Systems and methods for comprehensive analysis of molecular profiles across multiple tumor and germline exomes

Abstract

Omics patient data are analyzed using sequences or diff objects of tumor and matched normal tissue to identify patient and disease specific mutations, using transcriptomic data to identify expression levels of the mutated genes, and pathway analysis based on the so obtained omic data to identify specific pathway characteristics for the diseased tissue. Most notably, many different tumors have shared pathway characteristics, and identification of a pathway characteristic of a tumor may thus indicate effective treatment options ordinarily not considered when tumor analysis is based on anatomical tumor type only.

What is claimed is: 
     
         1 . A computer-executed method for identification of a treatment option based on omics data of tumor cells, comprising:
 identifying, by an analysis engine, shared pathway characteristics among tumor cells of a plurality of patients using a plurality of respective omics data sets of the tumor cells;   wherein each omics data set belongs to each of the plurality of patients, respectively, and wherein at least two of the plurality of patients are diagnosed with different tumors;   wherein each set of omics data comprises genomics information and transcriptomics information from tumor and matched normal cells of each of the plurality patients;   wherein the transcriptomics information comprises expression levels or sequences of transcripts;   stratifying the tumor cells as belonging to a class of tumors based on the shared pathway characteristics;   using the analysis engine to provide, based on the class, a treatment option to the tumor cells, wherein the treatment option is common to the tumor cells independently of an anatomical types of the tumor cells;   wherein the treatment option includes identification of a drug and indication that the tumor cells are treatable with the drug, or wherein the treatment option is selected based on known or available treatments for the anatomically unrelated and distinct tumors; and   treating the tumor cells using the drug or known or available treatment.   
     
     
         2 . The method of  claim 1  wherein the at least two sets of omics data are in a BAMBAM format, a SAMBAM format, a FASTQ format, or a FASTA format. 
     
     
         3 . The method of  claim 1  wherein the at least two sets of omics data are BAMBAM diff objects. 
     
     
         4 . The method of  claim 1  wherein the genomics information comprise mutation information, copy number information, insertion information, deletion information, orientation information and/or breakpoint information. 
     
     
         5 . The method of  claim 1  wherein the genomics information is whole genome sequencing information. 
     
     
         6 . The method of  claim 1  wherein the genomics information is exome sequencing information. 
     
     
         7 . The method of  claim 1  wherein the transcriptomics information covers at least 50% of all exomes in the genomics information from the tumor cells. 
     
     
         8 . The method of  claim 1  wherein the transcriptomics information covers at least 80% of all exomes in the genomics information from the tumor cells. 
     
     
         9 . The method of  claim 1  wherein the shared pathway characteristics are selected from the group consisting of a constitutively activated pathway, a functionally impaired pathway, and a dysregulated pathway. 
     
     
         10 . The method of  claim 1  wherein the shared pathway characteristics are characterized by a mutated non-functional protein, mutated dysfunctional protein, an overexpressed protein, or an underexpressed protein in a pathway. 
     
     
         11 . The method of  claim 1  wherein the transcriptomics information is used in the step of identifying to infer reduced or absence of function of a protein encoded by a mutated gene. 
     
     
         12 . The method of  claim 1  wherein the step of identifying is performed using PARADIGM. 
     
     
         13 . The method of  claim 1 , wherein the treatment option includes identification of a drug and indication that the tumor cells are treatable with the drug. 
     
     
         14 . The method of  claim 1 , wherein the treatment option for a first patient with a first tumor is based on shared pathway characteristics with a second patient with a distinct second tumor. 
     
     
         15 . The method of  claim 1 , further comprising analyzing information, by an analysis engine, on pathway usage or compensation where a pathway function is compromised. 
     
     
         16 . The method of  claim 1 , wherein the sequences of transcripts are used to identify RNA editing or RNA splicing. 
     
     
         17 . The method of  claim 1 , wherein the treatment option is selected based on known or available treatments for the anatomically unrelated and distinct tumors. 
     
     
         18 . The method of  claim 1 , wherein the treatment option target a mutated element common to the tumor cells. 
     
     
         19 . The method of  claim 1 , wherein the treatment option targets a non-mutated element, which compensates for a defect of a pathway where a mutated element common to the tumor cells is disposed. 
     
     
         20 . The method of  claim 1 , wherein the expression level comprises quantity of the transcripts.