Cancer Score for Assessment and Response Prediction from Biological Fluids

Abstract

Methods for analyzing omics data and using the omics data to determine prognosis of a cancer, to predict an outcome of a treatment, and/or to determine an effectiveness of a treatment are presented. In preferred methods, blood from a patient having a cancer or suspected to have a cancer is obtained and blood omics data for a plurality of cancer-related, inflammation-related, or DNA repair-related genes are obtained. A cancer score can be calculated based on the omics data, which then can be used to provide a cancer prognosis, a therapeutic recommendation, an effectiveness of a treatment.

What is claimed is: 
     
         1 . A method of selecting a treatment option for a cancer patient, comprising:
 obtaining blood from a patient having a cancer;   obtaining from the blood omics data of the cancer patient for a plurality of cancer genes, wherein the omics data comprise at least one of DNA sequence data, RNA sequence data, and RNA expression level;   wherein the omics data comprise an expression level of a cancer related gene, an expression level of an immune therapy related gene, and an expression level of a DNA or RNA sequence encoding a neoepitope;   providing an omics record computer system that includes at least one processor and at least one computer readable memory coupled to the processor and configured to digitally store the omics data for the plurality of cancer-related genes in the at least one memory;   analyzing, in silico, the omics data to generate a digital cancer gene score, wherein the digital cancer gene score is calculated in silico using the omics data; and   administering, when (1) the digital cancer gene score exceeds a threshold level and (2) the majority portion of the digital cancer gene score is weighted for the cancer related gene, the immune therapy related gene, or the DNA or RNA sequence encoding a neoepitope, a therapeutic agent that targets the cancer related gene, the immune therapy related gene, or the DNA or RNA sequence encoding the neoepitope.   
     
     
         2 . The method of  claim 1 , wherein the blood omics data are obtained from DNA/RNA that is enclosed in a vesicular structure or bound to non-nucleotide molecule. 
     
     
         3 . The method of  claim 1 , wherein the blood omics data are obtained from cell-free DNA or cell-free RNA. 
     
     
         4 . The method of  claim 1 , wherein the DNA sequence data are selected from the group consisting of mutation data, copy number data duplication, loss of heterozygosity data, and epigenetic status. 
     
     
         5 . The method of  claim 1 , wherein the RNA sequence data are selected from the group consisting of mRNA sequence data and splice variant data. 
     
     
         6 . The method of  claim 1 , wherein the RNA expression level data are selected from the group consisting of a quantity of RNA transcript and a quantity of a small noncoding RNA. 
     
     
         7 . The method of  claim 1 , wherein DNA sequence data are obtained from circulating free DNA. 
     
     
         8 . The method of  claim 1 , wherein the RNA sequence data are obtained from the group consisting of circulating tumor RNA and circulating free RNA. 
     
     
         9 . The method of  claim 1 , wherein the cancer related gene is selected form the group consisting of a gene encoding a protein kinase, a cancer-specific gene, a cancer associated gene, a DNA polymerase gene, a nuclease gene, a replicated associated gene, 
     
     
         10 . The method of  claim 1 , wherein the immune therapy related gene is selected form the group consisting of a DNA repair gene, an RNA repair gene, an inflammation-related gene, a chemokine gene, a cytokine gene, a chemokine receptor gene, a cytokine receptor gene, a homologous recombination gene, non-homologous end joining gene, 
     
     
         11 . The method of  claim 1 , wherein the DNA or RNA sequence encoding the neoepitope is a DNA or RNA sequence that encodes a patient-and tumor specific neoepitope, is a sequence that encodes a tumor type-specific neoepitope, or is a sequence that encodes a cancer-associated neoepitope. 
     
     
         12 . The method of  claim 1 , wherein the neoepitope is matched to the patient's HLA type. 
     
     
         13 . The method of  claim 1 , wherein the cancer related gene or the immune therapy related gene is selected form the group of genes presented in Table 1, Table 2, and Table 3. 
     
     
         14 . The method of  claim 1 , further comprising a step of processing the omics data using pathway analysis to thereby identify one or more pathways affected by the expression level. 
     
     
         15 . The method of  claim 1 , wherein the cancer score is a compound score reflecting status of the cancer related gene, the immune therapy related gene, and the DNA or RNA sequence encoding a neoepitope. 
     
     
         16 . The method of  claim 1 , wherein the therapeutic agent is an enzyme inhibitor, a receptor ligand. 
     
     
         17 . The method of  claim 1 , wherein the therapeutic agent is an immune therapy. 
     
     
         18 . The method of  claim 1 , wherein the treatment option is surgery or radiation therapy.