Genomic Data Sharing: Case Studies, Challenges, and Opportunities for Precision Medicine

232 Pages·2022·13.509 MB·English

by  Jennifer B. Mccormick, Jyotishman Pathak

Genomic Data Sharing

Genomic Data Sharing
Case Studies, Challenges, and
Opportunities for Precision Medicine
Edited by
Jennifer B. McCormick
AssociateProfessor,DepartmentofHumanities,
CollegeofMedicine,PennsylvaniaStateUniversity,
HersheyPA,UnitedStates
Jyotishman Pathak
ProfessorofMedicalInformatics,Professorof
Psychiatry,ChiefoftheDivisionofHealthInformatics,
ViceChairoftheDepartmentofPopulationHealth
Sciences,WeillCornellMedicine,NewYork-Presbyterian
Hospital,NewYork,UnitedStates
AcademicPressisanimprintofElsevier
125LondonWall,LondonEC2Y5AS,UnitedKingdom
525BStreet,Suite1650,SanDiego,CA92101,UnitedStates
50HampshireStreet,5thFloor,Cambridge,MA02139,UnitedStates
TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UnitedKingdom
Copyright©2023ElsevierInc.Allrightsreserved.
Nopartofthispublicationmaybereproducedortransmittedinanyformorbyanymeans,electronicor
mechanical,includingphotocopying,recording,oranyinformationstorageandretrievalsystem,without
permissioninwritingfromthepublisher.Detailsonhowtoseekpermission,furtherinformationaboutthe
Publisher’spermissionspoliciesandourarrangementswithorganizationssuchastheCopyrightClearanceCenter
andtheCopyrightLicensingAgency,canbefoundatourwebsite:www.elsevier.com/permissions.
ThisbookandtheindividualcontributionscontainedinitareprotectedundercopyrightbythePublisher(other
thanasmaybenotedherein).
Notices
Knowledgeandbestpracticeinthisfieldareconstantlychanging.Asnewresearchandexperiencebroadenour
understanding,changesinresearchmethods,professionalpractices,ormedicaltreatmentmaybecomenecessary.
Practitionersandresearchersmustalwaysrelyontheirownexperienceandknowledgeinevaluatingandusingany
information,methods,compounds,orexperimentsdescribedherein.Inusingsuchinformationormethodsthey
shouldbemindfuloftheirownsafetyandthesafetyofothers,includingpartiesforwhomtheyhaveaprofessional
responsibility.
Tothefullestextentofthelaw,neitherthePublishernortheauthors,contributors,oreditors,assumeanyliability
foranyinjuryand/ordamagetopersonsorpropertyasamatterofproductsliability,negligenceorotherwise,or
fromanyuseoroperationofanymethods,products,instructions,orideascontainedinthematerialherein.
ISBN:978-0-12-819803-2
ForInformationonallAcademicPresspublicationsvisitour
websiteathttps://www.elsevier.com/books-and-journals
Publisher:StacyMasucci
AcquisitionsEditor:PeterB.Linsley
EditorialProjectManager:SamanthaAllard
ProductionProjectManager:StalinViswanathan
CoverDesigner:MarkRogers
TypesetbyAptara,NewDelhi,India
Contents
Contributors xi
Chapter1:Introduction tothevolume 1
JenniferB.McCormickandJyotishmanPathak
Acknowledgments 6
References 6
Chapter2:Frompublicresources toimprovinghealth:Howgenomicdata
sharingempowersscience andmedicine 9
LauraLymanRodriguez,Ph.D.andElenaGhanaim,M.A.
2.1 Introduction 9
2.2 TheHumanGenomeProjectsettheparadigmforgenomicdatasharing 10
2.3 Genomicdatasharingenablesmultipleareasofresearch 13
2.3.1 Researchusingmodelorganisms 14
2.3.2 Researchusinghumandata 14
2.3.3 Technicalanalysisdevelopment 15
2.4 Puttingdatasharingintopractice 16
2.5 Datasharingwillpropelprecisionmedicine 17
2.6 Learninghealthcaresystemsanddatasharing 20
2.7 Needforresponsibledatastewardship 21
2.8 Barrierstogenomicdatasharing 23
2.9 Conclusion 24
References 25
Chapter3:Biobankcaseexample:Marshfieldclinic 31
CatherineA.McCartyandDeannaCross
3.1 Stakeholderengagement 31
3.1.1 Externalstakeholders 31
3.1.2 Internalstakeholders 32
3.2 Technicalprocedurestofacilitategenomicdatasharingwithcollaborators 33
3.3 Phase1—Sampleidentification,phenotyping,andqualitycontrols 33
3.3.1 Phenotypedataqualitycontrols 33
3.3.2 Sampledataqualitycontrols 34
3.4 Phase2—Dataintegrationandsamplereturn 34
3.5 Phase3—Finalizingdatasets 35
v
Contents
3.6 Phase4—Dataaccess 35
3.6.1 Pilotgenomicdatasharingprojectswithparticipants 35
3.7 Summary 36
References 37
Chapter4:Multidirectional geneticandgenomicdatasharinginthe All of Us
researchprogram 39
K.D.Blizinsky,S.Chandrasekharan,S.Jooma,J.A.ReuschandKimberlyA.Thomson
4.1 Introduction 39
4.2 Sharingdatawithresearchers 41
4.2.1 Relevantconsiderations 42
4.2.2 Guidingconceptsforsharingdatawithresearchers 43
4.2.3 Implementation 44
4.2.4 Lessonslearnedandfuturedirections 51
4.3 Returninggeneticandgenomicresultstoparticipants 54
4.3.1 Relevantconsiderations 54
4.3.2 Guidingconceptsforthereturnofgeneticandgenomicresults 56
4.3.3 Implementation 58
4.3.4 Lessonslearnedandfuturedirections 63
4.4 Concludingremarks 64
References 65
Chapter5:Acommunityapproachtostandards development:
TheGlobalAllianceforGenomicsandHealth(GA4GH) 71
AngelaPage,MelissaHaendelandRobertR.Freimuth
5.1 Introduction 71
5.2 Therationaleforandpromiseofaninternationalalliance(2012–2014) 71
5.3 Conveningthecommunity(2014–2017) 74
5.4 GA4GHconnect(2017–2019) 75
5.5 Gapanalysis(2019–2021) 78
5.5.1 Technicalalignment 82
5.5.2 Implementationsupport 82
5.5.3 Clinicalengagement 82
5.6 BeyondGA4GHconnect(2021andbeyond) 84
5.7 Anovelapproachtofundingandsupport 85
5.8 Threerecommendations 87
5.8.1 Communityneedsshoulddrivedevelopment 87
5.8.2 Createglobalequityandopportunitytoensurefit-for-purpose
development 87
5.8.3 Striveforconsensusandintentionaldecision-making 88
5.9 Conclusion 89
Acknowledgments 89
References 90
vi
Contents
Chapter6:ClinicalgenomicdataonFHIR®:Casestudies inthedevelopment
andadoptionoftheGenomics ReportingImplementationGuide 91
RobertR.Freimuth,RobertP.Milius,MullaiMuruganandMayTerry
6.1 Background 91
6.1.1 HealthLevel7(HL7) 91
6.1.2 HL7ClinicalGenomics 92
6.2 Casestudies:implementationofHL7FHIR 93
6.2.1 ExchangingHLAdataforhistocompatibilityandimmunogenetics 94
6.2.2 Electronicmedicalrecordsandgenomics(eMERGE)network 99
6.2.3 Minimumcommononcologydataelements(mCODE) 103
6.3 Conclusion 108
Acknowledgments 109
References 109
Chapter7:Genomicsdatasharing 111
JuditKumuthini,LyndonZass,MelekChaouch,FaisalM.Fadlelmola,NicolaMulder,
FouziaRadouani,VerenaRas,ChaimaeSamtal,MilaineS.S.Tchamga,DassenSathan,AnisahGhoorah,
RaphaelZ.Sangeda,LiberataA.Mwita,UpendoMasamu,SamarKamalKassim,ZoeGill,
ZahraMungloo-DilmohamudandGordonWells
7.1 Introduction 111
7.2 Currentpractices 112
7.3 Casestudy:H3Africamodel 114
7.3.1 Dataarchive 115
7.3.2 Datasharing,accessandreleasepolicy 118
7.3.3 Dataaccesscommittee 119
7.3.4 H3Africacatalog 120
7.4 Beacons 121
7.5 Datacommonsmodel 122
7.5.1 DatacommonsinAfrica 123
7.6 Commonchallengesingenomicdatasharingandmanagingrisks 125
7.6.1 ELSI 126
7.6.2 Motivationalchallenges 127
7.6.3 Technicalchallenges 127
7.6.4 Infrastructurechallenges 128
7.6.5 Economicandpoliticalchallenges 129
7.6.6 Intellectualpropertyrights 129
7.7 Executivesummary 130
References 131
Chapter8:Datastandardizationintheomicsfield 137
JuditKumuthini,LyndonZass,MelekChaouch,ZoeGill,VerenaRas,ZahraMungloo-Dilmohamud,
DassenSathan,AnisahGhoorah,FaisalFadlelmola,ChristopherFields,JohnVanHorn,
FouziaRadouani,MelissaKonopko,EmileR.ChimusaandShakuntalaBaichoo
8.1 Introduction 137
vii
Contents
8.1.1 Definingstandardization 137
8.2 Omicsdatastandardization 139
8.2.1 Existingstandardsandresources 141
8.2.2 DatastandardizationandFAIRdata 148
8.3 Challengestodatastandardization 150
8.3.1 Adoptionchallenges 150
8.3.2 Policychallenges 153
8.4 Executivesummary 153
Acknowledgments 154
ConflictofInterest 154
References 154
Chapter9:Datasharing: Thepublic’sperspective 157
JamesC.O’Leary
9.1 Publicwillingtoparticipate? 158
9.2 Concernsuniquetogenomicdata? 159
9.2.1 Dataconcerns 159
9.2.2 Mattersoftrust 160
9.3 Supportforbroaddatasharing 162
9.4 Aquestionofcontext 163
9.5 Policyforthepeople 166
9.6 Furtherresearch 166
References 167
Chapter10:GeneticdatasharingintheviewoftheEUgeneraldataprotection
regulation(GDPR) 171
PieterDeSmetandMahsaShabani
10.1 Introduction 171
10.2 Thespecialstatusofgenetic/genomicdata 172
10.3 TheGDPRframeworkforscientificresearch 173
10.4 ConsentforgeneticdatasharingunderEUlaw 175
10.4.1 (Informed)consentforgeneticdatasharing:twodistinct
requirementsarisingfromregulatoryandethicsframeworks 175
10.4.2 WhattypeofconsentisconsideredvalidundertheGDPR? 176
10.5 Alternativelegalbasesforgeneticdatasharing:shiftingattention
awayfromconsent 180
10.6 Concludingremarks 182
References 182
Chapter11:Genomicdatasharingandintellectualproperty 189
JorgeL.Contreras
11.1 Formsofintellectualpropertyprotectionforgenomicdata 189
11.1.1 Copyright 189
11.2 Databases,dataprotection,andtermsofuse 190
11.3 Patents 191
viii
Contents
11.3.1 Earlybiotechpatents 191
11.3.2 Geneticpatentsandutility 191
11.3.3 Bermudaandofficialpatentdeterrence 192
11.3.4 TheFt.Lauderdaleprinciples 193
11.3.5 NIH’sevolvingpolicytowardpatenting 194
11.3.6 PatentdeterrenceoutsidetheUnitedStates 194
11.3.7 Nongovernmentallimitationsonpatentinggenomicdata 195
11.3.8 TheSNPconsortiumanddefensivepatenting 195
11.3.9 GeneticsequencepatentsunderMyriad 196
11.3.10 DiagnosticpatentsunderMayo 198
11.3.11 Licensingofgenomicinventions 198
11.4 Conclusion 199
References 200
Chapter12:Datagovernance 203
DimitriPatrinos,MichaelLangandMa’nH.Zawati
12.1 Background:precisionmedicinegenomicsandgovernance 203
12.2 Howdatagovernanceshapesprecisionmedicine 204
12.2.1 Retrospectivedataintegration 205
12.2.2 Prospectivedatacollection 206
12.2.3 Dataaccess 208
12.3 Theroadahead:howdatagovernanceshouldshapethefutureof
precisionmedicine 211
References 213
Index 215
ix