1. Mapping copy number variation by population-scale genome sequencing
- Author
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L. McDade, Eric D. Green, Aravinda Chakravarti, Susan Lindsay, Justin Paschall, Aylwyn Scally, Deborah A. Nickerson, Chip Stewart, Stephen T. Sherry, Chunlin Xiao, Alex Reynolds, Carol Scott, H. M. Khouri, Pardis C. Sabeti, Xinmeng Jasmine Mu, Stephen B. Montgomery, Eric Banks, Gabor T. Marth, A. Caprio, Xiaole Zheng, Philip Awadalla, Qunyuan Zhang, Wei Chen, Matthew N. Bainbridge, Donna Muzny, Steven A. McCarroll, Jeffrey M. Kidd, Honglong Wu, Audrey Duncanson, Vladimir Makarov, Lilia M. Iakoucheva, Mark Gerstein, Han-Jun Jin, Can Alkan, Iman Hajirasouliha, T. J. Fennell, C. R. Juenger, J. Kidd, Chris Tyler-Smith, Qasim Ayub, D. Ashworth, Kristian Cibulskis, Yutao Fu, William M. McLaren, Sol Katzman, Yujun Zhang, Rajini R Haraksingh, A. Kebbel, Stuart L. Schreiber, Manual Rivas, Onur Sakarya, Tobias Rausch, Yuan Chen, M. Bachorski, Matthew E. Hurles, N. C. Clemm, Wei Wang, Xiangqun Zheng-Bradley, Adrian M. Sütz, Thomas M. Keane, E. Bank, Stephen F. McLaughlin, Javier Herrero, Jon Keebler, Simon Myers, Aleksandr Morgulis, James Nemesh, Jing Leng, Molly Przeworski, Alon Keinan, Lorraine Toji, Ilya Shlyakhter, Joshua M. Korn, Martine Zilversmit, Luke Jostins, Jun Wang, Jared Maguire, J. M. Korn, Ryan E. Mills, Seungtai Yoon, Bo Wang, F. M. De La Vega, Heng Li, L. Guccione, Laura Clarke, Huisong Zheng, Jeffrey K. Ichikawa, K. Kao, Kirill Rotmistrovsky, L. Gu, David B. Jaffe, David Haussler, Toby Bloom, Tara Skelly, S. Yoon, Gil McVean, Carrie Sougnez, Mark A. Batzer, A. De Witte, Ralf Herwig, Jane Wilkinson, Min Hu, K. Pareja, John V. Pearson, Robert E. Handsaker, Jerilyn A. Walker, Fuli Yu, Anthony A. Philippakis, Aniko Sabo, Jonathan Marchini, Ryan D. Hernandez, Guoqing Li, Peter Donnelly, Eric S. Lander, David J. Dooling, Jun Ding, Lukas Habegger, Pilar N. Ossorio, Andreas Dahl, Wilfried Nietfeld, Miriam F. Moffatt, Alexej Abyzov, Sebastian Zöllner, Ekta Khurana, Jean E. McEwen, Robert S. Fulton, Alexey Soldatov, Fiona Hyland, Philippe Lacroute, Richa Agarwala, Paul Flicek, Weichun Huang, Alison J. Coffey, Tony Cox, John W. Wallis, Robert Sanders, David Neil Cooper, Jason P. Affourtit, Mark A. DePristo, D Wheeler, Christopher Celone, Eugene Kulesha, Craig Elder Mealmaker, B. Desany, Zhengdong D. Zhang, Jonathan M. Manning, Cynthia L. Turcotte, Lisa D Brooks, Xiuqing Zhang, C. Coafra, Rajesh Radhakrishnan, Alan J. Schafer, Jonathan Sebat, Ken Chen, Andrew G. Clark, Alexis Christoforides, Edward V. Ball, Mark S. Guyer, Sharon R. Grossman, Philip Rosenstiel, J. Knowlton, Gonçalo R. Abecasis, Min Jian, James O. Burton, S. Wang, Lucinda Murray, George M. Weinstock, Mark Lathrop, Harold Swerdlow, Michael L. Metzker, Xiaowei Zhan, Yeyang Su, Ruibang Luo, Charles Lee, Huanming Yang, P. Marquardt, Charles N. Rotimi, Lynne V. Nazareth, Michael Snyder, Faheem Niazi, Quan Long, Jane Kaye, Michael Strömberg, Adam Auton, Michael Bauer, Cheng-Sheng Lee, S. Gabriel, Jim Stalker, Heather E. Peckham, D. Conners, Raffaella Smith, Yingrui Li, Niall Anthony Gormley, Megan Hanna, Jinchuan Xing, Hugo Y. K. Lam, S. Giles, Evan E. Eichler, Justin Jee, Loukas Moutsianas, Jiang Du, Hyun Min Kang, Eric F. Tsung, Ni Huang, Kai Ye, Stephen F. Schaffner, Suleyman Cenk Sahinalp, Xinghua Shi, Sean Humphray, Ahmet Kurdoglu, Amy L. McGuire, Sandra J. Lee, Linnea Fulton, Francis S. Collins, Huiqing Liang, S. C. Melton, A. Nawrocki, Aaron R. Quinlan, Tatjana Borodina, Lynn B. Jorde, Leopold Parts, Michael D. McLellan, Adrian M. Stütz, Paul Scheet, Amit Indap, Vyacheslav Amstislavskiy, Waibhav Tembe, S. Attiya, Jin Yu, Dmitri Parkhomchuk, Si Quang Le, Fabian Grubert, E. Buglione, Ruiqiang Li, Yan Zhou, Fiona Cunningham, Gilean McVean, Wan-Ping Lee, W. Song, Richard Durbin, Andrew Kernytsky, Stephen M. Beckstrom-Sternberg, Xin Ma, J. Jeng, Lauren Ambrogio, Carol Churcher, Ryan Poplin, William O.C.M. Cookson, Rasko Leinonen, Alexey N. Davydov, Kenny Ye, Paige Anderson, Alexander E. Urban, Adam Felsenfeld, Jeffrey S. Reid, Cornelis A. Albers, Jan O. Korbel, Senduran Balasubramaniam, Elaine R. Mardis, Gozde Aksay, Peter H. Sudmant, Aaron McKenna, M. Labrecque, Amanda J. Price, Vadim Zalunin, Donald F. Conrad, Florian Mertes, Christie Kovar, Danny Challis, A. D. Ball, Petr Danecek, Kiran V. Garimella, Bryan Howie, Scott Kahn, Shuaishuai Tai, E. P. Garrison, Robert D. Bjornson, Shankar Balasubramanian, Fereydoun Hormozdiari, Geng Tian, S. Clark, Joanna L. Kelley, Asif T. Chinwalla, Ramenani Ravi K, Ralf Sudbrak, Mark Kaganovich, Jeffrey C. Barrett, David Rio Deiros, Jeremiah D. Degenhardt, A. Palotie, Alistair Ward, Gianna Costa, Huyen Dinh, M. Minderman, R. Keira Cheetham, Jingxiang Li, Michael A. Quail, P. Koko-Gonzales, Alastair Kent, Martin Shumway, David R. Bentley, Ferran Casals, Leena Peltonen, Klaudia Walter, Christopher Hartl, Erica Shefler, Zhaolei Zhang, Hans Lehrach, Jessica L. Peterson, Roger Winer, Daniel C. Koboldt, D. Riches, Terena James, Wen Fung Leong, Michael Egholm, Thomas W. Blackwell, Peter D. Stenson, Anthony J. Cox, Andrew D. Kern, David M. Carter, M. Tolzmann, Daniel G. MacArthur, Jiantao Wu, Jennifer Stone, Angie S. Hinrichs, M. Albrecht, Jo Knight, Chang-Yun Lin, Adam R. Boyko, Dan Turner, Xiaodong Fang, Youssef Idaghdour, Liming Liang, Ryan N. Gutenkunst, David Craig, Mark J. Daly, Xiaosen Guo, Neda Gharani, Gerton Lunter, Shuli Kang, A. Burke, Shripad Sinari, Yongming A. Sun, Zoya Kingsbury, Robert M. Kuhn, Miriam K. Konkel, T. Li, Kevin McKernan, Simon Gravel, Brian L. Browning, C Sidore, Zamin Iqbal, Matthew Mort, Afidalina Tumian, Michael C. Wendl, Adam Phillips, Bernd Timmermann, Carlos Bustamante, H. Y. Lam, Deniz Kural, Richard A. Gibbs, Bartha Maria Knoppers, Emmanouil T. Dermitzakis, Lon Phan, Richard K. Wilson, D. L. Altshuler, S. Keenen, Assya Abdallah, Eric A. Stone, Michael A. Eberle, Li Ding, and Broad Institute of MIT and Harvard
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DNA Copy Number Variations ,Genotype ,Population ,Genomic Structural Variation ,Genomics ,Computational biology ,Biology ,Genome ,Article ,DNA sequencing ,structural variation segmental duplications short-read rearrangements disorders disease common schizophrenia polymorphism insertions ,03 medical and health sciences ,0302 clinical medicine ,Gene Duplication ,Insertional ,Genetics ,Humans ,Genetic Predisposition to Disease ,Copy-number variation ,1000 Genomes Project ,education ,Sequence Deletion ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Multidisciplinary ,Genome, Human ,Reproducibility of Results ,Sequence Analysis, DNA ,DNA ,Mutagenesis, Insertional ,Genetics, Population ,Mutagenesis ,Human genome ,Sequence Analysis ,030217 neurology & neurosurgery ,Human - Abstract
Summary Genomic structural variants (SVs) are abundant in humans, differing from other variation classes in extent, origin, and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (i.e., copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analyzing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.
- Published
- 2011