BRCA Challenge...Bartha Knoppers, McGill University, Montreal, Canada genomicsandhealth.org BRCA...
Transcript of BRCA Challenge...Bartha Knoppers, McGill University, Montreal, Canada genomicsandhealth.org BRCA...
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BRCAChallenge
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GA4GHDemonstra5onprojectincollabora5onwithENIGMAIni5ated2014bySirJohnBurn,NewcastleUniversity&StephenChanock,Na5onalCancerIns5tute
Current“Driver”team:AmandaSpurdle–QIMRBerghoferMedicalResearchIns5tute,Brisbane
GunnarRaetsch-ETHZurichDavidGoldgar,SeanTav5gian-HuntsmanCancerIns5tute,UniversityofUtah,SaltLakeCity
MelissaCline,BenedictPaten-UniversityofCalifornia,SantaCruzRachelLiao–BroadIns5tute,Cambridge,MassachuseYs
genomicsandhealth.org
BRCAChallenge–Ins5tu5ons:SteeringCommiYee
John Burn, Newcastle University, Newcastle upon Tyne, UK Stephen Chanock, National Cancer Institute, Rockville, USA Antonis Antoniou, University of Cambridge, Cambridge, UK Larry Brody, National Human Genome Research Institute, Bethesda, USA Robert Cook-Deegan, Duke University, Durham, USA Fergus Couch, Mayo Clinic, Rochester, USA Johan den Dunnen, Leiden University Medical Center, Leiden, Netherlands Susan Domchek, University of Pennsylvania, Philadelphia, USA Douglas Easton, University of Cambridge, Cambridge, UK William Foulkes, McGill University, Montreal, Canada Judy Garber, Dana-Farber Cancer Institute, Boston, USA David Goldgar, Huntsman Cancer Institute, Salt Lake City, USA Kazuto Kato, Osaka University, Osaka, Japan Delyth Jane Morgan, Breast Cancer Now, Cancer Research UK
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Interna5onalrepresenta5onRobert Nussbaum, University of California San Francisco, USA Kenneth Offit, Memorial Sloan Kettering Cancer Center, New York, USA Sharon Plon, Baylor College of Medicine, Houston, USA Gunnar Rätsch, ETH Zurich, Zurich, Switzerland Nazneen Rahman, Institute of Cancer Research, London, UK Heidi Rehm, Harvard Medical School, Boston, USA Mark Robson, Memorial Sloan Kettering Cancer Center, NY City, USA Wendy Rubinstein, National Institute of Health, Bethesda, USA Amanda Spurdle, QIMR Berghofer Medical Research Institute, BNE, Australia Dominique Stoppa-Lyonnet, Curie Institute, Paris, France Sean Tavtigian, Hunstman Cancer Institute, Salt Lake City, USA David Haussler, UC Santa Cruz Genomics Institute, Santa Cruz, USA Bartha Knoppers, McGill University, Montreal, Canada
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BRCAChallenge–Ins5tu5onsacrosstheglobe
JohnBurn,NewcastleUniversity,NewcastleuponTyne,UKStephenChanock,Na<onalCancerIns<tute,Rockville,USA
AntonisAntoniou,UniversityofCambridge,Cambridge,UK
LarryBrody,Na<onalHumanGenomeResearchIns<tute,Bethesda,USA
RobertCook-Deegan,DukeUniversity,Durham,USA
FergusCouch,MayoClinic,Rochester,USAJohandenDunnen,LeidenUniversityMedicalCenter,Leiden,Netherlands
SusanDomchek,UniversityofPennsylvania,Philadelphia,USA
DouglasEaston,UniversityofCambridge,Cambridge,UK
WilliamFoulkes,McGillUniversity,Montreal,Canada
JudyGarber,Dana-FarberCancerIns<tute,Boston,USADavidGoldgar,HuntsmanCancerIns<tute,SaltLakeCity,USA
KazutoKato,OsakaUniversity,Osaka,Japan
DelythJaneMorgan,BaronessMorganofDrefelin,BreastCancerNow,CancerResearchUK
RobertNussbaum,UniversityofCaliforniaSanFrancisco,SanFrancisco,USA
KennethOffit,MemorialSloanKeReringCancerCenter,NewYork,USASharonPlon,BaylorCollegeofMedicine,Houston,USA
GunnarRätsch,ETHZurich,Zurich,Switzerland
NazneenRahman,Ins<tuteofCancerResearch,London,UK
HeidiRehm,HarvardMedicalSchool,Boston,USA
MarkRobson,MemorialSloanKeReringCancerCenter,NewYorkCity,USAWendyRubinstein,Na<onalIns<tuteofHealth,Bethesda,USA
AmandaSpurdle,QIMRBerghoferMedicalResearchIns<tute,Herston,Australia
DominiqueStoppa-Lyonnet,CurieIns<tute,Paris,France
SeanTav<gian,HunstmanCancerIns<tute,SaltLakeCity,USADavidHaussler,UCSantaCruzGenomicsIns<tute,SantaCruz,USA
BarthaKnoppers,McGillUniversity,Montreal,Canada
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genomicsandhealth.org
BRCAChallenge–ProjectOverview
● Mission:Improvecareofpa<entsatriskofbreastandovariancancerusingglobaldatasharingandcollabora<onintheanalysisofBRCA1andBRCA2
1. ShareBRCA1andBRCA2variantspublicallyviaawebportal2. Addresssocial,ethical,legalchallengestoglobaldatasharing3. CreateaGA4GHmodelforalldiseasegenes
● ClinicalFocus:Germlinevariantclassifica<on
● Majormilestones:– BRCAExchange->17,900variants,mul<plesites– 1/3expert-classifiedwithsuppor<ngra<onale– comingsoon…mobileappwithalertfunc<on
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BRCAExchangeWebsite
GunnarRaetsch,MelissaCline,BenedictPaten&others
Features:• Flexiblesearching• Drilldowntoextrainfo-Tiledformat• Versioning...- Variantlevel-Datasetlevel
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BRCAChallengeMobileApp
GunnarRaetsch&FaisalAlquaddoomiFeatures:● Simplifiedpresenta<on● Followavariantfunc<onality
(intes<ngphase)
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BRCAChallenge–Goals&PreviousEngagement
● Goals:*Variantleveldata–classifica<on,ra<onale,other*Individualleveldata–clinicalinfo,differingaccess*Algorithmstoautomatecollec<on/classifica<on
● PreviousEngagementwithGA4GH:*Ethics®ulatory:-FDAguidance(NGStes<ng&publicvariantdatabases)-EthicsWGchairs-databaseliabilitypub(GIM19:839)*DataWG:AdoptedtheGA4GHAPI-ToallowotherstoaccessBRCA-Exchangedata*…..currentlyintegra<ngwiththeBeaconnetwork7
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BRCAChallenge–StandardsneededforDatasharing
● GenomicKnowledge&Clinical/Phenotypedata● genomicnomenclature“transla<on”● associatedclinicalinforma<on/phenotype
-includingpa<entascertainment● gene<c&clinicaldataprovenance/quality
● Datause&ResearcherIDs-view&re-useofdata● forclinical/researchpurpose● openaccessvscontrolled(howmuch/who)
● Cloud-interoperability● op<misingworkflow,GA4GHapprovalstamp
● Discovery-controllingforoverlappingdata8
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BRCAChallenge–WhatwecanoffertoGA4GH?
● FeedbackofBRCAChallengedevelopments● Algorithmsforautomatedvariant
priori<za<on/classifica<on● Fieldtes<ngofstandardsonvariant
representa<onandclinicaldata● Mobileappforvariantviewandclassifica<on
updates
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BRCAChallenge
Q&A
Gunnar,Benedict&Melissatochimein!
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