Cancer diagnostics using biomarkers

Abstract

Disclosed herein, in certain instances, are methods, systems and kits for the diagnosis, prognosis and determination of cancer progression of a cancer in a subject. Further disclosed herein, in certain instances, are methods, systems and kits for determining the treatment modality of a cancer in a subject. The methods, systems and kits comprise expression-based analysis of biomarkers. Further disclosed herein, in certain instances, are probe sets for use in assessing a cancer status in a subject.

1 . A method of diagnosing, prognosing, determining progression the cancer, or predicting benefit from therapy in a subject, comprising:
 (a) assaying an expression level in a sample from the subject for a plurality of targets, wherein the plurality of targets comprises one or more targets selected from Tables 2, 4, 11 or 55; and   (b) diagnosing, prognosing, determining progression the cancer, or predicting benefit from therapy in a subject based on the expression levels of the plurality of targets.   
     
     
         2 . A method of determining a treatment for a cancer in a subject, comprising:
 (a) assaying an expression level in a sample from the subject for a plurality of targets, wherein the plurality of targets comprises one or more targets selected from Tables 2, 4, 11 or 55; and   (b) determining the treatment for the cancer based on the expression level of the plurality of targets.   
     
     
         3 . The method of  claim 1 , wherein the cancer is selected from the group consisting of a carcinoma, sarcoma, leukemia, lymphoma, myeloma, and a CNS tumor. 
     
     
         4 . The method of  claim 1 , wherein the cancer is selected from the group consisting of skin cancer, lung cancer, colon cancer, pancreatic cancer, prostate cancer, liver cancer, thyroid cancer, ovarian cancer, uterine cancer, breast cancer, cervical cancer, kidney cancer, epithelial carcinoma, squamous carcinoma, basal cell carcinoma, melanoma, papilloma, and adenomas. 
     
     
         5 - 26 . (canceled) 
     
     
         27 . A probe set for assessing a cancer status of a subject comprising a plurality of probes, wherein the probes in the set are capable of detecting an expression level of one or more targets selected from Tables 2, 4, 11 or 55, wherein the expression level determines the cancer status of the subject with at least 40% specificity. 
     
     
         28 - 32 . (canceled) 
     
     
         33 . The probe set of  claim 27 , wherein the probe set further comprises a probe capable of detecting an expression level of at least one coding target. 
     
     
         34 . The probe set of  claim 33 , wherein the coding target is an exonic sequence. 
     
     
         35 . The probe set of  claim 27 , wherein the probe set further comprises a probe capable of detecting an expression level of at least one non-coding target. 
     
     
         36 . The probe set of  claim 35 , wherein the non-coding target is an intronic sequence or partially overlaps with an intronic sequence. 
     
     
         37 . The probe set of  claim 35 , wherein the non-coding target is a UTR sequence or partially overlaps with a UTR sequence. 
     
     
         38 - 40 . (canceled) 
     
     
         41 . The probe set of  claim 27 , wherein the target is a nucleic acid sequence. 
     
     
         42 . The probe set of  claim 41 , wherein the nucleic acid sequence is a DNA sequence. 
     
     
         43 . The probe set of  claim 41 , wherein the nucleic acid sequence is an RNA sequence. 
     
     
         44 - 59 . (canceled) 
     
     
         60 . The probe set of  claim 27 , wherein the non-coding target is a non-coding RNA transcript and the non-coding RNA transcript is non-polyadenylated. 
     
     
         61 . A system for analyzing a cancer, comprising:
 (a) a probe set comprising a plurality of target sequences, wherein
 (i) the plurality of target sequences hybridizes to one or more targets selected from Tables 2 or 4; or 
 (ii) the plurality of target sequences comprises one or more target sequences selected from Table 11; and 
   (b) a computer model or algorithm for analyzing an expression level and/or expression profile of the target hybridized to the probe in a sample from a subject suffering from a cancer.   
     
     
         62 . The system of  claim 61 , further comprising an electronic memory for capturing and storing an expression profile. 
     
     
         63 . The system of  claim 61 , further comprising a computer-processing device, optionally connected to a computer network. 
     
     
         64 - 78 . (canceled) 
     
     
         79 . A method of analyzing a cancer in an individual in need thereof, comprising:
 (a) obtaining an expression profile from a sample obtained from the individual, wherein the expression profile comprises one or more targets selected from Tables 2, 4, 11 or 55; and   (b) comparing the expression profile from the sample to an expression profile of a control or standard.   
     
     
         80 - 173 . (canceled) 
     
     
         174 . A kit for analyzing a cancer, comprising:
 (a) a probe set comprising a plurality of target sequences, wherein the plurality of target sequences comprises at least one target sequence listed in Table 11; and   (b) a computer model or algorithm for analyzing an expression level and/or expression profile of the target sequences in a sample.   
     
     
         175 - 184 . (canceled)