Genetic polymorphisms associated with liver fibrosis, methods of detection and uses thereof

Abstract

The present invention is based on the discovery of genetic polymorphisms that are associated with liver fibrosis and related pathologies. In particular, the present invention relates to nucleic acid molecules containing the polymorphisms, including groups of nucleic acid molecules that may be used as a signature marker set, 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 developing liver fibrosis, 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:91-358 or its complement, wherein the polymorphism indicates an altered risk for developing liver fibrosis. 
     
     
         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 7-11 and 13-20. 
     
     
         3 . The method of  claim 2 , wherein said polymorphism comprises a haplotype selected from the group consisting of the haplotypes set forth in at least one of Tables 8-10, 16, and 18. 
     
     
         4 . The method of  claim 1 , wherein said polymorphism comprises a polymorphism selected from the group consisting of hCV11722141 (rs1927911), hCV11722237 (rs4986791/T399I), hCV11722238 (rs4986790/D299G), hCV29292005 (rs7864330), hCV29816566 (rs10448253), hCV31783925(rs12375686), hCV31783982 (rs10818069), hCV31783985 (rs10818070), hCV31784008 (rs10759933), hCV8788444 (rs1252039), hDV71564063 (rs11536889), hCV26954831 (rs5030728), and hCV29292008 (rs7873784). 
     
     
         5 . The method of  claim 4 , wherein said polymorphism comprises a haplotype selected from the group consisting of:
 (a) haplotypes comprising polymorphisms hCV11722237 (rs4986791/T399I), hCV11722238 (rs4986790/D299G), and hDV71564063 (rs11536889); and   (b) the haplotypes of (a), further comprising polymorphisms hCV26954831 (rs5030728) and hCV29292008 (rs7873784).   
     
     
         6 . The method of  claim 1 , wherein the altered risk is an increased risk. 
     
     
         7 . The method of  claim 1 , wherein the altered risk is a decreased risk. 
     
     
         8 . The method of  claim 1 , wherein said nucleic acid is a nucleic acid extract from a biological sample from said human. 
     
     
         9 . The method of  claim 8 , wherein said biological sample is blood, saliva, or buccal cells. 
     
     
         10 . The method of  claim 8 , further comprising preparing said nucleic acid extract from said biological sample prior to said testing step. 
     
     
         11 . The method of  claim 8 , further comprising obtaining said biological sample from said human prior to said preparing step. 
     
     
         12 . The method of  claim 1 , wherein said testing step comprises nucleic acid amplification. 
     
     
         13 . The method of  claim 12 , wherein said nucleic acid amplification is carried out by polymerase chain reaction. 
     
     
         14 . The method of  claim 1 , further comprising correlating the presence or absence of the polymorphism with an altered risk for developing liver fibrosis. 
     
     
         15 . The method of  claim 14 , wherein said correlating step is performed by computer software. 
     
     
         16 . 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). 
     
     
         17 . The method of any one of  claim 1 , wherein said testing is performed using an allele-specific method. 
     
     
         18 . The method of  claim 17 , wherein said allele-specific method is allele-specific probe hybridization, allele-specific primer extension, or allele-specific amplification. 
     
     
         19 . The method of  claim 17 , wherein the method is performed using an allele-specific primer set forth in Table 3. 
     
     
         20 . The method of  claim 1  which is an automated method. 
     
     
         21 . A method of determining whether a human has an increased risk for progressing rapidly from minimal fibrosis to bridging fibrosis/cirrhosis, 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:91-358 or its complement, wherein the polymorphism indicates an altered risk for progressing rapidly from minimal fibrosis to bridging fibrosis/cirrhosis. 
     
     
         22 . The method of  claim 21 , further comprising correlating the presence or absence of the polymorphism with an increased risk for progressing rapidly from minimal fibrosis to bridging fibrosis/cirrhosis. 
     
     
         23 . The method of  claim 22 , wherein said correlating step is performed by computer software. 
     
     
         24 . A method of identifying a human having an increased risk for developing liver fibrosis, 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:91-358 or its complement, and wherein the first polymorphism identifies said human as having an increased risk for developing liver fibrosis. 
     
     
         25 . The method of  claim 24 , wherein the linkage disequilibrium is r 2 =1. 
     
     
         26 . The method of  claim 24 , wherein the first polymorphism is selected from the group consisting of the polymorphisms set forth in Table 4. 
     
     
         27 . The method of  claim 24 , further comprising correlating the presence or absence of said first polymorphism with an increased risk for developing liver fibrosis. 
     
     
         28 . The method of  claim 27 , wherein said correlating step is performed by computer software. 
     
     
         29 . A method for reducing risk of developing liver fibrosis 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 developing liver fibrosis 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:91-358. 
     
     
         30 . The method of  claim 29 , wherein the method comprises testing nucleic acid from said human for the presence or absence of said polymorphism. 
     
     
         31 . The method of  claim 1 , further comprising selecting said human for inclusion in a clinical trial of a therapeutic agent. 
     
     
         32 . A kit for carrying out the method of  claim 1 , wherein the kit comprises an enzyme, a buffer, and at least one polynucleotide detection reagent, and 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.