Genetic polymorphisms associated with cardiovascular disorders and drug response, methods of detection and uses thereof

• US 20070072821A1
• Filed: 09/22/2006
• Published: 03/29/2007
• Est. Priority Date: 09/23/2005
• Status: Active Grant

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Devlin, James, Iakoubova, Olga
• Granted Patent: US 7,799,530 B2
• Time in Patent Office: Days
• US Class Current: 514/44.R
• CPC Class Codes: A61K 31/70 Carbohydrates; Sugars; Derivatives thereof sorbitol A61K31/047
• CPC Class Codes: A61P 9/00 Drugs for disorders of the cardiovascular system
• CPC Class Codes: A61P 9/10 for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: C12Q 2600/172 Haplotypes

Abstract

The present invention is based on the discovery of genetic polymorphisms that are associated with cardiovascular disorders, particularly acute coronary events such as myocardial infarction and stroke, and genetic polymorphisms that are associated with responsiveness of an individual having a cardiovascular disorder to treatment of the disorder with statin. In particular, the present invention relates to nucleic acid molecules containing the polymorphisms, variant proteins encoded by such nucleic acid molecules, reagents for detecting the polymorphic nucleic acid molecules and proteins, and methods of using the nucleic acid and proteins as well as methods of using reagents for their detection.

Claims

1. A method of identifying an individual having an altered risk for developing an acute coronary event or a method of evaluating an individual'"'"'s likelihood of responding to statin treatment, comprising detecting the presence or absence of one or more alleles of a SNP in said individual'"'"'s nucleic acids, wherein the SNP is selected from any one of the nucleotide sequences of SEQ ID NOS:

121-200 and SEQ ID NOS;

251-410, and the presence or absence of the alleles are correlated with an individual'"'"'s risk for developing an acute coronary event or likelihood of responding to statin treatment.

2. The method of claim 1, wherein the SNP is selected from the group of nucleotide sequences consisting of SEQ ID NOs of 356, 282, 358, 270, 256, 252, 354, 357, 306, 363, 361, 295, 285, 290, 251, 293, 294, 305, 266, 409, 410, 284, 406, 276, 263, 271, 264, 353, 261, 399, and 265.

3. The method of claim 1, comprising contacting the nucleic acids of the individual with a detection reagent, and determining which nucleotide is present or absent at a specified SNP position.

4. The method of claim 3, in which the nucleic acids are prepared from blood cells of the individual.

5. The method of claim 3, in which the detection reagent is a polynucleotide probe.

6. The method of claim 5, in which the 3′

end of the probe hybridizes to the SNP in the nucleic acid.

7. The method of claim 5, in which the probe is labeled with a reporter dye.

8. A method of detecting a single nucleotide polymorphism (SNP) in a nucleic acid molecule, comprising contacting a test sample with a reagent which specifically hybridizes to a SNP in any one of the nucleotide sequences of SEQ ID NOS:

1-60 and 121-410 under stringent hybridization conditions, and detecting the formation of a hybridized duplex.

9. The method of claim 8 in which detection is carried out by a process selected from the group consisting of:

allele-specific probe hybridization, allele-specific primer extension, allele-specific amplification, sequencing, 5′

nuclease digestion, molecular beacon assay, oligonucleotide ligation assay, size analysis, and single-stranded conformation polymorphism.

10. A method of identifying an individual having an altered risk for developing an acute coronary event or a method of evaluating an individual'"'"'s likelihood of responding to statin treatment, comprising detecting the presence or absence of a polymorphism in said individual'"'"'s nucleic acids, wherein said polymorphism is in linkage disequilibrium with a SNP in any one of the nucleotide sequences of SEQ ID NOS:

121-200 and SEQ ID NOS;

251-410, and the presence or absence of the polymorphism is correlated with an individual'"'"'s risk for developing an acute coronary event or likelihood of responding to statin treatment.

11. The method of claim 10, wherein the SNP is selected from the group of nucleotide sequences consisting of SEQ ID NOs of 356, 282, 358, 270, 256, 252, 354, 357, 306, 363, 361, 295, 285, 290, 251, 293, 294, 305, 266, 409, 410, 284, 406, 276, 263, 271, 264, 353, 261, 399, and 265.

12. A method of treating a cardiovascular disorder in an individual, comprising administering to said individual an effective amount of statin based on said individual'"'"'s likelihood of responding to statin treatment, as predicted by the presence or absence of a SNP selected from the group consisting of SNPs disclosed in Tables 1-2.

13. A reagent for detecting a variant protein encoded by a SNP-containing nucleic acid molecule, said reagent selectively binds to the variant protein as compared to a protein encoded by another nucleic acid molecule, wherein the SNP-containing nucleic acid molecule contains a SNP in any one of the nucleotide sequences of SEQ ID NOS:

121-200 and SEQ ID NOS;

251-410.

14. The reagent of claim 13, wherein said reagent is an antibody, an antibody fragment, an aptamer, a peptide, a ligand, or a small molecule compound.

15. The reagent of claim 14, wherein said reagent is labeled with a reporter dye or an imaging agent.

16. A kit comprising the reagent of claim 13 and a buffer.

17. An amplified polynucleotide containing a single nucleotide polymorphism (SNP) selected from any one of the nucleotide sequences of SEQ ID NOS:

1-60 and 121-410, or a complement thereof, wherein the amplified polynucleotide is between about 16 and about 1,000 nucleotides in length.

18. The amplified polynucleotide of claim 17 in which the nucleotide sequence comprises any one of the nucleotide sequences of SEQ ID NOS:

1-60 and 121-410.

19. An isolated polynucleotide which specifically hybridizes to a nucleic acid molecule containing a single nucleotide polymorphism (SNP) in any one of the nucleotide sequences in SEQ ID NOS:

1-60 and 121-410.

20. The polynucleotide of claim 19 which is 8-70 nucleotides in length.

21. The polynucleotide of claim 19 which is an allele-specific probe.

22. The polynucleotide of claim 19 which is an allele-specific primer.

23. A kit for detecting a single nucleotide polymorphism (SNP) in a nucleic acid, comprising the polynucleotide of claim 19, a buffer, and an enzyme.

24. An isolated polypeptide comprising of an amino acid sequence selected from the group of amino acid sequences consisting of SEQ ID NOS:

61-120.

25. The isolated polypeptide of claim 24 wherein the polypeptide has the amino acid sequence selected from the group of amino acid sequences consisting of SEQ ID NOS:

61-120.

26. An antibody that selectively binds to a polypeptide of claim 24.

27. A method for identifying an agent useful in therapeutically or prophylactically treating myocardial infarction, comprising contacting the polypeptide of claim 24 with a candidate agent under conditions suitable to allow formation of a binding complex between the polypeptide and the candidate agent, and detecting the formation of the binding complex, wherein the presence of the complex identifies said agent.