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大小:426.42 KB
页数:27页
时间:2019-07-09
《Oral_Clefts__Imputation_Report》由会员上传分享,免费在线阅读,更多相关内容在行业资料-天天文库。
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
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