A Method to Address Differential Bias in Genotyping in Large-Scale Association Studies 英文参考文献.docVIP

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A Method to Address Differential Bias in Genotyping in Large-Scale Association Studies 英文参考文献.doc

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A Method to Address Differential Bias in Genotyping in Large-Scale Association Studies 英文参考文献

AMethodtoAddressDifferentialBias inGenotyping inLarge-ScaleAssociationStudies Vincent Plagnol*,Jason. D.Cooper, John A.Todd, David G. Clayton JuvenileDiabetesResearchFoundation/WellcomeTrustDiabetesandInflammationLaboratory,DepartmentofMedicalGenetics,CambridgeInstituteforMedicalResearch, UniversityofCambridge,Cambridge,UnitedKingdom In a previous paper we have shown that, when DNA samples for cases and controls are prepared in different laboratoriespriortohigh-throughputgenotyping,scoringinaccuraciescanleadtodifferentialmisclassificationand, consequently, to increased false-positive rates. Different DNA sourcing is often unavoidable in large-scale disease association studies of multiple case and control sets. Here, we describe methodological improvements to minimise suchbiases.Thesefallintotwocategories:improvementstothebasicclusteringmethodsforidentifyinggenotypes fromfluorescenceintensities,anduseof‘‘fuzzy’’callsinassociationtestsinordertomakeappropriateallowancefor calluncertainty.Wefindthatthemainimprovementisamodificationofthecallingalgorithmthatlinkstheclustering ofcasesandcontrolswhileallowingfordifferentDNAsourcing.Wealsofindthat,inthepresenceofdifferentDNA sourcing, biases associated withmissing data canincrease the false-positive rate. Therefore,we propose theuse of ‘‘fuzzy’’callstodealwithuncertaingenotypesthatwouldotherwisebelabeledasmissing. Citation:PlagnolV,CooperJD,ToddJA,ClaytonDG(2007)Amethodtoaddressdifferentialbiasingenotypinginlarge-scaleassociationstudies.PLoSGenet3(5):e74.doi:10. 1371/journal.pgen.0030074 approach is that it can generate a differential bias in genotypecallingbetweencaseandcontrolDNAsamplesthat Introduction Genome-wide association (GWA) studies are becoming more common because of rapid technological changes, decreasing costs and extensive single nucleotide polymor- phism (SNP) maps of the genome [1,2]. However, a major technological challenge is the fact that this ever-increasing number of SNPs is necessarily reliant on fu