Identification of Tumors and Tissues
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
determining the expression levels of about five to 49 transcribed sequences from cells in a cell containing sample obtained from a human subject, wherein said sample is not a frozen tissue section, and
classifying the sample as containing tumor cells of a type of tissue from a plurality of tumor types based on the expression levels of said sequences,
wherein the ratio, of transcribed sequences to the number of tumor types, used in said classifying is from about 1:2 to about 5:2 or higher.
2 . A method of classifying a cell containing sample as containing tumor cells of a type of tissue, said method comprising
determining the expression levels of about five to 49 transcribed sequences from cells in a cell containing sample obtained from a human subject, and
classifying the sample as containing tumor cells of a type of tissue from a plurality of tumor types based on the expression levels of said sequences,
wherein the ratio, of transcribed sequences to the number of tumor types, used in said classifying is from about 1:2 to about 5:2 or higher, and
wherein a) the expression of more than 50% of said transcribes sequences are not correlated with expression of another one of said transcribed sequences, or
b) the five to 49 transcribes sequences are not selected based upon supervised learning using known tumor samples, on the level of correlation between their expression and said plurality of tumor types, or on their rank in a correlation between their expression and said plurality of tumor types.
3 . The method of claim 1 wherein said ratio is up to about 20:1.
4 . The method of claim 1 wherein said ratio is from about 3:2 to about 5:2 and said number of tumor types ranges from two to 38.
5 . The method of claim 1 , further comprising determining the expression levels of an excess number of transcribed sequences beyond the number based on said ratio and the number of tumor types, is determined.
6 . The method of claim 5 wherein said expression levels are determined by use of a microarray.
7 . The method of claim 1 wherein said classifying is with an accuracy of 60% or higher.
8 . The method of claim 1 wherein said five to 49 transcribed sequences comprise two or more selected from the set of 74 genes.
9 . The method of claim 8 wherein said five to 49 transcribed sequences comprise five or more selected from the set of 74 genes.
10 . The method of claim 1 wherein said determining comprises measurement in comparison to one or more reference transcribed sequences.
11 . The method of claim 1 wherein said determining comprises measuring the expression of all or part of the transcribed sequences.
12 . 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.
13 . The method of claim 12 wherein said amplification comprises linear RNA amplification or quantitative PCR.
14 . The method of claim 12 wherein said amplification is of sequences present within 600 nucleotides of the polyadenylation sites of the transcripts.
15 . The method of claim 12 wherein said amplification is quantitative PCR amplification of at least 50 nucleotides of the transcripts.
16 . The method of claim 1 wherein said transcribed sequences are selected to be non-redundant.
17 . The method of claim 16 , further comprising determining the expression levels of an excess number of transcribed sequences which are redundant to those used for said classifying.
18 . The method of claim 1 , wherein said sample is a clinical sample from a human patient, such as where the sample is a fixed sample, like a formalin fixed, paraffin embedded (FFPE) sample.
19 . The method of claim 1 , further comprising, before said determining of the expression levels of about five to 49 transcribed sequences,
diagnosis of a human subject as in need of said determining; or
obtaining of a cell containing sample from a human subject; or
receipt of a cell containing sample; or
sectioning a cell containing sample; or
isolating cells from a cell containing sample; or
obtaining RNA from cells of a cell containing sample.
20 . The method of claim 1 , further comprising, after said determining of the expression levels of about five to 49 transcribed sequences and said classifying of the sample,
processing reimbursement or payment for said determining or classifying by indicating that 1) payment has been received, or 2) payment will be made by other payer, or 3) payment remains unpaid; or
receiving reimbursement for said determining or said classifying; or
forwarding or having forwarded a reimbursement request to an insurance company, health maintenance organization, federal health agency, or to said patient for said determining or classifying; or
receiving indication of approval for payment or denial of payment for said determining or classifying; or
sending a request for reimbursement for said determining or classifying; or
indicating the need for reimbursement or payment on a form or into a database for said determining or classifying; or
indicating the performance of said determining or classifying on a form or into a database; or
reporting the results of said determining or classifying, optionally to a health care facility, a health care provider, a doctor, a nurse, or said patient; or
receiving a payment from said patient for the performance of said determining or classifying.