Prognostic method

Abstract

A method for prognosing recurrence of prostate cancer (PCa) in a subject following prostatectomy using the outcomes of selected single nucleotide polymorphisms (SNPs) and clinical variables. A method for genotyping PCa associated genetic variations comprising use of a DNA microarray. A microarray for use in the described methods.

1 - 15 . (canceled) 
     
     
         16 . A method of prognosing PCa recurrence in a subject comprising determining the genotype of the subject at one or more positions of single nucleotide polymorphism selected from SNPs 9, 24, 25, 28, 34, 46, 47, 51, 58 and 80 in Table 1B. 
     
     
         17 - 108 . (canceled) 
     
     
         109 . The method of  claim 16 , wherein said method comprises determining the genotype of the subject at least the SNP 58 (rs1800247) or an SNP having R 2 >0.8 with said SNP 58 (rs1800247). 
     
     
         110 . The method of  claim 109 , wherein said method comprises determining the genotype of the subject at least the SNP 58 (rs1800247). 
     
     
         111 . The method of  claim 16 , wherein the presence said SNP 58 (rs1800247) is indicative of a likelihood of prostate cancer recurrence after prostatectomy in said subject. 
     
     
         112 . The method of  claim 16 , wherein the method further comprises obtaining or determining one or more clinical variables listed in Table 18. 
     
     
         113 . The method of  claim 16 , wherein said prognosing prostate cancer recurrence comprises determining the likelihood of prostate cancer recurrence within 5 years of said subject having had prostatectomy surgery. 
     
     
         114 . The method of  claim 16 , wherein determining the genotype of the subject comprises genotyping a sample which has been obtained from the subject, which sample has been obtained from blood, saliva, liver, kidney, pancreas, heart, urine or from cells from the buccal cavity. 
     
     
         115 . The method of  claim 114 , wherein said blood comprises serum, lymphocytes, Iymphoblastoid cells, fibroblasts, platelets, mononuclear cells or other blood cells. 
     
     
         116 . A method for identifying a human subject having an increased risk of prostate cancer recurrence, comprising:
 detecting in a DNA sample obtained from the subject the presence of at least one T allele of the rs1800247 single nucleotide polymorphism by amplifying a portion of the DNA sample with nucleic acid primers comprising SEQ ID NO: 417 and SEQ ID NO: 506; and   correlating the presence of the T allele of the rs1800247 single nucleotide polymorphism with an increased risk of prostate cancer recurrence in the subject.   
     
     
         117 . The method of  claim 116 , wherein said method comprises detecting two T alleles of the subject at the rs1800247 single nucleotide polymorphism. 
     
     
         118 . The method of  claim 116 , wherein the method further comprises obtaining or determining one or more clinical variables selected from the group consisting of prostate specific antigen level, onset age, clinical stage, prostatectomy Gleason grade, surgical oncologic margins, and surgical gland margins. 
     
     
         119 . The method of  claim 116 , wherein the increased risk of prostate cancer recurrence comprises increased risk of prostate cancer recurrence within 5 years of said subject having had prostatectomy surgery. 
     
     
         120 . The method of  claim 116 , wherein the DNA sample from the subject has been obtained from blood, saliva, liver, kidney, pancreas, heart, urine or from cells from the buccal cavity of the subject. 
     
     
         121 . The method of  claim 120 , wherein said blood comprises serum, lymphocytes, lymphoblastoid cells, fibroblasts, platelets, mononuclear cells or other blood cells. 
     
     
         122 . A method of treating a human post-operative prostate cancer subject, comprising:
 (a) (i) detecting in a DNA sample obtained from the subject the presence of at least one T allele of the rs1800247 single nucleotide polymorphism, wherein said detecting comprises sequencing the DNA sample or contacting the DNA sample with a probe that binds specifically to the T allele and not the C allele of the rs1800247 single nucleotide polymorphism; and
 (ii) correlating the presence of the T allele of the rs1800247 single nucleotide polymorphism with an increased risk of prostate cancer recurrence in the subject; and 
   (b) administering adjuvant therapy to the subject with increased risk of prostate cancer recurrence, wherein said adjuvant therapy comprises radiation, chemotherapy and/or androgen-deprivation therapy.   
     
     
         123 . A method of treating a human pre-operative prostate cancer subject, comprising:
 (a) (i) detecting in a DNA sample obtained from the subject the presence of at least one T allele of the rs1800247 single nucleotide polymorphism, wherein said detecting comprises sequencing the DNA sample or contacting the DNA sample with a probe that binds specifically to the T allele and not the C allele of the rs1800247 single nucleotide polymorphism; and
 (ii) correlating the presence of the T allele of the rs1800247 single nucleotide polymorphism with an increased risk of prostate cancer recurrence in the subject; and 
   (b) administering therapy without surgery to the subject with increased risk of prostate cancer recurrence, wherein said therapy without surgery comprises radiation, chemotherapy and/or androgen-deprivation therapy.