Oral_Clefts__Imputation_Report

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1、GENEVAOralCleftsProjectImputationReport–HapMapIIIreferencepanelAugust27,2010ContentsI.SummaryandrecommendationsfordbGaPusersII.Studydataa.Samplesb.SNPsIII.Referencepanela.Samplesb.SNPsIV.StrandalignmentV.ImputationsoftwareandcomputingresourcesVI.Imputationoutputa.Genotypeprobabi

2、litiesb.Qualitymetricsc.MaskedSNPanalysisd.Additionalimputationqualityassessmenti.Maximumunrelatedsii.Samplesetdivisioniii.MendelianerrorcheckingVII.SummaryanddiscussionVIII.ReferencesIX.WebresourcesX.TablesXI.FiguresXII.Supplementaryfiles1I.SummaryandrecommendationsfordbGaPuser

3、sGenotypeimputationistheprocessofinferringunobservedgenotypesinastudysamplebasedonthehaplotypesobservedinamoredenselygenotypedreferencesampleofsimilargeneticbackground(Lietal.2009;Huangetal.2009).TheGENEVACoordinatingCenter(CC)performedgenotypeimputationfortheOralCleftsprojectus

4、ingBEAGLEsoftware(BrowningandBrowning2009).ImputationwasperformedinsubjectsofEuropeanandAsianancestryusingaHapMapPhaseIIIreferencepanel.Imputedgenotypesareprovidedastheprobabilityofeachofthethreegenotypestates,reflectingthelevelofcertaintyinthegenotypeprediction.Qualitymetricsar

5、eprovidedforeachimputedSNPthatcanbeusedforfilteringimputationresultsonaper‐SNPlevelpriortodownstreamanalyses.Toreducecomputationtime,familieswereassignedatrandomtooneoftwogroupsandimputedseparately,exceptfor24triosthatwereimputedinbothgroups.Thecorrelationofimputedgenotypesbetwe

6、enindividualsthatoccurinbothgroupsisveryhigh.Nevertheless,usersshouldconsiderpossibledifferencesbetweenthegroupsindownstreamanalyses.II.Studydataa.SamplesTheGENEVAOralCleftsstudyconsistsofprimarilycase‐parenttriosrecruitedfrom13differentsitesacrosstheUnitedStates,Europe,Southeas

7、tandEastAsia.AfterexcludingHapMapcontrols,duplicates,andsamplesofquestionableidentity,therewere7,089uniquesubjects.Foradetaileddescriptionofgenotypequalitycontrol(QC)fortheOralCleftsproject,pleaseseethereportavailableondbGaP.Principalcomponentsanalysis(PCA,Figure1)showsthatmosts

8、ubjectshaveEuropeanand/orAsianancestrywithconsi