Identification of tumors
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 obtained from a subject as containing tumor cells of a type of tissue, said method comprising
selecting randomly 50 or more transcribed sequences of the subject;
producing cDNA copies of the 50 or more randomly selected transcribed sequences from cells in the cell-containing sample;
amplifying the cDNA copies to produce amplified molecules;
determining expression levels of the 50 or more transcribed sequences;
comparing the determined expression levels to expression levels of the same 50 or more transcribed sequences in a plurality of known tumor types comprising one or more tumor types selected from the group consisting of testicular germ cell, sarcoma, adrenal gland, brain, breast, carcinoid-intestine, cervix-adenocarcinoma, cervix-squamous, endometrium, gall bladder, germ cell-ovary, GIST (gastrointestinal stromal tumor), kidney, liver, lung-adenocarcinoma-large cell, lung-small cell, lung-squamous, lymphoma-B cell, lymphoma-Hodgkin's, lymphoma-T cell, meningioma, mesothelioma, ovary-clear cell, ovary-serous, pancreas, prostate, skin-basal cell, skin-melanoma, skin-squamous, small and large bowel, soft tissue-MFH (malignant fibrous histiocytoma), stomach-adenocarcinoma, thyroid-follicular-papillary, thyroid-medullary, and urinary bladder, and
classifying the sample as containing or not containing tumor cells of a tumor type or tissue in the plurality of known tumor types.
2. The method of claim 1 wherein said expression levels are determined by use of a microarray.
3. The method of claim 1 wherein said classifying is with an accuracy of 60% or higher.
4. The method of claim 1 wherein said determining comprises measurement in comparison to one or more reference transcribed sequences.
5. The method of claim 1 wherein said determining comprises measuring the expression of all or part of each one of the 50 or more transcribed sequences.
6. The method of claim 1 wherein said determining comprises amplification of all or part of each one of the 50 or more transcribed sequences, or reverse transcription and labeling RNA obtained from said transcribed sequences.
7. The method of claim 6 wherein said amplification comprises linear RNA amplification or quantitative PCR.
8. The method of claim 6 wherein said amplification is of sequences present within 600 nucleotides of the polyadenylation sites of the transcribed sequences.
9. The method of claim 6 wherein said amplification is quantitative PCR amplification of at least 50 nucleotides of the transcribed sequences.
10. A microarray comprising oligonucleotide probes to detect products of the amplification of claim 6 .
11. The method of claim 1 wherein said transcribed sequences are selected to be non-redundant.
12. The method of claim 11 , further comprising determining the expression levels of an excess number of transcribed sequences which are redundant to those used for said classifying.
13. The method of claim 1 , wherein said sample is a clinical sample from a human patient.
14. The method of claim 13 , wherein said sample is a formalin fixed, paraffin embedded (FFPE) sample.
15. The method of claim 1 , wherein the 50 or more transcribed sequences are 50 to 350 transcribed sequences.
16. The method of claim 1 , wherein at least one of the 50 or more transcribed sequences is not associated with tumor cells of the plurality of known tumor types.
17. The method of claim 1 , wherein the 50 or more transcribed sequences are not selected based upon a ranking of significance of correlation of the expression level of the transcribed sequence with any one of the known tumor types.
18. The method of claim 1 , wherein the 50 or more transcribed sequences are selected randomly from nucleotide sequences of
(a) SEQ ID NOs: 1 to 74, or
(b) SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 50, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 74, and SEQ ID NOs: 149-200.
19. The method of claim 1 , wherein the step of selecting is performed by randomly selecting more than 50 transcribed sequences of the subject and reducing the number of selected transcribed sequences to 50 or more transcribed sequences by removing one or more transcribed sequence whose expression level correlates with at least one other transcribed sequence.
20. The method of claim 19 , wherein the expression level of more than 10% of the 50 or more transcribed sequences are not correlated with another transcribed sequence of the 50 or more transcribed sequences.