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.

1 . A method for identifying a therapeutic for an individual with a condition comprising:
 (a) determining an expression level of a gene from a biological sample of said individual,
 wherein said gene is selected from the group consisting of HSP90, Survivin, RRM1, SSTRS3, DNMT3B, VEGFA, SSTR4, RRM2, SRC, RRM2B, HSP90AA1, STR2, FLT1, SSTR5, YES1, BRCA1, RRM1, DHFR, KDR, EPHA2, RXRG, and LCK; and, 
   (b) identifying a therapeutic that said individual has not previously been treated with for said condition, when said gene exhibits a change in expression as compared to a reference.   
   
   
       2 . The method of  claim 1 , wherein said expression level is determined by analysis of mRNA levels of said gene or protein levels of said gene. 
   
   
       3 . The method of  claim 1 , further comprising determining an expression level of a second gene. 
   
   
       4 . The method of  claim 1  or  3 , wherein determining is by immunohistochemistry (IHC) analysis, microarray analysis, in-situ hybridization (ISH) or real-time PCR. 
   
   
       5 . The method of  claim 3 , wherein said ISH is fluorescent in-situ hybridization (FISH). 
   
   
       6 . The method of  claim 3 , wherein determining an expression level of said second gene is by the same method used for said first gene. 
   
   
       7 . The method of  claim 3 , wherein determining an expression level of said second gene is by a different method than that used for said first gene. 
   
   
       8 . The method of  claim 3 , wherein determining an expression level of said first gene is by IHC and said second gene is by microarray. 
   
   
       9 . The method of  claim 1 , further comprising identifying a mutation, polymorphism, or deletion, or insertion in a gene. 
   
   
       10 . The method of  claim 9 , wherein said identifying is by IHC analysis, microarray analysis, ISH, PCR, real-time PCR, or sequencing. 
   
   
       11 . A method for identifying a therapeutic for an individual with a condition comprising:
 (a) determining an expression level of a gene by IHC from a biological sample of said individual,
 wherein said protein is selected from the group consisting of: SPARC, TOP2A, or PTEN; and, 
   (b) identifying a therapeutic that said individual has not previously been treated with for said condition, when said protein exhibits a change in expression as compared to a reference.   
   
   
       12 . The method of  claim 11 , further comprising determining an expression level of a second gene. 
   
   
       13 . The method of  claim 12 , wherein determining an expression level of said second gene is by IHC analysis, microarray analysis, ISH, or real-time PCR. 
   
   
       14 . The method of  claim 12 , wherein said ISH is FISH. 
   
   
       15 . The method of  claim 11 , further comprising identifying a mutation, polymorphism, deletion, or insertion in a gene. 
   
   
       16 . The method of  claim 15 , wherein said identifying is by IHC analysis, microarray analysis, ISH, PCR, real-time PCR, or sequencing. 
   
   
       17 . A method for identifying a therapeutic for an individual with a condition comprising:
 (a) determining an mRNA expression level of CD52 from a biological sample of said individual; and,   (b) identifying a therapeutic that said individual has not previously been treated with for said condition, when said mRNA expression level exhibits a change as compared to a reference.   
   
   
       18 . The method of  claim 17 , further comprising determining an expression level of a second gene. 
   
   
       19 . The method of  claim 18 , wherein determining an expression level of said second gene is by a same method used for determining said mRNA expression level of CD52. 
   
   
       20 . The method of  claim 18 , wherein determining an expression level of said second gene is by a different method than used for determining said mRNA expression level of CD52. 
   
   
       21 . The method of  claim 18 , wherein determining an expression level of said second gene is by IHC analysis, microarray analysis, ISH, or real-time PCR. 
   
   
       22 . The method of  claim 21 , wherein said ISH is FISH. 
   
   
       23 . The method of  claim 17 , further comprising identifying a mutation, polymorphism, deletion, or insertion in a gene. 
   
   
       24 . The method of  claim 23 , wherein said identifying is by IHC analysis, microarray analysis, ISH, PCR, real-time PCR, or sequencing. 
   
   
       25 . The method of  claim 4 ,  13 , or  21 , wherein said microarray analysis comprises using an expression microarray, a comparative genomic hybridization (CGH) microarray, a single nucleotide polymorphism (SNP) microarray, a proteomic array or an antibody array. 
   
   
       26 . The method of  claim 4 ,  13 , or  21 , wherein said microarray analysis comprises identifying whether said gene is up-regulated or down-regulated relative to a reference with a significance of p<0.001. 
   
   
       27 . The method of  claim 4 ,  11 ,  13 , or  21 , wherein said IHC analysis comprises determining whether 30% or more of said sample are +2 or greater in staining intensity.