Demographic history and rare allele sharing among human populations

著者: Simon Gravel, Brenna M. Henn, Ryan N. Gutenkunst, Amit Indap, Gábor Marth, Andrew G. Clark, Fuli Yu, Richard A. Gibbs, The 1000 Genomes Project, Carlos D. Bustamante, David L. Altshuler, Richard Durbin, Gonçalo R. Abecasis, David R. Bentley, Aravinda Chakravarti, Andrew G. Clark, Francis S. Collins, Francisco M. De La Vega, Peter Donnelly, Michael Egholm, Paul Flicek, Stacey Gabriel, Richard A. Gibbs, Bartha Maria Knoppers, Eric S. Lander, Hans Lehrach, Elaine R. Mardis, Gil McVean, Debbie A. Nickerson, Leena Peltonen, Alan J. Schafer, Stephen T. Sherry, Jun Wang, Richard K. Wilson, Richard A. Gibbs, David Rio Deiros, Mike Metzker, Donna M. Muzny, Jeff Reid, David A. Wheeler, Jun Wang, Jingxiang Li, Min Jian, Guoqing Li, Ruiqiang Li, Huiqing Liang, Geng Tian, Bó Wáng, Jian Wang, Wei Wang, Huanming Yang, Xiuqing Zhang, Huisong Zheng, Eric S. Lander, David L. Altshuler, Lauren Ambrogio, Toby Bloom, Kristian Cibulskis, Tim J. Fennell, Stacey B. Gabriel, David B. Jaffe, Erica Shefler, Carrie Sougnez, David R. Bentley, Niall Gormley, Sean Humphray, Zoya Kingsbury, Paula Koko-Gonzales, Jennifer Stone, Kevin McKernan, Gina L. Costa, Jeffry K. Ichikawa, Clarence Lee, Ralf Sudbrak, Hans Lehrach, Tatiana Borodina, Andreas Dahl, Alexey N. Davydov, P Marquardt, Florian Mertes, Wilfiried Nietfeld, Philip Rosenstiel, Stefan Schreiber, Aleksey V. Soldatov, Bernd Timmermann, Marius Tolzmann, Michael Egholm, Jason P. Affourtit, Dana Ashworth, Said Attiya, Melissa Bachorski, Eli Buglione, Adam Burke, Amanda Caprio, Christopher Celone, Shauna Clark, David Conners, Brian Desany, Lisa Gu, Lorri Guccione, Kalvin Kao, Andrew Kebbel, Jennifer Knowlton, Matthew T. Labrecque, Louise McDade, Craig Mealmaker, Melissa Minderman, Anne Nawrocki, Faheem Niazi, Kristen Pareja, Ravi Ramenani, David W. H. Riches, Wanmin Song, Cynthia Turcotte, Shally Wang, Elaine R. Mardis, Richard K. Wilson, David J. Dooling, Lucinda Fulton, Robert E. Fulton, George M. Weinstock, Richard Durbin, John H. Burton, David M. Carter, Carol Churcher, Alison J. Coffey, Anthony J. Cox, Aarno Palotie, Michael A. Quail, Tom Skelly, James Stalker, Harold Swerdlow, Daniel J. Turner, Anniek De Witte, Shane Giles, Richard A. Gibbs, David A. Wheeler, Matthew Bainbridge, Danny Challis, Aniko Sabo, Fuli Yu, Jin Yu, Jun Wang, Xiaodong Fang, Xiaosen Guo, Ruiqiang Li, Yingrui Li, Ruibang Luo, Shuaishuai Tai, Honglong Wu, Hancheng Zheng, Xiaole Zheng, Yan Zhou, Guoqing Li, Jian Wang, Huanming Yang, Gábor Marth, Erik P. Garrison, Weichun Huang, Amit Indap, Deniz Kural, Wan‐Ping Lee, Wen Fung Leong, Aaron R. Quinlan, Chip Stewart, Michael P. Strömberg, Alistair N. Ward, Jiantao Wu, Charles Lee, Ryan E. Mills, Xinghua Shi, Mark J. Daly, Mark A. DePristo, David L. Altshuler, Aaron D. Ball, Eric Banks, Toby Bloom, Brian L. Browning, Kristian Cibulskis, Tim J. Fennell, Kiran Garimella, Sharon R. Grossman, Robert E. Handsaker, Matt Hanna, Christopher Hartl, David B. Jaffe, Andrew Kernytsky, Joshua M. Korn, Heng Li, Jared Maguire, Steven A. McCarroll, Aaron McKenna, James Nemesh, Anthony Philippakis, Ryan Poplin, Alkes L. Price, Manuel A. Rivas, Pardis C. Sabeti, S. F. Schaffner, Erica Shefler, Ilya Shlyakhter, D.N. Cooper, Edward V. Ball, Matthew Mort, Andrew D. Phillips, Peter D. Stenson, Jonathan Sebat, Vladimir Makarov, Kenny Ye, Seungtai C. Yoon, Carlos D. Bustamante, Andrew G. Clark, Adam R. Boyko, Jeremiah Degenhardt, Simon Gravel, Ryan N. Gutenkunst, Mark Kaganovich, Alon Keinan, Phil Lacroute, Xin Ma, Andy Reynolds, Laura Clarke, Paul Flicek, Fiona Cunningham, Javier Herrero, Stephen Keenen, Eugene Kulesha, Rasko Leinonen, William McLaren, Rajesh Radhakrishnan, Richard E. Smith, Vadim Zalunin, Xiangqun Zheng-Bradley, Jan O. Korbel, Adrian M. Stütz, Sean Humphray, Markus Bauer, R. Keira Cheetham, Tony Cox, Michael A. Eberle, Terena James, Scott D. Kahn, Lisa Murray, Aravinda Chakravarti, Kai Ye, Francisco M. De La Vega, Yutao Fu, Fiona Hyland, Jonathan M. Manning, Stephen F. McLaughlin, Heather E. Peckham, Onur Sakarya, Yongming A. Sun, Eric F. Tsung, Mark A. Batzer, Miriam K. Konkel, Jerilyn A. Walker, Ralf Sudbrak, Marcus W. Albrecht, Vyacheslav Amstislavskiy, Ralf Herwig, Dimitri V. Parkhomchuk, Stephen T. Sherry, Richa Agarwala, Hoda Khouri, Aleksandr Morgulis, Justin Paschall, Lon Phan, Kirill E. Rotmistrovsky, Robert D. Sanders, Martin F. Shumway, Chunlin Xiao, Gil A. McVean, Adam Auton, Zamin Iqbal, Gerton Lunter, Jonathan Marchini, Loukas Moutsianas, Simon Myers, Afidalina Tumian, Brian Desany, James Knight, Roger Winer, David W. Craig, Steve M. Beckstrom-Sternberg, Alexis Christoforides, Ahmet Kurdoglu, John V. Pearson, Shripad Sinari, Waibhav Tembe, David Haussler, Angie S. Hinrichs, Sol Katzman, Andrew D. Kern, Robert M. Kuhn, Molly Przeworski, Ryan D. Hernandez, Bryan Howie, Joanna L. Kelley, Samuel Melton, Gonçalo R. Abecasis, Yun Li, Paul Anderson, Tom Blackwell, Wei Chen, William Cookson, Jun Ding, Hyun Min Kang, Mark Lathrop, Liming Liang, Miriam F. Moffatt, Paul Scheet, Carlo Sidore, Matthew Snyder, Xiaowei Zhan, Sebastian Zöllner, Philip Awadalla, Ferrán Casals, Youssef Idaghdour, John Keebler, Eric A. Stone, Martine Zilversmit, Lynn B. Jorde, Jinchuan Xing, Evan E. Eichler, Gozde Aksay, Can Alkan, Iman Hajirasouliha, Fereydoun Hormozdiari, Jeffrey M. Kidd, S. Cenk Şahinalp, Peter H. Sudmant, Elaine R. Mardis, Ken Chen, Asif Chinwalla, Ding Li, Daniel C. Koboldt, Mike D. McLellan, David J. Dooling, George M. Weinstock, John W. Wallis, Michael C. Wendl, Qunyuan Zhang, Richard Durbin, Cornelis A. Albers, Qasim Ayub, Senduran Balasubramaniam, Jeffrey C. Barrett, David M. Carter, Yuan Chen, Donald F. Conrad, Petr Danecek, Emmanouil T. Dermitzakis, Min Hu, Ni Huang, Matt Hurles, Han‐Jun Jin, Luke Jostins, Thomas Keane, Si Quang Le, Sarah Lindsay, Quan Long, Daniel G. MacArthur, Stephen B. Montgomery, Leopold Parts, James Stalker, Chris Tyler‐Smith, Klaudia Walter, Yujun Zhang, Mark B. Gerstein, Michael Snyder, Alexej Abyzov, Suganthi Balasubramanian, Robert Bjornson, Jiang Du, Fabian Grubert, Lukas Habegger, Rajini Haraksingh, Justin Jee, Ekta Khurana, Hugo Y. K. Lam, Jing Leng, Xinmeng Jasmine Mu, Alexander E. Urban, Zhengdong Zhang, Yingrui Li, Ruibang Luo, Gábor Marth, Erik P. Garrison, Deniz Kural, Aaron R. Quinlan, Chip Stewart, Michael P. Strömberg, Alistair N. Ward, Jiantao Wu, Charles Lee, Ryan E. Mills, Xinghua Shi, Steven A. McCarroll, Eric Banks, Mark A. DePristo, Robert E. Handsaker, Christopher Hartl, Joshua M. Korn, Heng Li, James Nemesh, Jonathan Sebat, Vladimir Makarov, Kenny Ye, Seungtai C. Yoon, Jeremiah Degenhardt, Mark Kaganovich, Laura Clarke, Richard E. Smith, Xiangqun Zheng-Bradley, Jan O. Korbel, Sean Humphray, R. Keira Cheetham, Michael A. Eberle, Scott D. Kahn, Lisa Murray, Kai Ye, Francisco M. De La Vega, Yutao Fu, Heather E. Peckham, Yongming A. Sun, Mark A. Batzer, Miriam K. Konkel, Jerilyn A. Walker, Chunlin Xiao, Zamin Iqbal, Brian Desany, Tom Blackwell, Matthew Snyder, Jinchuan Xing, Evan E. Eichler, Gozde Aksay, Can Alkan, Iman Hajirasouliha, Fereydoun Hormozdiari, Jeffrey M. Kidd, Ken Chen, Asif Chinwalla, Ding Li, Mike D. McLellan, John W. Wallis, Matt Hurles, Donald F. Conrad, Klaudia Walter, Yujun Zhang, Mark B. Gerstein, Michael Snyder, Alexej Abyzov, Jiang Du, Fabian Grubert, Rajini Haraksingh, Justin Jee, Ekta Khurana, Hugo Y. K. Lam, Jing Leng, Xinmeng Jasmine Mu, Alexander E. Urban, Zhengdong Zhang, Richard A. Gibbs, Matthew Bainbridge, Danny Challis, Cristian Coafra, Huyen Dinh, Christie Kovar, Sandy Lee, Donna M. Muzny, Lynne Nazareth, Jeff Reid, Aniko Sabo, Fuli Yu, Jin Yu, Gábor Marth, Erik Garrison, Amit Indap, Wen Fung Leong, Aaron R. Quinlan, Chip Stewart, Alistair N. Ward, Jiantao Wu, Kristian Cibulskis, Tim Fennell, Stacey B. Gabriel, Kiran Garimella, Christopher Hartl, Erica Shefler, Carrie Sougnez, Jane Wilkinson, Andrew G. Clark, Simon Gravel, Fabian Grubert, Laura Clarke, Paul Flicek, Richard E. Smith, Xiangqun Zheng-Bradley, Stephen T. Sherry, Hoda Khouri, Justin Paschall, Martin F. Shumway, Chunlin Xiao, Gil A. McVean, Sol Katzman, Gonçalo R. Abecasis, Tom Blackwell, Elaine R. Mardis, David J. Dooling, Lucinda Fulton, Robert E. Fulton, Daniel C. Koboldt, Richard M. Durbin, Senduran Balasubramaniam, Allison Coffey, Thomas Keane, Daniel G. MacArthur, Aarno Palotie, Carol Scott, James Stalker, Chris Tyler‐Smith, Mark Gerstein, Suganthi Balasubramanian, Aravinda Chakravarti, Bartha Maria Knoppers, Gonçalo R. Abecasis, Carlos D. Bustamante, Neda Gharani, Richard A. Gibbs, Lynn B. Jorde, Jane Kaye, Alastair Kent, Taosha Li, Amy L. McGuire, Gil McVean, Pilar N. Ossorio, Charles N. Rotimi, Yeyang Su, Lorraine H. Toji, Chris Tyler‐Smith, Lisa Brooks, Adam L. Felsenfeld, Jean E. McEwen, Assya Abdallah, Christopher R. Juenger, Nicholas C. Clemm, Francis S. Collins, Audrey Duncanson, Eric D. Green, Mark S. Guyer, Jane L. Peterson, Alan J. Schafer, Gonçalo R. Abecasis, David L. Altshuler, Adam Auton, Lisa Brooks, Richard M. Durbin, Richard A. Gibbs, Matt Hurles, Gil A. McVean - Proceedings of the National Academy of Sciences, PNAS 2011 被引用: 733

High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2-4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ∼1,000 sequenced chromosomes per population, whereas ∼2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence.