publication . Article . Other literature type . 2012

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

Alon Keinan;
Open Access English
  • Published: 01 Nov 2012
  • Publisher: Nature Publishing Group
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 carr...
Subjects
free text keywords: Genoma humà, Human genome, transcription factor, untranslated RNA, Binding Sites, Conserved Sequence, Continental Population Groups, Evolution, Molecular, Genetic Variation, Genetics, Medical, Genetics, Population, Genome, Human, Genome-Wide Association Study, Genomics, Haplotypes, Humans, Nucleotide Motifs, Polymorphism, Single Nucleotide, Sequence Deletion, Transcription Factors, Algorithm, Evolutionary biology, Genetic analysis, Human evolution, Integrated approach, Map, Natural selection, Polymorphism, Alleles, Evolution, Molecular, Genetics, Medical, Population, Genome, Human, Single Nucleotide, Binding Sites/genetics, Conserved Sequence/genetics, Continental Population Groups/genetics, Genetic Variation/genetics, Genome, Human/genetics, Haplotypes/genetics, Polymorphism, Single Nucleotide/genetics, Sequence Deletion/genetics, Transcription Factors/metabolism, Article, ddc:576.5
Funded by
WT| Statistical methods development and analysis of genomic data in health and disease.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 095552
  • Funding stream: Cellular and Molecular Neuroscience
,
NIH| Filling the data processing gap for exon-region specific data from 1000 Genomes
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01HG005211-02
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
NIH| Joint SNP and CNV calling in 1000 Genomes sequence data
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U01HG005208-02S1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
NIH| POSTDOCTORAL TRAINING IN MEDICAL INFORMATION SCIENCES
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5T15LM007033-02
  • Funding stream: NATIONAL LIBRARY OF MEDICINE
,
NIH| Population genetics and evolution of mobile elements
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM059290-16
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
47 references, page 1 of 4

Tennessen, JA. Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes. Science. 2012 [OpenAIRE]

A map of human genome variation from population-scale sequencing. Nature. 2010; 467: 1061-1073 [OpenAIRE] [PubMed]

Drmanac, R. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. 2010; 327: 78-81 [PubMed]

Mills, RE. Mapping copy number variation by population-scale genome sequencing. Nature. 2011; 470: 59-65 [OpenAIRE] [PubMed]

Marth, GT. The functional spectrum of low-frequency coding variation. Genome Biol. 2011; 12: R84 [OpenAIRE] [PubMed]

Nelson, MR. An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science. 2012; 337: 100-104 [OpenAIRE] [PubMed]

Mathieson, I, McVean, G. Differential confounding of rare and common variants in spatially structured populations. Nat Genet. 2012; 44: 243-246 [OpenAIRE] [PubMed]

Gravel, S. Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A. 2011; 108: 11983-11988 [OpenAIRE] [PubMed]

A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007; 449: 851-861 [OpenAIRE] [PubMed]

Salmela, E. Genome-wide analysis of single nucleotide polymorphisms uncovers population structure in Northern Europe. PLoS ONE. 2008; 3: e3519 [OpenAIRE] [PubMed]

Lupski, JR, Belmont, JW, Boerwinkle, E, Gibbs, RA. Clan genomics and the complex architecture of human disease. Cell. 2011; 147: 32-43 [OpenAIRE] [PubMed]

Lawson, DJ, Hellenthal, G, Myers, S, Falush, D. Inference of population structure using dense haplotype data. PLoS Genet. 2012; 8: e1002453 [OpenAIRE] [PubMed]

A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011; 9: e1001046 [OpenAIRE] [PubMed]

Sasaki, K. Expression cloning of a novel Gal beta (1-3/1-4) GlcNAc alpha 2,3-sialyltransferase using lectin resistance selection. J Biol Chem. 1993; 268: 22782-22787 [PubMed]

Marth, G. Sequence variations in the public human genome data reflect a bottlenecked population history. Proc Natl Acad Sci U S A. 2003; 100: 376-381 [OpenAIRE] [PubMed]

47 references, page 1 of 4
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 carr...
Subjects
free text keywords: Genoma humà, Human genome, transcription factor, untranslated RNA, Binding Sites, Conserved Sequence, Continental Population Groups, Evolution, Molecular, Genetic Variation, Genetics, Medical, Genetics, Population, Genome, Human, Genome-Wide Association Study, Genomics, Haplotypes, Humans, Nucleotide Motifs, Polymorphism, Single Nucleotide, Sequence Deletion, Transcription Factors, Algorithm, Evolutionary biology, Genetic analysis, Human evolution, Integrated approach, Map, Natural selection, Polymorphism, Alleles, Evolution, Molecular, Genetics, Medical, Population, Genome, Human, Single Nucleotide, Binding Sites/genetics, Conserved Sequence/genetics, Continental Population Groups/genetics, Genetic Variation/genetics, Genome, Human/genetics, Haplotypes/genetics, Polymorphism, Single Nucleotide/genetics, Sequence Deletion/genetics, Transcription Factors/metabolism, Article, ddc:576.5
Funded by
WT| Statistical methods development and analysis of genomic data in health and disease.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 095552
  • Funding stream: Cellular and Molecular Neuroscience
,
NIH| Filling the data processing gap for exon-region specific data from 1000 Genomes
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01HG005211-02
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
NIH| Joint SNP and CNV calling in 1000 Genomes sequence data
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U01HG005208-02S1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
NIH| POSTDOCTORAL TRAINING IN MEDICAL INFORMATION SCIENCES
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5T15LM007033-02
  • Funding stream: NATIONAL LIBRARY OF MEDICINE
,
NIH| Population genetics and evolution of mobile elements
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM059290-16
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
47 references, page 1 of 4

Tennessen, JA. Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes. Science. 2012 [OpenAIRE]

A map of human genome variation from population-scale sequencing. Nature. 2010; 467: 1061-1073 [OpenAIRE] [PubMed]

Drmanac, R. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. 2010; 327: 78-81 [PubMed]

Mills, RE. Mapping copy number variation by population-scale genome sequencing. Nature. 2011; 470: 59-65 [OpenAIRE] [PubMed]

Marth, GT. The functional spectrum of low-frequency coding variation. Genome Biol. 2011; 12: R84 [OpenAIRE] [PubMed]

Nelson, MR. An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science. 2012; 337: 100-104 [OpenAIRE] [PubMed]

Mathieson, I, McVean, G. Differential confounding of rare and common variants in spatially structured populations. Nat Genet. 2012; 44: 243-246 [OpenAIRE] [PubMed]

Gravel, S. Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A. 2011; 108: 11983-11988 [OpenAIRE] [PubMed]

A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007; 449: 851-861 [OpenAIRE] [PubMed]

Salmela, E. Genome-wide analysis of single nucleotide polymorphisms uncovers population structure in Northern Europe. PLoS ONE. 2008; 3: e3519 [OpenAIRE] [PubMed]

Lupski, JR, Belmont, JW, Boerwinkle, E, Gibbs, RA. Clan genomics and the complex architecture of human disease. Cell. 2011; 147: 32-43 [OpenAIRE] [PubMed]

Lawson, DJ, Hellenthal, G, Myers, S, Falush, D. Inference of population structure using dense haplotype data. PLoS Genet. 2012; 8: e1002453 [OpenAIRE] [PubMed]

A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011; 9: e1001046 [OpenAIRE] [PubMed]

Sasaki, K. Expression cloning of a novel Gal beta (1-3/1-4) GlcNAc alpha 2,3-sialyltransferase using lectin resistance selection. J Biol Chem. 1993; 268: 22782-22787 [PubMed]

Marth, G. Sequence variations in the public human genome data reflect a bottlenecked population history. Proc Natl Acad Sci U S A. 2003; 100: 376-381 [OpenAIRE] [PubMed]

47 references, page 1 of 4
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