Genetic polymorphisms associated with venous thrombosis, methods of detection and uses thereof

Abstract

The present invention is based on the discovery of genetic polymorphisms that are associated with venous thrombosis. 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.

1 . A method of determining whether a human has an altered risk for venous thrombosis (VT), 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:602-1587 or its complement, wherein the polymorphism indicates an altered risk for VT. 
     
     
         2 . The method of  claim 1 , wherein the VT is deep vein thrombosis (DVT). 
     
     
         3 . The method of  claim 1 , wherein said polymorphism is selected from the group consisting of the polymorphisms provided in at least one of Tables 5-9 and 11-30. 
     
     
         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 VT. 
     
     
         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 , wherein the VT is recurrent VT. 
     
     
         20 . The method of  claim 19 , wherein the polymorphism is selected from the group consisting of the polymorphisms provided in Table 24. 
     
     
         21 . The method of  claim 1 , wherein the VT includes pulmonary embolism (PE). 
     
     
         22 . The method of  claim 21 , wherein the polymorphism is selected from the group consisting of the polymorphisms provided in Table 25. 
     
     
         23 . The method of  claim 1 , wherein the human has cancer. 
     
     
         24 . The method of  claim 23 , wherein the polymorphism is selected from the group consisting of the polymorphisms provided in Table 26. 
     
     
         25 . A method for reducing risk of venous thrombosis (VT) 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 VT due to 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:602-1587 or its complement. 
     
     
         26 . The method of  claim 25 , wherein the method comprises testing nucleic acid from said human for the presence or absence of said polymorphism. 
     
     
         27 . The method of  claim 25 , wherein the therapeutic agent comprises an anticoagulant agent. 
     
     
         28 . The method of  claim 27 , wherein the anticoagulant agent is selected from the group consisting of coumarines (vitamin K antagonists) such as warfarin (coumadin), acenocoumarol, phenprocoumon, and phenindione; heparin and derivative substances such as low molecular weight heparin; factor Xa inhibitors such as Fondaparinux, Idraparinux, and other synthetic pentasaccharide inhibitors of factor Xa; and thrombin inhibitors such as argatroban, lepirudin, bivalirudin, and dabigatran. 
     
     
         29 . The method of  claim 25 , wherein the therapeutic agent comprises an antiplatelet agent. 
     
     
         30 . The method of  claim 29 , wherein the antiplatelet agent is selected from the group consisting of cyclooxygenase inhibitors such as aspirin, and ADP receptor inhibitors such as clopidogrel (Plavix) and prasugrel (Effient). 
     
     
         31 . A method of identifying a human having an increased risk for venous thrombosis (VT), 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:602-1587 or its complement, and wherein the first polymorphism identifies said human as having an increased risk for VT. 
     
     
         32 . The method of  claim 31 , wherein the linkage disequilibrium is r 2 =1. 
     
     
         33 . The method of  claim 31 , wherein the first polymorphism is selected from the group consisting of the polymorphisms set forth in Table 4. 
     
     
         34 . The method of  claim 31 , further comprising correlating the presence or absence of said first polymorphism with an increased risk for VT. 
     
     
         35 . The method of  claim 34 , wherein said correlating step is performed by computer software. 
     
     
         36 . The method of  claim 1 , further comprising at least one of:
 a) selecting said human for inclusion in a clinical trial of a therapeutic agent; and   b) assigning said human to a group within a clinical trial.   
     
     
         37 . The method of  claim 36 , wherein the therapeutic agent is an anticoagulant agent or an antiplatelet agent. 
     
     
         38 . A kit for determining whether a human has an altered risk for venous thrombosis (VT), 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:602-1587 or its complement. 
     
     
         39 . The kit of  claim 38 , 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.