Cancer biomarkers

Abstract

Biomarkers and methods using the biomarkers for the prediction of the recurrence risk of cancer in a patient are provided.

1 - 18 . (canceled) 
     
     
         19 . A method of detecting an increased or decreased likelihood of prostate cancer progression, comprising:
 a) assaying a prostate cancer ribonucleic acid sample by quantitative polymerase chain reaction to determine the normalized, combined expression of an assay gene panel;   b) combining the normalized, combined expression of the assay gene panel with one or more first clinical parameters to detect either an increased or decreased likelihood of prostate cancer progression,   
       wherein the assay gene panel comprises between 4 and 31 of the genes in Panel F, and the one or more first clinical parameters comprise at least one of: age at diagnosis, clinical stage, Gleason score and PSA. 
     
     
         20 . The method of  claim 19 , wherein assaying the prostate cancer ribonucleic acid sample by quantitative polymerase chain reaction to determine the normalized,
 combined expression of the assay gene panel comprises determining the mean of the expression values of each gene in the assay gene panel.   
     
     
         21 . The method of  claim 19 , wherein assaying the prostate cancer ribonucleic acid sample by quantitative polymerase chain reaction to determine the normalized, combined expression of the assay gene panel comprises normalizing the expression of the genes in the assay gene panel using the expression of a housekeeper gene panel. 
     
     
         22 . The method of  claim 21 , wherein the housekeeper gene panel comprises between 1 and 15 genes from Table 12. 
     
     
         23 . The method of  claim 19 , wherein assaying the prostate cancer ribonucleic acid sample by quantitative polymerase chain reaction to determine the normalized, combined expression of the assay gene panel comprises:
 a) determining the mean of the expression values of each gene in the assay gene panel;   b) determining the mean of the expression values of each gene in a housekeeper gene panel; and   c) normalizing the mean of the expression values of each gene in the assay gene panel using the mean of the expression values of each gene in a housekeeper gene panel,   
       wherein the housekeeper gene panel comprises between 1 and 15 genes from Table 12. 
     
     
         24 . The method of  claim 19 , wherein combining the normalized, combined expression of the assay gene panel with one or more first clinical parameters to detect either an increased or decreased likelihood of prostate cancer progression comprises detecting a higher likelihood of cancer progression than would be expected based on one or more second clinical parameters. 
     
     
         25 . The method of  claim 24 , wherein the one or more second clinical parameters comprise at least one of: age at diagnosis, clinical stage, Gleason score and PSA. 
     
     
         26 . The method of  claim 19 , wherein combining the normalized, combined expression of the assay gene panel with one or more first clinical parameters to detect either an increased or decreased likelihood of prostate cancer progression comprises detecting a lower likelihood of cancer progression than would be expected based on one or more second clinical parameters. 
     
     
         27 . The method of  claim 26 , wherein the one or more second clinical parameters comprise at least one of: age at diagnosis, clinical stage, Gleason score and PSA. 
     
     
         28 . The method of  claim 19 , wherein the assay gene panel comprises at least 50% cell cycle genes. 
     
     
         29 . The method of  claim 19 , wherein the assay gene panel comprises at least 75% cell cycle genes. 
     
     
         30 . The method of  claim 19 , wherein the assay gene panel comprises at least 85% cell cycle genes. 
     
     
         31 . The method of  claim 19 , wherein the assay gene panel comprises at least 95% cell cycle genes. 
     
     
         32 . A method of detecting an increased or decreased likelihood of prostate cancer progression, comprising:
 a) assaying a prostate cancer ribonucleic acid sample by quantitative polymerase chain reaction to determine: i) the mean of the expression values of each gene in an assay gene panel, and ii) the mean of the expression values of each gene in a housekeeper gene panel;   b) normalizing the mean of the expression values of each gene in the assay gene panel using the mean of the expression values of each gene in a housekeeper gene panel to produce a score;   c) combining the score with one or more first clinical parameters to detect either an increased or decreased likelihood of prostate cancer progression relative to the likelihood of cancer progression that would be expected based on one or more second clinical parameters,   wherein the assay gene panel comprises between 4 and 31 of the genes in Panel F, the housekeeper gene panel comprises between 1 and 15 genes from Table 12, the one or more first clinical parameters comprise at least one of: age at diagnosis, clinical stage, Gleason score and PSA, and the one or more second clinical parameters comprise at least one of: age at diagnosis, clinical stage, Gleason score and PSA.