Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

dc.contributorAalto-yliopistofi
dc.contributorAalto Universityen
dc.contributor.authorLees, John A.en_US
dc.contributor.authorVehkala, Minnaen_US
dc.contributor.authorVälimäki, Nikoen_US
dc.contributor.authorHarris, Simon R.en_US
dc.contributor.authorChewapreecha, Claireen_US
dc.contributor.authorCroucher, Nicholas J.en_US
dc.contributor.authorMarttinen, Pekkaen_US
dc.contributor.authorDavies, Mark R.en_US
dc.contributor.authorSteer, Andrew C.en_US
dc.contributor.authorTong, Steven Y Cen_US
dc.contributor.authorHonkela, Anttien_US
dc.contributor.authorParkhill, Julianen_US
dc.contributor.authorBentley, Stephen D.en_US
dc.contributor.authorCorander, Jukkaen_US
dc.contributor.departmentDepartment of Computer Scienceen
dc.contributor.groupauthorCentre of Excellence in Computational Inference, COINen
dc.contributor.organizationWellcome Trust Sanger Instituteen_US
dc.contributor.organizationUniversity of Helsinkien_US
dc.contributor.organizationUniversity of Cambridgeen_US
dc.contributor.organizationImperial College Londonen_US
dc.contributor.organizationUniversity of Melbourneen_US
dc.contributor.organizationMurdoch Children's Research Instituteen_US
dc.contributor.organizationCharles Darwin Universityen_US
dc.date.accessioned2017-05-11T08:21:26Z
dc.date.available2017-05-11T08:21:26Z
dc.date.issued2016-09-16en_US
dc.description.abstractBacterial genomes vary extensively in terms of both gene content and gene sequence. This plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. Here we introduce a computationally scalable and widely applicable statistical method (SEER) for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to tens of thousands of genomes by counting variable-length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogens Streptococcus pneumoniae and Streptococcus pyogenes, SEER identifies relevant previously characterized resistance determinants for several antibiotics and discovers potential novel factors related to the invasiveness of S. pyogenes. We thus demonstrate that our method can answer important biologically and medically relevant questions.en
dc.description.versionPeer revieweden
dc.format.extent8
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationLees, J A, Vehkala, M, Välimäki, N, Harris, S R, Chewapreecha, C, Croucher, N J, Marttinen, P, Davies, M R, Steer, A C, Tong, S Y C, Honkela, A, Parkhill, J, Bentley, S D & Corander, J 2016, ' Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes ', Nature Communications, vol. 7, 12797 . https://doi.org/10.1038/ncomms12797en
dc.identifier.doi10.1038/ncomms12797en_US
dc.identifier.issn2041-1723
dc.identifier.otherPURE UUID: 6aa1d751-f3c6-47d1-8722-0256dcc26953en_US
dc.identifier.otherPURE ITEMURL: https://research.aalto.fi/en/publications/6aa1d751-f3c6-47d1-8722-0256dcc26953en_US
dc.identifier.otherPURE LINK: http://www.scopus.com/inward/record.url?scp=84987941941&partnerID=8YFLogxKen_US
dc.identifier.otherPURE FILEURL: https://research.aalto.fi/files/11503202/ncomms12797.pdfen_US
dc.identifier.urihttps://aaltodoc.aalto.fi/handle/123456789/25580
dc.identifier.urnURN:NBN:fi:aalto-201705113964
dc.language.isoenen
dc.relation.ispartofseriesNATURE COMMUNICATIONSen
dc.relation.ispartofseriesVolume 7en
dc.rightsopenAccessen
dc.titleSequence element enrichment analysis to determine the genetic basis of bacterial phenotypesen
dc.typeA1 Alkuperäisartikkeli tieteellisessä aikakauslehdessäfi
dc.type.versionpublishedVersion
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