developing an ecosystem for precision medicine via …...shows a specific gene mutation for one’s...
TRANSCRIPT
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1FHIR®andthe FHIRIconaretrademarksofHL7,Inc.(http://hl7.org)
DevelopinganEcosystemforPrecisionMedicineviaFHIRGenomicsandBCOIntegration
GilAlterovitz
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Motivation UpdateVision Now
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Instances(Biocompute)
Workflows(CWL)
FDA
Clinical/PhenotypeCriteria
(FHIRQueryLanguage)
Labs
EMR/ClinicalPhenotype
FORWARD
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Instances(Biocompute)
Workflows(CWL)
Clinical/PhenotypeCriteria
(FHIRQueryLanguage)
Labs
EMR/ClinicalPhenotype
Clincian andPatientAppsFDA
REVERSE
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GenomicsintheClinicalSetting
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Reports…
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… evendetailedones
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Cannotdothis…ContextualDynamicRe-computableActionable
Showsaspecificgenemutationforone’slungcancerpatientagainstmostcommonKRASinlungcancerpopulations
Warner&Alterovitz,JAMIA2016
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Standards-basedStructureddata
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Deliverstructuredgenomicdata
Useresource-baseddatamodel
Adoptamodern,web-savvyAPI
Anopenindustrystandard
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ProposedSolution
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EMR
GenomicsLab
FHIRGenomics
Data
FHIRDiagnosticOrder
OrderPanelorSequencing
1
2 ReturnDataResults
3 SendDatatoClinicogenomicApp
Warner&Alterovitz,JAMIA2016
SMARTonFHIRApp
FastHealthcareInteroperabilityResources
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AnEncompassingStandard?
PayorData
GenomicsData
ClinicalData
ImagingData
AdminData
http://hl7.org/fhir/2017Jan/index.html
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• HL7ClinicalGenomicsDomainAnalysisModel(DAM)DocumentforClinicalSequencing– Listofusecasesandworkflowsfor
clinicalgenomics- withfocusonclinicalsequencing
– Approximately5yearsofworkinHL7ClinicalGenomicsWorkgroup
– Ballotedandreconciledbyinternationalstakeholders
– ~70pages
ClinicalGenomicsUseCases/Workflows
PublishedFeb2017
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Therearemanyusecases...
SpecimenIdentification + Germlinetestingforbiomarkers/mutations(usuallyinherited) + Tumortestingforbiomarkers/mutations(somatic/tumorspecific) +PediatricTesting + PrenatalTesting + InfectiousDiseaseTesting + EmergingSpecimenscenarios + Microbiomeanalysisofthepatient + Free-cellcell-freecirculatingtumorDNA(ctDNA) + Cell-freefetalDNA(cffDNA) + ClinicalSequencing– GermlineTesting + DescriptionofPrimaryClinicalSequenceWorkflow– GermlineTesting + AlternativeGermlineWorkflows + AlternativeFlow1:ChartReview +AlternativeFlow2:NewGeneticKnowledge + AlternativeFlow3:NewClinicalIndication + CancerProfiling– SomaticTesting + DescriptionofPrimaryClinicalSequenceWorkflow– SomaticTesting + AlternativeWorkflows– SomaticTesting +AlternateWorkflow1:Referral + AlternateWorkflow2:PathologistOrderedTesting+ DecisionMakingTools– FamilyHistoryandDrugDosageCalculators + PublicHealthReporting + DescriptionofPublicHealthReportingScenario + CancerRegistryworkflow + ClinicalandResearchDataWarehouses + CytogeneticMarkeridentificationviasequencing + Pharmacogenomics + DescriptionofScenario +Pharmacogenomics– SomaticProfiling + Pharmacogenomics– Germline + PrimaryGermlinePharmacogenomicsGermlineTestingWorkflow + AlternateGermlinePharmacogenomicWorkflow– PharmacistInvolvement + State&RegionalHealthInformationExchanges(HIE) + Humanleukocyteantigen(HLA)Typing + SummaryofChallenges + BackgroundonNMDP + HMLandHL7 + AdditionalUseCaseScenarios(fromSep2016) + BoneMarrowReport + Rare/UndiagnosedDiseases +PreimplantationTesting + FetalTesting– Cell-freeDNA-BasedNoninvasivePrenatalTesting + NewbornScreening + CurrentNewbornScreening + AlternativeResearch-BasedNewbornScreening + NewbornGenomeandTargetedPanelTesting+ PublicHealthTesting– Microbial
PublishedFeb2017
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AlternateWorkflows
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IncrementalAdoptionofFHIR
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+interpretationsonly
+variant/genesequencelocations
GeneticsLabTestResults
+wholesequence/reads
+variant/genenames
Observation+LOINCcodes
ObservationGeneticsProfile
SequenceResource
+RepositoryReads
+Variant/Geneextensions
TraditionalLabs
NGSLabs
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Motivation UpdateVision Now
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AnAssemblyProcess:PathwaytowardClinicalandGenomicIntegration
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ClinicalData à Argonaut
EHRSystem
SynchronizingClinicalCareandResearchStandards
SMARTonFHIRApps
Clinician&Patient
ClinicalCare
SMARTonFHIR
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ClinicalData à SyncforScience
EHRSystem
ResearchDataWarehouse
SynchronizingClinicalCareandResearchStandards
ClinicalCare
Research
FHIR
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AllofUs(PMICohortProgram),etc.
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ClinicalData à Argonaut
ClinicalData à SyncforScience
EHRSystem
ResearchDataWarehouse
SynchronizingClinicalCareandResearchStandards
SMARTonFHIRApps
Clinician&Patient
ClinicalCare
Research
SMARTonFHIR
FHIR
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AllofUs(PMICohortProgram),etc.
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Motivation UpdateVision Now
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http://www.himssconference.org/sites/himssconference/files/pdf/INV1_1.pdf
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ClinicalData à Argonaut
ClinicalData à SyncforScience
Sequence/PanelDiagnostics
Bioinformatics
EHRSystem
ResearchDataWarehouseAllofUs(PMICohort
Program),etc.
Single NationalStandardforClinicalCare&Research
SMARTonFHIRApps
Clinician&Patient
FHIRGenomicData
ClinicalCare
Research
SMARTonFHIR SMARTonFHIR
FHIRFHIR
GenomicData
GenomicData
ClinicogenomicsPharmacogenomicsCancerGenomicsPrecisionMedicine…
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SyncforGenes
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GenomicData
GenomicData
Sequence/PanelDiagnostics
Bioinformatics
EHRSystem
ResearchDataWarehouse
EnablingConsistencyandUsabilityinSharingofGenomic Data
SMARTonFHIRApps
Clinician&Patient
FHIRGenomicData
ClinicalCare
Research
SMARTonFHIR
FHIR
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AllofUs(PMICohortProgram),etc.
SyncforGenes
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GenomicData
GenomicData
Sequence/PanelDiagnostics
Bioinformatics
EHRSystem
ResearchDataWarehouse
EnablingConsistencyandUsabilityinSharingofGenomic Data
SMARTonFHIRApps
Clinician&Patient
FHIRGenomicData
ClinicalCare
Research
SMARTonFHIR
FHIR
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AllofUs(PMICohortProgram),etc.
SyncforGenes
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Motivation UpdateVision Now
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FHIRGenomicsNow
Jan2016May2016
Connectathons
Sep2015BallotComplete
DSTU2
Dec2016BallotComplete
STU3
Jan2017
Pilots
StandardforTrialUse(FHIRVersion3)
FHIRGenomicsFHIRMaturityAchieved:
“Substantiallycompleteandreadyforimplementation”
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BCOandFHIRGenomics
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HowtopreventnextVioxx (Rofecoxib)?
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Brownsteinetal,PLOSOne,2007
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FHIRResources
33
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ProvenanceResource
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ResourceUMLDiagramExample
35
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Provenance- CWLIntegration
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BCOObjects
38
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Idea(basedonFHIR-GA4GHSynergyProject)
• Worktogethertofindoverlapsandmappingsbetweendifferentstandards
• WritereviewpaperonhowvariouselementscanbeleveragedandwhichnewonesareneededforBCOobject
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44
GA4GH
SMART
FHIR
Systems/Security/Apps
ClinicalWorkflow/Genomics SequenceDatasets
FastHealthcareInteroperabilityResources
GlobalAllianceforGenomicsandHealth
SubstitutableMedicalAppsReusableTechnologies