RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm 英文参考文献.docVIP

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RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm 英文参考文献.doc

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RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm 英文参考文献

RNA-SeqMappingandDetectionofGeneFusionswitha SuffixArrayAlgorithm OnurSakarya1*,HeinzBreu1,MilanRadovich2,YongzhiChen1,YuleiN.Wang1,CatalinBarbacioru1, SowmiUtiramerur1,PennP.Whitley3,JoelP.Brockman3,PaoloVatta1,ZhengZhang1,LiviuPopescu1, MatthewW.Muller1,VidyaKudlingar1,NritiGarg1,Chieh-YuanLi1,BenjaminS.Kong1,JohnP.Bodeau1, RobertC.Nutter1,JianGu3,KelliS.Bramlett3,JeffreyK.Ichikawa1,FionaC.Hyland1*,AsimS.Siddiqui1* 1Life Technologies, Foster City, California, United States of America, 2Indiana University School of Medicine, Indianapolis, Indiana, United States of America, 3Life Technologies(Ambion),Austin,Texas,UnitedStatesofAmerica Abstract High-throughputRNAsequencingenablesquantificationoftranscripts(bothknownandnovel),exon/exonjunctionsand fusions of exons from different genes. Discovery of gene fusions–particularly those expressed with low abundance– is a challenge with short- and medium-length sequencing reads. To address this challenge, we implemented an RNA-Seq mapping pipeline within the LifeScope software. We introduced new features including filter and junction mapping, annotation-aidedpairingrescueandaccuratemappingqualityvalues.WecombinedthispipelinewithaSuffixArraySpliced Read(SASR)alignertodetectchimerictranscripts.Performingpaired-endRNA-SeqofthebreastcancercelllineMCF-7using theSOLiDsystem,wecalled40genefusionsamongover120,000splicingjunctions.Wevalidated36ofthese40fusions withTaqManassays,ofwhich25wereexpressedinMCF-7butnottheHumanBrainReference.Anintra-chromosomalgene fusioninvolvingtheestrogenreceptoralphageneESR1,andanotherinvolvingtheRPS6KB1(RibosomalproteinS6kinase beta-1)wererecurrentlyexpressedinanumberofbreasttumorcelllinesandaclinicaltumorsample. Citation:SakaryaO,BreuH,RadovichM,ChenY,WangYN,etal.(2012)RNA-SeqMappingandDetectionofGeneFusionswithaSuffixArrayAlgorithm.PLoS ComputBiol8(4):e1002464.doi:10.1371/journal.pcbi.1002464 Editor:WeixiongZhang,WashingtonUniversityinSaintLouis,UnitedStatesofAmerica ReceivedSeptember7,2011;AcceptedF