Use of marker panels for stratifying drug treatment options

Abstract

Personalized medicine involves the use of a patient's molecular markers to guide treatment regimens for the patient. The scientific literature provides multiple examples of correlations between drug treatment efficacy and the presence or absence of molecular markers in a patient sample. Methods are provided herein that permit efficient dissemination of scientific findings regarding treatment efficacy and molecular markers found in patient tumors to health care providers.

1 - 75 . (canceled) 
     
     
         76 . A method of determining personalized cancer treatment options for a subject, the method comprising:
 a. obtaining a sample from a subject, wherein the sample comprises molecular markers from a tumor cell;   b. determining a status of the molecular markers, wherein the molecular markers comprise c-kit, Kras, BRAF, microsatellite sequence, EGFR, chromosome 18q, thymidylate synthase, and Topol; and   c. stratifying one or more cancer drug treatment options in a report based on the status of the molecular markers.   
     
     
         77 . The method of  claim 76 , wherein the c-kit has an activating mutation. 
     
     
         78 . The method of  claim 76 , wherein the Kras has a mutation in exon 2. 
     
     
         79 . The method of  claim 78 , wherein the mutation in exon 2 is in codon 12 or 13. 
     
     
         80 . The method of  claim 76 , wherein the BRAF sequence encodes a V600E mutation. 
     
     
         81 . The method of  claim 76 , wherein the microsatellite sequence displays low-frequency microsatellite instability. 
     
     
         82 . The method of  claim 76 , wherein the microsatellite sequence displays high-frequency microsatellite instability. 
     
     
         83 . The method of  claim 76 , wherein EGFR copy number is increased relative to normal. 
     
     
         84 . The method of  claim 76 , wherein EGFR has mutations in exons 18-21. 
     
     
         85 . The method of  claim 76 , wherein the subject has chromosome 18q allelic loss. 
     
     
         86 . The method of  claim 76 , wherein thymidylate synthase levels are low. 
     
     
         87 . The method of  claim 76 , wherein thymidylate synthase levels are high. 
     
     
         88 . The method of  claim 76 , wherein Topol expression is moderate to high. 
     
     
         89 . The method of  claim 76 , wherein the one or more cancer drug treatment options comprise imatinib mesylate, cetuximab, panitumumab, bevacizumab, 5-FU, capecitabine, and/or irinotecan. 
     
     
         90 . The method of  claim 76 , wherein the sample comprises a tumor biopsy or a cell-free sample. 
     
     
         91 . The method of  claim 76 , wherein the tumor cell comprises a cell from a colon cancer, a bone cancer, a breast cancer, a central nervous system cancer, a gastric cancer, a cervical cancer, an esophageal cancer, a head and neck cancer, a kidney cancer, a skin cancer, a lung cancer, or a carcinoma. 
     
     
         92 . The method of  claim 76 , wherein the determining comprises nucleic acid amplification, DNA sequencing, fluorescent in-situ hybridization (FISH), quantitative PCR (qPCR), and/or immunohistochemistry (IHC). 
     
     
         93 . The method of  claim 76 , wherein the determining comprises determining an absence of one or more mutations or a presence of the one or more mutations in the molecular markers. 
     
     
         94 . The method of  claim 93 , wherein the one or more mutations comprise a de novo mutation, nonsense mutation, missense mutation, silent mutation, frameshift mutation, insertion, substitution, point mutation, single nucleotide polymorphism (SNP), deletion, rearrangement, amplification, chromosomal translocation, interstitial deletion, chromosomal inversion, loss of heterozygosity, loss of function mutation, gain of function mutation, dominant negative mutation, or lethal mutation.