Cancer biomarkers

Abstract

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

What is claimed is: 
     
         1 . A method of classifying cancer comprising determining in a cancer sample from a patient the status of a panel of genes comprising at least two cell-cycle genes, wherein an abnormal cell-cycle gene status indicates a poor prognosis. 
     
     
         2 . An in vitro diagnostic method comprising determining the status of a panel of genes comprising at least two cell-cycle genes in a sample obtained from a patient. 
     
     
         3 . The method of  claim 2 , further comprising determining at least one clinical parameter for the cancer patient. 
     
     
         4 . The method of  claim 2 , wherein said cell-cycle genes are chosen from the genes listed in Table 1 or in any of Panels A through G. 
     
     
         5 . The method of  claim 3 , wherein a recurrence-associated clinical parameter or an abnormal cell-cycle gene status indicates a poor prognosis. 
     
     
         6 . The method of  claim 1  further comprising determining the status of PTEN in a sample obtained from the patient, wherein either of abnormal cell-cycle gene status or abnormal PTEN status indicates a poor prognosis. 
     
     
         7 . The method of  claim 1 , wherein said cancer is prostate cancer. 
     
     
         8 . The method of  claim 1 , wherein said cancer is bladder cancer. 
     
     
         9 . The method of  claim 1 , wherein said cancer is brain cancer. 
     
     
         10 . The method of  claim 1 , wherein said cancer is lung cancer. 
     
     
         11 . The method of  claim 1 , wherein said panel comprises at least 15 cell-cycle genes. 
     
     
         12 . The method of  claim 11 , wherein said panel comprises at least 15 genes chosen from the group consisting of the genes in Table 1 or in any of Panels A through G. 
     
     
         13 . The method of  claim 11 , wherein said 15 genes comprise at least 75% of the genes in the panel. 
     
     
         14 . The method of  claim 11 , wherein said panel comprises the genes in Panel F. 
     
     
         15 . A method of treating a prostate cancer patient comprising determining at least one clinical parameter for said patient, determining the status of a plurality of cell-cycle genes in a sample obtained from the patient, and (a) recommending, prescribing or initiating active treatment if said patient has at least one risk-associated clinical parameter and an elevated status for said plurality of cell-cycle genes, or (b) recommending, prescribing or initiating watchful waiting if said patient has neither a risk-associated clinical parameter nor an elevated status for said plurality of cell-cycle genes. 
     
     
         16 . A computer-implemented method of determining whether a patient has an increased likelihood of cancer recurrence comprising:
 (a) accessing information on a patient's PTEN status or clinical parameters and CCG status stored in a computer-readable medium;   (b) querying this information to determine at least one of whether the patient has a low/negative PTEN status or whether the patient has a recurrence-associated clinical parameter;   (c) querying this information to determine whether a sample obtained from the patient shows increased expression of at least one CCG; and   (d) outputting an indication that the patient has an increased likelihood of recurrence if the patient has a low/negative PTEN status or a recurrence-associated clinical parameter and the sample shows increased expression of at least one CCG.   
     
     
         17 . A kit comprising a plurality of oligonucleotides for determining the expression level of a panel of genes, where said panel comprises at least 75% cell-cycle genes. 
     
     
         18 . A system for determining whether a patient has an increased likelihood of recurrence, comprising:
 a sample analysis device for determining, in a prostate cancer sample, the expression of a panel of genes having at least two cell-cycle genes chosen from the group consisting of the genes in Table 1, and Panels A through G; and   a computer processor programmed to execute the method of  claim 16 .