Sniper improved SNP discovery by multiply mapping deep sequenced reads 英文参考文献.docVIP

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Sniper improved SNP discovery by multiply mapping deep sequenced reads 英文参考文献.doc

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Sniper improved SNP discovery by multiply mapping deep sequenced reads 英文参考文献

SimolaandKimGenomeBiology2011,12:R55 /2011/12/6/R55 METHOD OpenAccess Sniper:improvedSNPdiscoverybymultiply mappingdeepsequencedreads DanielFSimola1,2 andJunhyongKim1,3* Abstract SNP(singlenucleotidepolymorphism)discoveryusingnext-generationsequencingdataremainsdifficultprimarily becauseofredundantgenomicregions,suchasinterspersedrepetitiveelementsandparalogousgenes,presentin alleukaryoticgenomes.Toaddressthisproblem,wedevelopedSniper,anovelmulti-locusBayesianprobabilistic modelandacomputationallyefficientalgorithmthatexplicitlyincorporatessequencereadsthatmaptomultiple genomicloci.Ourmodelfullyaccountsforsequencingerror,templatebias,andmulti-locusSNPcombinations, maintaininghighsensitivityandspecificityunderabroadrangeofconditions.AnimplementationofSniperis freelyavailableat/software/sniper.shtml. Background biasesinsequencingcoveragegeneratedduringgenomic The advent of next-generation, short-read sequencing DNA library preparation [9]. These practical issues (NGS)technologieshasenabledlarge-scale, whole-gen- makeitdifficult, evenwithsophisticatedprocedures,to ome resequencing studies that aim to discover novel discovertrueSNPsaccuratelywithoutconcurrentlypre- SNPs and other population genetic variations. Perhaps dicting many false SNPs. A recent study evaluated the themostambitiousofthesestudiesinvolvessequencing performance of three NGStechnologies (Illumina, ABI over 1,000 individual human genomes inorder to map Solid, 454) using near-saturating sequence coverage human genetic variation at a fine scale and to support (approximately188×)overthesamegenomicsequence, genome-widephenotypicanddiseaseassociationstudies reportingfalsepositiveandfalsenegativeSNPdiscovery [1]. Previous genome resequencing efforts have devel- rates of 3 to 12% and 1 to 8%, respectively [9]. While opedavarietyofapproachestoidentifySNPs,including theseerrorratesmayseemmanageable,theywereesti- straightforward decision rules suchasminimumcover- matedusingSNPsoccurri