Identification of Tumors

Abstract

The invention provides methods for the use of gene expression measurements to classify or identify tumors in samples obtained from a subject in a clinical setting, such as in cases of formalin fixed, paraffin embedded (FFPE) samples.

1 . A method of classifying a cell containing sample as containing tumor cells of a type of tissue, said method comprising
 detecting expressed RNA or cDNA copies thereof to determine the expression levels of 50 or more transcribed sequences from cells in a cell containing sample obtained from a human subject,   comparing said expression levels of 50 or more transcribed sequences to expression levels of the same 50 or more transcribed sequences in a plurality of known tumor tissue types, and   classifying the sample as containing, or not containing, tumor cells of a tumor from among said plurality of known tumor types,   wherein the 50 or more transcribed sequences comprises at least one transcribed sequence of a gene sequence selected from AA456140, AA745593, AA765597, AA782845, AA865917, AA946776, AA993639, AB038160, AF104032, AF133587, AF301598, AF332224, AI041545, AI147926, AI309080, AI341378, AI457360, AI620495, AI632869, AI683181, AI685931, AI802118, AI804745, AI952953, AI985118, AJ000388, AK025181, AK027147, AK054605, AL023657, AL039118, AL110274, AL157475, AW118445, AW194680, AW291189, AW298545, AW445220, AW473119, AY033998, BC000045, BC001293, BC001504, BC001639, BC002551, BC004331, BC004453, BC005364, BC006537, BC006811, BC006819, BC008764, BC008765, BC009084, BC009237, BC010626, BC011949, BC012926, BC013117, BC015754, BC017586, BE552004, BE962007, BF224381, BF437393, BF446419, BF592799, BI493248, H05388, H07885, H09748, M95585, N64339, NM — 000065, NM — 001337, NM — 003914, NM — 004062, NM — 004063, NM — 004496, NM — 006115, NM — 019894, NM — 033229, R15881, R45389, R61469, X69699, and X96757.   
     
     
         2 . The method of  claim 1 , wherein the 50 or more transcribed sequences includes at least one transcribed sequence of each gene sequence from the following: AA456140, AA745593, AA765597, AA782845, AA865917, AA946776, AA993639, AB038160, AF104032, AF133587, AF301598, AF332224, AI041545, AI147926, AI309080, AI341378, AI457360, AI620495, AI632869, AI683181, AI685931, AI802118, AI804745, AI952953, AI985118, AJ000388, AK025181, AK027147, AK054605, AL023657, AL039118, AL110274, AL157475, AW118445, AW194680, AW291189, AW298545, AW445220, AW473119, AY033998, BC000045, BC001293, BC001504, BC001639, BC002551, BC004331, BC004453, BC005364, BC006537, BC006811, BC006819, BC008764, BC008765, BC009084, BC009237, BC010626, BC011949, BC012926, BC013117, BC015754, BC017586, BE552004, BE962007, BF224381, BF437393, BF446419, BF592799, BI493248, H05388, H07885, H09748, M95585, N64339, NM — 000065, NM — 001337, NM — 003914, NM — 004062, NM — 004063, NM — 004496, NM — 006115, NM — 019894, NM — 033229, R15881, R45389, R61469, X69699, and X96757. 
     
     
         3 . The method of  claim 1  wherein said determining comprises measurement in comparison to one or more reference transcribed sequences. 
     
     
         4 . The method of  claim 1  wherein said determining comprises amplification of all or part of the transcribed sequences, or reverse transcription and labeling RNA corresponding to said transcribed sequences. 
     
     
         5 . The method of  claim 4  wherein said amplification comprises linear RNA amplification or quantitative PCR. 
     
     
         6 . The method of  claim 1 , wherein said sample is a formalin fixed, paraffin embedded (FFPE) sample.