GENE EXPRESSION PROFILING FROM FFPE SAMPLES
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 for amplification and analysis of expressed RNA from cells of a deparaffinized FFPE (formalin fixed paraffin embedded) sample, said method comprising:
synthesizing, with a primer comprising a sequence complementary to RNA extracted from said cells of said deparaffinized FFPE sample, to produce first cDNA strands;
amplifying said cDNA strands to produce amplified molecules;
hybridizing said amplified molecules to a microarray; and
producing signals from hybridized molecules, wherein the signals reflect expressed RNA in said cells.
2 . The method of claim 1 , wherein said RNA is extracted from said cells by a method comprising:
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.
3 . The method of claim 2 , further comprising heating said RNA extracted from said cells at about 70° C. before contacting said RNA with said primer.
4 . The method of claim 1 , further comprising synthesizing second cDNA strands, complementary to said first cDNA strands, by use of random primers.
5 . The method of claim 1 , wherein said primer is operably linked to a promoter sequence.
6 . The method of claim 4 , wherein said random primers are hexamers, heptamers, octamers, or nonamers.
7 . A method of comparing gene expression data to a gene expression profile, said method comprising:
obtaining gene expression data by the method of claim 1 ,
comparing said data to a gene expression profile generated by gene expression data from one or more FFPE samples from one or more other subjects, and
determining whether said data is the same or similar as said gene expression profile.
8 . The method of claim 1 , wherein said cells are microdissected from said FFPE sample prior to RNA extraction.
9 . The method of claim 1 , wherein said FFPE sample is of a fine needle aspirate (FNA).
10 . The method of claim 1 , wherein said FFPE sample is of a core biopsy.
11 . The method of claim 1 , wherein said FFPE sample is of a needle biopsy.
12 . The method of claim 1 , wherein said deparaffinized FFPE sample comprises tumor tissue and the cells of said deparaffinized FFPE sample are tumor cells.
13 . The method of claim 12 , wherein said tumor tissue is of the pancreas, large intestine, kidney, lung, brain, or a lymphoma.
14 . The method of claim 13 , wherein said tumor tissue is pancreas tissue.
15 . The method of claim 13 , wherein said tumor tissue is large intestine tissue.
16 . The method of claim 13 , wherein said tumor tissue is kidney tissue.
17 . The method of claim 13 , wherein said tumor tissue is lung tissue.
18 . The method of claim 13 , wherein said tumor tissue is brain tissue.
19 . The method of claim 13 , wherein said tumor tissue is of a lymphoma.
20 . The method of claim 12 , wherein said expressed RNA is polyadenylated RNA.
21 . (canceled)