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

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• dc.contributor.author Colonna, Vincenzaca
• dc.contributor.author Ayub, Qasimca
• dc.contributor.author Cheng, Yuanca
• dc.contributor.author Pagani, Lucaca
• dc.contributor.author Luisi, Pierre, 1985-ca
• dc.contributor.author Pybus Oliveras, Marc, 1985-ca
• dc.contributor.author Garrison, Erikca
• dc.contributor.author Xue, Yalica
• dc.contributor.author Tyler-Smith, Chrisca
• dc.contributor.author The 1000 Genomes Project Consortiumca
• dc.date.accessioned 2015-03-20T08:26:31Z
• dc.date.available 2015-03-20T08:26:31Z
• dc.date.issued 2014ca
• 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.en
• 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/pdfca
• dc.identifier.citation Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M et al. 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-r88ca
• dc.identifier.doi http://dx.doi.org/10.1186/gb-2014-15-6-r88
• dc.identifier.issn 1465-6906ca
• dc.identifier.uri http://hdl.handle.net/10230/23240
• dc.language.iso engca
• dc.publisher BioMed Centralca
• dc.relation.ispartof Genome Biology. 2014;15:R88
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/098051
• 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.ca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by/4.0
• dc.subject.other Genètica de poblacions humanesca
• dc.subject.other Genètica humana -- Variacióca
• dc.subject.other Selecció naturalca
• dc.title Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequencesen
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca