Molecular profiling of tumors

Abstract

Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.

What is claimed is: 
     
         1 . A system for generating a report identifying a therapeutic agent for an individual with ovarian cancer comprising:
 a. at least one device configured to assay a plurality of molecular targets in a biological sample from the individual to determine molecular profile test values for each member of the plurality of molecular targets, wherein the plurality of molecular targets comprises AR, BRCA2, c-KIT, EGFR, ER, HER2, PDGFRA, PR and TOP2A;   b. at least one computer database comprising:
 i. a reference value for each member of the plurality of molecular targets; and 
 ii. a listing of available therapeutic agents for the plurality of molecular targets; 
   c. a computer-readable program code comprising instructions to input the molecular profile test values and to compare each of the molecular profile test values with a corresponding reference value from the at least one computer database in (b)(i);   d. a computer-readable program code comprising instructions to access the at least one computer database and to identify at least one therapeutic agent from the listing of available therapeutic agents for the plurality of molecular targets wherein the comparison to the reference values in (c) indicates a likely benefit of the at least one therapeutic agent; and   e. a computer-readable program code comprising instructions to generate a report that comprises a listing of the molecular targets for which the comparison to the reference value indicated a likely benefit of the at least one therapeutic agent in (d) and the at least one therapeutic agent identified in (d).   
     
     
         2 . The system of  claim 1 , wherein the molecular profile test values are input into the system from a location that is remote from the at least one computer database. 
     
     
         3 . The system of  claim 1 , wherein the molecular profile test values are input into the system over an internet connection. 
     
     
         4 . The system of  claim 1 , wherein the report is in electronic or paper format. 
     
     
         5 . The system of  claim 1 , wherein the at least one computer database further comprises data corresponding to at least one clinical trial associated with at least one member of the plurality of molecular targets. 
     
     
         6 . The system of  claim 1 , wherein the reference value for each member of the plurality of molecular targets comprises a sequence, an expression level, or a copy number of a nucleic acid and/or a protein. 
     
     
         7 . The system of  claim 1 , wherein the molecular profile test values are determined after the individual has received a drug therapy for the ovarian cancer. 
     
     
         8 . The system of  claim 1 , wherein the molecular profile test values are determined by assessing a cell, a tissue sample, a blood sample or a combination thereof. 
     
     
         9 . The system of  claim 1 , wherein the molecular profile test values are determined by performing a test for a gene and/or a protein. 
     
     
         10 . The system of  claim 1 , wherein the plurality of molecular targets are assessed by nucleic acid sequencing. 
     
     
         11 . The system of  claim 1 , wherein each reference value is obtained from at least one individual without ovarian cancer. 
     
     
         12 . The system of  claim 1 , wherein the report further comprises a listing of at least one additional molecular target for which the comparison to the reference in (c) indicates a likely lack of benefit of at least one therapeutic agent and the at least one additional therapeutic agent. 
     
     
         13 . The system of  claim 1 , further comprising a computer-readable program code comprising instructions to prioritize the listing of the at least one therapeutic agent. 
     
     
         14 . The system of  claim 1 , wherein the plurality of molecular targets further comprises at least one of BRCA1 and RRM1. 
     
     
         15 . The system of  claim 1 , wherein the plurality of molecular targets further comprises at least one of BRAF, KRAS, MGMT, PGP, PIK3CA and ERCC1. 
     
     
         16 . The system of  claim 1 , wherein the comparison to the reference in (c) indicates at least one of a mutation, polymorphism, deletion, insertion, overexpression, underexpression, and gene amplification for each member of the plurality of molecular targets. 
     
     
         17 . The system of  claim 1 , wherein the at least one device configured to assay the plurality of molecular targets is configured to perform at least one of real-time PCR, nucleic acid sequencing, immunohistochemistry (IHC), an expression microarray analysis, a comparative genomic hybridization (CGH) microarray analysis, a single nucleotide polymorphism (SNP) microarray analysis, fluorescent in-situ hybridization (FISH), in-situ hybridization (ISH), and a proteomic array analysis. 
     
     
         18 . The system of  claim 1 , wherein the at least one device configured to assay the plurality of molecular targets is configured to perform at least one of polymerase chain reaction (PCR), pyrosequencing, NextGen sequencing, methylation specific PCR (MSPCR), restriction fragment length polymorphism (RFLP) analysis, and an immunoassay. 
     
     
         19 . The system of  claim 1 , wherein the at least one device configured to assay the plurality of molecular targets is configured to perform at least one of gene expression analysis, nucleic acid sequence analysis, nucleic acid methylation analysis, and proteomic analysis. 
     
     
         20 . The system of  claim 1 , wherein the at least one device configured to assay the plurality of molecular targets is configured to identify at least one of a mutation, polymorphism, deletion, insertion, substitution, translocation, fusion, break, duplication, amplification or repeat in a nucleic acid sequence corresponding to at least one member of the plurality of molecular targets.