Gene and gene expressed protein targets depicting biomarker patterns and signature sets by tumor type

Abstract

Provided herein are methods and systems for identifying a therapeutic for an individual, such as a therapeutic not previously identified for treating the individual. The therapeutic can be identified by molecular profiling, such as determining the biomarker patterns or signature sets of a biological sample of an individual.

What is claimed is: 
     
         1 . A system for generating a report identifying a therapeutic agent for an individual with a cancer comprising:
 a. one or more computer database comprising:
 i. a reference value for a plurality of molecular targets; 
 ii. a listing of available therapeutic agents for said plurality of molecular targets; 
   b. a computer-readable program code for inputting individualized molecular profile test values obtained for molecular targets comprising EGFR, VHL, TOPO1, MLH1, PTEN, PDGFRA, TP53, MGMT, RRM1, cKIT, SPARC and TOP2A in a biological sample from the individual and comparing said test values with a corresponding reference value in (a)(i);   c. a computer-readable program code for accessing the database in (a) and identifying one or more therapeutic agent in (a)(ii) for the molecular targets wherein said comparison to said reference in (b) indicates a likely benefit of the one or more therapeutic agent; and   d. a computer-readable program for generating a report that comprises a listing of the molecular targets wherein said comparison to said reference indicated a likely benefit of the one or more therapeutic agent in (c) along with the one or more therapeutic agent identified in (c).   
     
     
         2 . The system of  claim 1 , wherein the inputting in (b) is performed from a location that is remote from said database in (a). 
     
     
         3 . The system of  claim 1 , wherein the inputting is performed 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 one or more computer database further comprise data corresponding to one or more clinical trial of a molecular target. 
     
     
         6 . The system of  claim 1 , wherein the reference value for each of the plurality of molecular targets comprises a nucleic acid and/or protein. 
     
     
         7 . The system of  claim 1 , wherein the testing of the molecular target is performed after the individual has received drug therapy for the cancer. 
     
     
         8 . The system of  claim 1 , wherein the molecular profile comprises assessing a cell, tissue sample, blood sample or combination thereof. 
     
     
         9 . The system of  claim 1 , wherein the molecular profiling comprises performing a test for a gene and/or protein. 
     
     
         10 . The system of  claim 1 , wherein the reference is obtained from one or more normal individual without the cancer. 
     
     
         11 . The system of  claim 1 , wherein the individual has been treated by and failed to respond to one cancer therapeutic. 
     
     
         12 . The system of  claim 1 , wherein the individual has been treated by and failed to respond to more than one cancer therapeutic. 
     
     
         13 . The system of  claim 1 , wherein the molecular targets PTEN, EGFR and MGMT are assessed by protein and nucleic acid testing. 
     
     
         14 . The system of  claim 1 , wherein the EGFR molecular target is assessed by protein and nucleic acid testing. 
     
     
         15 . The system of  claim 1 , wherein the MGMT molecular target is assessed by protein and nucleic acid testing. 
     
     
         16 . The system of  claim 1 , wherein the molecular targets TOPO1, RRM1 and SPARC are assessed by immunohistochemistry testing. 
     
     
         17 . The system of  claim 1 , wherein the molecular target TOP2A is assessed by in-situ hybridization. 
     
     
         18 . The system of  claim 1 , wherein the molecular target PDGFRA, EGFR, MGMT and PTEN are assessed by sequencing. 
     
     
         19 . The system of  claim 1 , wherein the molecular targets further comprise HER2. 
     
     
         20 . The system of  claim 13 , wherein the testing comprises: (a) sequencing of the molecular targets EGFR, VHL, TP53, cKIT, PDGFRA and MLH1; (b) immunohistochemistry of the molecular targets TOPO1, RRM1 and SPARC; and (c) in-situ hybridization of the molecular target TOP2A. 
     
     
         21 . The system of  claim 1 , wherein said report further comprises a listing of one or more additional molecular target for which said comparison to said reference in (b) indicates a likely lack of benefit of one or more therapeutic agent in (a)(ii) for the one or more additional molecular target.