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A map of human genome variation from population-scale sequencing
- Source :
- Nature, Nature, 2010, 467 (7319), pp.1061-1073. ⟨10.1038/nature09534⟩, Nature; Vol 467, PMC, ResearcherID, Nature, 467(7319), 1061-1073, Durbin, R M, Altshuler, D, Abecasis, G R, Bentley, D R, Chakravarti, A, Clark, A G, Collins, F S, de la Vega, F M, Donnelly, P, Egholm, M, Flicek, P, Gabriel, S B, Gibbs, R A, Knoppers, B M, Lander, E S, Lehrach, H, Mardis, E R, McVean, G A, Nickerson, D A, Peltonen, L, Schafer, A J, Sherry, S T, Wang, J, Wilson, R K, Li, R & The 1000 Genomes Project Consortium 2010, ' A map of human genome variation from population-scale sequencing ', Nature, vol. 467, no. 7319, pp. 1061–1073 . https://doi.org/10.1038/nature09534, Nature, Vol. 467, No 7319 (2010) pp. 1061-73
- Publication Year :
- 2010
- Publisher :
- HAL CCSD, 2010.
-
Abstract
- April 1, 2011<br />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[superscript −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.<br />Ministry of Science and Technology of the People's Republic of China (973 program no. 2011CB809200)<br />National Natural Science Foundation (China) (30725008)<br />National Natural Science Foundation (China) (30890032)<br />National Natural Science Foundation (China) (30811130531)<br />National Natural Science Foundation (China) (30221004)<br />China (Chinese 863 program 2006AA02Z177)<br />China (Chinese 863 program 2006AA02Z334)<br />China (Chinese 863 program 2006AA02A302)<br />China (Chinese 863 program 2009AA022707)<br />National Institutes of Health (U.S.) (Grant U54HG2750)<br />National Institutes of Health (U.S.) (Grant U01HG5208)<br />National Institutes of Health (U.S.) (Grant U54HG3067)
- Subjects :
- Male
[SDV]Life Sciences [q-bio]
DNA Mutational Analysis
Pilot Projects
Chromosomes, Human, Y/genetics
DNA, Mitochondrial/genetics
0302 clinical medicine
ddc:576.5
2. Zero hunger
Genetics
Recombination, Genetic
0303 health sciences
Multidisciplinary
Genetics, Population/methods
Genomics
Polymorphism, Single Nucleotide/genetics
Recombination, Genetic/genetics
3. Good health
Genetic Variation/genetics
Sequence Analysis, DNA/methods
Calibration
Female
Mutation/genetics
Genotype
Haplotypes/genetics
Biology
Instability
DNA, Mitochondrial
Polymorphism, Single Nucleotide
Article
Selection, Genetic/genetics
Factor (chord)
Evolution, Molecular
03 medical and health sciences
Table (landform)
Humans
Selection, Genetic
Genetic Association Studies
030304 developmental biology
Genotype imputation
Chromosomes, Human, Y
Genome, Human
Computational Biology
Genetic Variation
Sequence Analysis, DNA
Genomics/methods
Genetics, Population
Haplotypes
Sample Size
wide association gene-expression recombination hotspots meiotic recombination genotype imputation rare variants haplotype map nucleotide diseases common
Mutation
Genome, Human/genetics
Trinucleotide repeat expansion
Sequence Alignment
030217 neurology & neurosurgery
Genome-Wide Association Study
Subjects
Details
- Language :
- English
- ISSN :
- 00280836 and 14764687
- Database :
- OpenAIRE
- Journal :
- Nature, Nature, 2010, 467 (7319), pp.1061-1073. ⟨10.1038/nature09534⟩, Nature; Vol 467, PMC, ResearcherID, Nature, 467(7319), 1061-1073, Durbin, R M, Altshuler, D, Abecasis, G R, Bentley, D R, Chakravarti, A, Clark, A G, Collins, F S, de la Vega, F M, Donnelly, P, Egholm, M, Flicek, P, Gabriel, S B, Gibbs, R A, Knoppers, B M, Lander, E S, Lehrach, H, Mardis, E R, McVean, G A, Nickerson, D A, Peltonen, L, Schafer, A J, Sherry, S T, Wang, J, Wilson, R K, Li, R & The 1000 Genomes Project Consortium 2010, ' A map of human genome variation from population-scale sequencing ', Nature, vol. 467, no. 7319, pp. 1061–1073 . https://doi.org/10.1038/nature09534, Nature, Vol. 467, No 7319 (2010) pp. 1061-73
- Accession number :
- edsair.doi.dedup.....3c837f74b531086923604e4fb1c1bab8