A Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing, and DNA Editing 英文参考文献.docVIP

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A Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing, and DNA Editing 英文参考文献.doc

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A Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing, and DNA Editing 英文参考文献

ASurveyofGenomicTracesRevealsaCommon SequencingError,RNAEditing,andDNAEditing AlexanderWaitZaranek1.*,ErezY.Levanon1,2.*,TomerZecharia3,TomClegg4,GeorgeM.Church1 1DepartmentofGenetics,HarvardMedicalSchool,Boston,Massachusetts,UnitedStatesofAmerica,2TheMinaandEverardGoodmanFacultyofLifeSciences,Bar-Ilan University,Ramat-Gan,Israel,3CompugenLtd.,TelAviv,Israel,4ScalableComputingExperts,Somerville,Massachusetts,UnitedStatesofAmerica Abstract Whileitiswidelyheldthatanorganism’sgenomicinformationshouldremainconstant,severalproteinfamiliesareknown tomodifyit.MembersoftheAID/APOBECproteinfamilycandeaminateDNA.Similarly,membersoftheADARfamilycan deaminateRNA.Characterizingthescopeoftheseeventsischallenging.Hereweuselargegenomicdatasets,suchasthe twobillionsequencesintheNCBITraceArchive,tolookforclustersofmismatchesofthesametype,whichareahallmarkof editingeventscausedbyAPOBEC3andADAR.Wealign603,249,815tracesfromtheNCBItracearchivetotheirreference genomes.Inclustersofmismatchesofincreasingsize,atleastonesystematicsequencingerrordominatestheresults(G-to- A).Itisstillpresentinmismatcheswith99%accuracyandonlyvanishesinmismatchesat99.99%accuracyorhigher.The error appears to have entered into about 1% of the HapMap, possibly affecting other users that rely on this resource. Furtherinvestigation,usingstringentqualitythresholds,uncoversthousandsofmismatchclusterswithnoapparentdefects intheirchromatograms.ThesetracesprovidethefirstreportedcandidatesofendogenousDNAeditinginhuman,further elucidating RNA editing in human and mouse and also revealing, for the first time, extensive RNA editing in Xenopus tropicalis.WeshowthattheNCBITraceArchiveprovidesavaluableresourcefortheinvestigationofthephenomenaofDNA and RNA editing, as well as setting the stage for a comprehensive mapping of editing events in large-scale genomic datasets. Citation:ZaranekAW,LevanonEY,ZechariaT,CleggT,ChurchGM(2010)ASurveyofGenomicTracesRevealsaCommonSequencingError,RNAEditing,and DNAEditing.PLoSGenet6(5):e100095