Methods and compositions for correlating genetic markers with risk of aggressive prostate cancer

Abstract

The present invention provides a method of identifying a subject as having an increased risk of having or developing aggressive prostate cancer, comprising detecting in the subject the presence of various polymorphisms associated with an increased risk of having or developing aggressive prostate cancer.

That which is claimed is: 
     
         1 . A method of identifying a human subject as having an increased risk of developing aggressive prostate cancer, comprising detecting in a nucleic acid sample from the subject a T allele at single nucleotide polymorphism rs4054823 in chromosome region 17p12, wherein the detection of said allele identifies the subject as having an increased risk of developing aggressive prostate cancer. 
     
     
         2 . A method of identifying a human subject as having an increased risk of developing aggressive prostate cancer, comprising detecting in a nucleic acid sample from the subject an allele that is in linkage disequilibrium with the T allele at single nucleotide polymorphism rs4054823 in chromosome region 17p12, wherein the detection of said allele identifies the subject as having an increased risk of developing aggressive prostate cancer. 
     
     
         3 . The method of  claim 1 , wherein the subject is homozygous for the T allele at single nucleotide polymorphism rs4054823. 
     
     
         4 . The method of  claim 1 , wherein detecting is carried out by an amplification reaction. 
     
     
         5 . The method of  claim 1 , wherein detecting is carried out by an amplification reaction and single base extension. 
     
     
         6 . The method of  claim 5 , wherein the product of the amplification reaction and single base extension is spotted on a silicone chip. 
     
     
         7 . The method of  claim 1 , wherein detecting is carried out by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS). 
     
     
         8 . The method of  claim 4 , wherein the amplification reaction is a polymerase chain reaction. 
     
     
         9 . The method of  claim 1 , wherein detecting is carried out by sequencing, hybridization, restriction endonuclease digestion analysis, electrophoresis, or any combination thereof. 
     
     
         10 . A computer-assisted method of identifying a proposed treatment for aggressive prostate cancer as an effective and/or appropriate treatment for a subject carrying a genetic marker correlated with aggressive prostate cancer, comprising the steps of:
 (a) storing a database of biological data for a plurality of subjects, the biological data that is being stored including for each of said plurality of subjects:
 (i) a treatment type, 
 (ii) at least one genetic marker associated with aggressive prostate cancer, and 
 (iii) at least one disease progression measure for prostate cancer from which treatment efficacy can be determined; and then 
   (b) querying the database to determine the dependence on said genetic marker of the effectiveness of a treatment type in treating prostate cancer, thereby identifying a proposed treatment as an effective and/or appropriate treatment for a subject carrying a genetic marker correlated with prostate cancer.   
     
     
         11 . The method of  claim 10 , wherein the genetic marker associated with aggressive prostate cancer is a T allele in single nucleotide polymorphism rs4054823 in chromosome region 17p12. 
     
     
         12 . The method of  claim 1 , wherein the subject has an elevated prostate serum antigen level. 
     
     
         13 . The method of  claim 1 , wherein the subject has a family history of prostate cancer. 
     
     
         14 . A kit comprising oligonucleotides to detect the T allele of single nucleotide polymorphism rs4054823 in chromosome region 17p12 and/or a risk allele of a single nucleotide polymorphism in linkage disequilibrium with single nucleotide polymorphism rs4054823 in chromosome region 17p12 in a nucleic acid sample.