Predicting Unobserved Phenotypes for Complex Traits from Whole-Genome SNP Data 英文参考文献.docVIP

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Predicting Unobserved Phenotypes for Complex Traits from Whole-Genome SNP Data 英文参考文献.doc

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Predicting Unobserved Phenotypes for Complex Traits from Whole-Genome SNP Data 英文参考文献

PredictingUnobservedPhenotypesforComplexTraits fromWhole-GenomeSNPData SangHongLee1,2,JuliusH.J.vanderWerf1,BenJ.Hayes3,MichaelE.Goddard3,4,PeterM.Visscher5* 1SchoolofEnvironmentalandRuralScience,UniversityofNewEngland,Armidale,NewSouthWales,Australia,2NationalInstituteofAnimalScience,RuralDevelopment Administration, Cheon An, Korea, 3Department of Primary Industry, Victoria, Australia, 4Faculty of Land and Food Resources, University of Melbourne, Melbourne, Australia,5QueenslandInstituteofMedicalResearch,Brisbane,Australia Abstract Genome-wideassociationstudies(GWAS)forquantitativetraitsanddiseaseinhumansandotherspecieshaveshownthat therearemanylocithatcontributetotheobservedresemblancebetweenrelatives.GWAStodatehavemostlyfocussedon discovery of genes or regulatory regions habouring causative polymorphisms, using single SNP analyses and setting stringent type-I error rates. Genome-wide marker data can also be used to predict genetic values and therefore predict phenotypes.Here,weproposeaBayesianmethodthatutilisesallmarkerdatasimultaneouslytopredictphenotypes.We applythemethodtothreetraits:coatcolour,%CD8cells,andmeancellhaemoglobin,measuredinaheterogeneousstock mousepopulation.Wefindthatamodelthatcontainsbothadditiveanddominanceeffects,estimatedfromgenome-wide markerdata,issuccessfulinpredictingunobservedphenotypesandissignificantlybetterthanapredictionbaseduponthe phenotypesofcloserelatives.Correlationsbetweenpredictedandactualphenotypeswereintherangeof0.4to0.9when halfofthenumberoffamilieswasusedtoestimateeffectsandtheotherhalfforprediction.PosteriorprobabilitiesofSNPs being associated with coat colour were high for regions that are known to contain loci for this trait. The prediction of phenotypes using large samples, high-density SNP data, and appropriate statistical methodology is feasible and can be appliedinhumanmedicine,forensics,orartificialselectionprograms. Citation:LeeSH,vanderWerfJHJ,HayesBJ,GoddardME,VisscherPM(2008)PredictingUnobservedPhenotypesfor