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OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis

dc.rights.licenseopenen_US
dc.contributor.authorTHIBORD, F.
dc.contributor.authorPERRET, C.
dc.contributor.authorROUX, M.
dc.contributor.authorSUCHON, P.
hal.structure.identifierBordeaux population health [BPH]
dc.contributor.authorGERMAIN, Marine
dc.contributor.authorDELEUZE, J. F.
dc.contributor.authorMORANGE, P. E.
hal.structure.identifierBordeaux population health [BPH]
dc.contributor.authorTREGOUET, David-Alexandre
dc.date.accessioned2020-07-15T08:34:53Z
dc.date.available2020-07-15T08:34:53Z
dc.date.issued2019-06
dc.identifier.issn1469-9001 (Electronic) 1355-8382 (Linking)en_US
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/10474
dc.description.abstractEnNext-generation sequencing is an increasingly popular and efficient approach to characterize the full set of microRNAs (miRNAs) present in human biosamples. MiRNAs' detection and quantification still remain a challenge as they can undergo different post transcriptional modifications and might harbor genetic variations (polymiRs) that may impact on the alignment step. We present a novel algorithm, OPTIMIR, that incorporates biological knowledge on miRNA editing and genome-wide genotype data available in the processed samples to improve alignment accuracy. OPTIMIR was applied to 391 human plasma samples that had been typed with genome-wide genotyping arrays. OPTIMIR was able to detect genotyping errors, suggested the existence of novel miRNAs and highlighted the allelic imbalance expression of polymiRs in heterozygous carriers. OPTIMIR is written in python, and freely available on the GENMED website (http://www.genmed.fr/index.php/fr/) and on Github (github.com/FlorianThibord/OptimiR).
dc.language.isoENen_US
dc.rightsAttribution 3.0 United States
dc.rights.urihttps://creativecommons.org/licenses/by/3.0/us/
dc.subject.enVINTAGE
dc.title.enOPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis
dc.title.alternativeRNAen_US
dc.typeArticle de revueen_US
dc.identifier.doi10.1261/rna.069708.118en_US
dc.subject.halSciences du Vivant [q-bio]/Santé publique et épidémiologieen_US
dc.identifier.pubmed30819774en_US
bordeaux.journalRNA (New York, N.Y.)en_US
bordeaux.page657-668en_US
bordeaux.volume25en_US
bordeaux.hal.laboratoriesBordeaux Population Health Research Center (BPH) - UMR 1219en_US
bordeaux.issue6en_US
bordeaux.institutionUniversité de Bordeauxen_US
bordeaux.peerReviewedouien_US
bordeaux.inpressnonen_US
hal.exportfalse
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=RNA%20(New%20York,%20N.Y.)&rft.date=2019-06&rft.volume=25&rft.issue=6&rft.spage=657-668&rft.epage=657-668&rft.eissn=1469-9001%20(Electronic)%201355-8382%20(Linking)&rft.issn=1469-9001%20(Electronic)%201355-8382%20(Linking)&rft.au=THIBORD,%20F.&PERRET,%20C.&ROUX,%20M.&SUCHON,%20P.&GERMAIN,%20Marine&rft.genre=article


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