Integrating CNV analysis into a NextGen sequencing clinical analytics platform

Abstract The goal of this project is to develop a commercial analysis software platform that features the ability to detect and interpret copy number variantsCNVsand other types of structural variationsSVsfrom short read NextGen SequenceNGSdata to enable comprehensivewidely accessibleand economical genetic testingThis capability is key in clinical and research applicationsFor examplecurrently clinical laboratories determine the presence of CNVs and SV by utilizing a wide array of specialized tests such a micro arrays or multiplex ligation dependent probe amplificationMLPAThis is required to completely understand the variation with a human genome possibly contributing to a diseaseSimilarlyresearchers are trying to understand the underlying association between such variations and diseasesThe difference being that clinicians are conducting analytics on a single sample or perhaps a small set of family sampleswhereas researchers often study larger cohortsIn both application areasit would be a significant simplification of clinical or research flowsif these types analysis could occur solely within the NGS paradigmSuch simplification would also provide for major cost savingsIn addition to thisthere is a clear trend in research and clinical application of NextGen sequencing moving towards whole genome sequencingWGSConceptuallyall genomic information is captured in a WGS sampleCurrentlythe adoption of this paradigm is hindered by the complexity of the analysis required to process and detect the full range of genomic variation from the raw sequence dataand the lack of an analysis platform tailored for small research and clinical labs that meets their needs for repeatable workflowsintuitive interfaces and long term archiving and data mining of their patient genomic and phenotypic dataWe are set out to provide a comprehensive solution to this problemIn PhaseSBIRwe have developed and successfully brought to market VS CNVa product for detecting CNVs in targeted gene panels and exomes based on CNV data based on coverage dataWe succeeded in all our aims and milestonesAt Golden Helixwe have a strong track record to create bioinformatics products that provide high end analytics capabilities that don t require specialized bioinformatics training to executeWe are uniquely positioned to build and commercialize a solution that removes the barrier to adoption of WGS as a singlecomprehensive test of all genomic variation and meets the needs of both clinical and research environmentsWe propose to build this solution by leveraging the Golden Helix VarSeq Product SuiteThis product line is a globally adopted filtering and annotation engine for genomic variationwith add ons for clinical reportingautomation of workflowsand data warehousing The goal of this project is to develop a commercial analysis software platform that features the ability to detect and interpret copy number variantsCNVsand other types of structural variationsSVsfrom short read NextGen SequenceNGSdatato enable comprehensivewidely accessibleand economical genetic testing