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

Publication ,  Journal Article
1000 Genomes Project Consortium, ; Abecasis, GR; Auton, A; Brooks, LD; DePristo, MA; Durbin, RM; Handsaker, RE; Kang, HM; Marth, GT; McVean, GA
Published in: Nature
November 2012

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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Published In

Nature

DOI

EISSN

1476-4687

ISSN

0028-0836

Publication Date

November 2012

Volume

491

Issue

7422

Start / End Page

56 / 65

Related Subject Headings

  • Transcription Factors
  • Sequence Deletion
  • Racial Groups
  • Polymorphism, Single Nucleotide
  • Nucleotide Motifs
  • Humans
  • Haplotypes
  • Genomics
  • Genome-Wide Association Study
  • Genome, Human
 

Citation

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1000 Genomes Project Consortium, ., Abecasis, G. R., Auton, A., Brooks, L. D., DePristo, M. A., Durbin, R. M., … McVean, G. A. (2012). An integrated map of genetic variation from 1,092 human genomes. Nature, 491(7422), 56–65. https://doi.org/10.1038/nature11632
1000 Genomes Project Consortium, T., Goncalo R. Abecasis, Adam Auton, Lisa D. Brooks, Mark A. DePristo, Richard M. Durbin, Robert E. Handsaker, Hyun Min Kang, Gabor T. Marth, and Gil A. McVean. “An integrated map of genetic variation from 1,092 human genomes.Nature 491, no. 7422 (November 2012): 56–65. https://doi.org/10.1038/nature11632.
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov;491(7422):56–65.
1000 Genomes Project Consortium, T., et al. “An integrated map of genetic variation from 1,092 human genomes.Nature, vol. 491, no. 7422, Nov. 2012, pp. 56–65. Epmc, doi:10.1038/nature11632.
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov;491(7422):56–65.
Journal cover image

Published In

Nature

DOI

EISSN

1476-4687

ISSN

0028-0836

Publication Date

November 2012

Volume

491

Issue

7422

Start / End Page

56 / 65

Related Subject Headings

  • Transcription Factors
  • Sequence Deletion
  • Racial Groups
  • Polymorphism, Single Nucleotide
  • Nucleotide Motifs
  • Humans
  • Haplotypes
  • Genomics
  • Genome-Wide Association Study
  • Genome, Human