Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants
Identifieur interne : 000509 ( Main/Exploration ); précédent : 000508; suivant : 000510Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants
Auteurs : Daniel S. Standage [États-Unis] ; C. Titus Brown [États-Unis] ; Fereydoun Hormozdiari [États-Unis]Source :
- iScience [ 2589-0042 ] ; 2019.
Abstract
Url:
DOI: 10.1016/j.isci.2019.07.032
PubMed: 31377530
PubMed Central: 6682328
Affiliations:
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Standage</name><affiliation wicri:level="1"><nlm:aff id="aff1">Population Health and Reproduction, University of California, Davis, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Population Health and Reproduction, University of California, Davis</wicri:regionArea><wicri:noRegion>Davis</wicri:noRegion></affiliation></author><author><name sortKey="Brown, C Titus" sort="Brown, C Titus" uniqKey="Brown C" first="C. Titus" last="Brown">C. Titus Brown</name><affiliation wicri:level="1"><nlm:aff id="aff1">Population Health and Reproduction, University of California, Davis, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Population Health and Reproduction, University of California, Davis</wicri:regionArea><wicri:noRegion>Davis</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2">Genome Center, University of California, Davis, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Center, University of California, Davis</wicri:regionArea><wicri:noRegion>Davis</wicri:noRegion></affiliation></author><author><name sortKey="Hormozdiari, Fereydoun" sort="Hormozdiari, Fereydoun" uniqKey="Hormozdiari F" first="Fereydoun" last="Hormozdiari">Fereydoun Hormozdiari</name><affiliation wicri:level="1"><nlm:aff id="aff2">Genome Center, University of California, Davis, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Center, University of California, Davis</wicri:regionArea><wicri:noRegion>Davis</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3">MIND Institute, University of California, Davis, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>MIND Institute, University of California, Davis</wicri:regionArea><wicri:noRegion>Davis</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:aff id="aff4">Biochemistry and Molecular Medicine, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biochemistry and Molecular Medicine, University of California, Davis, 1 Shields Avenue, Davis, CA 95616</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></analytic><series><title level="j">iScience</title><idno type="eISSN">2589-0042</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Summary</title><p><italic>De novo</italic> genetic variants are an important source of causative variation in complex genetic disorders. Many methods for variant discovery rely on mapping reads to a reference genome, detecting numerous inherited variants irrelevant to the phenotype of interest. To distinguish between inherited and <italic>de novo</italic> variation, sequencing of families (parents and siblings) is commonly pursued. However, standard mapping-based approaches tend to have a high false-discovery rate for <italic>de novo</italic> variant prediction. Kevlar is a mapping-free method for <italic>de novo</italic> variant discovery, based on direct comparison of sequences between related individuals. Kevlar identifies high-abundance <italic>k</italic>-mers unique to the individual of interest. Reads containing these <italic>k</italic>-mers are partitioned into disjoint sets by shared <italic>k</italic>-mer content for variant calling, and preliminary variant predictions are sorted using a probabilistic score. We evaluated Kevlar on simulated and real datasets, demonstrating its ability to detect both <italic>de novo</italic> single-nucleotide variants and indels with high accuracy.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bernardini, G" uniqKey="Bernardini G">G. Bernardini</name></author><author><name sortKey="Bonizzoni, P" uniqKey="Bonizzoni P">P. Bonizzoni</name></author><author><name sortKey="Denti, L" uniqKey="Denti L">L. Denti</name></author><author><name sortKey="Previtali, M" uniqKey="Previtali M">M. Previtali</name></author><author><name sortKey="Schonhuth, A" uniqKey="Schonhuth A">A. Schönhuth</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bray, N L" uniqKey="Bray N">N.L. Bray</name></author><author><name sortKey="Pimentel, H" uniqKey="Pimentel H">H. Pimentel</name></author><author><name sortKey="Melsted, P" uniqKey="Melsted P">P. 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Titus Brown</name><name sortKey="Hormozdiari, Fereydoun" sort="Hormozdiari, Fereydoun" uniqKey="Hormozdiari F" first="Fereydoun" last="Hormozdiari">Fereydoun Hormozdiari</name><name sortKey="Hormozdiari, Fereydoun" sort="Hormozdiari, Fereydoun" uniqKey="Hormozdiari F" first="Fereydoun" last="Hormozdiari">Fereydoun Hormozdiari</name><name sortKey="Hormozdiari, Fereydoun" sort="Hormozdiari, Fereydoun" uniqKey="Hormozdiari F" first="Fereydoun" last="Hormozdiari">Fereydoun Hormozdiari</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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