Analysis of Array-CGH Data Using the R and Bioconductor Software Suite英文文献资料.docVIP

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Analysis of Array-CGH Data Using the R and Bioconductor Software Suite英文文献资料.doc

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Analysis of Array-CGH Data Using the R and Bioconductor Software Suite英文文献资料

HindawiPublishingCorporation ComparativeandFunctionalGenomics Volume2009,ArticleID201325,8pages doi:10.1155/2009/201325 ResearchArticle AnalysisofArray-CGHDataUsing theRandBioconductorSoftwareSuite Winfried A. Hofmann, Anja Weigmann, Marcel Tauscher, Britta Skawran, Tim Focken, ReenaBuurman,LuzieU.Wingen,BrigitteSchlegelberger,andDorisSteinemann HannoverMedicalSchool,InstituteofCellandMolecularPathology,Carl-Neuberg-Str.1,30625Hannover,Germany CorrespondenceshouldbeaddressedtoDorisSteinemann,steinemann.doris@mh-hannover.de Received2December2008;Revised8May2009;Accepted5June2009 RecommendedbyEivindHovig Background.Array-basedcomparativegenomichybridization(array-CGH)isanemerginghigh-resolutionandhigh-throughput molecular genetic technique that allows genome-wide screening for chromosome alterations. DNA copy number alterations (CNAs)areahallmarkofsomaticmutationsintumorgenomesandcongenitalabnormalitiesthatleadtodiseasessuchasmental retardation.However,accurateidenti?cationofampli?edordeletedregionsrequiresasequenceofdi?erentcomputationalanalysis stepsofthemicroarraydata.Results.Wehavedevelopedauser-friendlyandversatiletoolforthenormalization,visualization, breakpointdetection,andcomparativeanalysisofarray-CGHdatawhichallowstheaccurateandsensitivedetectionofCNAs. Conclusion.Theimplementedoptionforthedeterminationofminimalalteredregions(MARs)fromaseriesoftumorsamplesis astepforwardintheidenti?cationofnewtumorsuppressorgenesoroncogenes. Copyright?2009WinfriedA.Hofmannetal.ThisisanopenaccessarticledistributedundertheCreativeCommonsAttribution License,whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperly cited. 1.Introduction environment R [4]. The methods for array-CGH analysis availablefromthisplatformaredescribedasfollows. The goal of array-CGH experiments is to detect and map genetic changes involving copy number aberrations of chromosomal segments at a high resolution along the genome. The computational analysis of t