Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation 英文参考文献.docVIP

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Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation 英文参考文献.doc

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Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation 英文参考文献

EfficiencyandPowerasaFunctionofSequence Coverage,SNPArrayDensity,andImputation JasonFlannick1,2,JoshuaM.Korn1,2,3,4,PierreFontanillas1,GeorgeB.Grant1,EricBanks1, MarkA.Depristo1,DavidAltshuler1,2,5* 1BroadInstituteofHarvardandMIT,Cambridge,Massachusetts,UnitedStatesofAmerica,2DepartmentofMolecularBiologyandDiabetesUnit,MassachusettsGeneral Hospital, Boston, Massachusetts, United States of America, 3Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, United States of America,4GraduatePrograminBiophysics,HarvardUniversity,Cambridge,Massachusetts,UnitedStatesofAmerica,5DepartmentofGeneticsandMedicine,Harvard MedicalSchool,Boston,Massachusetts,UnitedStatesofAmerica Abstract High coverage whole genome sequencing provides near complete information about genetic variation. However, other technologiescanbemoreefficientinsomesettingsby(a)reducingredundantcoveragewithinsamplesand(b)exploiting patternsofgeneticvariationacrosssamples.Tocharacterizeasmanysamplesaspossible,manygeneticstudiestherefore employ lower coverage sequencing or SNP array genotyping coupled to statistical imputation. To compare these approaches individually and in conjunction, we developed a statistical framework to estimate genotypes jointly from sequence reads, array intensities, and imputation. In European samples, we find similar sensitivity (89%) and specificity (99.6%)fromimputationwitheither16sequencingor1MSNParrays.Sensitivityisincreased,particularlyforlow-frequency polymorphisms (MAFv5%), when low coverage sequence reads are added to dense genome-wide SNP arrays — the converse,however,isnottrue.Atsiteswheresequencereadsandarrayintensitiesproducedifferentsamplegenotypes, joint analysis reduces genotype errors and identifies novel error modes. Our joint framework informs the use of next- generationsequencingingenomewideassociationstudiesandsupportsdevelopmentofimprovedmethodsforgenotype calling. Citation:FlannickJ,KornJM,FontanillasP,GrantGB,BanksE,etal.(2012)Efficiency