A global reference for human genetic variation View Full Text


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Article Info

DATE

2015-10

AUTHORS

Richard A. Gibbs, Eric Boerwinkle, Harsha Doddapaneni, Yi Han, Viktoriya Korchina, Christie Kovar, Sandra Lee, Donna Muzny, Jeffrey G. Reid, Yiming Zhu, Jun Wang, 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, Eric S. Lander, David M. Altshuler, Stacey B. Gabriel, Namrata Gupta, Neda Gharani, Lorraine H. Toji, Norman P. Gerry, Alissa M. Resch, Paul Flicek, Jonathan Barker, Laura Clarke, Laurent Gil, Sarah E. Hunt, Gavin Kelman, Eugene Kulesha, Rasko Leinonen, William M. McLaren, Rajesh Radhakrishnan, Asier Roa, Dmitriy Smirnov, Richard E. Smith, Ian Streeter, Anja Thormann, Iliana Toneva, Brendan Vaughan, Xiangqun Zheng-Bradley, David R. Bentley, Russell Grocock, Sean Humphray, Terena James, Zoya Kingsbury, Hans Lehrach, Ralf Sudbrak, Marcus W. Albrecht, Vyacheslav S. Amstislavskiy, Tatiana A. Borodina, Matthias Lienhard, Florian Mertes, Marc Sultan, Bernd Timmermann, Marie-Laure Yaspo, Elaine R. Mardis, Richard K. Wilson, Lucinda Fulton, Robert Fulton, Stephen T. Sherry, Victor Ananiev, Zinaida Belaia, Dimitriy Beloslyudtsev, Nathan Bouk, Chao Chen, Deanna Church, Robert Cohen, Charles Cook, John Garner, Timothy Hefferon, Mikhail Kimelman, Chunlei Liu, John Lopez, Peter Meric, Chris O’Sullivan, Yuri Ostapchuk, Lon Phan, Sergiy Ponomarov, Valerie Schneider, Eugene Shekhtman, Karl Sirotkin, Douglas Slotta, Hua Zhang, Gil A. McVean, Richard M. Durbin, Senduran Balasubramaniam, John Burton, Petr Danecek, Thomas M. Keane, Anja Kolb-Kokocinski, Shane McCarthy, James Stalker, Michael Quail, Jeanette P. Schmidt, Christopher J. Davies, Jeremy Gollub, Teresa Webster, Brant Wong, Yiping Zhan, Adam Auton, Christopher L. Campbell, Yu Kong, Anthony Marcketta, Richard A. Gibbs, Fuli Yu, Lilian Antunes, Matthew Bainbridge, Donna Muzny, Aniko Sabo, Zhuoyi Huang, Jun Wang, 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, Can Alkan, Elif Dal, Fatma Kahveci, Gabor T. Marth, Erik P. Garrison, Deniz Kural, Wan-Ping Lee, Wen Fung Leong, Michael Stromberg, Alistair N. Ward, Jiantao Wu, Mengyao Zhang, Mark J. Daly, Mark A. DePristo, Robert E. Handsaker, David M. Altshuler, Eric Banks, Gaurav Bhatia, Guillermo del Angel, Stacey B. Gabriel, Giulio Genovese, Namrata Gupta, Heng Li, Seva Kashin, Eric S. Lander, Steven A. McCarroll, James C. Nemesh, Ryan E. Poplin, Seungtai C. Yoon, Jayon Lihm, Vladimir Makarov, Andrew G. Clark, Srikanth Gottipati, Alon Keinan, Juan L. Rodriguez-Flores, Jan O. Korbel, Tobias Rausch, Markus H. Fritz, Adrian M. Stütz, Paul Flicek, Kathryn Beal, Laura Clarke, Avik Datta, Javier Herrero, William M. McLaren, Graham R. S. Ritchie, Richard E. Smith, Daniel Zerbino, Xiangqun Zheng-Bradley, Pardis C. Sabeti, Ilya Shlyakhter, Stephen F. Schaffner, Joseph Vitti, David N. Cooper, Edward V. Ball, Peter D. Stenson, David R. Bentley, Bret Barnes, Markus Bauer, R. Keira Cheetham, Anthony Cox, Michael Eberle, Sean Humphray, Scott Kahn, Lisa Murray, John Peden, Richard Shaw, Eimear E. Kenny, Mark A. Batzer, Miriam K. Konkel, Jerilyn A. Walker, Daniel G. MacArthur, Monkol Lek, Ralf Sudbrak, Vyacheslav S. Amstislavskiy, Ralf Herwig, Elaine R. Mardis, Li Ding, Daniel C. Koboldt, David Larson, Kai Ye, Simon Gravel, Anand Swaroop, Emily Chew, Tuuli Lappalainen, Yaniv Erlich, Melissa Gymrek, Thomas Frederick Willems, Jared T. Simpson, Mark D. Shriver, Jeffrey A. Rosenfeld, Carlos D. Bustamante, Stephen B. Montgomery, Francisco M. De La Vega, Jake K. Byrnes, Andrew W. Carroll, Marianne K. DeGorter, Phil Lacroute, Brian K. Maples, Alicia R. Martin, Andres Moreno-Estrada, Suyash S. Shringarpure, Fouad Zakharia, Eran Halperin, Yael Baran, Charles Lee, Eliza Cerveira, Jaeho Hwang, Ankit Malhotra, Dariusz Plewczynski, Kamen Radew, Mallory Romanovitch, Chengsheng Zhang, Fiona C. L. Hyland, David W. Craig, Alexis Christoforides, Nils Homer, Tyler Izatt, Ahmet A. Kurdoglu, Shripad A. Sinari, Kevin Squire, Stephen T. Sherry, Chunlin Xiao, Jonathan Sebat, Danny Antaki, Madhusudan Gujral, Amina Noor, Kenny Ye, Esteban G. Burchard, Ryan D. Hernandez, Christopher R. Gignoux, David Haussler, Sol J. Katzman, W. James Kent, Bryan Howie, Andres Ruiz-Linares, Emmanouil T. Dermitzakis, Scott E. Devine, Gonçalo R. Abecasis, Hyun Min Kang, Jeffrey M. Kidd, Tom Blackwell, Sean Caron, Wei Chen, Sarah Emery, Lars Fritsche, Christian Fuchsberger, Goo Jun, Bingshan Li, Robert Lyons, Chris Scheller, Carlo Sidore, Shiya Song, Elzbieta Sliwerska, Daniel Taliun, Adrian Tan, Ryan Welch, Mary Kate Wing, Xiaowei Zhan, Philip Awadalla, Alan Hodgkinson, Yun Li, Xinghua Shi, Andrew Quitadamo, Gerton Lunter, Gil A. McVean, Jonathan L. Marchini, Simon Myers, Claire Churchhouse, Olivier Delaneau, Anjali Gupta-Hinch, Warren Kretzschmar, Zamin Iqbal, Iain Mathieson, Androniki Menelaou, Andy Rimmer, Dionysia K. Xifara, Taras K. Oleksyk, Yunxin Fu, Xiaoming Liu, Momiao Xiong, Lynn Jorde, David Witherspoon, Jinchuan Xing, Evan E. Eichler, Brian L. Browning, Sharon R. Browning, Fereydoun Hormozdiari, Peter H. Sudmant, Ekta Khurana, Richard M. Durbin, Matthew E. Hurles, Chris Tyler-Smith, Cornelis A. Albers, Qasim Ayub, Senduran Balasubramaniam, Yuan Chen, Vincenza Colonna, Petr Danecek, Luke Jostins, Thomas M. Keane, Shane McCarthy, Klaudia Walter, Yali Xue, Mark B. Gerstein, Alexej Abyzov, Suganthi Balasubramanian, Jieming Chen, Declan Clarke, Yao Fu, Arif O. Harmanci, Mike Jin, Donghoon Lee, Jeremy Liu, Xinmeng Jasmine Mu, Jing Zhang, Yan Zhang, Yingrui Li, Ruibang Luo, Hongmei Zhu, Can Alkan, Elif Dal, Fatma Kahveci, Gabor T. Marth, Erik P. Garrison, Deniz Kural, Wan-Ping Lee, Alistair N. Ward, Jiantao Wu, Mengyao Zhang, Steven A. McCarroll, Robert E. Handsaker, David M. Altshuler, Eric Banks, Guillermo del Angel, Giulio Genovese, Chris Hartl, Heng Li, Seva Kashin, James C. Nemesh, Khalid Shakir, Seungtai C. Yoon, Jayon Lihm, Vladimir Makarov, Jeremiah Degenhardt, Jan O. Korbel, Markus H. Fritz, Sascha Meiers, Benjamin Raeder, Tobias Rausch, Adrian M. Stütz, Paul Flicek, Francesco Paolo Casale, Laura Clarke, Richard E. Smith, Oliver Stegle, Xiangqun Zheng-Bradley, David R. Bentley, Bret Barnes, R. Keira Cheetham, Michael Eberle, Sean Humphray, Scott Kahn, Lisa Murray, Richard Shaw, Eric-Wubbo Lameijer, Mark A. Batzer, Miriam K. Konkel, Jerilyn A. Walker, Li Ding, Ira Hall, Kai Ye, Phil Lacroute, Charles Lee, Eliza Cerveira, Ankit Malhotra, Jaeho Hwang, Dariusz Plewczynski, Kamen Radew, Mallory Romanovitch, Chengsheng Zhang, David W. Craig, Nils Homer, Deanna Church, Chunlin Xiao, Jonathan Sebat, Danny Antaki, Vineet Bafna, Jacob Michaelson, Kenny Ye, Scott E. Devine, Eugene J. Gardner, Gonçalo R. Abecasis, Jeffrey M. Kidd, Ryan E. Mills, Gargi Dayama, Sarah Emery, Goo Jun, Xinghua Shi, Andrew Quitadamo, Gerton Lunter, Gil A. McVean, Ken Chen, Xian Fan, Zechen Chong, Tenghui Chen, David Witherspoon, Jinchuan Xing, Evan E. Eichler, Mark J. Chaisson, Fereydoun Hormozdiari, John Huddleston, Maika Malig, Bradley J. Nelson, Peter H. Sudmant, Nicholas F. Parrish, Ekta Khurana, Matthew E. Hurles, Ben Blackburne, Sarah J. Lindsay, Zemin Ning, Klaudia Walter, Yujun Zhang, Mark B. Gerstein, Alexej Abyzov, Jieming Chen, Declan Clarke, Hugo Lam, Xinmeng Jasmine Mu, Cristina Sisu, Jing Zhang, Yan Zhang, Richard A. Gibbs, Fuli Yu, Matthew Bainbridge, Danny Challis, Uday S. Evani, Christie Kovar, James Lu, Donna Muzny, Uma Nagaswamy, Jeffrey G. Reid, Aniko Sabo, Jin Yu, Xiaosen Guo, Wangshen Li, Yingrui Li, Renhua Wu, Gabor T. Marth, Erik P. Garrison, Wen Fung Leong, Alistair N. Ward, Guillermo del Angel, Mark A. DePristo, Stacey B. Gabriel, Namrata Gupta, Chris Hartl, Ryan E. Poplin, Andrew G. Clark, Juan L. Rodriguez-Flores, Paul Flicek, Laura Clarke, Richard E. Smith, Xiangqun Zheng-Bradley, Daniel G. MacArthur, Elaine R. Mardis, Robert Fulton, Daniel C. Koboldt, Simon Gravel, Carlos D. Bustamante, David W. Craig, Alexis Christoforides, Nils Homer, Tyler Izatt, Stephen T. Sherry, Chunlin Xiao, Emmanouil T. Dermitzakis, Gonçalo R. Abecasis, Hyun Min Kang, Gil A. McVean, Mark B. Gerstein, Suganthi Balasubramanian, Lukas Habegger, Haiyuan Yu, Paul Flicek, Laura Clarke, Fiona Cunningham, Ian Dunham, Daniel Zerbino, Xiangqun Zheng-Bradley, Kasper Lage, Jakob Berg Jespersen, Heiko Horn, Stephen B. Montgomery, Marianne K. DeGorter, Ekta Khurana, Chris Tyler-Smith, Yuan Chen, Vincenza Colonna, Yali Xue, Mark B. Gerstein, Suganthi Balasubramanian, Yao Fu, Donghoon Kim, Adam Auton, Anthony Marcketta, Rob Desalle, Apurva Narechania, Melissa A. Wilson Sayres, Erik P. Garrison, Robert E. Handsaker, Seva Kashin, Steven A. McCarroll, Juan L. Rodriguez-Flores, Paul Flicek, Laura Clarke, Xiangqun Zheng-Bradley, Yaniv Erlich, Melissa Gymrek, Thomas Frederick Willems, Carlos D. Bustamante, Fernando L. Mendez, G. David Poznik, Peter A. Underhill, Charles Lee, Eliza Cerveira, Ankit Malhotra, Mallory Romanovitch, Chengsheng Zhang, Gonçalo R. Abecasis, Lachlan Coin, Haojing Shao, David Mittelman, Chris Tyler-Smith, Qasim Ayub, Ruby Banerjee, Maria Cerezo, Yuan Chen, Thomas W. Fitzgerald, Sandra Louzada, Andrea Massaia, Shane McCarthy, Graham R. Ritchie, Yali Xue, Fengtang Yang, Richard A. Gibbs, Christie Kovar, Divya Kalra, Walker Hale, Donna Muzny, Jeffrey G. Reid, Jun Wang, Xu Dan, Xiaosen Guo, Guoqing Li, Yingrui Li, Chen Ye, Xiaole Zheng, David M. Altshuler, Paul Flicek, Laura Clarke, Xiangqun Zheng-Bradley, David R. Bentley, Anthony Cox, Sean Humphray, Scott Kahn, Ralf Sudbrak, Marcus W. Albrecht, Matthias Lienhard, David Larson, David W. Craig, Tyler Izatt, Ahmet A. Kurdoglu, Stephen T. Sherry, Chunlin Xiao, David Haussler, Gonçalo R. Abecasis, Gil A. McVean, Richard M. Durbin, Senduran Balasubramaniam, Thomas M. Keane, Shane McCarthy, James Stalker, Walter Bodmer, Gabriel Bedoya, Andres Ruiz-Linares, Zhiming Cai, Yang Gao, Jiayou Chu, Leena Peltonen, Andres Garcia-Montero, Alberto Orfao, Julie Dutil, Juan C. Martinez-Cruzado, Taras K. Oleksyk, Kathleen C. Barnes, Rasika A. Mathias, Anselm Hennis, Harold Watson, Colin McKenzie, Firdausi Qadri, Regina LaRocque, Pardis C. Sabeti, Jiayong Zhu, Xiaoyan Deng, Pardis C. Sabeti, Danny Asogun, Onikepe Folarin, Christian Happi, Omonwunmi Omoniwa, Matt Stremlau, Ridhi Tariyal, Muminatou Jallow, Fatoumatta Sisay Joof, Tumani Corrah, Kirk Rockett, Dominic Kwiatkowski, Jaspal Kooner, Trâ`n Tịnh Hiê`n, Sarah J. Dunstan, Nguyen Thuy Hang, Richard Fonnie, Robert Garry, Lansana Kanneh, Lina Moses, Pardis C. Sabeti, John Schieffelin, Donald S. Grant, Carla Gallo, Giovanni Poletti, Danish Saleheen, Asif Rasheed

ABSTRACT

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. 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. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies. More... »

PAGES

68

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature15393

    DOI

    http://dx.doi.org/10.1038/nature15393

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1021812064

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/26432245


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