brca challenge...bartha knoppers, mcgill university, montreal, canada genomicsandhealth.org brca...

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genomicsandhealth.org BRCA Challenge 1 GA4GH Demonstra5on project in collabora5on with ENIGMA Ini5ated 2014 by Sir John Burn, Newcastle University & Stephen Chanock, Na5onal Cancer Ins5tute Current “Driver” team: Amanda Spurdle – QIMR Berghofer Medical Research Ins5tute, Brisbane Gunnar Raetsch - ETH Zurich David Goldgar, Sean Tav5gian - Huntsman Cancer Ins5tute, University of Utah, Salt Lake City Melissa Cline, Benedict Paten - University of California, Santa Cruz Rachel Liao – Broad Ins5tute, Cambridge, MassachuseYs

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Page 1: BRCA Challenge...Bartha Knoppers, McGill University, Montreal, Canada genomicsandhealth.org BRCA Challenge – Ins5tu5ons across the globe John Burn, Newcastle University, Newcastle

genomicsandhealth.org

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

Page 2: BRCA Challenge...Bartha Knoppers, McGill University, Montreal, Canada genomicsandhealth.org BRCA Challenge – Ins5tu5ons across the globe John Burn, Newcastle University, Newcastle

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

Page 3: BRCA Challenge...Bartha Knoppers, McGill University, Montreal, Canada genomicsandhealth.org BRCA Challenge – Ins5tu5ons across the globe John Burn, Newcastle University, Newcastle

genomicsandhealth.org

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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Page 4: BRCA Challenge...Bartha Knoppers, McGill University, Montreal, Canada genomicsandhealth.org BRCA Challenge – Ins5tu5ons across the globe John Burn, Newcastle University, Newcastle

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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Page 5: BRCA Challenge...Bartha Knoppers, McGill University, Montreal, Canada genomicsandhealth.org BRCA Challenge – Ins5tu5ons across the globe John Burn, Newcastle University, Newcastle

genomicsandhealth.org

BRCAExchangeWebsite

GunnarRaetsch,MelissaCline,BenedictPaten&others

Features:• Flexiblesearching• Drilldowntoextrainfo-Tiledformat• Versioning...- Variantlevel-Datasetlevel

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Page 6: BRCA Challenge...Bartha Knoppers, McGill University, Montreal, Canada genomicsandhealth.org BRCA Challenge – Ins5tu5ons across the globe John Burn, Newcastle University, Newcastle

genomicsandhealth.org

BRCAChallengeMobileApp

GunnarRaetsch&FaisalAlquaddoomiFeatures:● Simplifiedpresenta<on● Followavariantfunc<onality

(intes<ngphase)

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Page 7: BRCA Challenge...Bartha Knoppers, McGill University, Montreal, Canada genomicsandhealth.org BRCA Challenge – Ins5tu5ons across the globe John Burn, Newcastle University, Newcastle

genomicsandhealth.org

BRCAChallenge–Goals&PreviousEngagement

●  Goals:*Variantleveldata–classifica<on,ra<onale,other*Individualleveldata–clinicalinfo,differingaccess*Algorithmstoautomatecollec<on/classifica<on

●  PreviousEngagementwithGA4GH:*Ethics&regulatory:-FDAguidance(NGStes<ng&publicvariantdatabases)-EthicsWGchairs-databaseliabilitypub(GIM19:839)*DataWG:AdoptedtheGA4GHAPI-ToallowotherstoaccessBRCA-Exchangedata*…..currentlyintegra<ngwiththeBeaconnetwork7

Page 8: BRCA Challenge...Bartha Knoppers, McGill University, Montreal, Canada genomicsandhealth.org BRCA Challenge – Ins5tu5ons across the globe John Burn, Newcastle University, Newcastle

genomicsandhealth.org

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

Page 9: BRCA Challenge...Bartha Knoppers, McGill University, Montreal, Canada genomicsandhealth.org BRCA Challenge – Ins5tu5ons across the globe John Burn, Newcastle University, Newcastle

genomicsandhealth.org

BRCAChallenge–WhatwecanoffertoGA4GH?

●  FeedbackofBRCAChallengedevelopments●  Algorithmsforautomatedvariant

priori<za<on/classifica<on●  Fieldtes<ngofstandardsonvariant

representa<onandclinicaldata●  Mobileappforvariantviewandclassifica<on

updates

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Page 10: BRCA Challenge...Bartha Knoppers, McGill University, Montreal, Canada genomicsandhealth.org BRCA Challenge – Ins5tu5ons across the globe John Burn, Newcastle University, Newcastle

genomicsandhealth.org

BRCAChallenge

Q&A

Gunnar,Benedict&Melissatochimein!

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