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Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences

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dc.contributor.author Colonna, Vincenza
dc.contributor.author Ayub, Qasim
dc.contributor.author Cheng, Yuan
dc.contributor.author Pagani, Luca
dc.contributor.author Luisi, Pierre, 1985-
dc.contributor.author Pybus Oliveras, Marc, 1985-
dc.contributor.author Garrison, Erik
dc.contributor.author Xue, Yali
dc.contributor.author Tyler-Smith, Chris
dc.contributor.author The 1000 Genomes Project Consortium
dc.date.accessioned 2015-03-20T08:26:31Z
dc.date.available 2015-03-20T08:26:31Z
dc.date.issued 2014
dc.identifier.citation Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C; The 1000 Genomes Project Consortium. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biology. 2014; 15: R88. DOI 10.1186/gb-2014-15-6-r88
dc.identifier.issn 1465-6906
dc.identifier.uri http://hdl.handle.net/10230/23240
dc.description.abstract Background: Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. Results: We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively. Conclusions: We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.
dc.description.sponsorship This work was supported by The Wellcome Trust (098051), an Italian National Research Council (CNR) short-term mobility fellowship from the 2013 program to VC, and an EMBO Short Term Fellowship ASTF 324–2010 to VC
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof Genome Biology. 2014; 15: R88
dc.rights © 2014 Colonna et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.rights.uri http://creativecommons.org/licenses/by/4.0
dc.subject.other Genètica de poblacions humanes
dc.subject.other Genètica humana -- Variació
dc.subject.other Selecció natural
dc.title Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/gb-2014-15-6-r88
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/098051
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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