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dc.contributor.authorWhalen, Andrew
dc.contributor.authorRos Freixedes, Roger
dc.contributor.authorWilson, David L.
dc.contributor.authorGorjanc, Gregor
dc.contributor.authorHickey, John M.
dc.date.accessioned2020-02-03T10:07:27Z
dc.date.available2020-02-03T10:07:27Z
dc.date.issued2018-12-18
dc.identifier.issn0999-193X
dc.identifier.urihttp://hdl.handle.net/10459.1/67921
dc.description.abstractBackground: In this paper, we extend multi-locus iterative peeling to provide a computationally efficient method for calling, phasing, and imputing sequence data of any coverage in small or large pedigrees. Our method, called hybrid peeling, uses multi-locus iterative peeling to estimate shared chromosome segments between parents and their offspring at a subset of loci, and then uses single-locus iterative peeling to aggregate genomic information across multiple generations at the remaining loci. Results: Using a synthetic dataset, we first analysed the performance of hybrid peeling for calling and phasing geno- types in disconnected families, which contained only a focal individual and its parents and grandparents. Second, we analysed the performance of hybrid peeling for calling and phasing genotypes in the context of a full general pedigree. Third, we analysed the performance of hybrid peeling for imputing whole-genome sequence data to non- sequenced individuals in the population. We found that hybrid peeling substantially increased the number of called and phased genotypes by leveraging sequence information on related individuals. The calling rate and accuracy increased when the full pedigree was used compared to a reduced pedigree of just parents and grandparents. Finally, hybrid peeling imputed accurately whole-genome sequence to non-sequenced individuals. Conclusions: We believe that this algorithm will enable the generation of low cost and high accuracy whole- genome sequence data in many pedigreed populations. We make this algorithm available as a standalone program called AlphaPeel.
dc.description.sponsorshipThe authors acknowledge the financial support from the BBSRC ISPG to The Roslin Institute BB/J004235/1, from Genus PLC, and from Grant Nos. BB/M009254/1, BB/L020726/1, BB/N004736/1, BB/N004728/1, BB/L020467/1, BB/N006178/1 and Medical Research Council (MRC) Grant No. MR/M000370/1.
dc.format.mimetypeapplication/pdf
dc.language.isoeng
dc.publisherBMC (part of Springer Nature)
dc.relation.isformatofReproducció del document publicat a: https://doi.org/10.1186/s12711-018-0438-2
dc.relation.ispartofGenetics Selection Evolution, 2018, vol. 50, article number 67
dc.rightscc-by (c) Whalen, Andrew et al., 2018
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleHybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees
dc.typeinfo:eu-repo/semantics/article
dc.date.updated2020-02-03T10:07:28Z
dc.identifier.idgrec029235
dc.type.versioninfo:eu-repo/semantics/publishedVersion
dc.rights.accessRightsinfo:eu-repo/semantics/openAccess
dc.identifier.doihttps://doi.org/10.1186/s12711-018-0438-2


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cc-by (c) Whalen, Andrew et al., 2018
Except where otherwise noted, this item's license is described as cc-by (c) Whalen, Andrew et al., 2018