Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays 英文参考文献.docVIP

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Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays 英文参考文献.doc

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Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays 英文参考文献

EmpiricalEvaluationofOligonucleotideProbeSelection forDNAMicroarrays JenniferG.Mulle*,VirenC.Patel,StephenT.Warren,MadhuriR.Hegde,DavidJ.Cutler,MichaelE.Zwick DepartmentofHumanGenetics,EmoryUniversitySchoolofMedicine,Atlanta,Georgia,UnitedStatesofAmerica Abstract DNA-based microarrays are increasingly central to biomedical research. Selecting oligonucleotide sequences that will behaveconsistentlyacrossexperimentsisessentialtothedesign,productionandperformanceofDNAmicroarrays.Here ouraimwastoimproveonprobedesignparametersbyempiricallyandsystematicallyevaluatingprobeperformanceina multivariate context. We used experimental data from 19 array CGH hybridizations to assess the probe performance of 385,474probestiledintheDuchennemusculardystrophy(DMD)regionoftheXchromosome.Ourresultsdemonstratethat probemeltingtemperature,singlenucleotidepolymorphisms(SNPs),andhomocytosinemotifsallhaveastrongeffecton probe behavior. These findings, when incorporated into future microarray probe selection algorithms, may improve microarrayperformanceforawidevarietyofapplications. Citation:MulleJG,PatelVC,WarrenST,HegdeMR,CutlerDJ,etal.(2010)EmpiricalEvaluationofOligonucleotideProbeSelectionforDNAMicroarrays.PLoS ONE5(3):e9921.doi:10.1371/journal.pone.0009921 Editor:AmandaEwartToland,OhioStateUniversityMedicalCenter,UnitedStatesofAmerica ReceivedJune3,2009;AcceptedDecember4,2009;PublishedMarch29,2010 Copyright: ? 2010 Mulle et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding: J.G.M. was supported by a Kirschstein National Research Service Award (NRSA) fellowship and a NARSAD Young Investigator award (http://www. /).Thefundershadnoroleinstudydesign,datacollectionandanalysis,decisiontopublish,orpreparationofthemanuscript. CompetingInterests:Theauthorshavedeclaredthatnocompetinginterestsexist. *E-mail:jmulle@ I