hispanic community health study / study of latinos (hchs -sol) · national institute of...
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HispanicCommunityHealthStudy/StudyofLatinos(HCHS- SOL)
NationalHeart,Lung,andBloodInstituteNationalInstituteofDiabetesandDigestiveandKidneyDiseases
NationalInstituteofNeurologicalDisordersandStrokeNationalInstituteofDeafnessandOtherCommunicationDisorders
NationalInstituteofDentalandCraniofacialResearchNationalInstituteforMinorityHealthandHealthDisparities
OfficeofDietarySupplements
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ChallengestoHealthDisparitiesResearch
• Barriers– LegalStatus– PastTraumas–Discrimination–Marginalization–DistrustofGovernment– CulturalorLinguisticDifferences
2(USC, Center for Health Journalism)
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Hispanic/LatinoDefined
Jaimes, Londono, Halpern, JAMA Dermatol, 2013
A- Latino refers to persons whose origin or ancestries are from countries of Latin America.
B-The US Office of Management and Budget uses the terms Hispanic and Latino interchangeably to refer to persons who indicated that their origin is Mexican, Puerto Rican, Cuban, Central and South American, or other Spanishculture or Spanish-speaking country or origin, regardless of race.
C-Hispanic include individuals whose origin or ancestry comes from Hispania, or D-Spanish-speaking persons of Latin American descent living in the United States.
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GrowthanddiversificationofUSLatinopopulation
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USHispanic/Latinos
1980 1990
2000 2010Pew Hispanic Center (www.pewhispanic.org)
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HCHS- SOLcohortoverview• Multicenterprospectivecohortrecruitedin2008-2011
• N=16,415participantsaged18to74yearsold1/3ofparticipantswere18-45yearsatbaseline (undersampled)2/3ofparticipantswere>45yrs atbaseline(oversampled)AreabasedhouseholdsampleinfourUScities
• TOPMed contactPIs:RobertKaplanandKariNorth• GeneticSIGchairs:K.North,E.Boerwinkle,T.Sofer• GeneticAnalysisCenter:BruceWeirandCathyLaurie• OthersitePIs:M.Daviglus (Chicago),N.Schneiderman (Miami),G.Talavera(SanDiego),J.Cai(CC)
• SpirometryreadingcenterPIs:GrahamBarr,PaulEnright,JohnHankinson
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RecruitmentN=16,415,ages
18-74
Annualfollow-upinterviewstodetermineoutcomesandchangesinkeyexposures2009-
2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019
Secondclinicvisit2014-2017
Baselineclinicvisit2008-2011
StudyTimeline
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Diseaseandbiometricphenotypes• Prevalent and incident pulmonary diagnoses + exacerbations• Pulmonary Function Testing (basal and post-bronchodilator)• Mortality (total and cause-specific)• Prevalent and incident CVD (MI, stroke, heart failure)•Anthropometry/Weight loss/gain • Lab values: lipids, glucose, OGTT, insulin, inflammation, CBC, Hepatitis A, B C, Total and HDL cholesterol, LFT, renal, etc• Oral/dental health• Pregnancy complications•Hearing • Blood pressure, ECG, echocardiography• Sleep quality and disorders • Cognitive Function• Substance Abuse • Diabetes• Health behaviors (smoking, diet, physical activity, etc)
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StudyPopulation
Miami,FL
Chicago,IL
SanDiego,CA
Bronx,NY
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• HispanicCommunityHealthStudy/StudyofLatinos(HCHS/SOL)– Community-basedstudyof16,415menandwomen,18-76yearsofageatbaselineexamination(2008-2011)
– Complexsamplingdesign– Self-identifiedas
• CentralAmerican• Cuban• Dominican• Mexican• PuertoRican• SouthAmerican• Other/Multiple
Pew Hispanic Center (www.pewhispanic.org)
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4outof5cohortmemberswerebornoutsideofthe50states
Lengthoftimelivinginthe50statesondateofenrollment
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DemographicCharacteristics
All Cuba Domin.Republic
Mexico PuertoRico
Cent.Amer.
So.Amer.
N 16,415 2,201 1,400 6,232 2,590 1,634 1,022
Men,% 40 46 34 37 41 39 40
College,% 15 20 15 12 14 14 22
Income>$50K,% 11 8 7 14 14 7 11
PreferSpanish,% 77 91 80 81 42 89 89
USresidence<10years,% 31 55 27 27 8 38 47
Daviglus ML JAMA 2012
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Asthmaprevalence
Mexican PuertoRican
Cuban CentralAmerican
Dominican SouthAmerican
Physician-diagnosedasthma,ever
7.8(6.8–8.9)
30.9(27.8–34)
23.3(21.1–25.7)
12.8(10.7–15)
15.7(13.0–18.7)
10.4(7.9–13.5)
Physician-diagnosedasthma,current
3.4(2.7–4.1)
15.3(13.2–17)
8.6(7.1–10.4)
4.5(3.4–6.0)
6.7(5.3–8.5)
4.3(2.9–6.2)
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AsthmaprevalenceishighestinLatinoswhocametothe50statesduringearlychildhood
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Estimated prevalence of asthma by age immigrated to US
Age immigrated to US
Prev
alenc
e of
ever
asth
ma
diagn
osed
by M
D
●
0
10
20
30
40
50
60%
1 5 10 15 20 25 30 35 40 45 50 55 60 65 70US
born
Note: Prevalence estimates and 95% confidence intervals are from a survey data logistic regression model with effects for age(continuous), sex, Hispanic background, and age at immigration (grouped into 65 categories)
GrahamBarrAmJRespir Crit CareMed 2015
+
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ElinaJerschow AmericanJournalofPreventiveMedicine2017
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ElinaJerschow AmericanJournalofPreventiveMedicine2017
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SOLGeneticProjects
• Omics inLatinos(OLa)GWAS
• PAGEconsortium– Metabochip– MEGAchip
• Wholegenomesequencing
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SOLGeneticProjects
• Omics inLatinos(OLa)GWAS
• PAGEconsortium– Metabochip– MEGAchip
• Wholegenomesequencing
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OLa GWASProjectSNPMicroarrayData
12,803studyparticipantsprovidedconsentforgeneticstudies
Illumina Omni2.5M+~150kcustomcontent‘SoL_HCHS_Custom_15041502_B’
Arraydesign– Papanicolaou(NHLBI),RotterandTaylor(LABiomed)
GenotypingperformedbyIllumina &QCbyLABiomed
QAbySOLGeneticAnalysisCenter(Univ.Washington)
Imputationto1000Gphase3
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AnkleBrachialIndex Dental
Anthropometrics Diabetes
Anxiety/Depression Electrocardiography
BloodCellCount PulmonaryDisease
BloodPressure Sleep
ChronicKidneyDisease mtDNA/YChr
Lipids Reproductivetraits
Smoking
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SOLGeneticAnalysisWorkingGroups
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www.olgastudy.org
20ScrolldownforallworkinggroupsandtheirmembersDirectoryhascontactinformation
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1.EstimaterelatednessusingKING-robust,whichisrobusttodiscretepopulationstructurebutnottoadmixtureordeparturesfromHWEwithinsub-populations.
2.Partitionthesampleintoamutuallyunrelatedsetandtheremaining(relativesoftheunrelatedsetandpossiblyeachother)
3.Performstandardprincipalcomponentsanalysis(PCA)onthesetofunrelatedindividualsandprojectontorelatedindividuals
4.Re-estimaterelatednessusing‘PC-Relate’,whichprovidesunbiasedkinshipcoefficientsinthepresenceofpopulationstructure,admixtureandHWEdepartures,usingindividual-specificallelefrequenciesestimatedfromsampleeigenvectors.
5.Repeatsteps2-5togetfinalsetsofeigenvectorsandkinshipcoefficients
De-convolutionofancestryandrelatednessinadmixedpopulationsMattConomos andTimThornton(UniversityofWashington)
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GeneticAnalysisIssues1. Tieredconsentallowsvariablelevelsofdatasharing.Reconsentingat
eachinpersonvisitmaynecessitatewithdrawalofsubjects
1. Samplesurveydesign,2-stageprobabilitysamplinga. Primarysamplingunit=UScensusblockgroupb. Secondarysamplingunit=householdc. Householdbasedsampling(average1.8enrolledperHH)
2. Relatedness,populationstructureandadmixturea. ~85%ofsubjectsaremutuallyunrelatedb. ~15%areeachrelatedtosomeoneintheunrelatedsetc. SOLparticipantsareverydiverseethnicallyandgenetically
i. Caribbeangroups:Cuban,Dominican,PuertoRicanii. Mainlandgroups:Mexico,CentralAmerica,SouthAmerica
d. Novelmethodusedtode-convoluteancestryandrelatedness(Conomos &Thornton)
MixedmodelandGEEapproacheshavebeendevelopedtohandletheseissuesinassociationtests(GWAS).BothcontrolTypeIerrorwell,butmixedmodelhasmorepower.(Mixedmodel– Conomos +Thornton;GEE- Lin+Tao)
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Populationstructure
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Principalcomponentsanalysis(PCA)
Conomos 2016.
PCAplots(EV1-3)
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Proportionofancestralbackgrounds
Conomos etal.2016.
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ContinentalancestryproportionsestimatedusingADMIXTUREsoftwareAutosomal
Xchromosome
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SeparatePCAforeachofthe3ancestries
HCHS-SOLgroups
Referencepopulations
SharonBrowningG32016
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SeparateclusteringofAfricancomponentofHondurans/Guatemalans
• Garífuna population.
• MayhaveancestryfromspecificpartsofAfrica.
• Ordriftduetosmallpopulationsize.
HCHS-SOLgroups
Referencepopulations
Africa
SharonBrowningG32016
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ThreedistinctAmerindianclusters
• Mexico,CentralAmerica,SouthAmerica.
HCHS-SOLgroups
Referencepopulations
Americas
SharonBrowningG32016
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SeparateclusteringofEuropeancomponentofPuertoRicans
• MayincludeancestryfromNorthAfricanorMiddleEast.
• Ordriftduetosmallpopulationsize.
HCHS-SOLgroups
Referencepopulations
Europe
SharonBrowningG32016
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Eachofthefirst5Eigenvectorsdifferentiatesamongself-identifiedgroups
• Usethese5eigenvectorstoadjustforancestryinassociationtestsandtodefinegeneticanalysisgroupsforstratifiedanalysis• Comparedwithself-identifiedbackground(personalorfamilyplaceoforigin),thegroupsaremorehomogeneousgeneticallyandincludeindividualswithmissingor“other”self-identification 31
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SOLGeneticProjects
• Omics inLatinos(OLa)GWAS
• PAGEconsortium– Metabochip– MEGAchip
• Wholegenomesequencing
32
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KariNorthUNC-CH
CALiCOConsortium
PopulationArchitectureusingGenomicsandEpidemiology(PAGE)Study
RuthLoosMountSinaiSchoolofMedicine
MSSMBiobank
TaraMatiseRutgersUniversity
CoordinatingCenterCharlesKooperbergFHCRC
Women’sHealthInitiative
ChrisHaimanUSC
MultiethnicCohortStudy
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ThePAGEStudyPopulationArchitectureusingGenomicsandEpidemiologyIINetwork
• Goal:Investigateancestrallydiversepopulationstogainabetterunderstandingofhowgeneticfactorsinfluencesusceptibilitytodisease.
• FocusonUSminoritypopulations.
17,328
4,696
22,250
653
3,944
1,056
African-American
Asian
Hispanic/Latino
NativeAmerican
NativeHawaiian
Others
ILLUMINA ARRAY SEMINAR, SEPTEMBER 2016
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Common Low Frequency Rare
AAC
●
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●●●
●●●●
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Common Low Frequency Rare
AFR
●
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0.3
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0.6
0.7
0.8
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0.4, 0
.5
0.3, 0
.4
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AMR
●
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●●●
●●●●
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0.3
0.4
0.5
0.6
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0.4, 0
.5
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Common Low Frequency Rare
SAS
●
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●●●●
0.2
0.3
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0.5
0.6
0.7
0.8
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0.4, 0
.5
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EAS
●
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0.3
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0.8
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.5
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EUR
●
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●●●
●●●●●
0.2
0.3
0.4
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0.6
0.7
0.8
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0.4, 0
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.4
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0.02
0.005
, 0.01
Variant Frequency
Impu
tatio
n Ac
cura
cy, M
ean
r2
Array●
●
●
●
Omni1MOmniExpressAxiom.EURMEGA
ComparisonofMEGAImputationAccuracytoOtherCommercialChips(SupplementaryFigure)
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SOLGeneticProjects
• Omics inLatinos(OLa)GWAS
• PAGEconsortium– Metabochip– MEGAchip
• Wholegenomesequencing
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HCHS/SOLsampleselectionforwholegenomesequencingN=1917asthmacases(everdiagnosedbyaphysician)N=4503controls(neverdiagnosedbyaphysician)
NHGRI/PAGE ~270samplesselectedforhighAmerindianancestryPrimarilyCentralandSouthAmerican(onlyonePuertoRican)WashingtonU.sequencingcenter
NHGRI/CCDG ~4000samplesselectedatrandom Baylorsequencingcenter
TOPMed Totalapprovedallocationof2150 Baylorsequencingcenter1. Allever-asthmacasesnotpreviouslyselectedbyPAGEorCCDG,N=1277.(Bringing
totalofever-asthmacasesto1917acrossallthreesampleselections)
2. SixsamplespreviouslyselectedbyPAGE,whichwillserveascross-sequencingcentercontrols(onepergeneticanalysisgroupe.g.Cuban,Mexican,Dominican,etc),N=6
3. RemainingPuertoRicansnotincludedinPAGEorCCDGselections,N=867.
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WethanktheparticipantsandstaffoftheHispanicCommunityHealthStudy/StudyofLatinos(HCHS/SOL)fortheircontributionstothisstudy.ThebaselineexaminationofHCHS/SOLwascarriedoutasacollaborativestudysupportedbycontractsfromtheNHLBItotheUniversityofNorthCarolina(N01-HC65233),UniversityofMiami(N01-HC65234),AlbertEinsteinCollegeofMedicine(N01-HC65235),NorthwesternUniversity(N01-HC65236),andSanDiegoStateUniversity(N01-HC65237).Thefollowinginstitutes,centers,andofficescontributedtothefirstphaseofHCHS/SOLthroughatransferoffundstotheNHLBI:NationalInstituteonMinorityHealthandHealthDisparities,NationalInstituteonDeafnessandOtherCommunicationDisorders,NationalInstituteofDentalandCraniofacialResearch(NIDCR),NationalInstituteofDiabetesandDigestiveandKidneyDiseases(NIDDK),NationalInstituteofNeurologicalDisordersandStroke,andNIHOfficeof DietarySupplements.TheGeneticAnalysisCenterattheUniversityofWashingtonwassupportedbyNHLBI andNIDCRcontracts(HHSN268201300005CAM03and MOD03).Additional analysissupportwasprovidedby1R01DK101855-01and13GRNT16490017.GenotypingeffortsweresupportedbytheNIHDepartmentofHealthandHumanServices(HSN26220/20054C),NationalCenterforAdvancingTranslationalScienceClinicalTranslationalScienceInstitute(UL1TR000124),andNIDDKDiabetesResearchCenter(DK063491).