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

Colonna, V., Ayub, Q., Chen, Y., Pagani, L., Luisi, P., Pybus, M., et al. (2014). Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biology: Biology for the Post-Genomic Era, 15(6): R88. doi:10.1186/gb-2014-15-6-r88.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0025-B4AC-D Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-B04D-8
Genre: Journal Article

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© 2014 Colonna et al; licensee BioMed Central Ltd
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 Creators:
Colonna, V., Author
Ayub, Q., Author
Chen, Y., Author
Pagani, L., Author
Luisi, P., Author
Pybus, M., Author
Garrison, E., Author
Xue, Y., Author
Tyler-Smith, C., Author
1000 Genomes Project, Consortium1, Author
Sudbrak, R.1, 2, Author              
Albrecht, M.1, 3, Author              
Amstislavskiy, V.1, 4, Author              
Borodina, T. A.1, 5, Author              
Dahl, A.1, 2, Author              
Davydov, A.1, 5, Author              
Herwig, R.1, 3, Author              
Marquardt, P., Author
Mertes, F.1, 2, Author              
Nietfeld, W.1, 2, Author              
Parkhomchuk, D.1, 2, Author              Soldatov, A. V.1, 5, Author              Timmermann, B.1, 6, Author              Tolzmann, M., AuthorLehrach, H.1, 2, Author              Yaspo, M. L.1, 7, Author               more..
Affiliations:
1The 1000 Genomes Project Consortium, ou_persistent22              
2Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
3Bioinformatics (Ralf Herwig), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479648              
4Human Chromosome 21 (Marie-Laure Yaspo), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479652              
5Technology Development(Alexey Soldatov), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479657              
6Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479670              
7Gene Regulation and Systems Biology of Cancer (Marie-Laure Yaspo), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_2117287              

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 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.

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Language(s): eng - English
 Dates: 2014-06-30
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1186/gb-2014-15-6-r88
ISSN: 1465-6914 (Electronic)
 Degree: -

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Project name : 1000 Genomes Project
Grant ID : 01GS08201
Funding program : -
Funding organization : BMBF

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Title: Genome Biology : Biology for the Post-Genomic Era
Source Genre: Journal
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Publ. Info: London : BioMed Central Ltd.
Pages: - Volume / Issue: 15 (6) Sequence Number: R88 Start / End Page: - Identifier: ISSN: 1465-6906
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000224390