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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]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“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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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Self-citationFinding the missing heritability of complex diseases
Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., McCarthy, M. I., Ramos, E. M., Cardon, L. R., Chakravarti, A., et al. (2009) · Nature · doi:10.1038/nature08494 · Cited by 8,336
A haplotype map of the human genome
The International HapMap Consortium (2005) · Nature · doi:10.1038/nature04226 · Cited by 5,858
Self-citationFinishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03001 · Cited by 4,971
A second generation human haplotype map of over 3.1 million SNPs
The International HapMap Consortium (2007) · Nature · doi:10.1038/nature06258 · Cited by 4,438
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
The hitch-hiking effect of a favourable gene
Smith, J. M., & Haigh, J. (1974) · Genetical Research · doi:10.1017/s0016672300014634 · Cited by 3,415
Sequence Variations in PCSK9, Low LDL, and Protection against Coronary Heart Disease
Cohen, J. C., Boerwinkle, E., Mosley, T. H., & Hobbs, H. H. (2006) · New England Journal of Medicine · doi:10.1056/nejmoa054013 · Cited by 3,181
Integrating common and rare genetic variation in diverse human populations
The International HapMap 3 Consortium (2010) · Nature · doi:10.1038/nature09298 · Cited by 3,026
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
The International SNP Map Working Group, Laboratories:, C. S. H., Sachidanandam, R., Weissman, D., Schmidt, S. C., Kakol, J. M., Stein, L. D., National Center for Biotechnology Information:, Marth, G., Sherry, S., et al. (2001) · Nature · doi:10.1038/35057149 · Cited by 2,977
Flagged first, then by citations
Research works printed but not linked: 1
- Le, S. Q., Li, H. & Durbin, R. QCALL: SNP detection and genotyping from low coverage sequence data on multiple diploid samples. Genome Res. (in the press)
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Increased exonic de novo mutation rate in individuals with schizophrenia
Girard, S. L., Gauthier, J., Noreau, A., Xiong, L., Zhou, S., Jouan, L., Dionne-Laporte, A., Spiegelman, D., Henrion, E., Diallo, O., et al. (2011) · Nature Genetics · doi:10.1038/ng.886 · Cited by 438
Chromatin accessibility: a window into the genome
Tsompana, M., & Buck, M. J. (2014) · Epigenetics & Chromatin · doi:10.1186/1756-8935-7-33 · Cited by 473
Classic Selective Sweeps Were Rare in Recent Human Evolution
Hernandez, R. D., Kelley, J. L., Elyashiv, E., Melton, S., Auton, A., McVean, G., 1000 Genomes Project, Sella, G., & Przeworski, M. (2011) · Science · doi:10.1126/science.1198878 · Cited by 441
Next-generation diagnostics and disease-gene discovery with the Exomiser
Smedley, D., Jacobsen, J. O. B., Jäger, M., Köhler, S., Holtgrewe, M., Schubach, M., Siragusa, E., Zemojtel, T., Buske, O. J., Washington, N. L., et al. (2015) · Nature Protocols · doi:10.1038/nprot.2015.124 · Cited by 445
Identification of Genetic Variants That Affect Histone Modifications in Human Cells
McVicker, G., van de Geijn, B., Degner, J. F., Cain, C. E., Banovich, N. E., Raj, A., Lewellen, N., Myrthil, M., Gilad, Y., & Pritchard, J. K. (2013) · Science · doi:10.1126/science.1242429 · Cited by 436
wANNOVAR: annotating genetic variants for personal genomes via the web
Chang, X., & Wang, K. (2012) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2012-100918 · Cited by 442
Ensembl comparative genomics resources
Herrero, J., Muffato, M., Beal, K. M., Fitzgerald, S. F., Gordon, L., Pignatelli, M., Vilella, A. J., Searle, S. M. J., Amode, R., Brent, S., et al. (2016) · Database · doi:10.1093/database/bav096 · Cited by 583
Lo, M., Hinds, D. A., Tung, J. Y., Franz, C. E., Fan, C.-C., Wang, Y., Smeland, O. B., Schork, A. J., Holland, D., Kauppi, K., et al. (2016) · Nature Genetics · doi:10.1038/ng.3736 · Cited by 462
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Liu, X., & Fu, Y. (2020) · Genome biology · doi:10.1186/s13059-020-02196-9 · Cited by 492
A method to predict the impact of regulatory variants from DNA sequence
Lee, D., Gorkin, D. U., Baker, M., Strober, B. J., Asoni, A. L., McCallion, A. S., & Beer, M. (2015) · Nature Genetics · doi:10.1038/ng.3331 · Cited by 430
Induced pluripotent stem cells: the new patient?
Bellin, M., Marchetto, M. C., Gage, F. H., & Mummery, C. L. (2012) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3448 · Cited by 454
Leblond, C. S., Heinrich, J., Delorme, R., Proepper, C., Betancur, C., Huguet, G., Konyukh, M., Chaste, P., Ey, E., Rastam, M., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002521 · Cited by 429
Zeng, H., Shen, E. H., Hohmann, J. G., Oh, S. W., Bernard, A., Royall, J. J., Glattfelder, K. J., Sunkin, S. M., Morris, J. A., Guillozet-Bongaarts, A. L., et al. (2012) · Cell · doi:10.1016/j.cell.2012.02.052 · Cited by 426
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Luo, R., Wong, T. K. F., Zhu, J.-Q., Liu, C.-M., Zhu, X., Wu, E., Lee, L., Lin, H., Zhu, W., Cheung, D. W.-L., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065632 · Cited by 424
Duncan, L. E., Ratanatharathorn, A., Aiello, A. E., Almli, L. M., Amstadter, A. B., Ashley-Koch, A. E., Baker, D. G., Beckham, J. C., Bierut, L. J., Bisson, J., et al. (2018) · Molecular Psychiatry · doi:10.1038/mp.2017.77 · Cited by 425
Nielsen, R., Korneliussen, T., Albrechtsen, A., Li, Y., & Wang, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037558 · Cited by 424
“In fact, imputation based genotype calling will lead to a substantial increase in accuracy over other methods [7].”
BackgroundMethodInfluentialSystematic Transcriptome Wide Analysis of lncRNA-miRNA Interactions
Jalali, S., Bhartiya, D., Lalwani, M. K., Sivasubbu, S., & Scaria, V. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053823 · Cited by 424
Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications
Huang, L., Ma, F., Chapman, A. R., Lü, S., & Xie, X. S. (2015) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090413-025352 · Cited by 427
The Genetic Cost of Neanderthal Introgression
Harris, K., & Nielsen, R. (2016) · Genetics · doi:10.1534/genetics.116.186890 · Cited by 419
Tammimies, K., Marshall, C. R., Walker, S., Kaur, G., Thiruvahindrapuram, B., Lionel, A. C., Yuen, R. K. C., Uddin, M., Roberts, W., Weksberg, R., et al. (2015) · JAMA · doi:10.1001/jama.2015.10078 · Cited by 419
A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes
Moltke, I., Grarup, N., Jørgensen, M. E., Bjerregaard, P., Treebak, J. T., Fumagalli, M., Korneliussen, T. S., Andersen, M. A., Nielsen, T. S., Krarup, N. T., et al. (2014) · Nature · doi:10.1038/nature13425 · Cited by 418
PSORS2 Is Due to Mutations in CARD14
Jordan, C. T., Cao, L. H., Roberson, E. D. O., Pierson, K. C., Yang, C.-F., Joyce, C. E., Ryan, C., Duan, S., Helms, C. A., Liu, Y., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.03.012 · Cited by 417
Active Transposition in Genomes
Huang, C. R. L., Burns, K. H., & Boeke, J. D. (2012) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155616 · Cited by 430
Genome-wide association study identifies 143 loci associated with 25 hydroxyvitamin D concentration
Revez, J. A., Lin, T., Qiao, Z., Xue, A., Holtz, Y., Zhu, Z., Zeng, J., Wang, H., Sidorenko, J., Kemper, K. E., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15421-7 · Cited by 416
Personalized genomic analyses for cancer mutation discovery and interpretation
Jones, S., Anagnostou, V., Lytle, K., Parpart-Li, S. T., Nesselbush, M. C., Riley, D. R. J., Shukla, M., Chesnick, B., Kadan, M., Papp, E., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aaa7161 · Cited by 418
Aflitos, S. A., Schijlen, E. G. W. M., de Jong, H., de Ridder, D., Smit, S., Finkers, R., Wang, J., Zhang, G., Li, N., Mao, L., et al. (2014) · The Plant Journal · doi:10.1111/tpj.12616 · Cited by 423
Sausen, M., Leary, R. J., Jones, S., Wu, J., Reynolds, C. P., Liu, X., Blackford, A. L., Parmigiani, G., Diaz, L. A., Papadopoulos, N., et al. (2012) · Nature Genetics · doi:10.1038/ng.2493 · Cited by 417
Albers, C. A., Paul, D. S., Schulze, H., Freson, K., Stephens, J. C., Smethurst, P. A., Jolley, J. D., Cvejic, A., Kostadima, M. A., Bertone, P., et al. (2012) · Nature Genetics · doi:10.1038/ng.1083 · Cited by 415
Data integration in the era of omics: current and future challenges
Gómez-Cabrero, D., Abugessaisa, I., Maier, D., Teschendorff, A. E., Merkenschlager, M., Gisel, A., Ballestar, E., Bongcam‐Rudloff, E., Conesa, A., & Tegner, J. N. (2014) · BMC Systems Biology · doi:10.1186/1752-0509-8-s2-i1 · Cited by 426
Clavijo, B., Venturini, L., Schudoma, C., Accinelli, G. G., Kaithakottil, G., Wright, J., Borrill, P., Kettleborough, G., Heavens, D., Chapman, H., et al. (2017) · Genome Research · doi:10.1101/gr.217117.116 · Cited by 407
Natural selection interacts with recombination to shape the evolution of hybrid genomes
Schumer, M., Xu, C., Powell, D. L., Durvasula, A., Skov, L., Holland, C., Blazier, J. C., Sankararaman, S., Andolfatto, P., Rosenthal, G. G., et al. (2018) · Science · doi:10.1126/science.aar3684 · Cited by 412
Tian, C., Hromatka, B. S., Kiefer, A. K., Eriksson, N., Noble, S. M., Tung, J. Y., & Hinds, D. A. (2017) · Nature Communications · doi:10.1038/s41467-017-00257-5 · Cited by 413
Abundant contribution of short tandem repeats to gene expression variation in humans
Gymrek, M., Willems, T., Guilmatre, A., Zeng, H., Markus, B., Georgiev, S., Daly, M. J., Price, A. L., Pritchard, J. K., Sharp, A. J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3461 · Cited by 410
Noninvasive Whole-Genome Sequencing of a Human Fetus
Kitzman, J. O., Snyder, M. W., Ventura, M., Lewis, A. P., Qiu, R., Simmons, L. E., Gammill, H. S., Rubens, C. E., Santillan, D. A., Murray, J. C., et al. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3004323 · Cited by 410
Dindel: Accurate indel calls from short-read dataPreprint
Albers, C. A., Lunter, G. A., MacArthur, D. G., McVean, G., Ouwehand, W. H., & Durbin, R. M. (2010) · Genome Research · doi:10.1101/gr.112326.110 · Cited by 407
DNA methylation contributes to natural human variation
Heyn, H., Moran, S., Hernando-Herraez, I., Sayols, S., Gomez, A., Sandoval, J., Monk, D., Hata, K., Marques-Bonet, T., Wang, L., et al. (2013) · Genome Research · doi:10.1101/gr.154187.112 · Cited by 408
Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior
Ganna, A., Verweij, K. J. H., Nivard, M. G., Maier, R., Wedow, R., Busch, A. S., Abdellaoui, A., Guo, S., Sathirapongsasuti, J. F., 23andMe Research Team, et al. (2019) · Science · doi:10.1126/science.aat7693 · Cited by 406
SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it
Lachance, J., & Tishkoff, S. A. (2013) · BioEssays · doi:10.1002/bies.201300014 · Cited by 425
Pinto, D., Darvishi, K., Shi, X. M., Rajan, D., Rigler, D., Fitzgerald, T. W., Lionel, A. C., Thiruvahindrapuram, B., MacDonald, J. R., Mills, R. E., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1852 · Cited by 415
Sawcer, S. J., Franklin, R. J. M., & Ban, M. (2014) · The Lancet Neurology · doi:10.1016/s1474-4422(14)70041-9 · Cited by 432
Smith, B. H., Campbell, A., Linksted, P., Fitzpatrick, B., Jackson, C., Kerr, S. M., Deary, I. J., MacIntyre, D. J., Campbell, H., McGilchrist, M., et al. (2013) · International Journal of Epidemiology · doi:10.1093/ije/dys084 · Cited by 401
Wain, L. V., Shrine, N. R. G., Miller, S., Jackson, V. E., Ntalla, I., Artigas, M. S., Billington, C. K., Kheirallah, A. K., Allen, R. J., Cook, J. P., et al. (2015) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(15)00283-0 · Cited by 393
Exploring single-sample SNP and INDEL calling with whole-genomede novoassembly
Li, H. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts280 · Cited by 398
Gaulton, K. J., Ferreira, T. C., Lee, Y., Raimondo, A., Mägi, R., Reschen, M. E., Mahajan, A., Locke, A. E., Rayner, N. W., Robertson, N., et al. (2015) · Nature Genetics · doi:10.1038/ng.3437 · Cited by 399
Fuentes‐Pardo, A. P., & Ruzzante, D. E. (2017) · Molecular Ecology · doi:10.1111/mec.14264 · Cited by 417
What can exome sequencing do for you?
Majewski, J., Schwartzentruber, J., Lalonde, E., Montpetit, A., & Jabado, N. (2011) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2011-100223 · Cited by 417
Efficient storage of high throughput DNA sequencing data using reference-based compressionPreprint
Fritz, M. H.-Y., Leinonen, R., Cochrane, G., & Birney, E. (2011) · Genome Research · doi:10.1101/gr.114819.110 · Cited by 388
Genome-wide association studies of cancer: current insights and future perspectives
Sud, A., Kinnersley, B., & Houlston, R. S. (2017) · Nature reviews. Cancer · doi:10.1038/nrc.2017.82 · Cited by 391
Non-invasive prenatal measurement of the fetal genome
Fan, H. C., Gu, W., Wang, J., Blumenfeld, Y. J., El-Sayed, Y. Y., & Quake, S. R. (2012) · Nature · doi:10.1038/nature11251 · Cited by 393
Vaysse, A., Ratnakumar, A., Derrien, T., Axelsson, E., Pielberg, G., Sigurðsson, S., Fall, T., Seppälä, E. H., Hansen, M. S., Lawley, C., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002316 · Cited by 405
Whole-genome sequencing in health care
van El, C. G., Cornel, M. C., Borry, P., Hastings, R. J., Fellmann, F., Hodgson, S. V., Howard, H. C., Cambon‐Thomsen, A., Knoppers, B. M., Meijers-Heijboer, H. E. J., et al. (2013) · European Journal of Human Genetics · doi:10.1038/ejhg.2013.46 · Cited by 399
Wilde, A. A. M., Semsarian, C., Márquez, M. F., Shamloo, A. S., Ackerman, M. J., Ashley, E. A., Sternick, E. B., Barajas-Martínez, H., Behr, E. R., Bezzina, C. R., et al. (2022) · EP Europace · doi:10.1093/europace/euac030 · Cited by 421
The UK-PSCSC Consortium, Liu, J. Z., The International IBD Genetics Consortium, The International PSC Study Group, Hov, J. R., Folseraas, T., Ellinghaus, E., Rushbrook, S. M., Doncheva, N. T., Andreassen, O. A., et al. (2013) · Nature Genetics · doi:10.1038/ng.2616 · Cited by 391
Epidemiology, genetics, and subtyping of preserved ratio impaired spirometry (PRISm) in COPDGene
Wan, E. S., Castaldi, P. J., Cho, M. H., Hokanson, J. E., Regan, E. A., Make, B. J., Beaty, T. H., Han, M. K., Curtis, J. L., Curran‐Everett, D., et al. (2014) · Respiratory Research · doi:10.1186/s12931-014-0089-y · Cited by 390
Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis
Diabetes Genetics Replication and Meta-analysis Consortium, Stahl, E. A., Myocardial Infarction Genetics Consortium, Wegmann, D., Trynka, G., Gutierrez-Achury, J., Do, R., Voight, B. F., Kraft, P., Chen, R., et al. (2012) · Nature Genetics · doi:10.1038/ng.2232 · Cited by 388
TNF receptor 1 genetic risk mirrors outcome of anti-TNF therapy in multiple sclerosis
Gregory, A., Dendrou, C. A., Attfield, K. E., Haghikia, A., Xifara, D. K., Butter, F., Poschmann, G., Kaur, G., Lambert, L., Leach, O. A., et al. (2012) · Nature · doi:10.1038/nature11307 · Cited by 395
Accurate identification of human Alu and non-Alu RNA editing sites
Ramaswami, G., Lin, W., Piskol, R., Tan, M. H., Davis, C., & Li, J. B. (2012) · Nature Methods · doi:10.1038/nmeth.1982 · Cited by 384
Global reference mapping of human transcription factor footprints
Vierstra, J., Lazar, J., Sandstrom, R., Halow, J., Lee, K., Bates, D., Diegel, M., Dunn, D., Neri, F., Haugen, E., et al. (2020) · Nature · doi:10.1038/s41586-020-2528-x · Cited by 386
Differential confounding of rare and common variants in spatially structured populations
Mathieson, I., & McVean, G. (2012) · Nature Genetics · doi:10.1038/ng.1074 · Cited by 385
Three-dimensional reconstruction of protein networks provides insight into human genetic disease
Wang, X., Wei, X., Thijssen, B., Das, J., Lipkin, S. M., & Yu, H. (2012) · Nature Biotechnology · doi:10.1038/nbt.2106 · Cited by 385
Genome-wide association study of obsessive-compulsive disorder
Stewart, S. E., Yu, D., Scharf, J. M., Neale, B. M., Fagerness, J. A., Mathews, C. A., Arnold, P. D., Evans, P. D., Gamazon, E. R., Osiecki, L., et al. (2013) · Molecular Psychiatry · doi:10.1038/mp.2012.85 · Cited by 384
Reliable Identification of Genomic Variants from RNA-Seq Data
Piskol, R., Ramaswami, G., & Li, J. B. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.08.008 · Cited by 398
Zeitz, C., Robson, A. G., & Audo, I. S. (2014) · Progress in Retinal and Eye Research · doi:10.1016/j.preteyeres.2014.09.001 · Cited by 388
Development of a high density 600K SNP genotyping array for chicken
Kranis, A., Gheyas, A., Boschiero, C., Turner, F. S., Yu, L., Smith, S. E., Talbot, R., Pirani, A., Brew, F., Kaiser, P., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-59 · Cited by 399
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Gu, X., & Manautou, J. E. (2012) · Expert Reviews in Molecular Medicine · doi:10.1017/s1462399411002110 · Cited by 405
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Thompson, E. A. (2013) · Genetics · doi:10.1534/genetics.112.148825 · Cited by 401
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Downing, J. R., Wilson, R. K., Zhang, J., Mardis, E. R., Pui, C., Ding, L., Ley, T. J., & Evans, W. E. (2012) · Nature Genetics · doi:10.1038/ng.2287 · Cited by 390
The real cost of sequencing: higher than you think!
Sboner, A., Mu, X. J., Greenbaum, D. S., Auerbach, R. K., & Gerstein, M. (2011) · Genome biology · doi:10.1186/gb-2011-12-8-125 · Cited by 393
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Galinsky, K. J., Bhatia, G., Loh, P., Georgiev, S., Mukherjee, S., Patterson, N. J., & Price, A. L. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.12.022 · Cited by 374
Clan Genomics and the Complex Architecture of Human Disease
Lupski, J. R., Belmont, J. W., Boerwinkle, E., & Gibbs, R. A. (2011) · Cell · doi:10.1016/j.cell.2011.09.008 · Cited by 375
Howrigan, D. P., Simonson, M. A., & Keller, M. C. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-460 · Cited by 379
Capriotti, E., Calabrese, R., Fariselli, P., Martelli, P. L., Altman, R. B., & Casadio, R. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-s3-s6 · Cited by 379
The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biologyPreprint
Gardner, E. J., Lam, V. K. L., Harris, D., Chuang, N. T., Scott, E., Pittard, W. S., Mills, R. E., & Devine, S. E. (2017) · Genome Research · doi:10.1101/gr.218032.116 · Cited by 378
Grundberg, E., Meduri, E., Sandling, J. K., Hedman, Å. K., Keildson, S., Buil, A., Busche, S., Yuan, W., Nisbet, J., Sekowska, M., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.004 · Cited by 370
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Self-citationCasanova, J., Abel, L., & Quintana‐Murci, L. (2011) · Annual Review of Immunology · doi:10.1146/annurev-immunol-030409-101335 · Cited by 377
Stavropoulos, D. J., Merico, D., Jobling, R. K., Bowdin, S. C., Monfared, N., Thiruvahindrapuram, B., Nalpathamkalam, T., Pellecchia, G., Yuen, R. K. C., Szego, M. J., et al. (2016) · npj Genomic Medicine · doi:10.1038/npjgenmed.2015.12 · Cited by 366
Goriely, A., & Wilkie, A. O. M. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.12.017 · Cited by 365
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Khurana, E., Fu, Y., Colonna, V., Mu, X. J., Kang, H. M., Lappalainen, T., Sboner, A., Lochovsky, L., Chen, J., Harmanci, A. O., et al. (2013) · Science · doi:10.1126/science.1235587 · Cited by 368
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Leopold, J. A., & Loscalzo, J. (2018) · Circulation Research · doi:10.1161/circresaha.117.310782 · Cited by 380
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Wright, F. A., Sullivan, P. F., Brooks, A. I., Zou, F., Sun, W., Xia, K., Madar, V., Jansen, R., Chung, W., Zhou, Y.-H., et al. (2014) · Nature Genetics · doi:10.1038/ng.2951 · Cited by 362
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Lill, C. M. (2016) · Molecular and Cellular Probes · doi:10.1016/j.mcp.2016.11.001 · Cited by 387
Heitzer, E., Ulz, P., Belic, J., Gutschi, S., Quehenberger, F., Fischereder, K., Benezeder, T., Auer, M., Pischler, C., Mannweiler, S., et al. (2013) · Genome Medicine · doi:10.1186/gm434 · Cited by 362
Whole-genome sequencing in health care. Recommendations of the European Society of Human Genetics.
van El, C. G., Cornel, M. C., Borry, P., Hastings, R. J., Fellmann, F., Hodgson, S. V., Howard, H. C., Cambon‐Thomsen, A., Knoppers, B. M., Meijers-Heijboer, H. E. J., et al. (2013) · Europe PMC (PubMed Central) · Cited by 359
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Luxán, G., Casanova, J. C., Martı́nez-Poveda, B., Prados, B., D’Amato, G., MacGrogan, D., González-Rajal, Á., Dobarro, D., Torroja, C., Martínez, F., et al. (2013) · Nature Medicine · doi:10.1038/nm.3046 · Cited by 354
The UCSC Genome Browser database: extensions and updates 2011
Dreszer, T. R., Karolchik, D., Zweig, A. S., Hinrichs, A. S., Raney, B. J., Kuhn, R. M., Meyer, L. R., Wong, M., Sloan, C. A., Rosenbloom, K. R., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1055 · Cited by 349
Eberle, M. A., Fritzilas, E., Krusche, P., Källberg, M., Moore, B. L., Bekritsky, M. A., Iqbal, Z., Chuang, H., Humphray, S., Halpern, A. L., et al. (2016) · Genome Research · doi:10.1101/gr.210500.116 · Cited by 356
Sallari, R. C., Zhang, X., Wright, J. B., Bailey, S. D., Cole, M. D., Eeckhoute, J., Moore, J. H., & Lupien, M. (2012) · Nature Genetics · doi:10.1038/ng.2416 · Cited by 354
Whitcomb, D. C., LaRusch, J., Krasinskas, A. M., Klei, L., Smith, J. P., Brand, R. E., Neoptolemos, J. P., Lerch, M. M., Tector, M., Sandhu, B. S., et al. (2012) · Nature Genetics · doi:10.1038/ng.2466 · Cited by 354
Melin, B. S., Barnholtz‐Sloan, J. S., Wrensch, M., Johansen, C., Il’yasova, D., Kinnersley, B., Ostrom, Q. T., Labrèche, K., Chen, Y., Armstrong, G., et al. (2017) · Nature Genetics · doi:10.1038/ng.3823 · Cited by 351
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Manolio, T. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3523 · Cited by 363
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Yue, J., Li, J., Aigrain, L., Hallin, J., Persson, K. O., Oliver, K. L., Bergström, A., Coupland, P. G., Warringer, J., Lagomarsino, M. C., et al. (2017) · Nature Genetics · doi:10.1038/ng.3847 · Cited by 350
Hamdan, F. F., Gauthier, J., Araki, Y., Lin, D.-T., Yoshizawa, Y., Higashi, K., Park, A.-R., Spiegelman, D., Dobrzeniecka, S., Piton, A., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.02.001 · Cited by 349
Toperoff, G., Aran, D., Kark, J. D., Rosenberg, M. H., Dubnikov, T., Nissan, B., Wainstein, J., Friedlander, Y., Levy‐Lahad, E., Gläser, B., et al. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr472 · Cited by 353
Ellinghaus, D., Ellinghaus, E., Nair, R. P., Stuart, P. E., Esko, T., Metspalu, A., Debrus, S., Raelson, J., Tejasvi, T., Belouchi, M., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.02.020 · Cited by 356
Hirota, T., Takahashi, A., Kubo, M., Tsunoda, T., Tomita, K., Sakashita, M., Yamada, T., Fujieda, S., Tanaka, S., Doi, S., et al. (2012) · Nature Genetics · doi:10.1038/ng.2438 · Cited by 343
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Xuan, J., Yu, Y., Qing, T., Guo, L., & Shi, L. M. (2012) · Cancer Letters · doi:10.1016/j.canlet.2012.11.025 · Cited by 355
Seddon, J. M., Yu, Y., Miller, E. C., Reynolds, R. C., Tan, P. L., Gowrisankar, S., Goldstein, J. I., Triebwasser, M. P., Anderson, H. E., Zerbib, J., et al. (2013) · Nature Genetics · doi:10.1038/ng.2741 · Cited by 352
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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