A map of human genome variation from population-scale sequencing

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A map of human genome variation from population-scale sequencing
Autor: Abecasis, Gonçalo R ; Altshuler, David ; Auton, Adam ; Brooks, Lisa D ; Durbin, Richard M ; Gibbs, Richard A ; Hurles, Matt E ; McVean, Gil A
Assuntos: Biological and medical sciences ; Calibration ; Chromosomes, Human, Y - genetics ; Computational Biology ; Deoxyribonucleic acid ; Design ; DNA ; DNA Mutational Analysis ; DNA sequencing ; DNA, Mitochondrial - genetics ; Evolution, Molecular ; Female ; Fundamental and applied biological sciences. Psychology ; Genetic Association Studies ; Genetic Variation - genetics ; Genetics ; Genetics of eukaryotes. Biological and molecular evolution ; Genetics, Population - methods ; Genome, Human - genetics ; Genome-Wide Association Study ; Genomics ; Genomics - methods ; Genotype ; Haplotypes - genetics ; Human ; Human genome ; Human population genetics ; Humans ; Identification and classification ; Life Sciences ; Male ; Methods ; Mutation ; Mutation - genetics ; Nucleotide sequencing ; Pilot Projects ; Polymorphism, Single Nucleotide - genetics ; Population genetics, reproduction patterns ; Recombination, Genetic - genetics ; Sample Size ; Selection, Genetic - genetics ; Sequence Alignment ; Sequence Analysis, DNA - methods ; Studies
É parte de: Nature (London), 2010-10, Vol.467 (7319), p.1061-1073
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
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PMCID: PMC3042601
Analysis Group: Agilent Technologies Anniek De Witte28, Shane Giles28 Baylor College of Medicine Richard A. Gibbs (Principle Investigator)14, David Wheeler14, Matthew Bainbridge14, Danny Challis14, Aniko Sabo14, Fuli Yu14, Jin Yu14 BGI-Shenzhen Jun Wang (Principle Investigator)22,23, Xiaodong Fang22, Xiaosen Guo22, Ruiqiang Li22,23, Yingrui Li22, Ruibang Luo22, Shuaishuai Tai22, Honglong Wu22, Hancheng Zheng22, Xiaole Zheng22, Yan Zhou22, Guoqing Li22, Jian Wang22, Huanming Yang22 Boston College Gabor T. Marth (Principle Investigator)29, Erik P. Garrison29, Weichun Huang30, Amit Indap29, Deniz Kura29l, Wan-Ping Lee29, Wen Fung Leong29, Aaron R. Quinlan31, Chip Stewart29, Michael P. Stromberg6, Alistair N. Ward29, Jiantao Wu29 Brigham and Women's Hospital Charles Lee (Principle Investigator)32, Ryan E. Mills32, Xinghua Shi32 Broad Institute of MIT and Harvard Mark J. Daly (Principle Investigator)2, David L. Altshuler23-4, Aaron D. Ball2, Eric Banks2, Toby Bloom2, Brian L. Browning33, Kristian Cibulskis2, Mark A. DePristo2, Tim J. Fennell2, Kiran V. Garimella2, Sharon R. Grossman2,34, Robert E. Handsaker2, Matt Hanna2, Chris Hartl2, Andrew M. Kernytsky2, Joshua M. Korn2, Heng Li2, Jared R. Maguire2, Steve A. McCarroll2, Aaron McKenna2, James C. Nemesh2, Anthony A. Philippakis2, Ryan E. Poplin2, Manuel A. Rivas2, Pardis C. Sabeti2,34, Stephen F. Schaffner2, Erica Shefler2, Ilya A. Shlyakhter2,34 Cardiff University, The Human Gene Mutation Database David N. Cooper (Principle Investigator)35, Edward V. Ball35, Matthew Mort35, Andrew D. Phillips35, Peter D. Stenson35 Cold Spring Harbor Laboratory Jonathan Sebat (Principle Investigator)36, Vladimir Makarov37, Kenny Ye38, Seungtai C. Yoon39 Cornell and Stanford Universities Carlos D. Bustamante (Co-Principle Investigator)40, Andrew G. Clark (Co-Principle Investigator)8, Alon Keinan (Co-Principle Investigator)8, Michael Snyder (Co-Principle Investigator)40, Adam Boyko40, Jeremiah Degenhardt8, Simon Gravel40, Fabian Grubert40, Ryan N. Gutenkunst41, Mark Kaganovich40, Phil Lacroute40, Xin Ma8, Andy Reynolds8, Alexander Urban40 European Bioinformatics Institute Laura Clarke (Project Leader)13, Paul Flicek (Co-Chair, DCC) (Principle Investigator)13, Fiona Cunningham13, Javier Herrero13, Stephen Keenen13, Eugene Kulesha13, Rasko Leinonen13, William M. McLaren13, Rajesh Radhakrishnan13, Richard E. Smith13, Vadim Zalunin13, Xiangqun Zheng-Bradley13 European Molecular Biology Laboratory Jan O. Korbel (Principle Investigator)42, Adrian M. Stütz42 Illumina Sean Humphray (Project Leader)6, Markus Bauer6, R. Keira Cheetham6, Tony Cox6, Michael Eberle6, Terena James6, Scott Kahn6, Lisa Murray6 Johns Hopkins University Aravinda Chakravarti7 Leiden University Medical Center Kai Ye43 Life Technologies Francisco M. De La Vega (Principle Invesigator)10, Yutao Fu24, Fiona C.L. Hyland10, Jonathan M. Manning24, Stephen F. McLaughlin24, Heather E. Peckham24, Onur Sakarya10, Yongming A. Sun10, Eric F. Tsung24 Louisiana State University Mark A. Batzer (Principle Investigator)44, Miriam K. Konkel44, Jerilyn A. Walker44 Max Planck Institute for Molecular Genetics Ralf Sudbrak (Project Leader)16, Marcus W. Albrecht16, Vyacheslav S. Amstislavskiy16, Ralf Herwig16, Dimitri Parkhomchuk16 US National Institutes of Health Stephen T. Sherry (Co-Chair, DCC) (Principle Investigator)21, Richa Agarwala21, Hoda M. Khouri21, Aleksandr O. Morgulis21, Justin E. Paschall21, Lon D. Phan21, Kirill E. Rotmistrovsky21, Robert D. Sanders21, Martin F. Shumway21, Chunlin Xiao21 Oxford University Gil A. McVean (Co-Chair) (Co-Chair, Population Genetics) (Principle Investigator)11,18, Adam Auton11, Zamin Iqbal11, Gerton Lunter11, Jonathan L. Marchini11,18, Loukas Moutsianas18, Simon Myers11,18, Afidalina Tumian18 Roche Applied Science Brian Desany (Project Leader)27, James Knight27, Roger Winer27 The Translational Genomics Research Institute David W. Craig (Principle Investigator)45, Steve M. Beckstrom-Sternberg45, Alexis Christoforides45, Nils Homer46, Ahmet A. Kurdoglu45, James O. Long45, Barry Merriman46, Stan F. Nelson46, John V. Pearson45, Shripad A. Sinari45, Waibhav D. Tembe45 University of California, Santa-Cruz David Haussler (Principle Investigator)47, Angie S. Hinrichs47, Sol J. Katzman47, Andrew Kern47, Robert M. Kuhn47 University of Chicago Molly Przeworski (Co-Chair, Population Genetics) (Principle Investigator)48, Ryan D. Hernandez49, Bryan Howie50, Joanna L. Kelley50, John C. Marioni50, S. Cord Melton50 University of Michigan Gonçalo R. Abecasis (Co-Chair) (Principle Investigator)5, Hyun M. Kang (Project Leader) 5, Paul Anderson5, Tom Blackwell5, Wei Chen5, William O. Cookson51, Jun Ding5, Mark Lathrop52, Yun Li5, Liming Liang53, Miriam F. Moffatt51, Paul Scheet54, Carlo Sidore5, Matthew Snyder5, Xiaowei Zhan5, Sebastian Zoellner5 University of Montreal Philip Awadalla (Principle Investigator)55, Ferran Casals56, Youssef Idaghdour56, John Keebler56, Eric A. Stone56, Martine Zilversmit56 University of Utah Lynn Jorde (Principle Investigator)57, Jinchuan Xing57 University of Washington Evan E. Eichler (Principle Investigator)58, Can Alkan58, Iman Hajirasouliha59, Fereydoun Hormozdiari59, Jeffrey M. Kidd40, S. Cenk Sahinalp59, Peter H. Sudmant19 Washington University in St. Louis Elaine R. Mardis (Principle Investigator)17, Ken Chen17, Asif Chinwalla17, Li Ding17, Daniel C. Koboldt17, Mike D. McLellan17, David Dooling17, George Weinstock17, John W. Wallis17, Michael C. Wendl17, Qunyuan Zhang17 Wellcome Trust Sanger Institute Richard M. Durbin (Principle Investigator)1, Cornelis Albers60, Qasim Ayub1, Senduran Balasubramaniam1, Jeffrey C. Barrett1, David M. Carter1, Yuan Chen1, Donald F. Conrad1, Petr Danecek1, Emmanouil T. Dermitzakis61, Min Hu1, Ni Huang1, Matt E. Hurles1, Hanjun Jin62, Luke Jostins1, Thomas M. Keane1, Quang Le1, Sarah Lindsay1, Quan Long1, Daniel G. MacArthur1, Stephen B. Montgomery61, Leopold Parts1, James Stalker1, Chris Tyler-Smith1, Klaudia Walter1, Yali Xue1, Bryndis, Yngvadottir1, Yujun Zhang1 Yale University Mark B. Gerstein (Principle Investigator)63,64, Alexej Abyzov63, Suganthi Balasubramanian65, Robert Bjornson64, Jiang Du64, Lukas Habegger63, Rajini Haraksingh63, Justin Jee63, Ekta Khurana65, Hugo Y.K. Lam40, Jing Leng63, Xinmeng Jasmine Mu63, Zhengdong Zhang65
Sequencing Centres:Baylor College of Medicine Richard A. Gibbs (Principle Investigator)14, David Deiros14, Mike Metzker14, Donna Muzny14, Jeff Reid14, David Wheeler14 BGI-Shenzhen Jun Wang (Principle Investigator)22,23, Jingxiang Li22, Min Jian22, Guoqing Li22, Ruiqiang Li22,23, Huiqing Liang22, Geng Tian22, Bo Wang22, Jian Wang22, Wei Wang22, Huanming Yang22, Xiuqing Zhang22, Huisong Zheng22 Broad Institute of MIT and Harvard Eric S. Lander (Principal Investigator)2, David L. Altshuler23-4, Lauren Ambrogio2, Toby Bloom2, Kristian Cibulskis2, Tim J. Fennell2, Stacey B. Gabriel (Co-chair)2, Erica Shefler2, Carrie L. Sougnez2 Illumina David R. Bentley (Principle Investigator)6, Niall Gormley6, Sean Humphray6, Zoya Kingsbury6, Paula Koko-Gonzales6, Jennifer Stone6 Life Technologies Kevin J. McKernan (Principle Investigator)24, Gina L. Costa24, Jeffry K. Ichikawa24, Clarence C. Lee24 Max Planck Institute for Molecular Genetics Ralf Sudbrak (Project Leader)16, Hans Lehrach (Principal Investigator)16, Tatiana A. Borodina16, Andreas Dahl25, Alexey N. Davydov16, Peter Marquardt16, Florian Mertes16, Wilfiried Nietfeld16, Philip Rosenstiel26, Stefan Schreiber26, Aleksey V. Soldatov16, Bernd Timmermann16, Marius Tolzmann16 Roche Applied Science Michael Egholm (Principle Investigator)12, Jason Affourtit27, Dana Ashworth27, Said Attiya27, Melissa Bachorski27, Eli Buglione27, Adam Burke27, Amanda Caprio27, Christopher Celone27, Shauna Clark27, David Conners27, Brian Desany27, Lisa Gu27, Lorri Guccione27, Kalvin Kao27, Andrew Kebbel27, Jennifer Knowlton27, Matthew Labrecque27, Louise McDade27, Craig Mealmaker27, Melissa Minderman27, Anne Nawrocki27, Faheem Niazi27, Kristen Pareja27, Ravi Ramenani27, David Riches27, Wanmin Song27, Cynthia Turcotte27, Shally Wang27 Washinton University in St. Louis Elaine R. Mardis (Co-Chair) (Co-Principle Investigator) 17, Richard K. Wilson (Co-Principle Investigator)17, David Dooling17, Lucinda Fulton17, Robert Fulton17, George Weinstock17 Wellcome Trust Sanger Institute Richard M. Durbin (Principle Investigator)1, John Burton1, David M. Carter1, Carol Churcher1, Alison Coffey1, Anthony Cox1, Aarno Palotie1, Michael Quail1, Tom Skelly1, James Stalker1, Harold P. Swerdlow1, Daniel Turner1
Steering Committee: David L. Altshuler(Co-Chair)23-4, Richard M. Durbin(Co-Chair)1, Gonçalo R. Abecasis5, David R. Bentley6, Aravinda Chakravarti7, Andrew G. Clark8, Francis S. Collins9, Francisco M. De La Vega10, Peter Donnelly11, Michael Egholm12, Paul Flicek13, Stacey B. Gabriel2, Richard A. Gibbs14, Bartha M. Knoppers15, Eric S. Lander2, Hans Lehrach16, Elaine R. Mardis17, Gil A. McVean11,18, Debbie A. Nickerson19, Leena Peltonen*, Alan J. Schafer20, Stephen T. Sherry21, Jun Wang22,23, Richard K. Wilson17
Structural Variation Group: BGI-Shenzhen Yingrui Li22 Boston College Gabor T. Marth (Principle Investigator)29, Erik P. Garrison29, Deniz Kura29l, Aaron R. Quinlan31, Chip Stewart29, Michael P. Stromberg6, Alistair N. Ward29, Jiantao Wu29 Brigham and Women's Hospital Charles Lee (Co-Chair) (Principle Investigator)32, Ryan E. Mills32, Xinghua Shi32 Broad Institute of MIT and Harvard Eric Banks2, Mark A. DePristo2, Robert E. Handsaker2, Chris Hartl2, Joshua M. Korn2, Heng Li2, Steve A. McCarroll2, James C. Nemesh2 Cold Spring Harbor Laboratory Jonathan Sebat (Principle Investigator)36, Vladimir Makarov37, Kenny Ye38, Seungtai C. Yoon39 Cornell and Stanford Universities Michael Snyder (Co-Principle Investigator)40, Jeremiah Degenhardt8, Fabian Grubert40, Mark Kaganovich40, Alexander Urban40 European Bioinformatics Institute Laura Clarke (Project Leader)13, Richard E. Smith13, Xiangqun Zheng-Bradley13 European Molecula
Descrição: 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.
Editor: London: Nature Publishing Group
Idioma: Inglês

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A map of human genome variation from population-scale sequencing

Abecasis, Gonçalo R ; Altshuler, David ; Auton, Adam ; Brooks, Lisa D ; Durbin, Richard M ; Gibbs, Richard A ; Hurles, Matt E ; McVean, Gil A

London: Nature Publishing Group

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