Abundant Human DNA Contamination Identified in Non-Primate Genome Databases 英文参考文献.docVIP

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Abundant Human DNA Contamination Identified in Non-Primate Genome Databases 英文参考文献.doc

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Abundant Human DNA Contamination Identified in Non-Primate Genome Databases 英文参考文献

AbundantHumanDNAContaminationIdentifiedinNon- PrimateGenomeDatabases MarkS.Longo,MichaelJ.O’Neill,RachelJ.O’Neill* DepartmentofMolecularandCellBiology,UniversityofConnecticut,Storrs,Connecticut,UnitedStatesofAmerica Abstract During routine screens of the NCBI databases using human repetitive elements we discovered an unlikely level of nucleotide identity across a broad range of phyla. To ascertain whether databases containing DNA sequences, genome assemblies and trace archive reads were contaminated with human sequences, we performed an in depth search for sequences of human origin in non-human species. Using a primate specific SINE, AluY, we screened 2,749 non-primate publicdatabasesfromNCBI,Ensembl,JGI,andUCSCandhavefound492tobecontaminatedwithhumansequence.These representspeciesrangingfrombacteria(B.cereus)toplants(Z.mays)tofish(D.rerio)withexamplesfoundfrommostphyla. The identification of such extensive contamination of human sequence across databases and sequence types warrants cautionamongthesequencingcommunityinfuturesequencingefforts,suchashumanre-sequencing.Wediscussissues thismayraiseaswellaspresentdatathatgivesinsightastohowthismaybeoccurring. Citation:LongoMS,O’NeillMJ,O’NeillRJ(2011)AbundantHumanDNAContaminationIdentifiedinNon-PrimateGenomeDatabases.PLoSONE6(2):e16410. doi:10.1371/journal.pone.0016410 Editor:NajibEl-Sayed,TheUniversityofMaryland,UnitedStatesofAmerica ReceivedSeptember1,2010;AcceptedDecember23,2010;PublishedFebruary16,2011 Copyright: ? 2011 Longo 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: This work was funded by the NSF (). The funders had no role in study design, data collection and analysis, decision to publish, or preparationofthemanuscript. CompetingInterests:Theauthorshavedeclaredthatnocompetinginterestsexist. *E-mail:rachel.oneill@ Introdu