Sampling genotypes in large pedigrees with loops 英文参考文献.docVIP

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Sampling genotypes in large pedigrees with loops 英文参考文献.doc

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Sampling genotypes in large pedigrees with loops 英文参考文献

Genet. Sel. Evol. 33(2001) 337–367 ?INRA, EDP Sciences, 2001 337 Original article Samplinggenotypesinlargepedigrees withloops SoledadA.FERNáNDEZ a,b,RohanL.FERNANDO a,c,?, BerntGULDBRANDTSEN d,LiviuR.TOTIRa, AliciaL.CARRIQUIRY b,c aDepartmentofAnimalScience,IowaStateUniversity, 225KildeeHall,Ames,IA50011,USA bDepartmentofStatistics,IowaStateUniversity, 225KildeeHall,Ames,IA50011,USA cLawrenceH.BakerCenterforBioinformaticsandBiologicalStatistics, IowaStateUniversity,Ames,IA50011,USA dDanishInstituteofAnimalScience,Foulum,Denmark (Received19October2000;accepted23February2001) Abstract– MarkovchainMonteCarlo(MCMC)methodshavebeenproposedtoovercome computationalproblemsinlinkageandsegregationanalyses. Thisapproachinvolvessampling genotypesatthemarkerandtraitloci. Scalar-Gibbsiseasytoimplement,anditiswidelyused ingenetics.However,theMarkovchainthatcorrespondstoscalar-Gibbsmaynotbeirreducible whenthemarkerlocushasmorethantwoalleles,andevenwhenthechainisirreducible,mixing hasbeenobservedtobeslow.Theseproblemsdonotariseifthegenotypesaresampledjointly fromtheentirepedigree.Thispaperproposesamethodtojointlysamplegenotypes.Themethod combinestheElston-Stewartalgorithmanditerativepeeling,andiscalledtheESIPsampler. Forahypotheticalpedigree,genotypeprobabilitiesareestimatedfromsamplesobtainedusing ESIPandalsoscalar-Gibbs. Approximateprobabilitieswerealsoobtainedbyiterativepeel- ing. ComparisonsofthesewithexactgenotypicprobabilitiesobtainedbytheElston-Stewart algorithmshowedthatESIPanditerativepeelingyieldedgenotypicprobabilitiesthatwerevery closetotheexactvalues. Nevertheless,estimatedprobabilitiesfromscalar-Gibbswithachain oflength235000,includingaburn-inof200000steps,werelessaccuratethanprobabilities estimatedusingESIPwithachainoflength10000,withaburn-inof5000steps.Theeffective chainsize(ECS)wasestimatedfromthelast25000elementsofthechainoflength125000. ForoneoftheESIPsamplers,theECSrangedfrom21579to22741,whileforthescalar-Gibbs sampler,theECSrangedfrom64to671.Genoty