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A map of human genome variation from population-scale sequencing.
Open accessAbstract
The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother–father–child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10−8 per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research. This issue of Nature contains the first publication from The 1000 Genomes Project, an international collaboration that will produce an extensive public catalogue of human genetic variation. The plan, in fact, is to sequence about 2,000 unidentified individuals from 20 populations around the world. This first paper presents the results from the project's pilot phase, testing three different strategies for genome-wide sequencing with high-throughput platforms: low-coverage whole-genome sequencing of 179 individuals in three population groups, high-coverage sequencing of two mother–father–child trios, and exon-targeted sequencing of 697 individuals from seven populations. The goal of the 1000 Genomes Project is to provide in-depth information on variation in human genome sequences. In the pilot phase reported here, different strategies for genome-wide sequencing, using high-throughput sequencing platforms, were developed and compared. The resulting data set includes more than 95% of the currently accessible variants found in any individual, and can be used to inform association and functional studies.
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“To show that our estimates are not the result of Ancestry Composition errors or biases, we validated the estimates of low levels of African ancestry in European Americans comparing to f4 statistics,64 1000 Genomes Project consensus estimates,78 and ADMIXTURE estimates.66”
From The genetic ancestry of African Americans, Latinos, and European Americans across the United States (2015) · cites this paper as [78]
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“This underestimates the true number of common polymorphisms in the saola, as a large number of sites were conservatively removed to reduce errors, including all transition mutations, which typically account for approximately 2/3 of all SNPs.41”
From Genomes of critically endangered saola are shaped by population structure and purging (2025) · cites this paper as [41]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“We chose panTro4 as an ancestral sequence rather than a composite ancestral sequence as some other studies have done [e.g., (57)] because it allowed us to more easily estimate branch lengths, at the cost of discarding some sites.”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [57]
Experimental — accuracy not yet measuredIn the citing paper
“Similarly, two frame-shift mutations and one splice site mutation of SHANK2 are listed in dbSNP and in the 1000 genomes project [71].”
From Genetic and Functional Analyses of SHANK2 Mutations Suggest a Multiple Hit Model of Autism Spectrum Disorders (2012) · cites this paper as [71]
In the citing paper
“Initial results from the 1000 genomes project has estimated that, on average, each person carries approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders [71].”
From Genetic and Functional Analyses of SHANK2 Mutations Suggest a Multiple Hit Model of Autism Spectrum Disorders (2012) · cites this paper as [71]
In the citing paper
“eight callsets (three deletion, four insertion, and one tandem duplication callset) met the pre-specified specificity threshold33 (FDR≤10%), whereas the other callsets yielded lower specificity (FDRs of 13%-89%).”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [33]
In the citing paper
“The 1000GP recently generated 4.1 Terabases of raw sequence in pilot projects targeting whole human genomes33”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [33]
In the citing paper
“The published results for ASD 83–85 and unpublished data on SCZ suggest these issues will be important and underscore the need for sequencing studies to have the same emphasis on statistical rigor and large sample sizes that has enabled GWAS to realize success for multiple psychiatric disorders. 154”
From Genetic architectures of psychiatric disorders: the emerging picture and its implications (2012) · cites this paper as [154]
In the citing paper
“This analysis identified a single strong association (r2=.99), between rs10490924, a coding variant in the ARMS2 gene which is the peak of association in 10q26, and a 3′ UTR indel polymorphism associated with ARMS2 mRNA instability40.”
From Seven new loci associated with age-related macular degeneration (2013) · cites this paper as [39]
In the citing paper
“Consistent with observations for other complex diseases39, the majority of common disease susceptibility alleles do not alter protein sequences and are not associated with insertions or deletions of coding sequence or with copy number variation.”
From Seven new loci associated with age-related macular degeneration (2013) · cites this paper as [39]
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Metadata
- Authors
- The 1000 Genomes Project Consortium
- Venue
- Nature
- Published
- 2010-10-27
- Volume
- 467
- Issue
- 7319
- Pages
- 1061-1073
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3042601
- OpenAlex
- W2171777347
- Cited by
- 7,877
- References
- 50
- Citations by year
- 2026: 126 · 2025: 209 · 2024: 298 · 2023: 229 · 2022: 258 · 2021: 323 · 2020: 305 · 2019: 398 · 2018: 428 · 2017: 500 · 2016: 585 · 2015: 736 · 2014: 828 · 2013: 964 · 2012: 978
- FWCI
- 476.44
- Type
- journal article
- Language
- en
- Update notices
- erratum (2011-05-26)
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by-nc-sa)
- Archive ouverte UNIGE (University of Geneva) (publishedVersion, other-oa)
- PubMed Central (acceptedVersion)
- ANU Open Research (Australian National University) (submittedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Civil War Book Review (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- Max Planck Institute for Plasma Physics (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Funders
- National Science Foundation
- Howard Hughes Medical Institute
- Doris Duke Charitable Foundation
- Pew Charitable Trusts
- Wellcome Trust (085532, /WT081407/Z/06/Z, 086084, WT086084/Z/08/Z, 075491, 089062, 077009, WT075491/Z/04, 077192, WT085532AIA, WT089088/Z/09/Z, 077014, 89305, 081407, 089061, 089088)
- Translational Genomics Research Institute
- National Institute for Health and Care Research (NF-SI-0508-10212)
- British Heart Foundation (RG/09/012/28096)
- Leverhulme Trust
- European Commission (242257)
- Deutsche Forschungsgemeinschaft
- Louis-Jeantet Foundation
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (28096)
- National Natural Science Foundation of China (973 Program, 30890032, 30221004, 30725008, 30811130531)
- Bundesministerium für Bildung und Forschung (01GS08201, 0315428A)
- Government of Jiangxi Province
- Max-Planck-Gesellschaft
- Ministero dello Sviluppo Economico
- National Institutes of Health (5p41hg004221-03, n01hg62088-6-0-1)
- Medical Research Council
- Engineering and Physical Sciences Research Council
- National High-tech Research and Development Program
- National Key Research and Development Program of China (“973” Program)
- National Institute on Alcohol Abuse and Alcoholism (R21AA022707)
- National Institute of Mental Health (01MH84698, R01MH084698)
- National Human Genome Research Institute (P41HG2371, U54HG002750, P41HG004222, U54HG003067, U54HG002757, R01HG2651, U01HG005211, P50HG002357, R01HG4719, U01HG5214, R01HG004333, U54HG3273, RC2HG5552, R01HG003229, R01HG003698, U54HG003079, U01HG5209, P01HG004120, U41HG002371, P01HG4120, U54HG3067, U01HG5210, R01HG4333, R01HG002651, U54HG003273, U01HG005210, R01HG004719, U54HG2750, R01HG3698, U01HG5211, U01HG005214, 01HG3229, P41HG4221, U01HG005209, U41HG4568, U01HG5208, RC2HG005552, R01HG002510, N01 HG062088, P41HG002371, P41HG4222, U54HG2757, R01HG004960, F31HG005201, U01HG005208, U54HG3079, R01HG4960, P50HG2357, U41HG004568, U24HG002371, P41-HG004221)
- National Institute of General Medical Sciences (R01GM72861, T32GM007753, R01GM059290, R01 GM59290, R01GM072861)
- National Institute of Environmental Health Sciences (28096)
- U.S. National Library of Medicine
- National Center for Research Resources (S10RR025056)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- human genetic variation, 1000 Genomes Project, single nucleotide polymorphisms, indels, structural variants, loss-of-function mutations, de novo mutations, natural selection signatures, haplotype structure, allele frequency, population genetic variation, genotype-phenotype correlation
- MeSH terms
- Calibration, DNA Mutational Analysis, DNA, Mitochondrial, Female, Genetics, Population, Genotype, Haplotypes, Humans, Male, Mutation, Pilot Projects, Recombination, Genetic, Selection, Genetic, Genetic Variation, Genome, Human, Sequence Alignment, Sequence Analysis, DNA, Sample Size, Evolution, Molecular, Computational Biology, Polymorphism, Single Nucleotide, Genomics, Chromosomes, Human, Y, Genome-Wide Association Study, Genetic Association Studies
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