one that confers a significant risk of Type 2 diabetes.
  • significance associated with a haplotype is measured by an odds ratio.
  • the significance is measured by a percentage.
  • a significant risk is measured as an odds ratio of at least about 1.2, including but not limited to: 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8 and 1.9.
  • an odds ratio of at least 1.2 is significant.
  • an odds ratio of at least 1.5 is significant.
  • a significant increase in risk of at least about 1.7 is significant.
  • a significant increase in risk is at least about 20%, including but not limited to about 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% and 98%. In a further embodiment, a significant increase in risk is at least about 50%. It is understood, however, that identifying whether a risk is medically significant may also depend on a variety of factors, including the specific disease, the haplotype, and often, environmental factors.
  • the method comprises assessing in an individual the presence or frequency of SNPs, wherein an excess or higher frequency of the SNPs compared to a healthy control individual is indicative that the individual has Type 2 diabetes, or is susceptible to Type 2 diabetes.
  • the presence of two or more SNPs may indicate the presence of an at-risk haplotype that can be used to screen individuals.
  • an at-risk haplotype can include the haplotypes identified in Figure 2, a combination of SNPs identified in Figure 1, or a combination of the SNPs identified in Figures 1 or 2.
  • the presence of an at-risk haplotype is indicative of a susceptibility to Type 2 diabetes, and therefore is indicative of an individual who falls within a target population for the treatment methods described herein.
  • Example 9 SNPs Relating To Peripheral Vascular Disease
  • PVD peripheral vascular disease
  • the population attributable risk for both SNPs was - 23%, indicating that approximately one quarter of the population with at least 1 'G' allele at either of these SNPs are protected from PVD.

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Abstract

L'invention concerne l'association du diabète de type 2 avec des polymorphismes et des haplotypes à simple nucléotide. L'invention concerne également des applications diagnostiques permettant d'identifier les patients souffrant d'un diabète de type 2 ou présentant des risques de développer un diabète de type 2 ainsi que la découverte d'agents thérapeutiques et de méthodes de traitement.
PCT/EP2005/012986 2004-12-13 2005-12-05 Polymorphisme a simple nucleotide (snp) WO2006063703A2 (fr)

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JP2007544791A JP2008522597A (ja) 2004-12-13 2005-12-05 Ｉｉ型糖尿病に関連する単一ヌクレオチド多型（ｓｎｐ）
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WO2008122670A2 (fr) * 2007-04-10 2008-10-16 Integragen Gène tnfrsf10b de susceptibilité au diabète chez l'homme
WO2008122673A2 (fr) * 2007-04-10 2008-10-16 Integragen Gène tnfrsf10a de susceptibilité au diabète chez l'homme
WO2008122671A1 (fr) * 2007-04-10 2008-10-16 Integragen Gène tnfrsf10c de susceptibilité au diabète chez l'homme
WO2008122672A1 (fr) * 2007-04-10 2008-10-16 Integragen Gène tnfrsf10d de susceptibilité au diabète chez l'homme
WO2008135508A2 (fr) * 2007-05-04 2008-11-13 Integragen Gène eefsec humain de prédisposition au diabète
CN103882127A (zh) * 2014-03-13 2014-06-25 河北联合大学 用于预测患2型糖尿病肾病发生风险的试剂盒

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Cited By (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2008087204A1 (fr) * 2007-01-19 2008-07-24 Integragen Gène btbd9 de susceptibilité au diabète humain
WO2008122670A2 (fr) * 2007-04-10 2008-10-16 Integragen Gène tnfrsf10b de susceptibilité au diabète chez l'homme
WO2008122673A2 (fr) * 2007-04-10 2008-10-16 Integragen Gène tnfrsf10a de susceptibilité au diabète chez l'homme
WO2008122671A1 (fr) * 2007-04-10 2008-10-16 Integragen Gène tnfrsf10c de susceptibilité au diabète chez l'homme
WO2008122672A1 (fr) * 2007-04-10 2008-10-16 Integragen Gène tnfrsf10d de susceptibilité au diabète chez l'homme
WO2008122670A3 (fr) * 2007-04-10 2008-12-11 Integragen Sa Gène tnfrsf10b de susceptibilité au diabète chez l'homme
WO2008122673A3 (fr) * 2007-04-10 2008-12-11 Integragen Sa Gène tnfrsf10a de susceptibilité au diabète chez l'homme
WO2008135508A2 (fr) * 2007-05-04 2008-11-13 Integragen Gène eefsec humain de prédisposition au diabète
WO2008135508A3 (fr) * 2007-05-04 2009-01-08 Integragen Sa Gène eefsec humain de prédisposition au diabète
CN103882127A (zh) * 2014-03-13 2014-06-25 河北联合大学 用于预测患2型糖尿病肾病发生风险的试剂盒

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