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 evaluating an effectiveness of a treatment for a cancer patient, comprising:
 obtaining blood from a patient having a cancer;   obtaining from the blood omics data of the cancer patient before and after the treatment for a plurality of cancer-related genes, wherein the omics data comprise at least one of DNA sequence data, RNA sequence data, and RNA expression level;   analyzing the omics data to generate first and second cancer gene scores, wherein the first and cancer gene scores correspond to the omics data before and after the treatment, respectively; and   providing the effectiveness of the treatment based on a comparison of the first and second cancer gene scores.   
     
     
         2 . The method of  claim 1 , wherein the plurality of cancer-related genes comprises at least one of a cancer-related gene, a cancer-specific gene, a DNA-repair gene, a neoepitope, and a gene not associated with a disease. 
     
     
         3 . The method of  claim 2 , wherein the neoepitope is tumor specific and patient specific. 
     
     
         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 4 , wherein the plurality of cancer-related genes includes a cancer-specific gene, and the score is calculated based on a presence or an absence of a mutation in the cancer-specific gene. 
     
     
         10 . The method of  claim 9 , wherein the presence of the mutation in the cancer-specific gene weighs more than the presence of the mutation in the cancer-related genes other than the cancer-specific gene. 
     
     
         11 . The method of  claim 5 , wherein the score is calculated based on a type of a splice variant of the cancer gene or a ratio between a plurality of splice variants of the cancer gene. 
     
     
         12 . The method of  claim 1 , wherein the treatment is a drug, and at least one of the plurality of cancer gene is a predicted target of the drug. 
     
     
         13 . The method of  claim 1 , wherein the treatment is an immune therapy, and at least one of the plurality of cancer gene is a receptor of an immune cell or a ligand of the receptor. 
     
     
         14 . The method of  claim 1 , wherein the treatment is a surgery or a radiation therapy, and at least one of the plurality of cancer gene is a neoepitope that is tumor-specific and patient-specific. 
     
     
         15 . The method of  claim 1 , wherein the effectiveness of the treatment is determined by comparing the cancer gene score after the treatment with a predetermined threshold value. 
     
     
         16 . The method of  claim 1 , wherein the effectiveness of the treatment is determined by a difference between the cancer gene score before and after the treatment. 
     
     
         17 . The method of  claim 16 , wherein the treatment is determined effective when the difference is higher than a predetermined threshold value.