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

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 populati...

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Detalles Bibliográficos
Autores: Colonna, Vincenza, Ayub, Qasim, Cheng, Yuan, Pagani, Luca, Luisi, Pierre, 1985-, Pybus Oliveras, Marc, 1985-, Garrison, Erik, Xue, Yali, Tyler-Smith, Chris, The 1000 Genomes Project Consortium
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2014
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/23240
Acceso en línea:http://hdl.handle.net/10230/23240
http://dx.doi.org/10.1186/gb-2014-15-6-r88
Access Level:acceso abierto
Palabra clave:Genètica de poblacions humanes
Genètica humana -- Variació
Selecció natural
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spelling Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequencesColonna, VincenzaAyub, QasimCheng, YuanPagani, LucaLuisi, Pierre, 1985-Pybus Oliveras, Marc, 1985-Garrison, ErikXue, YaliTyler-Smith, ChrisThe 1000 Genomes Project ConsortiumGenètica de poblacions humanesGenètica humana -- VariacióSelecció naturalBackground: 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.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 VCBioMed Central201520152014info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/23240http://dx.doi.org/10.1186/gb-2014-15-6-r88reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésGenome Biology. 2014;15:R88info:eu-repo/grantAgreement/EC/FP7/098051© 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.http://creativecommons.org/licenses/by/4.0info:eu-repo/semantics/openAccessoai:recercat.cat:10230/232402026-05-29T05:05:01Z
dc.title.none.fl_str_mv Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
title Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
spellingShingle Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
Colonna, Vincenza
Genètica de poblacions humanes
Genètica humana -- Variació
Selecció natural
title_short Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
title_full Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
title_fullStr Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
title_full_unstemmed Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
title_sort Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
dc.creator.none.fl_str_mv Colonna, Vincenza
Ayub, Qasim
Cheng, Yuan
Pagani, Luca
Luisi, Pierre, 1985-
Pybus Oliveras, Marc, 1985-
Garrison, Erik
Xue, Yali
Tyler-Smith, Chris
The 1000 Genomes Project Consortium
author Colonna, Vincenza
author_facet Colonna, Vincenza
Ayub, Qasim
Cheng, Yuan
Pagani, Luca
Luisi, Pierre, 1985-
Pybus Oliveras, Marc, 1985-
Garrison, Erik
Xue, Yali
Tyler-Smith, Chris
The 1000 Genomes Project Consortium
author_role author
author2 Ayub, Qasim
Cheng, Yuan
Pagani, Luca
Luisi, Pierre, 1985-
Pybus Oliveras, Marc, 1985-
Garrison, Erik
Xue, Yali
Tyler-Smith, Chris
The 1000 Genomes Project Consortium
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Genètica de poblacions humanes
Genètica humana -- Variació
Selecció natural
topic Genètica de poblacions humanes
Genètica humana -- Variació
Selecció natural
description 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.
publishDate 2014
dc.date.none.fl_str_mv 2014
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/23240
http://dx.doi.org/10.1186/gb-2014-15-6-r88
url http://hdl.handle.net/10230/23240
http://dx.doi.org/10.1186/gb-2014-15-6-r88
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Genome Biology. 2014;15:R88
info:eu-repo/grantAgreement/EC/FP7/098051
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
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