A Genotype-Phenotype Archiving and Communication System

Despite major advances in genome sequencing and identification of the genetic basis of diseaseclinical use of genomic analysis is limited in part by the costs and coordination associated with correlating genome results with phenotypic findingsSegalClinicians are overwhelmed by the huge amounts of information needed to assess a genomeand laboratory scientists are hampered by getting sparse information about patient findingsphenotypic elements on physical examinationhistoryand testingWe have developed components of a process to address these issuesThese components include the SimulConsult Genome Phenome AnalyzerSegal et alwith its ad hoc Electronic Health RecordEHRintegrationSegal et alAs part of a Geisinger led teamwe have demonstrated that Geisinger s GenomeCOMPASS tool for Return of Genomic Resultsintegrated with the Genome Phenome Analyzerenhances understanding of those results by families and referring cliniciansWilliams et alStuckey et alSeparatelyGeisinger has developed methods for mining the findings in the EHRHoweverlack of access to clinical genomic data and lack of standardization in genome analysis and frequent changes in capabilities have made it challenging to use such componentsAccordinglywe propose to develop a prototype platform for a Genotype Phenotype Archiving and Communication SystemG PACSanalogous to the radiology PACSwith archiving and communication oftypes of informationpatient findings and annotated genomic variantsenabling genome phenome analysis using these componentsAIMDevelop phenotype processingarchiving and communicationA Patient Finding List will be built in the G PACSdistinct from the EHR s Problem ListThe Patient Finding List will have a Candidate findings section populated by the Phenotype Builder EHR text mining program being implemented at Geisingerand an Accepted findings section to which Candidate Findings can be accepted or be added using applications such as SimulConsultApplications will save Session snapshots to the G PACSwhich can be used to re launch using that dataor for a new analysisusing parts of the Patient Finding ListIn all casesthe application will have access to the Candidate and Accepted Findingsand highlight information on SimulConsult s Useful Findings screen to signal what information may already be known about the patientAIMEmpower clinicians to use full data in genomic diagnosisA pipeline will be built for annotating and combining variant fileswith archival capabilityoptimized for speedThis and findings chosen using the Patient Finding List or Session snapshotsplus those entered with the Useful Findings feature of SimulConsult will enable the clinician to do a full Genome Phenome analysisand report using GenomeCOMPASSAimEvaluate the end to end G PACS solutionA mixed methods approach will be used forclinicians to testde identified cases with known diagnosesusing G PACS and Epic s development environment This study aims to develop a prototype Genotype Phenotype Archiving and Communication SystemG PACSThe rationale is that the current state of genome analysis and clinical use is lagging in part due to a situation of siloed information and capabilitiesa situation that Clayton Christensen characterizes as requiring end to end integration to set the stage for a subsequent environment of interoperable standardsWhile analogous to the radiology PACSthe G PACS will also have advanced analysis capabilities and sophisticated handling oftypes of informationpatient findings and annotated genomic variants to enable genomephenome analysis by clinicians and laboratorians using these components