Observa(onal Health Data Sciences and Informa(cs · PDF fileObserva(onal Health Data Sciences...
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Observa(onalHealthDataSciencesandInforma(cs
(OHDSI)GeorgeHripcsak,MD,MS
ColumbiaUniversityMedicalCenter
NewYork-PresbyterianHospital
Sea>leSymposiumonHealthCareDataAnalyBcs
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Observa(onalHealthDataSciencesandInforma(cs(OHDSI,as“Odyssey”)
AmulB-stakeholder,interdisciplinary,
internaBonalcollaboraBvewithacoordinaBng
centeratColumbiaUniversity
Mission:Toimprovehealth,byempoweringa
communitytocollaboraBvelygeneratethe
evidencethatpromotesbe>erhealthdecisions
andbe>ercare
Aimingfor1,000,000,000paBentdatanetwork
h>p://ohdsi.org
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OHDSI’sglobalresearchcommunity
• >140collaboratorsfrom20differentcountries
• ExpertsininformaBcs,staBsBcs,epidemiology,clinicalsciences
• AcBveparBcipaBonfromacademia,government,industry,providers
• Currently600millionpaBentrecordsin52databases
h>p://ohdsi.org/who-we-are/collaborators/
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Whylarge-scaleanalysisisneededin
healthcare
Alldrugs
Allhealthoutcomesofinterest
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PaBent-levelpredicBonsforpersonalizedevidencerequires
bigdata
2millionpaBentsseemexcessiveorunnecessary?
• ImagineaproviderwantstocompareherpaBentwithotherpaBentswiththe
samegender(50%),inthesame10-yearagegroup(10%),andwiththesame
comorbidityofType2diabetes(5%)
• ImaginethepaBentisconcernedabouttheriskofketoacidosis(0.5%)
associatedwithtwoalternaBvetreatmentstheyareconsidering
• With2millionpaBents,you’donlyexpecttoobserve25similarpaBentswith
theevent,andwouldonlybepoweredtoobservearelaBverisk>2.0
Aggregateddataacrossahealthsystemof1,000providersmaycontain2,000,000paBents
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EvidenceOHDSIseekstogeneratefrom
observaBonaldata• Clinicalcharacteriza(on
– Naturalhistory:Whohasdiabetes,andwhotakesme`ormin?
– Qualityimprovement:WhatproporBonofpaBentswithdiabetesexperiencecomplicaBons?
• Popula(on-leveles(ma(on– Safetysurveillance:Doesme`ormincauselacBcacidosis?
– ComparaBveeffecBveness:Doesme`ormincauselacBcacidosismorethanglyburide?
• Pa(ent-levelpredic(on– Precisionmedicine:Giveneverythingyouknowaboutme,ifItakeme`ormin,whatisthechanceIwillgetlacBcacidosis?
– DiseaseintercepBon:Giveneverythingyouknowaboutme,whatisthechanceIwilldevelopdiabetes?
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OHDSI’sapproachtoopenscience
Open
source
socware
Open
science
Enableusers
todo
something
Generate
evidence
• OpenscienceisaboutsharingthejourneytoevidencegeneraBon
• Open-sourcesocwarecanbepartofthejourney,butit’snotafinaldesBnaBon
• Openprocessescanenhancethejourneythroughimprovedreproducibilityof
researchandexpandedadopBonofscienBficbestpracBces
Data+AnalyBcs+DomainexperBse
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Standardizingworkflowstoenable
transparent,reproducibleresearch
Open
science
Generate
evidence
Databasesummary
Cohortdefini(on
Cohortsummary
Comparecohorts
Exposure-outcomesummary
Effectes(ma(on
&calibra(on
Comparedatabases
Definedinputs:• Targetexposure
• Comparatorgroup
• Outcome
• Time-at-risk
• ModelspecificaBon
PopulaBon-levelesBmaBonforcomparaBve
effecBvenessresearch:
Is<intervenBonX>be>erthan<intervenBonY>
inreducingtheriskof<condiBonZ>?
Consistentoutputs:• analysisspecificaBonsfortransparencyand
reproducibility(protocol+sourcecode)
• onlyaggregatesummarystaBsBcs
(nopaBent-leveldata)
• modeldiagnosBcstoevaluateaccuracy
• resultsasevidencetobedisseminated
• staBcforreporBng(e.g.viapublicaBon)
• interacBveforexploraBon(e.g.viaapp)
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OHDSIDisBnguishingFeatures
• InternaBonaleffort(size&coverage)– 43sourcesterminologiesfromaroundtheworld
• Openscience(depth)– Infrastructureservesthescience– Stack:Terminology,CDM,ETL,QA,VisualizaBon,
NovelanalyBcmethods,Clinicalresearch
• FullinformaBonmodel
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HowOHDSIWorks
Sourcedata
warehouse,with
idenBfiable
paBent-leveldata
Standardized,de-
idenBfiedpaBent-
leveldatabase
(OMOPCDMv5)
ETL
Summary
staBsBcsresults
repository
OHDSI.org
Consistency
Temporality
Strength Plausibility
Experiment
Coherence
Biologicalgradient Specificity
Analogy
Compara(veeffec(veness
Predic(vemodeling
OHDSIDataPartners
OHDSICoordinaBngCenter
Standardized
large-scale
analyBcs
Analysis
results
AnalyBcs
development
andtesBng
Researchand
educaBon
Data
network
support
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DeepinformaBonmodelOMOPCDMv5.0.1
Concept
Concept_relaBonship
Concept_ancestor
Vocabulary
Source_to_concept_map
RelaBonship
Concept_synonym
Drug_strength
Cohort_definiBon
Standardizedvocabularies
A>ribute_definiBon
Domain
Concept_class
Cohort
Dose_era
CondiBon_era
Drug_era
Cohort_a>ribute
Standardizedderivedelem
ents
Stan
dardized
clin
icaldata
Drug_exposure
CondiBon_occurrence
Procedure_occurrence
Visit_occurrence
Measurement
ObservaBon_period
Payer_plan_period
Provider
Care_siteLocaBon
Death
Cost
Device_exposure
ObservaBon
Note
Standardizedhealthsystemdata
Fact_relaBonship
SpecimenCDM_source
Standardizedmeta-data
Standardizedhealtheconom
ics
Person
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Extensivevocabularies
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Preparingyourdataforanalysis
PaBent-level
datainsource
system/schema
PaBent-level
datain
OMOPCDM
ETL
design
ETL
implementETLtest
WhiteRabbit:profileyour
sourcedata
RabbitInAHat:mapyoursource
structureto
CDMtablesand
fields
ATHENA:standardized
vocabularies
forallCDM
domains
ACHILLES:profileyour
CDMdata;
reviewdata
quality
assessment;
explore
populaBon-
levelsummaries
OHDSItoolsbuilttohelp
CDM:
DDL,index,
constraintsfor
Oracle,SQL
Server,
PostgresQL;
Vocabularytables
withloading
scripts
h>p://github.com/OHDSI
OHDSIForums:PublicdiscussionsforOMOPCDMImplementers/developers
Usagi:mapyour
sourcecodes
toCDM
vocabulary
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ACHILLESHeelDataValidaBon
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ATLAStobuild,visualize,andanalyze
cohorts
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Characterizethecohortsofinterest
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LAERTES:Knowledgebaseofwhatweknow:
literature,labeling,spontaneousreporBng
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OHDSIinAcBon
• Generateevidence– Randomizedtrialisthegoldstandard
– ObservaBonalresearchissupporBng• Canitbecomeapartnership?
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CharacterizaBon
• TodaywecarryoutRCTswithoutclearknowledgeofactualpracBce
• TherewillbenoRCTswithoutanobservaBonalprecursor
– ItwillberequiredtocharacterizeapopulaBonusinglarge-scaleobservaBonaldatabeforedesigninganRCT
– Diseaseburden– ActualtreatmentpracBce
– Timeontherapy
– CourseandcomplicaBonrate
– Donenowsomewhatthroughliteratureandpilotstudies
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TreatmentPathways
Public
Industry
Regulator
AcademicsRCT,Obs
Literature
Laypress
Socialmedia
Guidelines
Formulary
Labels
AdverBsing Clinician
PaBent
Family
Consultant
IndicaBon
Feasibility
Cost
Preference
Localstakeholders
Globalstakeholders Conduits
Inputs
Evidence
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Networkprocess
1. JointhecollaboraBve2. ProposeastudytotheopencollaboraBve3. Writeprotocol
– h>p://www.ohdsi.org/web/wiki/doku.php?id=research:studies
4. Codeit,runitlocally,debugit(minimizeothers’work)
5. Publishit:h>ps://github.com/ohdsi
6. EachnodevoluntarilyexecutesontheirCDM
7. Centrallyshareresults8. CollaboraBvelyexploreresultsandjointlypublish
findings
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OHDSIinacBon:
Chronicdiseasetreatmentpathways
• ConceivedatAMIA
• Protocolwri>en,codewri>enandtestedat2
sites
• Analysissubmi>edto
OHDSInetwork
• Resultssubmi>edfor7
databases
15Nov2014
30Nov2014
2Dec2014
5Dec2014
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OHDSIparBcipaBngdatapartnersAbbre-via(on
Name Descrip(on Popula(on,millions
AUSOM AjouUniversitySchoolofMedicine SouthKorea;inpaBenthospital
EHR2
CCAE MarketScanCommercialClaimsand
EncountersUSprivate-payerclaims 119
CPRD UKClinicalPracBceResearchDatalink UK;EHRfromgeneralpracBce 11CUMC ColumbiaUniversityMedicalCenter US;inpaBentEHR 4GE GECentricity US;outpaBentEHR 33INPC RegenstriefInsBtute,IndianaNetworkfor
PaBentCareUS;integratedhealthexchange15
JMDC JapanMedicalDataCenter Japan;private-payerclaims 3MDCD MarketScanMedicaidMulB-State US;public-payerclaims 17MDCR MarketScanMedicareSupplementaland
CoordinaBonofBenefitsUS;privateandpublic-payer
claims9
OPTUM OptumClinFormaBcs US;private-payerclaims 40STRIDE StanfordTranslaBonalResearchIntegrated
DatabaseEnvironmentUS;inpaBentEHR 2
HKU HongKongUniversity HongKong;EHR 1
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Treatmentpathwayeventflow
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ProceedingsoftheNaBonalAcademyofSciences,2016
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T2DM:Alldatabases
Treatmentpathwaysfordiabetes
Firstdrug
Seconddrug
Onlydrug
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Type2DiabetesMellitus Hypertension Depression
OPTUM
GE
MDCDCUMC
INPC
MDCR
CPRD
JMDC
CCAE
PopulaBon-levelheterogeneityacrosssystems,
andpaBent-levelheterogeneitywithinsystems
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HTN:Alldatabases
PaBent-levelheterogeneity
25%ofHTNpaBents(10%ofothers)have
auniquepathdespite250Mpop
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Monotherapy–diabetes
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
1989 1994 1999 2004 2009
AUSOM(SKorea*) CCAE(US#) CPRD(UK*) CUMC(US*)
GE(US*) INPC(US*#) JMDC(Japan#) MDCD(US#)
MDCR(US#) OPTUM(US#) STRIDE(US*)
General
upwardtrend
in
monotherapy
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Monotherapy–HTN
AUSOM(SKorea*) CCAE(US#) CPRD(UK*) CUMC(US*)
GE(US*) INPC(US*#) JMDC(Japan#) MDCD(US#)
MDCR(US#) OPTUM(US#) STRIDE(US*)
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
1989 1994 1999 2004 2009
Academic
medical
centers
differfrom
general
pracBces
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Monotherapy–diabetes
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
1989 1994 1999 2004 2009
AUSOM(SKorea*) CCAE(US#) CPRD(UK*) CUMC(US*)
GE(US*) INPC(US*#) JMDC(Japan#) MDCD(US#)
MDCR(US#) OPTUM(US#) STRIDE(US*)
General
pracBces,
whether
EHRor
claims,have
similar
profiles
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Conclusions:Networkresearch
• ItisfeasibletoencodetheworldpopulaBoninasingledatamodel
– Over600,000,000recordsbyvoluntaryeffort(682,000,000)
• GeneraBngevidenceisfeasible• Stakeholderswillingtoshareresults• Abletoaccommodatevastdifferencesin
privacyandresearchregulaBon