Genome-wide meta-analysis of 158000 individuals of European ancestry identifies three loci

23 Pages·1999·1.67 MB·English

RESEARCHARTICLE
Genome-wide meta-analysis of 158,000
individuals of European ancestry identifies
three loci associated with chronic back pain
PradeepSuriID1,2,3*,MelodyR.PalmerID4,YakovA.TsepilovID5,6,7,MaximB.FreidinID8,
CindyG.BoerID9,MichelleS.Yau10,11,DanielS.Evans12,AndreaGelemanovicID13,
TraciM.BartzID14,15,MariaNethanderID16,LiubovArbeeva17,LennartKarssenID5,
TuhinaNeogi18,ArchieCampbellID19,DanMellstrom20,ClaesOhlsson21,
LynnM.MarshallID22,EricOrwoll23,AndreUitterlinden9,JeromeI.RotterID24,25,
a1111111111
GordanLaucID26,27,BruceM.Psaty14,28,29,30,MagnusK.Karlsson31,NancyE.Lane32,
a1111111111
GailP.JarvikID4,33,OzrenPolasek13,34,MarcHochberg35,JoanneM.Jordan17,
a1111111111 JoyceB.J.VanMeurs9,RebeccaJackson36,CarrieM.Nielson37,BraxtonD.Mitchell35,38,
a1111111111 BlairH.SmithID39,CarolineHayward40,NicholasL.Smith1,29,30,YuriiS.AulchenkoID5,
a1111111111 FrancesM.K.WilliamsID8
1 SeattleEpidemiologicResearchandInformationCenter(ERIC),DepartmentofVeteransAffairsOfficeof
ResearchandDevelopment,Seattle,Washington,UnitedStatesofAmerica,2 DivisionofRehabilitationCare
Services,VAPugetSoundHealthCareSystem,Seattle,Washington,UnitedStatesofAmerica,
3 DepartmentofRehabilitationMedicine,UniversityofWashington,Seattle,Washington,UnitedStatesof
OPENACCESS America,4 MedicalGenetics,DepartmentofMedicine,UniversityofWashington,Seattle,Washington,
UnitedStatesofAmerica,5 Polyomica,‘s-Hertogenbosch,theNetherlands,6 LaboratoryofTheoreticaland
Citation:SuriP,PalmerMR,TsepilovYA,Freidin
AppliedFunctionalGenomics,NovosibirskStateUniversity,Novosibirsk,Russia,7 Laboratoryof
MB,BoerCG,YauMS,etal.(2018)Genome-wide
RecombinationandSegregationAnalysis,InstituteofCytologyandGeneticsSDRAS,Novosibirsk,Russia,
meta-analysisof158,000individualsofEuropean
8 DepartmentofTwinResearchandGeneticEpidemiology,King’sCollegeLondon,London,United
ancestryidentifiesthreelociassociatedwith
Kingdom,9 DepartmentofInternalMedicine,ErasmusMedicalCenter,Rotterdam,theNetherlands,
chronicbackpain.PLoSGenet14(9):e1007601. 10 InstituteforAgingResearch,HebrewSeniorLife,Boston,Massachusetts,UnitedStatesofAmerica,
https://doi.org/10.1371/journal.pgen.1007601 11 DepartmentofMedicine,BethIsraelDeaconessMedicalCenterandHarvardMedicalSchool,Boston,
Massachusetts,UnitedStatesofAmerica,12 CaliforniaPacificMedicalCenterResearchInstitute,San
Editor:RuthJ.F.Loos,IcahnSchoolofMedicine
Francisco,California,UnitedStatesofAmerica,13 DepartmentofPublicHealth,UniversityofSplitMedical
atMountSinai,UNITEDSTATES
School,Split,Croatia,14 CardiovascularHealthResearchUnitandDepartmentofMedicine,Universityof
Washington,Seattle,Washington,UnitedStatesofAmerica,15 DepartmentofBiostatistics,Universityof
Received:January30,2018
Washington,Seattle,Washington,UnitedStatesofAmerica,16 DepartmentofMedicine,Universityof
Accepted:August2,2018 Go¨teborg,Go¨teborg,Sweden,17 DepartmentofMedicine,SchoolofMedicine,UniversityofNorthCarolina,
ChapelHill,NorthCarolina,UnitedStatesofAmerica,18 ClinicalEpidemiologyUnit,Departmentof
Published:September27,2018 Medicine,BostonUniversitySchoolofMedicine,Boston,Massachusetts,UnitedStatesofAmerica,
19 CentreforGenomicandExperimentalMedicine,MRCInstituteofGenetics&MolecularMedicine,
Copyright:Thisisanopenaccessarticle,freeofall
UniversityofEdinburgh,Edinburgh,UnitedKingdom,20 GeriatricMedicine,DepartmentofInternalMedicine
copyright,andmaybefreelyreproduced,
andClinicalNutrition,InstituteofMedicine,UniversityofGothenburg,Sweden,21 DepartmentofInternal
distributed,transmitted,modified,builtupon,or MedicineandClinicalNutrition,InstituteofMedicine,UniversityofGothenburg,Go¨teborg,Sweden,
otherwiseusedbyanyoneforanylawfulpurpose. 22 DepartmentofOrthopedicsandRehabilitation,OregonHealthandScienceUniversity,Portland,Oregon,
TheworkismadeavailableundertheCreative UnitedStatesofAmerica,23 DepartmentofMedicine,OregonHealthandScienceUniversity,Portland,
CommonsCC0publicdomaindedication. Oregon,UnitedStatesofAmerica,24 InstituteforTranslationalGenomicsandPopulationSciences,Los
AngelesBiomedicalResearchInstitute,Harbor-UCLAMedicalCenter,Torrance,California,UnitedStatesof
DataAvailabilityStatement:Meta-GWASdataare
America,25 DivisionofGenomicOutcomes,DepartmentsofPediatricsandMedicine,Harbor-UCLAMedical
availablefromthedbGaPCHARGESummary Center,Torrance,California,UnitedStatesofAmerica,26 GenosLtd,Osijek,Croatia,27 Facultyof
Resultssiteunderaccessionnumberphs000930, PharmacyandBiochemistry,UniversityofZagreb,Zagreb,Croatia,28 DepartmentofHealthServices,
andcanbeaccessedasdescribedinRichSS, UniversityofWashington,Seattle,Washington,UnitedStatesofAmerica,29 DepartmentofEpidemiology,
WangZY,SturckeA,ZiyabariL,FeoloM,O’Donnell UniversityofWashington,Seattle,Washington,UnitedStatesofAmerica,30 KaiserPermanente
CJ,etal.Rapidevaluationofphenotypes,SNPs WashingtonHealthResearchInstitute,KaiserPermanenteWashington,Seattle,UnitedStatesofAmerica,
andresultsthroughthedbGaPCHARGESummary 31 DepartmentofOrthopedics,SkaneUniversityHospital,LundUniversity,Malmo¨,Sweden,
32 DepartmentsofMedicineandRheumatology,UniversityofCaliforniaDavis,Sacramento,California,
Resultssite.NatGenet.2016;48(7):702-3.doi:10.
UnitedStatesofAmerica,33 DepartmentofGenomeSciences,UniversityofWashington,Seattle,
1038/ng.3582.PubMedPMID:27350599;PubMed
Washington,UnitedStatesofAmerica,34 Hospital“SvetiIvan”,Zagreb,Croatia,35 Departmentsof
CentralPMCID:PMC5787851.Thedatasetcan
MedicineandEpidemiology,UniversityofMaryland,Baltimore,Maryland,UnitedStatesofAmerica,
alsobeaccessedfromhttps://gwasarchive.org
36 DepartmentofMedicine,TheOhioStateUniversity,Columbus,Ohio,UnitedStatesofAmerica,
under’Chronicbackpain’.
PLOSGenetics|https://doi.org/10.1371/journal.pgen.1007601 September27,2018 1/23
Genome-widemeta-analysisofchronicbackpain
Funding:InfrastructurefortheCHARGE 37 SchoolofPublicHealth,OregonHealthandScienceUniversity,Portland,Oregon,UnitedStatesof
ConsortiumissupportedinpartbytheNational America,38 GeriatricResearch,EducationandClinicalCenter,VeteransAffairsMedicalCenter,Baltimore,
Heart,Lung,andBloodInstitutegrants Maryland,UnitedStatesofAmerica,39 DivisionofPopulationHealthSciences,SchoolofMedicine,
R01HL105756.Thisstudywassupportedbythe UniversityofDundee,Dundee,UnitedKingdom,40 MRCHumanGeneticsUnit,MRCInstituteofGenetics&
MolecularMedicine,UniversityofEdinburgh,UnitedKingdom
EuropeanCommissions’SeventhFramework
ProgrammefundedprojectPainOmics(Grant
*[email protected]
agreementn.602736)Dr.Suriwassupportedby
VACareerDevelopmentAward#1IK2RX001515
fromtheUnitedStates(U.S.)Departmentof
Abstract
VeteransAffairsRehabilitationResearchand
Development(RR&D)Service.Dr.SuriisaStaff
PhysicianattheVAPugetSoundHealthCare Backpainisthe#1causeofyearslivedwithdisabilityworldwide,yetsurprisinglylittleis
System.Thecontentsofthisworkdonotrepresent
knownregardingthebiologyunderlyingthissymptom.Weconductedagenome-wideasso-
theviewsoftheU.S.DepartmentofVeterans
ciationstudy(GWAS)meta-analysisofchronicbackpain(CBP).AdultsofEuropeanances-
AffairsortheUnitedStatesGovernment.
CardiovascularHealthStudy:ThisCHSresearch trywereincludedfrom15cohortsintheCohortsforHeartandAgingResearchinGenomic
wassupportedbyNHLBIcontracts Epidemiology(CHARGE)consortium,andfromtheUKBiobankinterimdatarelease.CBP
HHSN268201200036C,HHSN268200800007C,
casesweredefinedasthosereportingbackpainpresentfor(cid:21)3–6months;non-cases
HHSN268200960009C,N01HC55222,
wereincludedascomparisons(“controls”).Eachcohortconductedgenotypingusingcom-
N01HC85079,N01HC85080,N01HC85081,
N01HC85082,N01HC85083,N01HC85086;and merciallyavailablearraysfollowedbyimputation.GWASusedlogisticregressionmodels
NHLBIgrantsU01HL080295,R01HL087652, withadditivegeneticeffects,adjustingforage,sex,study-specificcovariates,andpopulation
R01HL105756,R01HL103612,R01HL120393,
substructure.Thethresholdforgenome-widesignificanceinthefixed-effectinverse-vari-
R01HL085251,andR01HL130114withadditional
contributionfromtheNationalInstituteof anceweightedmeta-analysiswasp<5×10−8.Suggestive(p<5×10−7)andgenome-widesig-
NeurologicalDisordersandStroke(NINDS). nificant(p<5×10−8)variantswerecarriedforwardforreplicationorfurtherinvestigationinthe
Additionalsupportwasprovidedthrough
remainingUKBiobankparticipantsnotincludedinthediscoverysample.Thediscoverysam-
R01AG023629fromtheNationalInstituteonAging
plecomprised158,025individuals,including29,531CBPcases.Agenome-widesignificant
(NIA).AfulllistofprincipalCHSinvestigatorsand
institutionscanbefoundatCHS-NHLBI.org.The associationwasfoundfortheintronicvariantrs12310519inSOX5(OR1.08,p=7.2×10−10).
provisionofgenotypingdatawassupportedinpart Thiswassubsequentlyreplicatedin283,752UKBiobankparticipantsnotincludedinthedis-
bytheNationalCenterforAdvancingTranslational coverysample,including50,915cases(OR1.06,p=5.3×10−11),andexceededgenome-
Sciences,CTSIgrantUL1TR000124,andthe
widesignificanceinjointmeta-analysis(OR1.07,p=4.5×10−19).Wefoundsuggestiveasso-
NationalInstituteofDiabetesandDigestiveand
KidneyDiseaseDiabetesResearchCenter(DRC) ciationsatthreeotherlociinthediscoverysample,twoofwhichexceededgenome-widesig-
grantDK063491totheSouthernCalifornia nificanceinjointmeta-analysis:anintergenicvariant,rs7833174,locatedbetweenCCDC26
DiabetesEndocrinologyResearchCenter.The
andGSDMC(OR1.05,p=4.4×10−13),andanintronicvariant,rs4384683,inDCC(OR0.97,
contentissolelytheresponsibilityoftheauthors
anddoesnotnecessarilyrepresenttheofficial p=2.4×10−10).Inthisfirstreportedmeta-analysisofGWASforCBP,weidentifiedandrepli-
viewsoftheNationalInstitutesofHealth. catedageneticlocusassociatedwithCBP(SOX5).Wealsoidentified2otherlocithat
FraminghamHeartStudy:FromtheFramingham
reachedgenome-widesignificanceina2-stagejointmeta-analysis(CCDC26/GSDMCand
HeartStudyoftheNationalHeartLungandBlood
DCC).
InstituteoftheNationalInstitutesofHealthand
BostonUniversitySchoolofMedicine.Thiswork
wassupportedbytheNationalHeart,Lungand
BloodInstitute’sFraminghamHeartStudy
(ContractNo.N01-HC-25195)anditscontractwith
Authorsummary
Affymetrix,Incforgenotypingservices(Contract
No.N02-HL-6-4278),andbygrantsfromthe
Backpainisthe#1causeofyearslivedwithdisabilityworldwideandoneofthemostcom-
NationalInstituteofNeurologicalDisordersand
monreasonsforhealthcarevisitsindevelopedcountries,yetsurprisinglylittleisknown
Stroke(NS17950)andtheNationalInstituteof
regardingthebiologyunderlyingthissymptom.Chronicbackpainisthemajordriverof
Aging,(AG08122,AG16495).Thecontentissolely
theresponsibilityoftheauthorsanddoesnot thesocietalburdenofbackpain.Identifyingbiologicalpathwaysinvolvedinchronicback
necessarilyrepresenttheofficialviewsofthe painthroughgeneticassociationstudiesmightrevealinsightsintotheunderlyingmecha-
FraminghamHeartStudyorBostonUniversity nismsinvolvedorsuggestpotentialavenuesforthedevelopmentofnewtreatments.We
SchoolofMedicine.GenerationScotland:
conductedthefirstgenome-wideassociationstudymeta-analysistoexaminegeneticvari-
GenerationScotland(GS)receivedcorefunding
antsassociatedwithchronicbackpain.Weidentifiedvariantsassociatedwithchronic
PLOSGenetics|https://doi.org/10.1371/journal.pgen.1007601 September27,2018 2/23
Genome-widemeta-analysisofchronicbackpain
fromtheChiefScientistOfficeoftheScottish
GovernmentHealthDirectoratesCZD/16/6andthe backpainin158,025individualsofEuropeanancestryfrom16cohortsinEuropeand
ScottishFundingCouncilHR03006.Genotypingof NorthAmerica,andreplicatedourfindingsin283,752UKBiobankparticipantsofEuro-
sampleswascarriedoutbytheGeneticsCore
peanancestrynotincludedinthediscoverysample.Ourstudyidentifiesthreenovel
LaboratoryattheWellcomeTrustClinicalResearch
genome-widesignificantassociationswithchronicbackpain,andsuggestspossibleshared
Facility,Edinburgh,Scotlandandwasfundedby
geneticmechanismswithothertraitssuchascartilage,osteoarthritis,lumbardiscdegen-
theMedicalResearchCouncilUKandthe
WellcomeTrust(WellcomeTrustStrategicAward eration,depression,andheight/vertebraldevelopment.
“STratifyingResilienceandDepression
Longitudinally”(STRADL)Reference104036/Z/14/
Z).JohnstonCountyOsteoarthritisProject:The
JoCoissupportedinpartbyS043,S1734,& Introduction
S3486fromtheCDC/AssociationofSchoolsof
PublicHealth;5-P60-AR30701&5-P60-AR49465- Backpaincausesmoreyearslivedwithdisabilitythananyotherhealthconditionworldwide.
03fromNIAMS/NIH;genotypingwassupportedby [1]Althoughmostadultsexperienceanew(‘acute’)episodeofbackpainatsomepointin
Algynomics,Inc.Mr.OsSweden:MrOSSwedenis theirlives,thesocietalburdenofbackpainisdrivenbytheminorityofindividualswhofailto
supportedbytheSwedishResearchCouncil,the
recoverfromsuchepisodesandgoontodeveloppersistent(‘chronic’)backpain.[2]Chronic
SwedishFoundationforStrategicResearch,the
backpain(CBP)hasanumberofdefinitionsbutismostoftenconsideredasbackpainofdura-
ALF/LUAresearchgrantinGothenburg,the
LundbergFoundation,theKnutandAlice tion(cid:21)3monthsinclinicalpractice,andadurationof(cid:21)6monthsisalsocommonlyusedin
WallenbergFoundation,theTorstenSoderberg research.[3,4]
Foundation,andtheNovoNordiskFoundation,the Backpainismoderatelyheritable.Meta-analysisof11twinstudiesofbackpainindicatesa
ALF/FoUUresearchgrantinSkane,Herman
heritabilityof40%,withapatternofmonozygotic(r =0.56)anddizygotic(r =0.28)twin
Ja¨rnhardts,KocksandO¨sterludsFoundations. MZ DZ
correlationssuggestinganadditivegeneticmodel(2r =r ).[5,6]Heritabilityisgreaterfor
OsteoporoticFracturesinMen(MrOs)US:The DZ MZ
chronicthanforacutebackpain.[7]Nevertheless,geneticstudiesattemptingtoidentifyspe-
OsteoporoticFracturesinMen(MrOS)Studyis
supportedbyNationalInstitutesofHealthfunding. cificgeneticmarkersforCBPhavetodatebeenlimitedtosmallstudiesusingthecandidate
Thefollowinginstitutesprovidesupport:the geneapproach.[8,9]AlthoughCBPisoftenattributedtoanatomicchangessuchasinterverte-
NationalInstituteofArthritisandMusculoskeletal braldiscdegenerationordischerniation,suchfindingshaveonlyweakassociationwithCBP,
andSkinDiseases(NIAMS),theNationalInstitute
[10,11]andexplainonlyasmallproportion(7–23%)ofthegeneticinfluenceonbackpain
onAging(NIA),theNationalCenterforResearch
[12].TheunexplainedgeneticcontributiontoCBPmayinvolvenotonlyspinepathologybut
Resources(NCRR),andNIHRoadmapforMedical
Researchunderthefollowinggrantnumbers:U01 alsofunctionalpredispositiontochronicpaininvolvinghigher-orderneurologicprocesses
AR45580,U01AR45614,U01AR45632,U01 relatedtothegenerationandmaintenanceofpain.[13–15]Furthermore,psychologicalfactors
AR45647,U01AR45654,U01AR45583,U01 suchasdepressionarewidelyrecognizedasimportantriskfactorsforCBP.[16]Giventhe
AG18197,U01-AG027810,U01AG042140,U01
rangeofprocessesthatmightcontributetoCBP,theagnosticgenome-wideassociation
AG042143,U01AG042124,U01AG042145,U01
approachmayidentifynovelgeneticvariantsassociatedwithCBPandprovideinsightsinto
AG042139,U01AG042168,U01AR066160,UL1
underlyingbiologicalmechanismsnotpreviouslyconsidered.
TR000128,andUL1RR024140.TheNational
InstituteofArthritisandMusculoskeletalandSkin ThisresearchwasaninternationalcollaborationbetweeninvestigatorsfromtheCohorts
Diseases(NIAMS)providesfundingfortheMrOS forHeartandAgingResearchinGenomicEpidemiology(CHARGE)ConsortiumMusculo-
ancillarystudy‘GWASinMrOSandSOF’underthe skeletalWorkgroup[17]andtheEuropeanUnionFP7projectPain-OMICS(‘Multi-dimen-
grantnumberRC2ARO58973.Osteoarthritis
sionalomicsapproachtostratificationofpatientswithlowbackpain’).Weconductedameta-
Initiative(OAI):Thisstudywassupportedbythe
analysisofGWASofCBPinadultsofEuropeanancestryfrom16community-andpopula-
AmericanRecoveryandReinvestmentAct(ARRA)
throughgrantnumberRC2-AR-058950from tion-basedcohorts,includingthosefromtheCHARGEandPainOmicsconsortia,andthe
NIAMS/NIH.TheOAIispublic-privatepartnership UKBiobank.Theaimwastoidentifynovelassociationsbetweenspecificgeneticmarkersand
comprisedoffivecontracts(N01-AR-2-2258;N01- CBP,andelucidatethebiologicalmechanismsunderlyingthiscondition.
AR-2-2259;N01-AR-2-2260;N01-AR-2-2261;
N01-AR-2-2262)fundedbytheNIH.Additional
supportwasprovidedbyNIHgrantP30- Results
DK072488.RotterdamStudy:TheRotterdam
Studyoverview
StudyissupportedbytheErasmusMedicalCenter
andErasmusUniversity,Rotterdam;the Genome-widediscoverymeta-analysiswascomprisedofadultsofEuropeanancestryfrom16
NetherlandsOrganizationforScientificResearch
cohorts(n=158,025including29,531CBPcases;Table1),including15CHARGEcohorts
(NWO),theNetherlandsOrganizationforHealth
andparticipantsfromtheUKBiobank(UKB)interimdatarelease(UKB1).Afterqualitycon-
ResearchandDevelopment(ZonMw),the
trol,thenumberofSNPsincludedinthemeta-analysisrangedfrom6,205,227to9,775,703,
PLOSGenetics|https://doi.org/10.1371/journal.pgen.1007601 September27,2018 3/23
Genome-widemeta-analysisofchronicbackpain
ResearchInstituteforDiseasesintheElderly dependingonthecohort(S1andS2Tables).Linkagedisequilibrium(LD)scoreregression
(RIDE),theMinistryofEducation,Cultureand (LDsr)wasuseddistinguishpolygenicityfrompotentialconfounding,[18]usingLDscores
Science,theMinistryforHealth,Welfareand
fromEuropeanancestry1000Genomesdata.Thegenome-widesignificancelevelwasdefined
Sports,theEuropeanCommission(DGXII),and
asp<5×10−8,andsuggestivesignificancelevelwasdefinedasp<5×10−7,afterusingtheLDsr
theMunicipalityofRotterdam.Thegenerationand
interceptasacorrectionfactor.ForthoseSNPsofgenome-widesuggestivesignificanceinthe
managementofGWASgenotypedataforthe
RotterdamStudy(RSI,RSII,RSIII)wasexecuted discoveryphase,replicationwasconductedinasampleofUKBEuropeanancestryparticipants
bytheHumanGenotypingFacilityoftheGenetic (UKB2)whowerenotpartoftheinterimdatarelease(n=283,752subjects,including50,915
LaboratoryoftheDepartmentofInternalMedicine, CBPcases),andajoint(discovery-replication)meta-analysiswasperformed.Wethencon-
ErasmusMC,Rotterdam,TheNetherlands.The
ductedfunctionalcharacterizationofvariantsandlociachievinggenome-widesignificancein
GWASdatasetsaresupportedbytheNetherlands
thejointmeta-analysis.
OrganisationofScientificResearchNWO
Investments(nr.175.010.2005.011,911-03-012),
theGeneticLaboratoryoftheDepartmentof
InternalMedicine,ErasmusMC,theResearch
InstituteforDiseasesintheElderly(014-93-015; Meta-analysisofGWASofCBP
RIDE2),theNetherlandsGenomicsInitiative(NGI)/
Thecharacteristicsofcohortsincludedinthediscoverymeta-analysisareshowninTable1.
NetherlandsOrganisationforScientificResearch
(NWO)NetherlandsConsortiumforHealthyAging Themeanageofparticipantsineachcohortrangedbetween53–76years.Withincohorts,
(NCHA),projectnr.050-060-810.Studyof meanage,BMI,andproportionoffemaleswasmoreoftenhigheramongCBPcasesthan
OsteoporoticFractures:TheStudyofOsteoporotic amongthosewithoutCBP.Aquantile-quantileplotcomparingthemeta-analysisassociation
Fractures(SOF)issupportedbyNationalInstitutes
resultswiththoseexpectedbychanceispresentedinS1Fig.TheLDsrinterceptwas1.007
ofHealthfunding.TheNationalInstituteonAging
(standarderror0.006),λwas1.114,andtheLDsrratiowas0.0581(standarderror0.053),pro-
(NIA)providessupportunderthefollowinggrant
numbers:R01AG005407,R01AR35582,R01 vidingnoevidenceofinflationofp-valuesfrompopulationstratification.Meta-analysisresults
AR35583,R01AR35584,R01AG005394,R01 aresummarizedintheManhattanplotshowninFig1.
AG027574,andR01AG027576.TheNational Agenome-widesignificantassociation(OR1.08,p=7.2×10−10)wasfoundforrs12310519
InstituteofArthritisandMusculoskeletalandSkin
onchromosome12inanintronicregionofSOX5,withlittleevidenceforheterogeneity
Diseases(NIAMS)providesfundingfortheMrOS
(I2=0,p=0.95)(Table2,S2Fig).SeveralothersignalswereinhighLD(r2>0.8)withthetop
ancillarystudy‘GWASinMrOSandSOF’underthe
signal(S3Fig),butnonewereindependentlyassociatedwithCBPinanalysesconditionalon
grantnumberRC2ARO58973.10,001Dalmatians:
SupportforfieldworkfromUniversityofSplitand rs12310519.
ZagrebMedicalSchools,theInstitutefor Noothervariantsachievedgenome-widesignificance,butvariantsinthreeotherloci
AntropologicalResearchinZagrebandtheCroatian reachedsuggestivesignificance(Table2,S3Table,S4–S9Figs):rs1453867(OR0.95,
InstituteforPublicHealth.TheSNPgenotypingfor p=7.7×10−8),locatedinanintronicregionofchromosome2withinDIS3L2;rs7833174(OR
theViscohortwasperformedinthecore
1.06,p=1.0×10−7),locatedinanintergenicregiononchromosome8betweenCCDC26(a
genotypinglaboratoryoftheWellcomeTrust
ClinicalResearchFacilityattheWesternGeneral longnon-codingRNA)andGSDMC;andrs4384683(OR0.95,p=3.2×10−7),locatedinan
Hospital,Edinburgh,Scotland.TheSNP intronicregionofchromosome18withinDCC.Ineachofthese3regions,therewasnoother
genotypingfortheKorculacohortwasperformed variantreachingthesuggestivesignificancelevelinanalysesconditionalontheleadSNPinthe
inHelmholtzZentrumMu¨nchen,Neuherberg,
region.Posthocsecondaryanalysesofthediscoverysampleshowedeffectsofsimilarmagni-
Germany.TheSNPgenotypingwasperformedby
tudeanddirectionbetweentheCHARGEcohortsandtheUKBinterimdatareleaseforassoci-
AROSAppliedBiotechnology,Aarhus,Denmark.
ationsbetweentheleadvariantsinthetop4lociandCBP(S4Table).
ThestudywasfundedbytheMedicalResearch
CouncilUK,TheCroatianMinistryofScience, Weexaminedthese4topvariantsin283,752UKBindividualsnotincludedinthediscovery
EducationandSports(grant216-1080315-0302), sample(UKB2),including50,915cases(Table2).Forall4variants,thedirectionofassociation
theEuropeanUnionframeworkprogram6 wasthesameindiscoveryandreplication.Theassociationforrs12310519inSOX5replicated
EUROSPANproject(contractno.LSHG-CT-2006- inUKB2(OR1.06,p=5.3×10−11),andexceededgenome-widesignificanceinthejointanaly-
018947),theCroatianScienceFoundation(grant
sis(OR=1.07,p=4.5×10−19).Ofthe3suggestive-significancevariantsfromthediscovery
8875),theCentreforResearchExcellencein
PersonalizedMedicineandtheCentreof stage,rs7833174atCCDC26/GSDMC(OR1.05,p=4.4×10−13)andrs4384683inDCC(OR
CompetenciesforIntegrativeTreatment, 0.97,p=2.4×10−10)exceededgenome-widesignificanceinthejointmeta-analysis,but
PreventionandRehabilitationusingTMS. rs1453867inDISL32(OR0.98,p=3.9×10−7)didnot(Table2).Thus,wedemonstrate
TwinsUK:TwinsUKreceivesfundingfromthe
genome-widesignificantassociationsofCBPwithlocitaggedbyrs12310519(SOX5),
WellcomeTrust;EuropeanCommunity’sSeventh
rs7833174(CCDC26/GSDMC),andrs4384683(DCC),withreplicationforrs12310519in
FrameworkProgramme(FP7/2007-2013toTwins
UK);theNationalInstituteforHealthResearch SOX5.
PLOSGenetics|https://doi.org/10.1371/journal.pgen.1007601 September27,2018 4/23
Genome-widemeta-analysisofchronicbackpain
(NIHR)ClinicalResearchFacilityatGuy’s&St CharacterizationofvariantsinSOX5,CCDC26/GSDMC,andDCC
Thomas’NHSFoundationTrustandNIHR
Functionalcharacterizationfollowedthesamestepsforeachofthe3locithatachieved
BiomedicalResearchCentrebasedatGuy’sandSt
Thomas’NHSFoundationTrustandKing’sCollege genome-widesignificanceinthejointmeta-analysis.First,weexaminedcross-phenotype
London.UKBiobank:Thisresearchhasbeen geneticassociationsbetweeneachleadSNPandtraitswithpossibleconceptuallinkstoCBP,
conductedusingtheUKBiobankResource(project inlook-upsofpubliclyandprivatelyavailableGWASdatasets.WheretheleadSNPwasnot
#18219).WearegratefultotheUKBiobank
presentinadataset,weexaminedassociationswiththevariantinhighestLDwiththelead
participantsformakingsuchresearchpossible.Dr.
SNP.Second,weannotatedleadvariantsandthoseinLD(r2(cid:21)0.6)forconsequencesongene
SmithisaResearchScientistattheVAPuget
functions(usingthecombinedannotationdependentdepletion[CADD]score[21]),potential
SoundHealthCareSystem.TheworkofDr.
TsepilovwaspartlysupportedbytheRussian regulatoryfunctions(usingRegulomeDBscore[22]),andeffectsongeneexpression(using
MinistryofScienceandEducationunderthe5-100 GTExv6[23,24]),andexaminedwhetherthesevariantsresidedinenhancerregionsfor
ExcellenceProgramme.Thefundershadnorolein
selectedtissueswithconnectionstothespineorpainprocessing(usingdatafromtheRoad-
studydesign,datacollectionandanalysis,decision
mapEpigenomicsConsortium[25,26])(Methods,S1Text).
topublish,orpreparationofthemanuscript.
SOX5. AmongCBP-relatedtraitsexamined,theleadSNPinSOX5,rs12310519,was
Competinginterests:BMPservesontheDSMBof
moststronglyassociatedwithimaging-detectedlumbarintervertebraldiscdegeneration
aclinicaltrialfundedbyZollLifeCorandonthe
(p=1.1×10−4;S5Table)[27].ThehighestCADDscoreamongSOX5variantswas10.52forthe
SteeringCommitteeoftheYaleOpenDataAccess
leadSNPintheregionrs12310519,indicatingitispredictedtobeamongthe10%mostdelete-
ProjectfundedbyJohnson&Johnson;YSAand
LKarefoundersandco-ownersofPolyOmica,a riouspossiblesubstitutionsinthehumangenome(S1Appendix).However,theoverallregula-
privategenomicsresearchorganization;these torypotentialofthesevariantswaslowaccordingtoRegulomeDBscore(scoresof6[‘minimal
relationshipsdonotposeknownconflictswiththe bindingevidence’])(S1Appendix).Therewerenomeaningfulassociationswithgeneexpres-
contentofthisworkpresented.Wetheauthorsdo sionusingGTExv6.TheleadSNPrs12310519andvariantsinLD(r2>0.6)containedactive
nothaveanyotherfinancialintereststhatcould
enhancermarksinchondrogeniccellsusingRoadmapEpigenomicsConsortiumdata(Fig2,
createapotentialconflictortheappearanceofa
S1Appendix).
potentialconflictofinterestwithregardtothis
work. CCDC26/GSDMC. Inlook-upsofGWASofselectedtraitswithpossiblelinkstoCBP
(S5Table),theleadSNPrs7833174wasmoststronglyassociatedwithheightinUKB[28]
(p=1.3×10−59)andhipcircumferenceinUKB[28](p=1.8×10−5).TheleadSNPrs7833174
wasalsoassociatedwithradiographichiposteoarthritis[29](p=4.9×10−4)(S5Table).Allvari-
antsinCCDC26/GSDMCthatweresuggestivelyassociatedwithCBPshowedcross-phenotypic
associationswithlumbarmicrodiscectomyforsciaticainarecentGWASofIcelandicadults
[30](S6Table,lowestp=5.6×10−12).Thedirectionofeffectontheseotherphenotypeswasthe
sameasthedirectionofeffectonCBP(i.e.theTalleleassociatedwithgreaterheight,greater
riskofradiographichiposteoarthritis,andgreaterriskoflumbardiscectomyforsciaticawas
alsoassociatedwithgreaterCBPrisk).ThehighestCADDscoreamongCBP-associatedvari-
antsatCCDC26/GSDMCwas18.75forrs6470778,indicatingthatthisSNPispredictedtobe
amongthe5%mostdeleterioussubstitutionsinthehumangenome,andtheoverallregulatory
potentialofthesevariantswassubstantialaccordingtoRegulomeDBscore(highestRegulo-
meDBscoreof2b[‘likelytoaffectbinding’])(S1Appendix).Inexaminationofeffectson
geneexpressionusingGTExv6,variantsinLDwithrs7833174(r2>0.6)werealsoeQTLs
forGSDMCexpressioninesophagealmucosa,skin,andskeletalmuscle(S1Appendix,
p<5×10−8).TheleadSNPrs7833174andvariantsinLD(r2>0.6)containedactiveenhancer
markslocatedinregulatoryregionsformesodermalcells,astrocytes,chondrogeniccells,and
osteoblastsindatafromtheRoadmapEpigenomicsConsortium(Fig2,S1Appendix).
DCC. Inlook-upsofGWASofselectedtraitswithpossiblelinkstoCBP(S5Table),the
leadSNPrs4384683wasassociatedwithdepressivesymptoms[31](p=5.9×10−4),withthe
samedirectionofeffect(i.etheAallelewasassociatedwithlessdepressivesymptomsand
lowerCBPrisk).ThehighestCADDscoreamongvariantsatDCCthatweresuggestivelyasso-
ciatedwithCBPwas11.21forrs2116378,indicatingthatrs2116378ispredictedtobeamong
the10%mostdeleterioussubstitutionsinthehumangenome,buttheoverallregulatorypoten-
tialofthesevariantswaslowaccordingtoRegulomeDBscore(highestRegulomeDBscoreof
PLOSGenetics|https://doi.org/10.1371/journal.pgen.1007601 September27,2018 5/23
Genome-widemeta-analysisofchronicbackpain
Table1. Cohortsinmeta-analysisofgenome-wideassociationstudiesofchronicbackpain(Europeanancestry).
Cohort Studysetting Country Sample Chronicbackpain Prevalence Age(yr) BMI(kg/ Women
size definition (%) m2) (%)
CardiovascularHealth Community USA 2849 (cid:21)1monthofback 14.2% Cases(n=404) 72.1±5.1 27.3±5.0 73.3%
Study(CHS) paininconsecutive
Controls 72.1±5.2 26.1±4.3 59.6%
years
(n=2445)
FraminghamHeart Community USA 2673 (cid:21)6monthsofback 21.0% Cases(n=561) 67.7±9.3 28.8±5.8 62.2%
Study[19] pain
Controls 66.4±9.1 28.0±52 52.9%
(n=2112)
GenerationScotland Population UK 5071 (cid:21)3monthsofback 26.0% Cases 54.9±11.8 28.1±5.7 66.7%
pain (n=1322)
Controls 52.4±12.7 26.4±4.6 55.4%
(n=3749)
JohnstonCounty Population USA 480 (cid:21)6monthsofback 38.8% Cases(n=186) 72.0±8.0 31.4±6.3 65.0%
OsteoarthritisProject pain
Controls 73.0±8.0 29.3±5.2 58.4%
(JoCo)
(n=294)
Mr.OsSweden
Gothenburg Population Sweden 920 (cid:21)6monthsofback 14.2% Cases(n=131) 75.3±3.2 26.7±3.9 0%
pain
Controls 75.3±3.2 26.1±3.4 0%
(n=789)
Malmo Population Sweden 948 (cid:21)6monthsofback 10.8% Cases(n=102) 75.8±3.1 27.2±3.7 0%
pain
Controls 75.6±3.2 26.4±3.6 0%
(n=846)
Mr.OsUS Community USA 4615 (cid:21)6monthsofback 14.1% Cases(n=653) 74.6±6.1 28.0±4.1 0%
pain
Controls 73.9±5.9 27.3±3.8 0%
(n=3962)
OsteoarthritisInitiative Community USA 2474 (cid:21)1monthofback 13.5% Cases(n=335) 61.0±9.1 28.9±4.7 57.9%
(OAI) paininconsecutive
Controls 61.7±9.1 28.1±4.5 53.2%
years
(n=2139)
RotterdamStudy(RS)
RS-1 Community Netherlands 5965 (cid:21)6monthsofback 14.7% Cases(n=877) 69.1±9.2 26.7±4.0 72.0%
pain
Controls 70.0±9.4 26.2±3.7 58.3%
(n=5088)
RS-2 Community Netherlands 1566 (cid:21)6monthsofback 36.7% Cases(n=574) 65.3±8.0 27.7±4.2 66.7%
pain
Controls 64.6±8.0 27.3±4.1 55.4%
(n=992)
RS-3 Community Netherlands 3019 (cid:21)6monthsofback 38.2% Cases 57.4±6.9 28.1±4.8 59.5%
pain (n=1154)
Controls 56.9±6.7 27.4±4.5 54.3%
(n=1865)
StudyofOsteoporotic Community USA 3615 (cid:21)6monthsofback 16.3% Cases(n=589) 72.1±5.6 27.6±5.3 100%
Fractures(SOF) pain
Controls 71.4±5.2 26.6±4.4 100%
(n=3026)
10,001Dalmatians
Vis Population Croatia 251 (cid:21)3monthsofback 22.3% Cases(n=56) 67.3±13.2 27.8±4.4 69.6%
pain
Controls 63.7±12.1 26.7±4.0 52.8%
(n=195)
Korcula Population Croatia 773 (cid:21)3monthsofback 21.2% Cases(n=164) 64.3±12.9 28.0±4.3 70.7%
pain
Controls 58.0±14.9 27.0±41 64.0%
(n=609)
UKBiobank Population United 120,024 (cid:21)3monthsofback 18.0% Cases 57.3±7.9 28.5±5.4 54.0%
Kingdom pain (n=21,600)
Controls 57.0±7.9 27.4±4.8 52.4%
(n=98,424)
(Continued)
PLOSGenetics|https://doi.org/10.1371/journal.pgen.1007601 September27,2018 6/23
Genome-widemeta-analysisofchronicbackpain
Table1. (Continued)
Cohort Studysetting Country Sample Chronicbackpain Prevalence Age(yr) BMI(kg/ Women
size definition (%) m2) (%)
TwinsUK Population-based United 2782 (cid:21)3monthsofback 29.6% Cases(n=823) 56.7±12.6 27.4±5.3 90.3%
twinregistry Kingdom pain
Controls 54.3±13.9 26.0±4.9 90.0%
(n=1959)
Totalofallcohorts - - 158,025 - - Cases - - -
(n=29,531)
Controls - - -
(n=128,494)
https://doi.org/10.1371/journal.pgen.1007601.t001
5)(S1Appendix).TherewerenomeaningfulassociationswithgeneexpressionusingGTExv6.
IndatafromtheRoadmapEpigenomicsConsortium,theleadSNPrs4384683andvariantsin
LD(r2>0.6)containedactiveenhancermarksinH9humanembryonicstemcell-derivedneu-
ralcells(Fig2,S1Appendix).
Secondaryanalysestoexamineinterrelationshipswithheight
PosthocanalysesamongUKB1participantsfromthediscoverysample(n=120,023)indicated
thatassociationswithCBPfortheleadvariantinSOX5weresimilarwithandwithoutadjust-
mentforheightasacovariate,andinconditionalanalysesaccountingforheight(S1Text,
S7Table).AssociationswithCBPfortheleadvariantinCCDC26/GSDMCwerealsosimilar
withandwithoutadjustmentforheightasacovariate.However,associationswithCBPwere
markedlydiminishedwhenconditionalontheleadheight-associatedvariantintheregion,
andassociationswithheightweremarkedlydiminishedwhenconditionedontheleadCBP-
associatedvariantintheregion(S7Table).Thissuggeststhatthesamefunctionalvariantis
responsibleforassociationofCCDC26/GSDMClocuswithheightandCBP,althoughanalter-
nativeexplanationistwofunctionalvariantsintightLD.AssociationswithCBPforthelead
variantinDCCweresimilarwithandwithoutadjustmentforheightasacovariate,andincon-
ditionalanalysesaccountingforheight(S7Table).
ToexaminepossiblecausaleffectsofheightonCBP,weconductedatwo-sampleMende-
lianrandomization(MR)analysisusinggeneticvariantsassociatedwithstandingheightinthe
GIANTconsortiumastheexposure,andthediscoveryphaseGWASmeta-analysisofCBPas
theoutcome.Resultsofthetwo-sampleMRusing326SNPsandtheinstrumentsinvolvedare
availableintheS2Appendix.Theseinstrumentsexplained10.1%ofthevarianceinheight,
withanaverageSNP-heightF-statisticof78.5,indicatingsubstantialinstrumentstrength.ORs
forCBPwere1.10perstandarddeviationincreaseinheightwithinversevarianceweighted
(IVW)regression(p<0.0001).However,therewassignificantheterogeneityamongSNPs
(I2=0.35;p<0.0001),suggestinghorizontalpleiotropyforatleastsomeSNPs(S3Appendix).
EstimateswithotherMRmethodsweredirectionallyconsistent,andallbutMR-Eggerregres-
sionwerestatisticallysignificant:anORforCBPof1.09perstandarddeviationincreasein
heightwithMR-Eggerregression(p=0.19);1.14perstandarddeviationincreaseinheight
withtheweightedmedianmethod(p<0.0001),and1.17perstandarddeviationincreasein
heightwiththeweightedmodemethod(p=0.02)(S3Appendix).ThemagnitudeofMResti-
matesafterexcluding14outlierSNPswereverysimilartothetwo-sampleMRusing326
SNPs,butwithsubstantiallylessheterogeneityamongstSNPs(I2=0.12;p=0.04),just
exceedingnominalsignificance(S2andS3Appendices).MR-Eggerinterceptswerecloseto0
withboththe326SNPand312SNPinstruments,andneitherwerestatisticallysignificant,
PLOSGenetics|https://doi.org/10.1371/journal.pgen.1007601 September27,2018 7/23
Genome-widemeta-analysisofchronicbackpain
Fig1.Manhattanplotformeta-analysis(discovery)ofGWASofchronicbackpain(n=158,025).GWAS=genome-wideassociationstudy.Results
usethelinkagedisequilibriumscoreregression(LDSR)interceptasacorrectionfactor.Redlinedepictsgenome-widestatisticalsignificance(P
<5×10−8).Bluelinedepictssuggestivesignificance(P<5×10−7).
https://doi.org/10.1371/journal.pgen.1007601.g001
suggestingnostrongdirectionalhorizontalpleiotropyundertheInSIDE(InstrumentStrength
IndependentonDirectEffect)assumption(S3Appendix).
SecondaryanalysestoexamineforinfluenceofrelatednessinUKBiobank. GWAS
analysesusinglinearmixed-effectmodelsinUKB1yieldedassociationsbetweenthe3lead
SNPsandCBPthatwereverysimilartotheoriginalanalysesusinglogisticregressioninterms
Table2. Associationresultsforchronicbackpain:Meta-analysis(discovery),replication,andjointmeta-analysis(cid:3).
Discovery(Meta-analysisofCHARGEand Replication(UKB2)b JointMeta-Analysis
PainOmicscohorts+UKB1)a (n=283,752) (Discovery-
(n=158,025) Replication)c
(n=441,777)
SNPrsID Chr:Posd NearestGene Location Alleles EAF OR SE p-value I2 Het.p- OR SE p-valueb OR SE p-value
value
rs12310519e 12:23975219 SOX5 intronic T/C 0.16 1.08 0.013 7.2x 0 0.95 1.06 0.009 5.3x 1.07 0.008 4.5x
10−10 10−11 10−19
rs1453867 2:232917899 DIS3L2 intronic T/C 0.65 0.95 0.010 7.7x10−8 13 0.31 0.98 0.007 0.021 0.97 0.006 3.9x10−7
rs7833174 8:130718772 CCDC26/ intergenic T/C 0.77 1.06 0.011 1.0x10−7 0 0.71 1.04 0.008 3.7x10−7 1.05 0.007 4.4x
GSDMC 10−13
rs4384683 18:50379032 DCC intronic A/G 0.54 0.95 0.009 3.2x10−7 0 0.86 0.97 0.007 4.2x10−5 0.97 0.006 2.4x
10−10
CHARGE=CohortsforHeartandAgingResearchinGenomicEpidemiology,UKB1=UKBiobankparticipantsfromtheinterimdatarelease[20],UKB2=UK
Biobankparticipantsnotincludedintheinterimdatarelease,chr:pos=chromosome:position,alleles=effect/other,EAF=effectallelefrequencyOR=oddsratio,het.=
heterogeneity
(cid:3)Topvariantateachlocusmeetingsuggestiveorgenome-widesignificancelevelindiscoverystage(p<5.0x10-7).
aAftergenomiccontrolusingtheLDscoreregressionintercept
bReplicationforrs12310519.Thethresholdforsignificanceinreplicationofrs12310519wasp<0.05(0.05/1)
cThethresholdforgenome-widesignificanceinjointanalysiswasp<5×10−8
dBuildGRCh37/hg19
ers115392701hasmergedintors12310519
https://doi.org/10.1371/journal.pgen.1007601.t002
PLOSGenetics|https://doi.org/10.1371/journal.pgen.1007601 September27,2018 8/23
Genome-widemeta-analysisofchronicbackpain
Fig2.Significantvariantsareco-localizedwithpotentialgeneregulatorymarkers.Theheatmapdepictsthe
percentageofvariantsingeneregulatoryregions(associatedwithenhancers/promotors)inLD(r2>0.6)with
rs7833174(CCDC26/GSDMC),rs12310519(SOX5),andrs4384683(DCC).Weexaminedepigenetichistonemarksin
selectedcelltypes/tissuesincludingchondrogenic,bone-related,neuronalandbraincells/tissues;mesodermalcells
(relatedtonotochord);andpsoasmuscle(locatedproximaltothelumbarspine).
https://doi.org/10.1371/journal.pgen.1007601.g002
ofstatisticalsignificance,indicatingnomeaningfulinfluenceonthestudyresultsduetorelat-
edness(S8Table).
HeritabilityofCBPandgeneticcorrelations
SNPheritabilityofCBPontheliabilityscalewas7.6%.Partitionedheritabilitybyfunctional
categoryusingstratifiedLDscoreregressionshowedsignificantenrichment(p=0.0004)for
regionsconservedinmammals,with2.6%ofSNPsexplaining40%oftheSNPheritabilityof
CBP,withoutsignificantenrichmentforotherfunctionalcategories,includingcodingregions
(S4Appendix).Thispatternofpartitionedheritabilitywasbroadlysimilaracrosscelltype
groups,includingcentralnervoussystem(CNS),connectivetissueandbone,andskeletalmus-
cle,amongothers(S4Appendix).Geneticcorrelationsofnominalsignificance(rangeofr
g
0.17–0.31,p<0.05)werefoundwithanthropometrictraitsinvolvingobesityorbodyfatdistri-
bution(waistcircumference,hipcircumference,waist-hipratios,overweight/obesityclasses,
andBMI),butnotwithheight(S9Table).Largermagnitudenominallysignificant(p<0.05)
geneticcorrelationswerealsofoundwithdepression-relatedphenotypes(rangeofr 0.46–
g
0.52),self-reportedosteoarthritis(r =0.63),andICD-10-definedosteoarthritis(r =0.49)
g g
phenotypes.
Discussion
Thisstudyisthefirstmeta-GWASofCBP.Thiscollaborationbetweentwointernationalcon-
sortiaforgenomicstudiesofcomplextraitsintheUSAandEuropeincorporateddatafrom
16cohortsandmorethan441,000participantsofEuropeanancestryacrossdiscoveryand
replicationsamples.OurstudyidentifiesthreenovelassociationswithCBPforlociatSOX5,
CCDC26/GSDMC,andDCC.
CBPwasmoststronglyassociatedwithrs12310519inanintronicregionoftheSOX5gene.
TheSOXgenesareafamilyoftranscriptionfactorsinvolvedinvirtuallyallphasesofembry-
onicdevelopment,andarethoughttodeterminethefateofmanycelltypes.TheSOXgenes
aredefinedbycontainingtheHMG(‘highmobilitygroup’)boxofageneinvolvedinsex
determinationcalledSRY(‘sexdeterminingregion’)[32].SOX5andSOX6haveoverlapping
PLOSGenetics|https://doi.org/10.1371/journal.pgen.1007601 September27,2018 9/23
Genome-widemeta-analysisofchronicbackpain
functionsandworktogetherinclosecoordinationthatisnecessaryforefficientchondrogen-
esis[33].InactivationofSOX5leadstominordefectsincartilageandskeletogenesisinmice,
whereasSOX5/SOX6doubleknockoutshaveseverechondrodysplasia[34].Togetherwith
SOX9,SOX5andSOX6aresometimesreferredtoasthe‘masterchondrogenicSOXtrio’[33,
35].PriorworkindicatesanimportantroleforSOX5inarticularcartilageandosteoarthritis
[36,37],andsucharolewasalsosupportedbyourfunctionalannotationshowingthat
rs12310519(andSNPsinhighLD)overlappedwithpotentialregulatoryregionsforchondro-
geniccells.SOX5/6arealsoessentialfornotochorddevelopment,andthroughthisrolethey
arecriticalintheformationofthevertebralcolumn,includingtheintervertebraldiscs[33,35,
38].InactivationofSOX5and/orSOX6inmiceleadstoarangeofabnormalitiesinthedevel-
opmentofspinalstructures[38].AlthoughvariantsinSOX5havenotbeenreportedinprior
GWASoflimbosteoarthritis(knee,hip,orhand)[39–46],theassociationofSOX5withCBP
mayinvolvethespinalstructuresspecifically.Consistentwiththis,wefoundacross-pheno-
typicassociationfortheleadCBP-associatedvariantinSOX5withimaging-detectedlumbar
intervertebraldiscdegenerationinapriorGWASmeta-analysis[27].FutureGWASmayalso
beusefultocharacterizeotherspine-relatedphenotypesbesidesdiscdegeneration,suchas
osteoarthritisofthezygapophyseal(‘facet’)joint,theonlytruesynovialjointinthespine[47].
TheintergenicvariantsatCCDC26/GSDMCassociatedwithCBPinthecurrentstudywere
alsopreviouslyfoundassociatedwithlumbarmicrodiscectomyforsciaticaduetointerverte-
braldischerniation.[30]Thesefindingsareintriguing,giventhatlumbardischerniations(an
aspectoflumbardiscdegeneration)havelongbeenimplicatedasacauseofsomeformsof
backpain.[48]Recentstudieshaveconcludedthatassociationsbetweenimaging-detected
lumbardischerniationandCBPareofmodestmagnitude.[10,11]Thismightexplainthe
smallmagnitudeassociationofthetopvariantatCCDC26/GSDMCwithCBPinthecurrent
study(OR1.08indiscovery),incontrasttothelargermagnitudeassociationseenwithmicro-
discectomyforsciatica(OR1.23).Functionalcharacterizationoftheseintergenicvariantssug-
gestthelikelyinvolvementofthegeneGSDMC.GSDMCencodestheproteinGasderminC,
partoftheGSDMfamilyofgenesthatisexpressedinepithelialtissues.Althoughthespecific
roleofGSDMCinlumbardischerniationand/orsciaticaisunclear,GSDMCisassociatedwith
differentialmethylationpatternsinosteoarthritis-relatedcartilageandsubchondralbonecarti-
lage,[49,50]consistentwithourfindingsthatvariantsinLDwithrs4384683werelocatedin
potentialregulatoryregionsinchondrocytesandosteoblasts.Ourexaminationofunivariate
cross-phenotypicgeneticassociationsforCBP-associatedvariantsatCCDC26/GSDMCalso
suggestpleiotropywithradiographichipOAforrs6470763.[29]Takentogether,thesedata
suggestinterconnectionsbetweenvariantsatCCDC26/GSDMCandCBPinvolvingcartilage,
osteoarthritis,and/orlumbardiscdegeneration.
ThethirdsignificantCBP-associatedvariantinourstudywasrs4384683,anintronicvari-
antinthegeneDCC(DeletedinColorectalCarcinoma),whichco-localizedwithregulatory
regionsinneuralembryonicstemcells.DCCencodesatransmembraneproteinthatisarecep-
torfornetrin-1,anaxonalguidancemoleculeinvolvedinthedevelopmentofspinalandcorti-
calcommissuralneurons.[51]InteractionsbetweenDCCandnetrin-1areamongthebest-
studiedaxonalguidanceprocesses,withkeyrolesduringdevelopmentandinadulthood,and
theyalsoaffectangiogenesis.[52,53]Increasedexpressionofnetrin-1andDCCoccursin
degeneratehumanintervertebraldiscscomparedtohealthycontroldiscs,andinnucleus
pulposuscomparedtoannulusfibrosis.[54]Netrin-1/DCCmightthereforemediateneurovas-
cularingrowthintotheintervertebraldisc,whichhaslongbeenimplicatedasapossiblemech-
anismofchronicdiscogenicbackpain.[54,55]Giventhewell-knownphenotypiccorrelation
betweendepressionandCBP[56],however,anotherpossibleexplanationforthelinkbetween
CBPandDCC(suggestedbythecross-phenotypeassociationofrs4384683withdepressive
PLOSGenetics|https://doi.org/10.1371/journal.pgen.1007601 September27,2018 10/23