Genetic polymorphisms associated with stroke, methods of detection and uses thereof

Abstract

The present invention provides compositions and methods based on genetic polymorphisms that are associated with vascular diseases such as stroke. In particular, the present invention relates to genetic polymorphisms that have utility for such uses as predicting disease risk or predicting an individual's response to a treatment such as statins, including groups of polymorphisms that may be used as a signature marker set for such uses, as well as 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.

What is claimed is: 
     
         1 . A method of determining whether a human has an altered risk for stroke, comprising testing nucleic acid from said human for the presence or absence of a polymorphism selected from the group consisting of the polymorphisms represented by position 101 of any one of the nucleotide sequences of SEQ ID NOS:436-1566 or its complement, wherein the polymorphism indicates an altered risk for stroke. 
     
     
         2 . The method of  claim 1 , wherein said polymorphism is selected from the group consisting of the polymorphisms set forth in at least one of Tables 6-9, 11-14, 16-22, 24, 26, 28-30, and 33-38. 
     
     
         3 . The method of  claim 2 , wherein the polymorphism is selected from the group consisting of the MYH15 polymorphism rs3900940 (hCV7425232), the CALM1 polymorphism rs3814843 (hCV11476411), the chromosome 4q25 polymorphism rs2200733 (hCV16158671), and the chromosome 9p21 polymorphism rs10757274 (hCV26505812). 
     
     
         4 . The method of  claim 1 , wherein the altered risk is an increased risk. 
     
     
         5 . The method of  claim 1 , wherein the altered risk is a decreased risk. 
     
     
         6 . The method of  claim 1 , wherein said nucleic acid is a nucleic acid extract from a biological sample from said human. 
     
     
         7 . The method of  claim 6 , wherein said biological sample is blood, saliva, or buccal cells. 
     
     
         8 . The method of  claim 6 , further comprising preparing said nucleic acid extract from said biological sample prior to said testing step. 
     
     
         9 . The method of  claim 8 , further comprising obtaining said biological sample from said human prior to said preparing step. 
     
     
         10 . The method of  claim 1 , wherein said testing step comprises nucleic acid amplification. 
     
     
         11 . The method of  claim 10 , wherein said nucleic acid amplification is carried out by polymerase chain reaction. 
     
     
         12 . The method of  claim 1 , further comprising correlating the presence or absence of the polymorphism with an altered risk for stroke. 
     
     
         13 . The method of  claim 12 , wherein said correlating step is performed by computer software. 
     
     
         14 . The method of  claim 1 , wherein said testing is performed using sequencing, 5′ nuclease digestion, molecular beacon assay, oligonucleotide ligation assay, size analysis, single-stranded conformation polymorphism analysis, or denaturing gradient gel electrophoresis (DGGE). 
     
     
         15 . The method of any one of  claim 1 , wherein said testing is performed using an allele-specific method. 
     
     
         16 . The method of  claim 15 , wherein said allele-specific method is allele-specific probe hybridization, allele-specific primer extension, or allele-specific amplification. 
     
     
         17 . The method of  claim 16 , wherein the method is performed using an allele-specific primer provided in Table 3. 
     
     
         18 . The method of  claim 1  which is an automated method. 
     
     
         19 . The method of  claim 1 , further comprising correlating the presence of the polymorphism with a reduction of risk for stroke by an HMG-CoA reductase inhibitor. 
     
     
         20 . The method of  claim 19 , wherein said correlating step is performed by computer software. 
     
     
         21 . The method of  claim 19 , wherein said HMG-CoA reductase inhibitor is a hydrophilic statin. 
     
     
         22 . The method of  claim 19 , wherein said HMG-CoA reductase inhibitor is a hydrophobic statin. 
     
     
         23 . The method of  claim 19 , wherein said HMG-CoA reductase inhibitor is selected from the group consisting of pravastatin, atorvastatin, simvastatin, cerevastatin, lovastatin, storvastatin, rosuvastatin, and fluvastatin, or a combination thereof. 
     
     
         24 . The method of  claim 19 , wherein the polymorphism is selected from the group consisting of the polymorphisms provided in Tables 23, 25, 27, 31-32, and 37-38. 
     
     
         25 . The method of  claim 24 , wherein the polymorphism is the chromosome 9p21 polymorphism rs10757274 (hCV26505812). 
     
     
         26 . A method for reducing risk of stroke in a human, comprising administering to said human an effective amount of a therapeutic agent, said human having been identified as having an increased risk for stroke due to the presence or absence of a polymorphisms selected from the group consisting of the polymorphisms represented by position 101 of any one of the nucleotide sequences of SEQ ID NOS:436-1566 or its complement. 
     
     
         27 . The method of  claim 26 , wherein the method comprises testing nucleic acid from said human for the presence or absence of said polymorphism. 
     
     
         28 . The method of  claim 26 , wherein said therapeutic agent comprises an HMG-CoA reductase inhibitor. 
     
     
         29 . The method of  claim 28 , wherein said HMG-CoA reductase inhibitor is a hydrophilic statin. 
     
     
         30 . The method of  claim 28 , wherein said HMG-CoA reductase inhibitor is a hydrophobic statin. 
     
     
         31 . The method of  claim 28 , wherein said HMG-CoA reductase inhibitor is selected from the group consisting of pravastatin, atorvastatin, simvastatin, cerevastatin, lovastatin, storvastatin, rosuvastatin, and fluvastatin, or a combination thereof. 
     
     
         32 . The method of  claim 28 , wherein the polymorphism is selected from the group consisting of the polymorphisms provided in Tables 23, 25, 27, 31-32, and 37-38. 
     
     
         33 . The method of  claim 32 , wherein the polymorphism is the chromosome 9p21 polymorphism rs10757274 (hCV26505812). 
     
     
         34 . A method of identifying a human having an increased risk for stroke, comprising testing a nucleic acid sample from said human for the presence or absence of a first polymorphism which is in linkage disequilibrium with a second polymorphism, wherein the second polymorphism is a polymorphism selected from the group consisting of the polymorphisms represented by position 101 of any one of the nucleotide sequences of SEQ ID NOS:436-1566 or its complement, and wherein the first polymorphism identifies said human as having an increased risk for stroke. 
     
     
         35 . The method of  claim 34 , wherein the linkage disequilibrium is r 2 =1. 
     
     
         36 . The method of  claim 34 , wherein the first polymorphism is selected from the group consisting of the polymorphisms set forth in Table 4. 
     
     
         37 . The method of  claim 34 , further comprising correlating the presence or absence of said first polymorphism with an increased risk for stroke. 
     
     
         38 . The method of  claim 37 , wherein said correlating step is performed by computer software. 
     
     
         39 . The method of  claim 1 , further comprising selecting said human for inclusion in a clinical trial of a therapeutic agent. 
     
     
         40 . A kit for determining whether a human has an altered risk for stroke, wherein the kit comprises at least one container and at least one polynucleotide detection reagent stored in said container, wherein the polynucleotide detection reagent is capable of detecting the presence or absence of a polymorphism selected from the group consisting of the polymorphisms represented by position 101 of any one of the nucleotide sequences of SEQ ID NOS:436-1566 or its complement. 
     
     
         41 . The kit of  claim 40 , wherein the polynucleotide detection reagent selectively hybridizes to said nucleic acid in the presence of said polymorphism and does not hybridize to said nucleic acid in the absence of said polymorphism.