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1 FHIR® and the FHIR Icon are trademarks of HL7, Inc. (http://hl7.org) Developing an Ecosystem for Precision Medicine via FHIR Genomics and BCO Integration Gil Alterovitz

Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

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Page 1: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

1FHIR®andthe FHIRIconaretrademarksofHL7,Inc.(http://hl7.org)

DevelopinganEcosystemforPrecisionMedicineviaFHIRGenomicsandBCOIntegration

GilAlterovitz

Page 2: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

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Motivation UpdateVision Now

Page 3: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

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

Page 5: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

GenomicsintheClinicalSetting

5

Page 6: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

6

Reports…

Page 7: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

7

… evendetailedones

Page 8: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

8

Cannotdothis…ContextualDynamicRe-computableActionable

Showsaspecificgenemutationforone’slungcancerpatientagainstmostcommonKRASinlungcancerpopulations

Warner&Alterovitz,JAMIA2016

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9

Standards-basedStructureddata

Page 10: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

Deliverstructuredgenomicdata

Useresource-baseddatamodel

Adoptamodern,web-savvyAPI

Anopenindustrystandard

10

ProposedSolution

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11

EMR

GenomicsLab

FHIRGenomics

Data

FHIRDiagnosticOrder

OrderPanelorSequencing

1

2 ReturnDataResults

3 SendDatatoClinicogenomicApp

Warner&Alterovitz,JAMIA2016

SMARTonFHIRApp

FastHealthcareInteroperabilityResources

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12

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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14

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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15

Page 16: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

AlternateWorkflows

16

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IncrementalAdoptionofFHIR

17

+interpretationsonly

+variant/genesequencelocations

GeneticsLabTestResults

+wholesequence/reads

+variant/genenames

Observation+LOINCcodes

ObservationGeneticsProfile

SequenceResource

+RepositoryReads

+Variant/Geneextensions

TraditionalLabs

NGSLabs

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Motivation UpdateVision Now

Page 19: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

AnAssemblyProcess:PathwaytowardClinicalandGenomicIntegration

19

Page 20: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

ClinicalData à Argonaut

EHRSystem

SynchronizingClinicalCareandResearchStandards

SMARTonFHIRApps

Clinician&Patient

ClinicalCare

SMARTonFHIR

20

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ClinicalData à SyncforScience

EHRSystem

ResearchDataWarehouse

SynchronizingClinicalCareandResearchStandards

ClinicalCare

Research

FHIR

21

AllofUs(PMICohortProgram),etc.

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ClinicalData à Argonaut

ClinicalData à SyncforScience

EHRSystem

ResearchDataWarehouse

SynchronizingClinicalCareandResearchStandards

SMARTonFHIRApps

Clinician&Patient

ClinicalCare

Research

SMARTonFHIR

FHIR

22

AllofUs(PMICohortProgram),etc.

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23

Motivation UpdateVision Now

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http://www.himssconference.org/sites/himssconference/files/pdf/INV1_1.pdf

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Page 26: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

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…

26

SyncforGenes

Page 27: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

GenomicData

GenomicData

Sequence/PanelDiagnostics

Bioinformatics

EHRSystem

ResearchDataWarehouse

EnablingConsistencyandUsabilityinSharingofGenomic Data

SMARTonFHIRApps

Clinician&Patient

FHIRGenomicData

ClinicalCare

Research

SMARTonFHIR

FHIR

27

AllofUs(PMICohortProgram),etc.

SyncforGenes

Page 28: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

GenomicData

GenomicData

Sequence/PanelDiagnostics

Bioinformatics

EHRSystem

ResearchDataWarehouse

EnablingConsistencyandUsabilityinSharingofGenomic Data

SMARTonFHIRApps

Clinician&Patient

FHIRGenomicData

ClinicalCare

Research

SMARTonFHIR

FHIR

28

AllofUs(PMICohortProgram),etc.

SyncforGenes

Page 29: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

29

Motivation UpdateVision Now

Page 30: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

30

FHIRGenomicsNow

Jan2016May2016

Connectathons

Sep2015BallotComplete

DSTU2

Dec2016BallotComplete

STU3

Jan2017

Pilots

StandardforTrialUse(FHIRVersion3)

FHIRGenomicsFHIRMaturityAchieved:

“Substantiallycompleteandreadyforimplementation”

Page 31: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

BCOandFHIRGenomics

Page 32: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

HowtopreventnextVioxx (Rofecoxib)?

32

Brownsteinetal,PLOSOne,2007

Page 33: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

FHIRResources

33

Page 34: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

ProvenanceResource

34

Page 35: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

ResourceUMLDiagramExample

35

Page 36: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

Provenance- CWLIntegration

Page 37: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

37

Page 38: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

BCOObjects

38

Page 39: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

39

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40

Page 41: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

41

Page 42: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

Idea(basedonFHIR-GA4GHSynergyProject)

• Worktogethertofindoverlapsandmappingsbetweendifferentstandards

• WritereviewpaperonhowvariouselementscanbeleveragedandwhichnewonesareneededforBCOobject

42

44

GA4GH

SMART

FHIR

Systems/Security/Apps

ClinicalWorkflow/Genomics SequenceDatasets

FastHealthcareInteroperabilityResources

GlobalAllianceforGenomicsandHealth

SubstitutableMedicalAppsReusableTechnologies

Page 43: Developing an Ecosystem for Precision Medicine via …...Shows a specific gene mutation for one’s lung cancer patient against most common KRAS in lung cancer populations Warner &

43

Contact

GilAlterovitz

[email protected]

[email protected]

LinkedIn:


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MONOGRAPH ON LUNG CANCER - Lung Center of the …lcp.gov.ph/images/Scientific_Proceedings/Monograph_on_Lung_Cancer_July14.pdfMONOGRAPH ON LUNG CANCER: LUNG CANCER REGISTRY DATA OF

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