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  An integrated map of genetic variation from 1,092 human genomes

Abecasis, G. R., Auton, A., Brooks, L. D., DePristo, M. A., Durbin, R. M., Handsaker, R. E., et al. (2012). An integrated map of genetic variation from 1,092 human genomes. Nature, 491(7422), 56-65. doi:10.1038/nature11632.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-CA29-B Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0028-E6FE-9
Genre: Journal Article

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2012
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© 2012 Nature Publishing Group, a division of Macmillan Publishers Limited

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 Creators:
Abecasis, Goncalo R., Author
Auton, Adam, Author
Brooks, Lisa D., Author
DePristo, Mark A., Author
Durbin, Richard M., Author
Handsaker, Robert E., Author
Kang, Hyun Min, Author
Marth, Gabor T., Author
McVean, Gil A., Author
The 1000 Genomes Project Consortium, Author
Sudbrak, Ralf1, Author              
Albrecht, Marcus2, Author              
Amstislavskiy, Vyacheslav3, Author              
Borodina, Tatiana A.4, Author              
Davydov, Alexey4, Author              
Herwig, Ralf2, Author              
Lienhard, Matthias2, Author              
Mertes, Florian1, Author              
Sultan, Marc3, Author              
Timmermann, Bernd5, Author              
Yaspo, Marie L.3, Author              Lehrach, Hans1, Author               more..
Affiliations:
1Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
2Bioinformatics (Ralf Herwig), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479648              
3Human Chromosome 21 (Marie-Laure Yaspo), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479652              
4Technology Development(Alexey Soldatov), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479657              
5Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479670              

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 Abstract: By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations.

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Language(s): eng - English
 Dates: 2012-07-042012-10-012012-10-312012-11-01
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1038/nature11632
ISSN: 1476-4687
 Degree: -

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Title: Nature
Source Genre: Journal
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Publ. Info: Nature Publishing Group
Pages: - Volume / Issue: 491 (7422) Sequence Number: - Start / End Page: 56 - 65 Identifier: ISSN: 0028-836