SNPdetector A Software Tool for Sensitive and Accurate SNP Detection 英文参考文献.docVIP

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SNPdetector A Software Tool for Sensitive and Accurate SNP Detection 英文参考文献.doc

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SNPdetector:ASoftwareToolforSensitive andAccurateSNPDetection Jinghui Zhang1*,David A.Wheeler2,Imtiaz Yakub2,Sharon Wei2,Raman Sood3,William Rowe1,Paul P.Liu3, Richard A.Gibbs2,Kenneth H.Buetow1 1LaboratoryofPopulationGenetics,NationalCancerInstitute,NationalInstitutesofHealth,Bethesda,Maryland,UnitedStatesofAmerica,2HumanGenomeSequencing CenterandDepartmentofMolecularandHumanGenetics,BaylorCollegeofMedicine,Houston,Texas,UnitedStatesofAmerica,3GeneticsandMolecularBiologyBranch, NationalHumanGenomeResearchInstitute,NationalInstitutesofHealth,Bethesda,Maryland,UnitedStatesofAmerica Identification of single nucleotide polymorphisms (SNPs) and mutations is important for the discovery of genetic predispositiontocomplexdiseases.PCRresequencingisthemethodofchoicefordenovoSNPdiscovery.However, manualcurationofputativeSNPshasbeenamajorbottleneckintheapplicationofthismethodtohigh-throughput screening.ThereforeitiscriticaltodevelopamoresensitiveandaccuratecomputationalmethodforautomatedSNP detection. We developed a software tool, SNPdetector, for automated identification of SNPs and mutations in fluorescence-basedresequencingreads.SNPdetectorwasdesignedtomodeltheprocessofhumanvisualinspection andhasaverylowfalsepositiveandfalsenegativerate.WedemonstratethesuperiorperformanceofSNPdetectorin SNPandmutationanalysisbycomparingitsresultswiththosederivedbyhumaninspection,PolyPhred(apopularSNP detection tool), and independent genotype assays in three large-scale investigations. The first study identified and validatedinter-andintra-subspeciesvariationsin4,650tracesof25inbredmousestrainsthatbelongtoeithertheMus musculusspeciesortheM.spretusspecies.UnexpectedheterozgyosityinCAST/Eistrainwasobservedintwooutof 1,167mouseSNPs.Thesecondstudyidentified11,241candidateSNPsinfiveENCODEregionsofthehumangenome covering 2.5 Mb of genomic sequence. Approximately 50% of the candidate SNPs were selected for experimental genotyping; the validation rate exceeded 95%. The third study detected ENU