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1、PLINK:atoolsetfor wholegenomeassociationanalysisShaunPurcellshaun@pngu.mgh.harvard.eduCenterforHumanGeneticResearch,MassachusettsGeneralHospitalBroadInstituteofHarvard&MITPurcelletal(2007)AJHGDatamanagementSummarystatisticsPopulationstratificationAssociationanalysisLinkagedise
2、quilibriumandhaplotypeanalysisSharedsegmentanalysisCopynumberanalysisDatamanagementRecodedataset(A,C,G,T→1,2)Reorder,reformatdatasetFlipDNAstrandExtract/removeindividuals/SNPsSwapinnewphenotypes,covariatesFilteroncovariatesMerge2ormorefilesetsP1AAACCGTTAATTP2ACAACGGTACTTP3CCAC
3、GGTTAATTP4CCAAGGGTAATTS1AAACCCCCS2ACAAACAAS3CGCGGGGGS4TTCGTTGTS5AAGTAAAAS6TTACTTTTP1S1AAP1S2ACP1S3CGP2S4ACP2S5CCP1S1A2C0P1S2A1C1P1S3C0G1P2S4A3C1P2S5C2C201010100101010101011010011101010101010110111010100101010111010010111011010101101010101010111010←PeopleSNPs→←GenotypesSNPsinCN
4、PsCompactbinaryformat←SNPsPeople→S1A/AP1P2P7P8S1A/CP3P4S1C/CP5S2G/TP5S2G/GP1P2P3P4ListbygenotypeS1S2S3S4P10121P20NA02P32121P40120NumericcodingSummarystatisticsFiltersandreportsforstandardmetricsGenotypingrateAllele,genotype,haplotypefrequenciesHardy-WeinbergMendelerrorsTestsof
5、non-randommissingnessbyphenotypeandby(unobserved)genotypeIndividualhomozygosityestimatesCheck/imputesexbasedonXchromosomeLD-baseddetectionofstrandflipsA/TandC/GSNPspotentiallyambiguousAutomatedsearchforplateeffectsw/subsequentmaskingofspecificSNP/individualgenotypesHanChineseJ
6、apaneseReferenceSamepopulationDifferentpopulationPairwiseallele-sharingmetricHierarchicalclusteringMultidimensionalscaling/PCAEstimationofIBDsharing(relatedness)ABACABACIBS=1IBD=0ParentsMostrecentcommonancestorfromhomogeneousrandommatingpopulationABACAssociationanalysisPopulat
7、ion-basedAllelic,trend,genotypic,Fisher’sexactStratifiedtests(Cochran-Mantel-Haenszel,Breslow-Day)Linear&logisticregressionmodelsmultiplecovariates,interactions,jointtests,etcFamily-basedDiseasetraits:TDT/sib-TDTContinuoustraits:QFAM(between/withinmodel,QTDT)Permutationprocedu
8、res“adaptive”,max(T),gene-dropping,between/within,rank-based,
