Methods and systems for interpretation and reporting of sequence-based genetic tests

Abstract

Disclosed herein are system, method, and computer program product embodiments for aiding in the interpretation of variants observed in clinical sequencing data. An embodiment operates by receiving clinical trial enrollment criteria from a user, including but not limited to genetic targeting criteria; searching a knowledge base of patient test information received from a plurality of independent entities for patients that match the clinical trial enrollment criteria; and providing to the user search results for consented patients that match the clinical trial enrollment criteria.

What is claimed is: 
     
         1 . A method for multi-variant classification, comprising:
 receiving test information of a patient;   determining a significance category of a genomic variant included in the test information based on a co-occurrence of the genomic variant with one or more other genomic variants in the patient using a knowledge base including information about the genomic variant and the one or more other genomic variants,   wherein information about the one or more genomic variants indicates whether a genomic variant of the one or more genomic variants modifies a severity of a phenotype, and   providing the significance category to a user,   wherein at least one of the receiving, determining, or providing are performed by one or more computers.   
     
     
         2 . The method of  claim 1 , wherein the information about the one or more other genomic variants is structured according to an ontology. 
     
     
         3 . The method of  claim 2 , wherein the knowledge base comprises curated biomedical content. 
     
     
         4 . The method of  claim 1 , wherein the one or more other genomic variants are known to confer additional sensitivity or resistance to phenotypic effects of the genomic variant. 
     
     
         5 . The method of  claim 1 , wherein the genomic variant is at least one of a somatic variant in oncology or a heredity variant that predisposes the patient to a genetic disorder. 
     
     
         6 . The method of  claim 1 , further comprising:
 modifying the significance category of the genomic variant based on the co-occurrence of the one or more other genomic variants in the patient.   
     
     
         7 . A system, comprising:
 a memory; and   at least one processor coupled to the memory and configured to:   receive test information of a patient;   determine a significance category of a genomic variant included in the test information based on a co-occurrence of the genomic variant with one or more other genomic variants in the patient using a knowledge base including information about the genomic variant and the one or more other genomic variants,   wherein information about the one or more genomic variants indicates whether a genomic variant of the one or more genomic variants modifies a severity of a phenotype; and   provide the significance category to a user.   
     
     
         8 . The system of  claim 7 , wherein the information about the one or more other genomic variants is structured according to an ontology. 
     
     
         9 . The system of  claim 8 , wherein the knowledge base comprises curated biomedical content. 
     
     
         10 . The system of  claim 7 , wherein the one or more other genomic variants are known to confer additional sensitivity or resistance to phenotypic effects of the genomic variant. 
     
     
         11 . The system of  claim 7 , wherein the genomic variant is at least one of a somatic variant in oncology or a heredity variant that predisposes the patient to a genetic disorder. 
     
     
         12 . The system of  claim 7 , the at least one processor further configured to:
 modify the significance category of the genomic variant based on the co-occurrence of the one or more other genomic variants in the patient.   
     
     
         13 . A non-transitory computer readable medium having instructions stored thereon that, when executed by at least one computing device, cause the at least one computing device to perform operations comprising:
 receiving test information of a patient;   determining a significance category of a genomic variant included in the test information based on a co-occurrence of the genomic variant with one or more other genomic variants in the patient using a knowledge base including information about the genomic variant and the one or more other genomic variants,   wherein information about the one or more genomic variants indicates whether a genomic variant of the one or more genomic variants modifies a severity of a phenotype; and   providing the significance category to a user.   
     
     
         14 . The non-transitory computer readable medium of  claim 13 , wherein the information about the one or more other genomic variants is structured according to an ontology. 
     
     
         15 . The non-transitory computer readable medium of  claim 14 , wherein the knowledge base comprises curated biomedical content. 
     
     
         16 . The non-transitory computer readable medium of  claim 14 , wherein the one or more other genomic variants are known to confer additional sensitivity or resistance to phenotypic effects of the genomic variant. 
     
     
         17 . The non-transitory computer readable medium of  claim 14 , wherein the genomic variant is at least one of a somatic variant in oncology or a heredity variant that predisposes the patient to a genetic disorder. 
     
     
         18 . The non-transitory computer readable medium of  claim 14 , the operations further comprising: modifying the significance category of the genomic variant based on the co-occurrence of the one or more other genomic variants in the patient.