ISSN 1476-4687 (online) The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Its current structure is a linear composite of merged haplotypes from more than 20 . is affiliated with Vertex Pharmaceuticals, E.A. Systematic analysis of the patterns in which genetic variants are shared among individuals and populations provides detailed accounts of population history. Type: Article. These same technical advances are enabling the application of whole genome sequencing to a variety of medically important samples. An integrated map of structural variation in 2,504 human genomes ), R01GM104390 (L.B.J., M.Y.Y. This file contains Supplementary Methods, Supplementary References and Supplementary Tables 1-12. Genome Res. A global reference for human genetic variation. b, The average number of tagging variants (r2 > 0.8) as a function of physical distance for common (top), low frequency (middle), and rare (bottom) variants. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination . 40, 892896 (2008), The ENCODE Project Consortium. A global reference for human genetic variation - ResearchGate ), T32GM7790 (C.D.B., A.R.M. ), the British Heart Foundation (C.A.A. A map of human genome variation from population-scale sequencing. and JavaScript. ), the Japan Society for the Promotion of Science Fellowship number PE13075 (N.P. The number of alleles associated with a disease or phenotype in each genome did not follow this pattern of increased diversity in Africa (Extended Data Fig. At lower frequencies, comparison with >60,000 European haplotypes from the Haplotype Reference Consortium9 suggests 75% power to detect SNPs with frequency of 0.1%. 10.1038/nature15393. is an advisor for DNAnexus, F.M.D.L.V. 4d), consistent with improved localization. Deep catalogues of potentially functional variants will help ensure that downstream functional analyses include the true candidate variants, and will aid analyses that integrate complex disease associations with functional genomic elements31. USA 107, 74017406 (2010), Wakefield, J. Bayes factors for genome-wide association studies: comparison with P-values. is a member of the scientific advisory board of Omicia, M.G. Press ReleaseFebruary 25, 2021 Exactly 20 years after the successful completion of the "Human Genome Project," an international group of researchers, the Human Genome Structural Variation Consortium (HGSVC), has now sequenced 32 human genomes at high resolution. 123, 177187 (2008), Mathias, R. A. et al. a, The number of variants within the phase 3 sample as a function of alternative allele frequency. To provide a measure of uncertainty, one curve is plotted for each chromosome. Note the x axis shows the number of polymorphic sites within the maximal comparison. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. ), WT090770/Z/09/Z (D.K. Linkage disequilibrium was calculated around 10,000 randomly selected polymorphic sites in each population, having first thinned each population down to the same sample size (61 individuals). Bayesian refinement of association signals for 14 loci in 3 common diseases. ), NIJ Grant 2014-DN-BX-K089 (Y.E. ), WT0855322/Z/08/Z (R.L. is a co-founder of Genomics and a partner in Peptide Groove. Nature 526 (7571), 68, 2015. ), R01HG2898 (S.E.D. A global reference for human genetic variation - UCL Discovery Dashed lines indicate populations sampled outside of their ancestral continental region. Thank you for visiting nature.com. "A Global Reference for Human Genetic Variation." Nature 526 (7571) (September 30): 68-74. doi:10.1038/nature15393. Faculty of Medical Sciences, Cave Hill Campus, The University of the West Indies. A global reference for human genetic variation - Harvard University Nature, 526(7571), 68 . (1) A high-quality haplotype scaffold was constructed using statistical methods applied to SNP microarray genotypes (black circles) and, where available, genotypes for first degree relatives (available for 52% of samples; Supplementary Table 11)38. Nevertheless, the majority of variants observed in a single genome are common: just 40,000 to 200,000 of the variants in a typical genome (14%) have a frequency <0.5% (Fig. Nature Genet. Many thanks to the people who contributed to this project: P. Maul, T. Maul, and C. Foster; Z. Chong, X. Justine Hospital Research Centre, Montreal, H3T 1C5, Quebec, Canada, Philip Awadalla (Principal Investigator)&Alan Hodgkinson, Department of Genetics, Department of Biostatistics, Department of Computer Science, University of Chapel Hill, North Carolina, 27599, USA, Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, 28223, North Carolina, USA, Xinghua Shi (Principal Investigator),Andrew Quitadamo,Xinghua Shi (Principal Investigator)&Andrew Quitadamo, Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands, Department of Biology, University of Puerto Rico at Mayagez, Mayagez, 00680, Puerto Rico, USA, Taras K. Oleksyk (Principal Investigator),Juan C. Martinez-Cruzado&Taras K. Oleksyk, Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, 84112, Utah, USA, Lynn Jorde (Principal Investigator),David Witherspoon,David Witherspoon&Lynn Jorde, Department of Genetics, Rutgers University, Piscataway, New Jersey, 08854, USA, Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, 98195, Washington, USA, Brian L. Browning (Principal Investigator), Department of Biostatistics, University of Washington, Seattle, 98195, Washington, USA, Sharon R. Browning (Principal Investigator). the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in 1, Heidelberg, Germany, Jan O. Korbel,Jan O. Korbel (Principal Investigator),Tobias Rausch (Project Leader),Adrian M. Sttz,Jan O. Korbel (Principal Investigator) (Co-Chair),Sascha Meiers,Benjamin Raeder,Tobias Rausch,Adrian M. Sttz&Jan O. Korbel, The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, 06032, Connecticut, USA, Charles Lee,Charles Lee (Principal Investigator),Eliza Cerveira,Jaeho Hwang,Ankit Malhotra (Co-Project Lead),Dariusz Plewczynski,Kamen Radew,Mallory Romanovitch,Chengsheng Zhang (Co-Project Lead),Charles Lee (Principal Investigator) (Co-Chair),Eliza Cerveira,Ankit Malhotra,Jaeho Hwang,Dariusz Plewczynski,Kamen Radew,Mallory Romanovitch,Chengsheng Zhang,Charles Lee,Eliza Cerveira,Ankit Malhotra,Mallory Romanovitch&Chengsheng Zhang, Department of Life Sciences, Ewha Womans University, Ewhayeodae-gil, Seodaemun-gu, Seoul, South Korea, 120-750, Charles Lee,Charles Lee (Principal Investigator),Charles Lee (Principal Investigator) (Co-Chair)&Charles Lee, Max Planck Institute for Molecular Genetics, D-14195 Berlin-Dahlem, Germany, Hans Lehrach,Hans Lehrach (Principal Investigator),Vyacheslav S. Amstislavskiy,Matthias Lienhard,Florian Mertes,Marc Sultan,Bernd Timmermann,Marie-Laure Yaspo,Vyacheslav S. Amstislavskiy,Ralf Herwig&Matthias Lienhard, Dahlem Centre for Genome Research and Medical Systems Biology, D-14195 Berlin-Dahlem, Germany, Hans Lehrach&Hans Lehrach (Principal Investigator), McDonnell Genome Institute at Washington University, Washington University School of Medicine, St Louis, 63108, Missouri, USA, Elaine R. Mardis,Richard K. Wilson,Elaine R. Mardis (Co-Principal Investigator) (Co-Chair),Richard K. Wilson (Co-Principal Investigator),Lucinda Fulton,Robert Fulton,Elaine R. Mardis (Co-Principal Investigator),Li Ding,Daniel C. Koboldt,David Larson,Kai Ye,Li Ding (Principal Investigator),Ira Hall,Kai Ye,Elaine R. Mardis (Principal Investigator),Robert Fulton,Daniel C. Koboldt&David Larson, USTAR Center for Genetic Discovery & Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, 84112, Utah, USA, Gabor T. Marth,Gabor T. Marth (Principal Investigator),Alistair N. Ward,Gabor T. Marth (Principal Investigator),Alistair N. Ward,Jiantao Wu,Mengyao Zhang,Gabor T. Marth (Principal Investigator) (Co-Chair),Wen Fung Leong&Alistair N. Ward, Affymetrix, Santa Clara, California, 95051, USA, Jeanette P. Schmidt,Jeanette P. Schmidt (Principal Investigator),Christopher J. Davies,Jeremy Gollub,Teresa Webster,Brant Wong&Yiping Zhan, US National Institutes of Health, National Center for Biotechnology Information, 45 Center Drive, Bethesda, 20892, Maryland, USA, Stephen T. Sherry,Stephen T. Sherry (Principal Investigator),Victor Ananiev,Zinaida Belaia,Dimitriy Beloslyudtsev,Nathan Bouk,Chao Chen,Robert Cohen,Charles Cook,John Garner,Timothy Hefferon,Mikhail Kimelman,Chunlei Liu,John Lopez,Peter Meric,Yuri Ostapchuk,Lon Phan,Sergiy Ponomarov,Valerie Schneider,Eugene Shekhtman,Karl Sirotkin,Douglas Slotta,Hua Zhang,Stephen T. Sherry (Principal Investigator),Chunlin Xiao,Chunlin Xiao,Stephen T. Sherry (Principal Investigator),Chunlin Xiao,Stephen T. Sherry (Principal Investigator) (Co-Chair)&Chunlin Xiao, Jun Wang,Jun Wang (Principal Investigator),Yuqi Chang,Qiang Feng,Xiaodong Fang,Xiaosen Guo,Min Jian,Hui Jiang,Xin Jin,Tianming Lan,Guoqing Li,Jingxiang Li,Yingrui Li,Shengmao Liu,Xiao Liu,Yao Lu,Xuedi Ma,Meifang Tang,Bo Wang,Guangbiao Wang,Honglong Wu,Renhua Wu,Xun Xu,Ye Yin,Dandan Zhang,Wenwei Zhang,Jiao Zhao,Meiru Zhao,Xiaole Zheng,Jun Wang (Principal Investigator),Lachlan J. M. Coin,Lin Fang,Xiaosen Guo,Xin Jin,Guoqing Li,Qibin Li,Yingrui Li,Zhenyu Li,Haoxiang Lin,Binghang Liu,Ruibang Luo,Haojing Shao,Yinlong Xie,Chen Ye,Chang Yu,Fan Zhang,Hancheng Zheng,Hongmei Zhu,Yingrui Li,Ruibang Luo,Hongmei Zhu,Xiaosen Guo,Wangshen Li,Yingrui Li,Renhua Wu,Jun Wang (Principal Investigator),Xu Dan,Xiaosen Guo,Guoqing Li,Yingrui Li,Chen Ye,Xiaole Zheng,Hongyu Cai,Hongzhi Cao,Yingrui Li,Yeyang Su,Zhongming Tian,Yuhong Wang,Huanming Yang,Ling Yang,Jiayong Zhu,Zhiming Cai,Jiayong Zhu,Jun Wang&Huanming Yang, Department of Biology, University of Copenhagen, Ole Maales Vej 5, Copenhagen, 2200, Denmark, Jun Wang,Jun Wang (Principal Investigator),Qiang Feng,Xiaodong Fang,Xiaosen Guo,Min Jian,Hui Jiang,Xiao Liu,Jun Wang (Principal Investigator),Lin Fang,Xiaosen Guo,Jun Wang (Principal Investigator),Xiaosen Guo,Hongzhi Cao&Jun Wang, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 80205, Saudi Arabia, Jun Wang,Jun Wang (Principal Investigator),Jun Wang (Principal Investigator),Jun Wang (Principal Investigator)&Jun Wang, Macau University of Science and Technology, Avenida Wai long, Taipa, 999078, Macau, China, Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, 21 Sassoon Road, Hong Kong, Coriell Institute for Medical Research, Camden, 08103, New Jersey, USA, Neda Gharani,Lorraine H. Toji,Norman P. Gerry,Alissa M. Resch,Christine Beiswanger,Norman P. Gerry,Neda Gharani,Alissa M. Resch&Lorraine H. Toji, European Centre for Public Heath Genomics, UNU-MERIT, Maastricht University, PO Box 616, Maastricht, 6200, MD, The Netherlands, Ralf Sudbrak (Project Leader),Ralf Sudbrak (Project Leader),Ralf Sudbrak (Project Lead)&Ralf Sudbrak, Alacris Theranostics, D-14195 Berlin-Dahlem, Germany, Marcus W. Albrecht,Tatiana A. Borodina&Marcus W. Albrecht, Personalis, Menlo Park, California, 94025, USA, US National Institutes of Health, National Human Genome Research Institute, 50 South Drive, Bethesda, 20892, Maryland, USA, Department of Computer Engineering, Bilkent University, Bilkent, TR-06800, Ankara, Turkey, Can Alkan,Elif Dal,Fatma Kahveci,Can Alkan,Elif Dal&Fatma Kahveci, Seven Bridges Genomics, 1 Broadway, 14th floor, Cambridge, 02142, Massachusetts, USA, Deniz Kural,Wan-Ping Lee,Deniz Kural&Wan-Ping Lee, Department of Agronomy, Kansas State University, Manhattan, 66506, Kansas, USA, Illumina, San Diego, 92122, California, USA, Michael Stromberg,Jiantao Wu,Bret Barnes,Scott Kahn,Bret Barnes,Scott Kahn&Scott Kahn, Department of Genetics, Harvard Medical School, Cambridge, 02142, Massachusetts, USA, Mengyao Zhang,Robert E. Handsaker (Project Leader),Seva Kashin,Steven A. McCarroll,Steven A. McCarroll (Principal Investigator),Robert E. Handsaker (Project Leader),Seva Kashin,Robert E. Handsaker,Seva Kashin&Steven A. McCarroll, SynapDx, Four Hartwell Place, Lexington, 02421, Massachusetts, USA, Mark A. DePristo (Project Leader)&Mark A. DePristo, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA, Seungtai C. Yoon (Principal Investigator),Jayon Lihm,Seungtai C. Yoon (Principal Investigator)&Jayon Lihm, Seaver Autism Center and Department of Psychiatry, Mount Sinai School of Medicine, New York, 10029, New York, USA, Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, 14853, New York, USA, Srikanth Gottipati,Haiyuan Yu (Principal Investigator)&Danielle Jones, Department of Genetic Medicine, Weill Cornell Medical College, New York, 10044, New York, USA, Juan L. Rodriguez-Flores,Juan L. Rodriguez-Flores&Juan L. Rodriguez-Flores, European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, Heidelberg, 69117, Germany, Tobias Rausch (Project Leader),Markus H. Fritz,Markus H. Fritz&Tobias Rausch, Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, WC1E 6DD, UK, Center for Systems Biology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, 02138, Massachusetts, USA, Pardis C. Sabeti (Principal Investigator),Ilya Shlyakhter,Stephen F. Schaffner,Pardis C. Sabeti,Pardis C. Sabeti,Matt Stremlau,Ridhi Tariyal&Pardis C. Sabeti, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, 02138, Massachusetts, USA, Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK, David N. Cooper (Principal Investigator),Edward V. Ball&Peter D. Stenson, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, 10029-6574, New York, USA, Department of Biological Sciences, Louisiana State University, Baton Rouge, 70803, Louisiana, USA, Mark A. Batzer (Principal Investigator),Miriam K. Konkel,Jerilyn A. Walker,Mark A. Batzer (Principal Investigator),Miriam K. Konkel&Jerilyn A. Walker, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, 02114, Massachusetts, USA, Daniel G. MacArthur (Principal Investigator),Monkol Lek&Daniel G. MacArthur (Principal Investigator), McGill University and Genome Quebec Innovation Centre, 740, Avenue du Dr. Penfield, Montreal, H3A 0G1, Quebec, Canada, Simon Gravel,Simon Gravel&Simon Gravel, National Eye Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA, New York Genome Center, 101 Avenue of the Americas, 7th floor, New York, 10013, New York, USA, Tuuli Lappalainen (Principal Investigator),Yaniv Erlich (Principal Investigator),Melissa Gymrek,Yaniv Erlich&Melissa Gymrek, Department of Systems Biology, Columbia University, New York, 10032, NY, USA, Tuuli Lappalainen (Principal Investigator), Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, New York, USA, Yaniv Erlich (Principal Investigator)&Yaniv Erlich, HarvardMIT Division of Health Sciences and Technology, Cambridge, 02139, Massachusetts, USA, General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA, Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, 02142, Massachusetts, USA, Thomas Frederick Willems&Thomas Frederick Willems, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, M5G 0A3, Ontario, Canada, Jared T. Simpson&Philip Awadalla (Principal Investigator), Department of Anthropology, Penn State University, University Park, Pennsylvania, 16802, USA, Rutgers Cancer Institute of New Jersey, New Brunswick, 08903, New Jersey, USA, Jeffrey A. Rosenfeld (Principal Investigator)&Carlos D. Bustamante (Principal Investigator), Department of Genetics, Stanford University, Stanford, 94305, California, USA, Francisco M. De La Vega (Principal Investigator),Phil Lacroute,Brian K. Maples,Alicia R. Martin,Andres Moreno-Estrada,Suyash S. Shringarpure,Fouad Zakharia,Phil Lacroute,Carlos D. Bustamante (Principal Investigator),Carlos D. Bustamante (Principal Investigator) (Co-Chair),Fernando L. Mendez,Peter A. Underhill,Carlos D. Bustamante,Andres Moreno-Estrada&Karla Sandoval, Departments of Genetics and Pathology, Stanford University, Stanford, 94305-5324, California, USA, Stephen B. Montgomery (Principal Investigator),Marianne K. DeGorter,Stephen B. Montgomery (Principal Investigator)&Marianne K. DeGorter, Ancestry.com, San Francisco, 94107, California, USA, DNAnexus, 1975 West El Camino Real STE 101, Mountain View California, 94040, USA, Laboratorio Nacional de Genmica para la Biodiversidad (LANGEBIO), CINVESTAV, Irapuato, 36821, Guanajuato, Mexico, Andres Moreno-Estrada&Andres Moreno-Estrada, Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel, Eran Halperin (Principal Investigator)&Yael Baran, Department of Microbiology, Tel-Aviv University, Tel-Aviv, 69978, Israel, International Computer Science Institute, Berkeley, 94704, California, USA, Thermo Fisher Scientific, 200 Oyster Point Boulevard, South San Francisco, 94080, California, USA, The Translational Genomics Research Institute, Phoenix, 85004, Arizona, USA, David W. Craig (Principal Investigator),Alexis Christoforides,Tyler Izatt,Ahmet A. Kurdoglu,Shripad A. Sinari,David W. Craig (Principal Investigator),David W. Craig (Principal Investigator),Alexis Christoforides,Tyler Izatt,David W. Craig (Principal Investigator),Tyler Izatt&Ahmet A. Kurdoglu, Life Technologies, Beverly, 01915, Massachusetts, USA, Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, 90024, California, USA, Department of Psychiatry, University of California, San Diego, La Jolla, 92093, California, USA, Jonathan Sebat (Principal Investigator),Danny Antaki,Madhusudan Gujral,Amina Noor,Jonathan Sebat (Principal Investigator)&Danny Antaki, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, 92093, California, USA, Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, 10461, New York, USA, Departments of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, 94158, San Francisco, USA, Esteban G. Burchard (Principal Investigator),Ryan D. Hernandez (Principal Investigator),Christopher R. Gignoux,Esteban G. Burchard&Christopher R. Gignoux, Institute for Quantitative Biosciences (QB3), University of California, San Francisco, 1700 4th Street, San Francisco, 94158, California, USA, Ryan D. Hernandez (Principal Investigator), Institute for Human Genetics, University of California, San Francisco, 1700 4th Street, San Francisco, 94158, California, USA, Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, 95064, California, USA, David Haussler (Principal Investigator),Sol J. Katzman,W. James Kent&David Haussler (Principal Investigator), Howard Hughes Medical Institute, Santa Cruz, 95064, California, USA, David Haussler (Principal Investigator)&David Haussler (Principal Investigator), Department of Human Genetics, University of Chicago, Chicago, 60637, Illinois, USA, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK, Andres Ruiz-Linares (Principal Investigator)&Andres Ruiz-Linares, Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland, Emmanouil T. Dermitzakis (Principal Investigator),Olivier Delaneau,Andy Rimmer&Emmanouil T. Dermitzakis (Principal Investigator), Institute for Genetics and Genomics in Geneva, University of Geneva, 1211 Geneva, Switzerland, Emmanouil T. Dermitzakis (Principal Investigator)&Emmanouil T. Dermitzakis (Principal Investigator), Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, 21201, Maryland, USA, Scott E. Devine (Principal Investigator),Scott E. Devine (Principal Investigator)&Eugene J. Gardner (Project Leader), Department of Computational Medicine and Bioinfomatics, University of Michigan, Ann Arbor, 48109, Michigan, USA, Jeffrey M. Kidd (Principal Investigator),Shiya Song,Jeffrey M. Kidd (Principal Investigator),Ryan E. Mills (Principal Investigator)&Gargi Dayama, Department of Human Genetics, University of Michigan Medical School, Ann Arbor, 48109, Michigan, USA, Jeffrey M. Kidd (Principal Investigator),Sarah Emery,Elzbieta Sliwerska,Jeffrey M. Kidd (Principal Investigator),Ryan E. Mills (Principal Investigator),Gargi Dayama&Sarah Emery, Department of Pediatrics, University of Pittsburgh, Pittsburgh, 15224, Pennsylvania, USA, The University of Texas Health Science Center at Houston, Houston, 77030, Texas, USA, Goo Jun,Yunxin Fu (Principal Investigator),Xiaoming Liu,Momiao Xiong&Goo Jun, Vanderbilt University School of Medicine, Nashville, 37232, Tennessee, USA, University of Michigan Sequencing Core, University of Michigan, Ann Arbor, 48109, Michigan, USA, Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, 09042, Cagliari, Italy, Dipartimento di Scienze Biomediche, Universit delgi Studi di Sassari, Sassari, 07100, Italy, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, 75390, Texas, USA, Department of Pediatrics, University of Montreal, Ste.
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