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Somatic mutation detection: a critical evaluation through simulations and reanalyses in oaks

hal.structure.identifierEcologie des forêts de Guyane [UMR ECOFOG]
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorSCHMITT, Sylvain
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierInstitut de Recherche en Horticulture et Semences [IRHS]
dc.contributor.authorLEROY, Thibault
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorHEUERTZ, Myriam
hal.structure.identifierEcologie des forêts de Guyane [UMR ECOFOG]
dc.contributor.authorTYSKLIND, Niklas
dc.date.issued2022
dc.identifier.issn2804-3871
dc.description.abstractEn1. Mutation, the source of genetic diversity, is the raw material of evolution; however,the mutation process remains understudied, especially in plants. Using both a simulationand reanalysis framework, we set out to explore and demonstrate the improved perfor-mance of variant callers developed for cancer research compared to single nucleotidepolymorphism (SNP) callers in detecting de novo somatic mutations.2. In an in silico experiment, we generated Illumina-like sequence reads spiked withsimulated mutations at different allelic fractions to compare the performance of sevencommonly-used variant callers to recall them. More empirically, we then reanalyzedtwo of the largest datasets available for plants, both developed for identifying within-individual variation in long-lived pedunculate oaks.3. Based on thein silico experiment, variant callers developed for cancer research outper-form SNP callers regarding plant mutation recall and precision, especially at low allele fre-quency. Such variants at low allelic fractions are typically expected for within-individualde novo plant mutations, which initially appear in single cells. Reanalysis of publishedoak data with Strelka2, the best-performing caller based on our simulations, identifiedup to 3.4x more candidate somatic mutations than reported in the original studies.4. Our results advocate the use of cancer research callers to boost de novo mutationresearch in plants, and to reconcile empirical reports with theoretical expectations.
dc.language.isoen
dc.publisherPeer Community In
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.title.enSomatic mutation detection: a critical evaluation through simulations and reanalyses in oaks
dc.typeArticle de revue
dc.identifier.doi10.24072/pcjournal.187
dc.subject.halSciences du Vivant [q-bio]/Génétique/Génétique des plantes
bordeaux.journalPeer Community Journal
bordeaux.pagee68
bordeaux.volume2
bordeaux.peerReviewedoui
hal.identifierhal-03887919
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03887919v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Peer%20Community%20Journal&rft.date=2022&rft.volume=2&rft.spage=e68&rft.epage=e68&rft.eissn=2804-3871&rft.issn=2804-3871&rft.au=SCHMITT,%20Sylvain&LEROY,%20Thibault&HEUERTZ,%20Myriam&TYSKLIND,%20Niklas&rft.genre=article


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