The DOI matches its Crossref record; 50 of the 50 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
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
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)
Cited by
Sorted by citations
Items 801–900 of 1,090
Identification of Multiple Genetic Susceptibility Loci in Takayasu Arteritis
Saruhan‐Direskeneli, G., Hughes, T. K., Aksu, K., Keser, G., Coit, P., Aydın, S. Z., Alıbaz-Öner, F., Kamalı, S., İnanç, M., Carette, S., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.05.026 · Cited by 173
A Recurrent PDGFRB Mutation Causes Familial Infantile Myofibromatosis
Cheung, Y. H., Gayden, T., Campeau, P. M., LeDuc, C. A., Russo, D., Nguyễn, V. H., Guo, J., Qi, M., Guan, Y., Albrecht, S., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.04.026 · Cited by 173
Merelli, I., Pérez‐Sánchez, H., Gesing, S., & D’Agostino, D. (2014) · BioMed Research International · doi:10.1155/2014/134023 · Cited by 172
Resource profile and user guide of the Polygenic Index Repository
Becker, J., Burik, C. A. P., Goldman, G., Wang, N., Jayashankar, H., Bennett, M., Belsky, D. W., Linnér, R. K., Ahlskog, R., Kleinman, A., et al. (2021) · Nature Human Behaviour · doi:10.1038/s41562-021-01119-3 · Cited by 179
Refaat, M. M., Lubitz, S. A., Makino, S., Islam, Z., Frangiskakis, J. M., Mehdi, H., Gutmann, R. A., Zhang, M. L., Bloom, H. L., MacRae, C. A., et al. (2011) · Heart Rhythm · doi:10.1016/j.hrthm.2011.10.016 · Cited by 170
Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios
Besenbacher, S., Liu, S. M., Izarzugaza, J. M. G., Grove, J., Belling, K., Bork‐Jensen, J., Huang, S., Als, T. D., Li, S., Yadav, R., et al. (2015) · Nature Communications · doi:10.1038/ncomms6969 · Cited by 169
Roth, A. J. L., Ding, J., Morin, R. D., Crisan, A., Ha, G., Giuliany, R., Bashashati, A., Hirst, M., Turashvili, G., Oloumi, A., et al. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts053 · Cited by 173
Genome-wide association study identifies three novel loci for type 2 diabetes
Hara, K., Fujita, H., Johnson, T. A., Yamauchi, T., Yasuda, K., Horikoshi, M., Chen, P., Hu, C., Ronald, C. W., Imamura, M., et al. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt399 · Cited by 171
Reddy, T. E., Gertz, J., Pauli, F., Kucera, K. S., Varley, K. E., Newberry, K. M., Marinov, G. K., Mortazavi, A., Williams, B. A., Song, L., et al. (2012) · Genome Research · doi:10.1101/gr.131201.111 · Cited by 175
The mitochondrial ADP/ATP carrier (SLC25 family): Pathological implications of its dysfunction
Clémençon, B., Babot, M., & Trézéguet, V. (2013) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2012.05.006 · Cited by 173
Majithia, A. R., Flannick, J. A., Shahinian, P., Guo, M. H., Bray, M., Fontanillas, P., Gabriel, S., NHGRI JHS/FHS Allelic Spectrum Project, Rosen, E. D., Altshuler, D., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1410428111 · Cited by 172
Comment on “Widespread RNA and DNA Sequence Differences in the Human Transcriptome”
Pickrell, J. K., Gilad, Y., & Pritchard, J. K. (2012) · Science · doi:10.1126/science.1210484 · Cited by 167
Identification of 12 genetic loci associated with human healthspan
Zenin, A., Tsepilov, Y., Sharapov, S., Getmantsev, E., Menshikov, L. I., Fedichev, P. O., & Aulchenko, Y. (2019) · Communications Biology · doi:10.1038/s42003-019-0290-0 · Cited by 170
Cerhan, J. R., Berndt, S. I., Vijai, J., Ghesquières, H., McKay, J., Wang, S., Wang, Z., Yeager, M., Conde, L., de Bakker, P. I. W., et al. (2014) · Nature Genetics · doi:10.1038/ng.3105 · Cited by 174
Next Generation Sequencing and the Future of Genetic Diagnosis
Lohmann, K., & Klein, C. (2014) · Neurotherapeutics · doi:10.1007/s13311-014-0288-8 · Cited by 170
A decade of structural variants: description, history and methods to detect structural variation
Escaramís, G., Docampo, E., & Rabionet, R. (2015) · Briefings in Functional Genomics · doi:10.1093/bfgp/elv014 · Cited by 184
Iqbal, Z., Vandeweyer, G., van der Voet, M., Waryah, A., Zahoor, M., Besseling, J., Roca, L. T., Silfhout, A. T. V.-V., Nijhof, B., Kramer, J. M., et al. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt043 · Cited by 175
Churko, J. M., Mantalas, G. L., Snyder, M. P., & Wu, J. C. (2013) · Circulation Research · doi:10.1161/circresaha.113.300939 · Cited by 183
Poultney, C. S., Goldberg, A. P., Drapeau, E., Kou, Y., Harony-Nicolas, H., Kajiwara, Y., De Rubeis, S., Durand, S., Stevens, C., Rehnström, K., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.09.001 · Cited by 169
Self-citationSeeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome
van Oven, M., Geystelen, A. V., Kayser, M., Decorte, R., & Larmuseau, M. (2013) · Human Mutation · doi:10.1002/humu.22468 · Cited by 169
FLAGS, frequently mutated genes in public exomes
Shyr, C., Tarailo‐Graovac, M., Gottlieb, M., Lee, J. J. Y., van Karnebeek, C., & Wasserman, W. W. (2014) · BMC Medical Genomics · doi:10.1186/s12920-014-0064-y · Cited by 174
Arking, D., Junttila, M. J., Goyette, P., Huertas-Vázquez, A., Eijgelsheim, M., Blom, M., Newton-Cheh, C., Reinier, K., Teodorescu, C. A., Uy-Evanado, A., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002158 · Cited by 150
Mutations in SLC34A3/NPT2c Are Associated with Kidney Stones and Nephrocalcinosis
Dasgupta, D., Wee, M. J., Reyes, M., Li, Y., Simm, P. J., Sharma, A., Schlingmann, K. P., Janner, M., Biggin, A., Lazier, J., et al. (2014) · Journal of the American Society of Nephrology · doi:10.1681/asn.2013101085 · Cited by 169
Genetic and environmental exposures constrain epigenetic drift over the human life coursePreprint
Shah, S. H., McRae, A. F., Marioni, R. E., Harris, S. E., Gibson, J., Henders, A. K., Redmond, P. H., Cox, S. R., Pattie, A., Corley, J., et al. (2014) · Genome Research · doi:10.1101/gr.176933.114 · Cited by 169
Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers
Sánchez-Quinto, F., Schroeder, H., Ramirez, O., Ávila-Arcos, M. C., Pybus, M., Olalde, I., Velazquez, A. M. V., Marcos, M. E. P., Encinas, J. M. V., Bertranpetit, J., et al. (2012) · Current Biology · doi:10.1016/j.cub.2012.06.005 · Cited by 142
Variants inDENND1AAre Associated with Polycystic Ovary Syndrome in Women of European Ancestry
Welt, C. K., Styrkársdóttir, U., Ehrmann, D. A., Þorleifsson, G., Arason, G., Guðmundsson, J. A., Ober, C., Rosenfield, R. L., Saxena, R., Þorsteinsdóttir, U., et al. (2012) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2011-3478 · Cited by 170
Toddie-Moore, D., Onoufriadis, A., Shoemark, A., Simpson, M. A., Lage, P. Z., de Castro, S. C., Bartoloni, L., Gallone, G., Petridi, S., Woollard, W. J., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.07.009 · Cited by 168
Biomarkers for the Prediction of Type 2 Diabetes and Cardiovascular Disease
Herder, C., Karakas, M., & Köenig, W. (2011) · Clinical Pharmacology & Therapeutics · doi:10.1038/clpt.2011.93 · Cited by 168
Evolutionary Biology for the 21st Century
Losos, J. B., Arnold, S. J., Bejerano, G., Brodie, E. D., Hibbett, D. S., Hoekstra, H. E., Mindell, D. P., Monteiro, A., Moritz, C. C., Orr, H. A., et al. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001466 · Cited by 176
Metspalu, M., Romero, I. G., Yunusbayev, B., Chaubey, G., Mallick, C. B., Hudjashov, G., Nelis, M., Mägi, R., Metspalu, E., Remm, M., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.11.010 · Cited by 170
A novel Fanconi anaemia subtype associated with a dominant-negative mutation in RAD51
Ameziane, N., May, P., Haitjema, A., van de Vrugt, H. J., van Rossum-Fikkert, S. E., Ristić, D., Williams, G. J., Balk, J. A., Rockx, D., Li, H., et al. (2015) · Nature Communications · doi:10.1038/ncomms9829 · Cited by 173
Large-scale contamination of microbial isolate genomes by Illumina PhiX control
Mukherjee, S., Huntemann, M., Ivanova, N., Kyrpides, N. C., & Pati, A. (2015) · Standards in Genomic Sciences · doi:10.1186/1944-3277-10-18 · Cited by 166
Variant Callers for Next-Generation Sequencing Data: A Comparison Study
Liu, X., Han, S., Wang, Z., Gelernter, J. E., & Yang, B. (2013) · PLoS ONE · doi:10.1371/journal.pone.0075619 · Cited by 166
Payne, F., Lim, K., Girousse, A., Brown, R. J., Kory, N., Robbins, A. L., Xue, Y., Sleigh, A., Cochran, E. K., Adams, C., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1408523111 · Cited by 167
Archaic human ancestry in East Asia
Skoglund, P., & Jakobsson, M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1108181108 · Cited by 170
A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome
Mathias, R. A., Taub, M. A., Gignoux, C. R., Fu, W., Musharoff, S. A., O’Connor, T. D., Vergara, C., Torgerson, D. G., Pino-Yanes, M. D. M., Shringarpure, S., et al. (2016) · Nature Communications · doi:10.1038/ncomms12522 · Cited by 170
Understanding inflammatory bowel disease via immunogenetics
de Lange, K. M., & Barrett, J. C. (2015) · Journal of Autoimmunity · doi:10.1016/j.jaut.2015.07.013 · Cited by 168
Best, T., Li, D., Skol, A. D., Kirchhoff, T., Jackson, S. A., Yasui, Y., Bhatia, R., Strong, L. C., Domchek, S. M., Nathanson, K. L., et al. (2011) · Nature Medicine · doi:10.1038/nm.2407 · Cited by 170
Blood Pressure Loci Identified with a Gene-Centric Array
Johnson, T., Gaunt, T. R., Newhouse, S., Padmanabhan, S., Tomaszewski, M., Meena Kumari, B., Morris, R. W., Tzoulaki, I., O'Brien, E. T., Poulter, N. R., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.10.013 · Cited by 168
MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing
Mort, M. E., Sterne-Weiler, T., Li, B., Ball, E. V., Cooper, D. N., Predrag Radivojac, A., Sanford, J. R., & Mooney, S. D. (2014) · Genome biology · doi:10.1186/gb-2014-15-1-r19 · Cited by 161
Takeuchi, M., Mizuki, N., Meguro, A., Ombrello, M. J., Kirino, Y., Satorius, C., Le, J., Blake, M., Erer, B., Kawagoe, T., et al. (2017) · Nature Genetics · doi:10.1038/ng.3786 · Cited by 167
A female Viking warrior confirmed by genomics
Hedenstierna‐Jonson, C., Kjellström, A., Zachrisson, T., Krzewińska, M., Sobrado, V., Price, N. S., Günther, T., Jakobsson, M., Götherström, A., & Storå, J. (2017) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23308 · Cited by 186
Coffinier, C., Hull, L. E., Lynch, J. A., DuVall, S. L., Damrauer, S. M., Cunningham, F. E., Voight, B. F., Matheny, M. E., Oslin, D. W., Icardi, M. S., et al. (2019) · JAMA Network Open · doi:10.1001/jamanetworkopen.2019.5345 · Cited by 166
H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in AfricaPreprint
Mulder, N., Adebiyi, E. F., Alami, R., Benkahla, A., Brandful, J., Doumbia, S., Everett, D., Fadlelmola, F. M., Gaboun, F., Gaseitsiwe, S., et al. (2015) · Genome Research · doi:10.1101/gr.196295.115 · Cited by 172
Evidence for recent, population-specific evolution of the human mutation rate
Harris, K. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1418652112 · Cited by 165
A Connectome Computation System for discovery science of brain
Xu, T., Yang, Z., Jiang, L., Xing, X.-X., & Zuo, X. (2015) · 中国科学通报：英文版 · doi:10.1007/s11434-014-0698-3 · Cited by 173
Cordell, H. J., Bentham, J., Töpf, A., Zélénika, D., Heath, S. C., Mamasoula, C., Cosgrove, C., Blue, G. M., Granados-Riveron, J. T., Setchfield, K., et al. (2013) · Nature Genetics · doi:10.1038/ng.2637 · Cited by 165
Structural haplotypes and recent evolution of the human 17q21.31 region
Boettger, L. M., Handsaker, R. E., Zody, M. C., & McCarroll, S. A. (2012) · Nature Genetics · doi:10.1038/ng.2334 · Cited by 167
Using ERDS to Infer Copy-Number Variants in High-Coverage Genomes
Zhu, M., Need, A. C., Han, Y., Ge, D., Maia, J. M., Zhu, Q., Heinzen, E. L., Cirulli, E. T., Pelak, K., He, M., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.07.004 · Cited by 168
Bainbridge, M. N., Hu, H., Muzny, D. M., Musante, L., Lupski, J. R., Graham, B. H., Chen, W., Gripp, K. W., Jenny, K., Wienker, T. F., et al. (2013) · Genome Medicine · doi:10.1186/gm415 · Cited by 165
Epilepsy genetics — past, present, and future
Poduri, A., & Lowenstein, D. H. (2011) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2011.01.005 · Cited by 170
Krishna, A., Biryukov, M., Trefois, C., Antony, P. M. A., Hussong, R., Lin, J., Heinäniemi, M., Glusman, G., Köglsberger, S., Boyd, O., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-1154 · Cited by 174
Genome-wide association study of colorectal cancer identifies six new susceptibility loci
Schumacher, F. R., Schmit, S. L., Jiao, S., Edlund, C. K., Wang, H., Zhang, B., Hsu, L., Huang, S.-C., Fischer, C. P., Harju, J. F., et al. (2015) · Nature Communications · doi:10.1038/ncomms8138 · Cited by 167
The Human Genome Project changed everything
Gibbs, R. A. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0275-3 · Cited by 165
Comparison of somatic mutation calling methods in amplicon and whole exome sequence data
Xu, H., DiCarlo, J., Satya, R. V., Peng, Q., & Wang, Y. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-244 · Cited by 163
Genetics of type 2 diabetes: the GWAS era and future perspectives [Review]
Imamura, M., & Maeda, S. (2011) · Endocrine Journal · doi:10.1507/endocrj.ej11-0113 · Cited by 167
Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences
Fumagalli, M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0079667 · Cited by 168
The challenges, advantages and future of phenome‐wide association studies
Hebbring, S. J. (2013) · Immunology · doi:10.1111/imm.12195 · Cited by 166
Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples
Riley, D. R. J., Sieber, K. B., Robinson, K. M., White, J. R., Ganesan, A., Nourbakhsh, S., & Hotopp, J. C. D. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003107 · Cited by 165
An informatics approach to analyzing the incidentalome
Berg, J., Adams, M. C., Nassar, N., Bizon, C., Lee, K., Schmitt, C., Wilhelmsen, K., & Evans, J. P. (2012) · Genetics in Medicine · doi:10.1038/gim.2012.112 · Cited by 175
Extending reference assembly models
Church, D. M., Schneider, V., Steinberg, K. M., Schatz, M. C., Quinlan, A. R., Chin, C.-S., Kitts, P., Aken, B. L., Marth, G., Hoffman, M. M., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0587-3 · Cited by 164
Current status of genome-wide association studies in cancer
Chung, C. C., & Chanock, S. J. (2011) · Human Genetics · doi:10.1007/s00439-011-1030-9 · Cited by 166
Measuring cancer evolution from the genome
Graham, T. A., & Sottoriva, A. (2016) · The Journal of Pathology · doi:10.1002/path.4821 · Cited by 182
Common variants associated with general and MMR vaccine–related febrile seizures
Feenstra, B., Pasternak, B., Geller, F., Carstensen, L., Wang, T., Huang, F., Eitson, J. L., Hollegaard, M. V., Svanström, H., Vestergaard, M., et al. (2014) · Nature Genetics · doi:10.1038/ng.3129 · Cited by 152
Long-Read DNA Sequencing: Recent Advances and Remaining Challenges
Warburton, P. E., & Sebra, R. P. (2023) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-101722-103045 · Cited by 163
(2012) · Biological Psychiatry · doi:10.1016/j.biopsych.2012.05.035 · Cited by 170
Ding, J., Sidore, C., Butler, T. J., Wing, M. K., Qian, Y., Meirelles, O., Busonero, F., Tsoi, L. C., Maschio, A., Angius, A., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005306 · Cited by 160
Structures of human phosphofructokinase-1 and atomic basis of cancer-associated mutations
Webb, B. A., Forouhar, F., Szu, F.-E., Seetharaman, J., Tong, L., & Barber, D. L. (2015) · Nature · doi:10.1038/nature14405 · Cited by 163
Krupp, M., Marquardt, J. U., Şahin, U., Galle, P. R., Castle, J. C., & Teufel, A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts084 · Cited by 162
Lionel, A. C., Tammimies, K., Vaags, A. K., Rosenfeld, J. A., Ahn, J. W., Merico, D., Noor, A., Runke, C. K., Pillalamarri, V. K., Carter, M. T., et al. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddt669 · Cited by 163
Initiative, A. D. N., Ebbert, M., Wadsworth, M. E., Staley, L. A., Hoyt, K. L., Pickett, B. D., Miller, J. B., Duce, J., Kauwe, J. S. K., & Ridge, P. G. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1097-3 · Cited by 163
Genetic insights into the morass of metastatic heterogeneity
Hunter, K. W., Amin, R., Deasy, S. K., Ha, N., & Wakefield, L. M. (2018) · Nature reviews. Cancer · doi:10.1038/nrc.2017.126 · Cited by 167
XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data
Kluin, R. J. C., Kemper, K., Kuilman, T., de Ruiter, J. R., Iyer, V., Forment, J. V., Cornelissen‐Steijger, P., de Rink, I., ter Brugge, P., Song, J., et al. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2353-5 · Cited by 167
RNA editing in the human ENCODE RNA-seq dataPreprint
Park, E., Williams, B. A., Wold, B. J., & Mortazavi, A. (2012) · Genome Research · doi:10.1101/gr.134957.111 · Cited by 163
Terao, C. C., Yoshifuji, H., Kimura, A., Matsumura, T., Ohmura, K., Takahashi, M., Shimizu, M., Kawaguchi, T., Chen, Z., Naruse, T. K., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.05.024 · Cited by 162
Impacts of Variation in the Human Genome on Gene Regulation
Haraksingh, R., & Snyder, M. P. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.07.015 · Cited by 169
Addressing challenges in the production and analysis of illumina sequencing data
Kircher, M., Heyn, P. C., & Kelso, J. F. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-382 · Cited by 172
Neurofibromatosis type 1: from genotype to phenotype
Pasmant, É., Vidaud, M., Vidaud, D., & Wolkenstein, P. (2012) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2012-100978 · Cited by 169
DGAT1 mutation is linked to a congenital diarrheal disorder
Haas, J. T., Winter, H. S., Lim, E. T., Kirby, A. W., Blumenstiel, B. S., DeFelice, M. T., Gabriel, S., Jalas, C., Branski, D., Grueter, C. A., et al. (2012) · Journal of Clinical Investigation · doi:10.1172/jci64873 · Cited by 161
Oishi, M., Oishi, A., Gotoh, N., Ogino, K., Higasa, K., Iida, K., Makiyama, Y., Morooka, S., Matsuda, F., & Yoshimura, N. (2014) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.14-15458 · Cited by 161
Cao, H., Hastie, A., Cao, D., Lam, E. T., Sun, Y., Huang, H., Lin, L., Lin, L., Andrews, W., Chan, S., et al. (2014) · GigaScience · doi:10.1186/2047-217x-3-34 · Cited by 156
Compression of next-generation sequencing reads aided by highly efficient de novo assembly
Jones, D. C., Ruzzo, W. L., Peng, X., & Katze, M. G. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks754 · Cited by 161
A disease-associated gene desert directs macrophage inflammation through ETS2
Stankey, C. T., Bourges, C., Haag, L.-M., Turner‐Stokes, T., Piedade, A. P., Palmer-Jones, C., Papa, I., dos Santos, M. S., Zhang, Q., Cameron, A. J., et al. (2024) · Nature · doi:10.1038/s41586-024-07501-1 · Cited by 163
Pinel, P., Fauchereau, F., Moreno, A., Barbot, A., Lathrop, M. G., Zélénika, D., Bihan, D. L., Poline, J., Bourgeron, T., & Dehaene, S. (2012) · Journal of Neuroscience · doi:10.1523/jneurosci.5996-10.2012 · Cited by 169
Hoffmann, T. J., Zhan, Y., Kvale, M. N., Hesselson, S., Gollub, J., Iribarren, C., Lu, Y., Mei, G., Purdy, M. M., Quesenberry, C. P., et al. (2011) · Genomics · doi:10.1016/j.ygeno.2011.08.007 · Cited by 155
Large Scale Library Generation for High Throughput Sequencing
Borgström, E., Lundin, S., & Lundeberg, J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019119 · Cited by 161
Genetic Variation and Adaptation in Africa: Implications for Human Evolution and DiseasePreprint
Gomez, F., Hirbo, J. B., & Tishkoff, S. A. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a008524 · Cited by 161
Private Computation on Encrypted Genomic Data
Lauter, K., López-Alt, A., & Naehrig, M. (2015) · Lecture notes in computer science · doi:10.1007/978-3-319-16295-9_1 · Cited by 159
SIFT Indel: Predictions for the Functional Effects of Amino Acid Insertions/Deletions in Proteins
Hu, J., & Ng, P. C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077940 · Cited by 156
Genetic Testing for Dilated Cardiomyopathy in Clinical Practice
Lakdawala, N. K., Funke, B., Baxter, S. M., Cirino, A. L., Roberts, A. E., Judge, D. P., Johnson, N. M., Mendelsohn, N. J., Morel, C. F., Care, M. E., et al. (2012) · Journal of Cardiac Failure · doi:10.1016/j.cardfail.2012.01.013 · Cited by 164
Wang, X., Wang, H., Sun, V., Tuan, H.-F., Keser, V., Wang, K., Ren, H., Lopez, I., Zaneveld, J. E., Siddiqui, S., et al. (2013) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2013-101558 · Cited by 159
Lih, C., Harrington, R. D., Sims, D. J., Harper, K. N., Bouk, C. H., Datta, V., Yau, J., Singh, R. R., Routbort, M. J., Luthra, R., et al. (2017) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2016.10.007 · Cited by 161
Zhu, X., & Stephens, M. (2017) · The Annals of Applied Statistics · doi:10.1214/17-aoas1046 · Cited by 151
A glimpse into past, present, and future DNA sequencing
Morey, M., Marmiesse, A. F., Castiñeiras, D. E., Fraga, J. M., Couce, M. L., & Cocho, J. A. (2013) · Molecular Genetics and Metabolism · doi:10.1016/j.ymgme.2013.04.024 · Cited by 177
Extensive genetic variation in somatic human tissues
O’Huallachain, M., Karczewski, K. J., Weissman, S. M., Urban, A. E., & Snyder, M. P. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1213736109 · Cited by 156
Schmidt, E. M., Zhang, J., Zhou, W., Chen, J., Mohlke, K. L., Chen, Y., & Willer, C. J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv201 · Cited by 152
Genetic Diversity and Population Structure of Cucumber (Cucumis sativus L.)
Lv, J., Qi, J., Shi, Q., Shen, D., Zhang, S., GuangJin, S., Li, H., Sun, Z., Weng, Y., Shang, Y., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046919 · Cited by 158
Human olfactory receptor responses to odorants
Mainland, J. D., Li, Y. R., Zhou, T., Liu, W. L. L., & Matsunami, H. (2015) · Scientific Data · doi:10.1038/sdata.2015.2 · Cited by 155
Computational approaches to disease‐gene prediction: rationale, classification and successes
Piro, R. M., & Cunto, F. D. (2012) · FEBS Journal · doi:10.1111/j.1742-4658.2012.08471.x · Cited by 156
Molecular tools and analytical approaches for the characterization of farm animal genetic diversity
Lenstra, J. A., Groeneveld, L. F., Eding, H., Kantanen, J., Williams, J. L., Taberlet, P., Nicolazzi, E. L., Sölkner, J., Simianer, H., Ciani, E., et al. (2012) · Animal Genetics · doi:10.1111/j.1365-2052.2011.02309.x · Cited by 164
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.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
