Gene expression profiling from ffpe samples

Abstract

Methods and compositions relating to the generation and use of gene expression data from tissue samples that have been fixed and embedded are provided. The data can electronically stored and implemented as well as used to augment diagnosis and treatment of diseases.

1 . A method of synthesizing cDNA from the polyadenylated RNA from cells of an FFPE sample comprising
 a) extracting said RNA from said cells; and   b) contacting said extracted RNA with a primer comprising an oligo dT sequence under conditions that result in the synthesis of a first cDNA strand complementary to said extracted RNA.   
     
     
         2 . The method of  claim 1  further comprising heating said RNA extracted from said cells at about 70° C. before contacting said RNA with said primer. 
     
     
         3 . The method of  claim 1  wherein said extracting of RNA from said cells comprises
 obtaining said cells from said sample; 
 digesting said cells with proteinase K to produce digested material; 
 contacting the digested material with a guanidinium containing compound to produce a mixture; 
 contacting the mixture with a silica matrix to permit RNA binding to the matrix; and 
 eluting the bound RNA after removal of unbound matter. 
 
     
     
         4 . The method of  claim 2  wherein said heating is for about 3 to about 8 hours. 
     
     
         5 . The method of  claim 4  wherein said heating is for about 3 hours. 
     
     
         6 . The method of  claim 1  further comprising synthesis of the second cDNA strand by use of random primers. 
     
     
         7 . The method of  claim 1  further comprising synthesis of the second cDNA strand in the absence of random primers. 
     
     
         8 . The method of  claim 1  wherein said primer is operably linked to a promoter sequence. 
     
     
         9 . The method of  claim 6  wherein said random primers are hexamers, heptamers, octamers, or nonamers. 
     
     
         10 . The method of  claim 2  wherein said extracting of RNA from said cells comprises
 obtaining said cells from said sample; 
 digesting said cells with proteinase K to produce digested material; 
 contacting the digested material with a guanidinium containing compound to produce a mixture; 
 contacting the mixture with a silica matrix to permit RNA binding to the matrix; and 
 eluting the bound RNA after removal of unbound matter. 
 
     
     
         11 . The method of  claim 10  wherein said heating is for about 3 to about 8 hours. 
     
     
         12 . The method of  claim 11  wherein said heating is for about 3 hours. 
     
     
         13 - 14 . (canceled) 
     
     
         15 .A computer readable medium containing a gene expression profile represented as a data structure, said medium having a plurality of data fields stored on the medium and comprising
 a first data field representing gene expression profile data that is to be analyzed, said first data field being stored in a range of addresses in said computer readable medium;   one or more receiver objects that will receive test sample expression data for analysis with said gene expression profile data, each receiver object being stored in a separate range of addresses in said computer readable medium,   wherein each receiver object comprises a data field adapted for storing input information for correlation or analysis with said first data field.   
     
     
         16 . The medium of claim  15  wherein said first data field is stored in a range of addresses used by one of said one or more receiver objects. 
     
     
         17 . The medium of claim  15  further comprising a prompt field adapted for storing one or more data prompts to elicit entry of test sample expression data. 
     
     
         18 . The medium of claim  15  wherein said test sample expression data is obtained from cells of a tissue containing sample from a human patient. 
     
     
         19 . The medium of claim  15  wherein said gene expression profile data is derived from amplification of polyadenylated mRNA from one or more FFPE samples. 
     
     
         20 . A system for correlating gene expression data from an FFPE sample with a disease or treatment outcome experienced by the subject from which said sample was obtained comprising
 means for generating said gene expression data by amplification of polyadenylated mRNA from said FFPE sample; and   means for identifying one or more gene expression levels correlated with at least one disease or treatment outcome experienced by said subject.