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3. A global reference for human genetic variation

Author

Colonna V. (1000 Genomes Project Consortium) Adam Auton, Gonçalo R Abecasis, David M Altshuler, Richard M Durbin, David R Bentley, Aravinda Chakravarti, Andrew G Clark, Peter Donnelly, Evan E Eichler, Paul Flicek, Stacey B Gabriel, Richard A Gibbs, Eric D Green, Matthew E Hurles, Bartha M Knoppers, Jan O Korbel, Eric S Lander, Charles Lee, Hans Lehrach, Elaine R Mardis, Gabor T Marth, Gil A McVean, Deborah A Nickerson, Jeanette P Schmidt, Stephen T Sherry, Jun Wang, Richard K Wilson, Eric Boerwinkle, Harsha Doddapaneni, Yi Han, Viktoriya Korchina, Christie Kovar, Sandra Lee, Donna Muzny, Jeffrey G Reid, Yiming Zhu, 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, Namrata Gupta, Neda Gharani, Lorraine H Toji, Norman P Gerry, Alissa M Resch, 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, Russell Grocock, Sean Humphray, Terena James, Zoya Kingsbury, Ralf Sudbrak, Marcus W Albrecht, Vyacheslav S Amstislavskiy, Tatiana A Borodina, Matthias Lienhard, Florian Mertes, Marc Sultan, Bernd Timmermann, Marie-Laure Yaspo, Lucinda Fulton, Robert Fulton, 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, Senduran Balasubramaniam, John Burton, Petr Danecek, Thomas M Keane, Anja Kolb-Kokocinski, Shane McCarthy, James Stalker, Michael Quail, Christopher J Davies, Jeremy Gollub, Teresa Webster, Brant Wong, Yiping Zhan, Adam Auton, Christopher L Campbell, Yu Kong, Anthony Marcketta, Fuli Yu, Lilian Antunes, Matthew Bainbridge, Aniko Sabo, Zhuoyi Huang, Lachlan J M Coin, Lin Fang, Qibin 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, 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, Eric Banks, Gaurav Bhatia, Guillermo Del Angel, Giulio Genovese, Heng Li, Seva Kashin, Steven A McCarroll, James C Nemesh, Ryan E Poplin, Seungtai C Yoon, Jayon Lihm, Vladimir Makarov, Srikanth Gottipati, Alon Keinan, Juan L Rodriguez-Flores, Tobias Rausch, Markus H Fritz, Adrian M Stütz, Kathryn Beal, Avik Datta, Javier Herrero, Graham R S Ritchie, Daniel Zerbino, Pardis C Sabeti, Ilya Shlyakhter, Stephen F Schaffner, Joseph Vitti, David N Cooper, Edward V Ball, Peter D Stenson, Bret Barnes, Markus Bauer, R Keira Cheetham, Anthony Cox, Michael Eberle, 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 Herwig, 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, 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, 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, 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, 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, Brian L Browning, Sharon R Browning, Fereydoun Hormozdiari, Peter H Sudmant, Ekta Khurana, Chris Tyler-Smith, Cornelis A Albers, Qasim Ayub, Yuan Chen, Vincenza Colonna, Luke Jostins, 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, Chris Hartl, Khalid Shakir, Jeremiah Degenhardt, Sascha Meiers, Benjamin Raeder, Francesco Paolo Casale, Oliver Stegle, Eric-Wubbo Lameijer, Ira Hall, Vineet Bafna, Jacob Michaelson, Eugene J Gardner, Ryan E Mills, Gargi Dayama, Ken Chen, Xian Fan, Zechen Chong, Tenghui Chen, Mark J Chaisson, John Huddleston, Maika Malig, Bradley J Nelson, Nicholas F Parrish, Ben Blackburne, Sarah J Lindsay, Zemin Ning, Yujun Zhang, Hugo Lam, Cristina Sisu, Danny Challis, Uday S Evani, James Lu, Uma Nagaswamy, Jin Yu, Wangshen Li, Lukas Habegger, Haiyuan Yu, Fiona Cunningham, Ian Dunham, Kasper Lage, Jakob Berg Jespersen, Heiko Horn, Donghoon Kim, Rob Desalle, Apurva Narechania, Melissa A Wilson Sayres, Fernando L Mendez, G David Poznik, Peter A Underhill, Lachlan Coin, David Mittelman, Ruby Banerjee, Maria Cerezo, Thomas W Fitzgerald, Sandra Louzada, Andrea Massaia, Graham R Ritchie, Fengtang Yang, Divya Kalra, Walker Hale, Xu Dan, Kathleen C Barnes, Christine Beiswanger, Hongyu Cai, Hongzhi Cao, Brenna Henn, Danielle Jones, Jane S Kaye, Alastair Kent, Angeliki Kerasidou, Rasika Mathias, Pilar N Ossorio, Michael Parker, Charles N Rotimi, Charmaine D Royal, Karla Sandoval, Yeyang Su, Zhongming Tian, Sarah Tishkoff, Marc Via, Yuhong Wang, Huanming Yang, Ling Yang, Jiayong Zhu, Walter Bodmer, Gabriel Bedoya, Zhiming Cai, Yang Gao, Jiayou Chu, Leena Peltonen, Andres Garcia-Montero, Alberto Orfao, Julie Dutil, Juan C Martinez-Cruzado, Rasika A Mathias, Anselm Hennis, Harold Watson, Colin McKenzie, Firdausi Qadri, Regina LaRocque, Xiaoyan Deng, 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, Trân T?nh Hiên, Sarah J Dunstan, Nguyen Thuy Hang, Richard Fonnie, Robert Garry, Lansana Kanneh, Lina Moses, John Schieffelin, Donald S Grant, Carla Gallo, Giovanni Poletti, Danish Saleheen, Asif Rasheed, Lisa D Brooks, Adam L Felsenfeld, Jean E McEwen, Yekaterina Vaydylevich, Audrey Duncanson, Michael Dunn, Jeffery A Schloss, 1000 Genomes Project Consortium, Institute for Medical Engineering and Science, Broad Institute of MIT and Harvard, Lincoln Laboratory, Massachusetts Institute of Technology. Department of Biology, Gabriel, Stacey, Lander, Eric Steven, Daly, Mark J, Banks, Eric, Bhatia, Gaurav, Kashin, Seva, McCarroll, Steven A, Nemesh, James, Poplin, Ryan E., Sabeti, Pardis, Shlyakhter, Ilya, Schaffner, Stephen F, Vitti, Joseph, Gymrek, Melissa A, Hartler, Christina M., and Tariyal, Ridhi

Subjects
demography, genetic association, genotype, Human genomics, Genome-wide association study, Review, SUSCEPTIBILITY, DISEASE, polymorphism, 0302 clinical medicine, quantitative trait locus, INDEL Mutation, genetics, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), MUTATION, Exome sequencing, 0303 health sciences, public health, Sequence analysis, High-Throughput Nucleotide Sequencing, standard, Genomics, Reference Standards, Physical Chromosome Mapping, 3. Good health, priority journal, Science & Technology - Other Topics, BAYES FACTORS, Molecular Developmental Biology, Genotype, Genetics, Medical, Quantitative Trait Loci, DNA sequence, rare disease, human genetics, information processing, Article, 03 medical and health sciences, SDG 3 - Good Health and Well-being, POPULATION HISTORY, human genome, Humans, retroposon, Genetic variability, human, GENOME-WIDE ASSOCIATION, 1000 Genomes Project, Demography, Science & Technology, ancestry, disease predisposition, Genetic Variation, MACULAR DEGENERATION, major clinical study, gene linkage disequilibrium, purl.org/pe-repo/ocde/ford#3.01.02 [https], Genetics, Population, 030217 neurology & neurosurgery, haplotype, Internationality, VARIANT, Datasets as Topic, Human genetic variation, COMPLEMENT FACTOR-H, single nucleotide polymorphism, genetic variability, Exome, chromosome map, Genetics, Variant Call Format, Genome, Multidisciplinary, 1000 Genomes Project Consortium, international cooperation, Multidisciplinary Sciences, standards, Disease Susceptibility, medical genetics, General Science & Technology, Population, Computational biology, Biology, gene frequency, Polymorphism, Single Nucleotide, high throughput sequencing, Rare Diseases, promoter region, MD Multidisciplinary, Genetic variation, QH426, 030304 developmental biology, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Genome, Human, population genetics, population structure, Sequence Analysis, DNA, gene structure, INDIVIDUALS, Haplotypes, Genome-Wide Association Study, purl.org/pe-repo/ocde/ford#1.06.07 [https]
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., Wellcome Trust (London, England) (Core Award 090532/Z/09/Z), Wellcome Trust (London, England) (Senior Investigator Award 095552/Z/11/Z ), Wellcome Trust (London, England) (WT095908), Wellcome Trust (London, England) (WT109497), Wellcome Trust (London, England) (WT098051), Wellcome Trust (London, England) (WT086084/Z/08/Z), Wellcome Trust (London, England) (WT100956/Z/13/Z ), Wellcome Trust (London, England) (WT097307), Wellcome Trust (London, England) (WT0855322/Z/08/Z ), Wellcome Trust (London, England) (WT090770/Z/09/Z ), Wellcome Trust (London, England) (Major Overseas program in Vietnam grant 089276/Z.09/Z), Medical Research Council (Great Britain) (grant G0801823), Biotechnology and Biological Sciences Research Council (Great Britain) (grant BB/I02593X/1), Biotechnology and Biological Sciences Research Council (Great Britain) (grant BB/I021213/1), Zhongguo ke xue ji shu qing bao yan jiu suo. Office of 863 Programme of China (2012AA02A201), National Basic Research Program of China (2011CB809201), National Basic Research Program of China (2011CB809202), National Basic Research Program of China (2011CB809203), National Natural Science Foundation of China (31161130357), Shenzhen Municipal Government of China (grant ZYC201105170397A), Canadian Institutes of Health Research (grant 136855), Quebec Ministry of Economic Development, Innovation, and Exports (PSR-SIIRI-195), Germany. Bundesministerium für Bildung und Forschung (0315428A), Germany. Bundesministerium für Bildung und Forschung (01GS08201), Germany. Bundesministerium für Bildung und Forschung (BMBF-EPITREAT grant 0316190A), Deutsche Forschungsgemeinschaft (Emmy Noether Grant KO4037/1-1), Beatriu de Pinos Program (2006 BP-A 10144), Beatriu de Pinos Program (2009 BP-B 00274), Spanish National Institute for Health (grant PRB2 IPT13/0001-ISCIII-SGEFI/FEDER), Japan Society for the Promotion of Science (fellowship number PE13075), Marie Curie Actions Career Integration (grant 303772), Fonds National Suisse del la Recherche, SNSF, Scientifique (31003A_130342), National Center for Biotechnology Information (U.S.) (U54HG3067), National Center for Biotechnology Information (U.S.) (U54HG3273), National Center for Biotechnology Information (U.S.) (U01HG5211), National Center for Biotechnology Information (U.S.) (U54HG3079), National Center for Biotechnology Information (U.S.) (R01HG2898), National Center for Biotechnology Information (U.S.) (R01HG2385), National Center for Biotechnology Information (U.S.) (RC2HG5552), National Center for Biotechnology Information (U.S.) (U01HG6513), National Center for Biotechnology Information (U.S.) (U01HG5214), National Center for Biotechnology Information (U.S.) (U01HG5715), National Center for Biotechnology Information (U.S.) (U01HG5718), National Center for Biotechnology Information (U.S.) (U01HG5728), National Center for Biotechnology Information (U.S.) (U41HG7635), National Center for Biotechnology Information (U.S.) (U41HG7497), National Center for Biotechnology Information (U.S.) (R01HG4960), National Center for Biotechnology Information (U.S.) (R01HG5701), National Center for Biotechnology Information (U.S.) (R01HG5214), National Center for Biotechnology Information (U.S.) (R01HG6855), National Center for Biotechnology Information (U.S.) (R01HG7068), National Center for Biotechnology Information (U.S.) (R01HG7644), National Center for Biotechnology Information (U.S.) (DP2OD6514), National Center for Biotechnology Information (U.S.) (DP5OD9154), National Center for Biotechnology Information (U.S.) (R01CA166661), National Center for Biotechnology Information (U.S.) (R01CA172652), National Center for Biotechnology Information (U.S.) (P01GM99568), National Center for Biotechnology Information (U.S.) (R01GM59290), National Center for Biotechnology Information (U.S.) (R01GM104390), National Center for Biotechnology Information (U.S.) (T32GM7790), National Center for Biotechnology Information (U.S.) (R01HL87699), National Center for Biotechnology Information (U.S.) (R01HL104608), National Center for Biotechnology Information (U.S.) (T32HL94284), National Center for Biotechnology Information (U.S.) (HHSN268201100040C), National Center for Biotechnology Information (U.S.) (HHSN272201000025C), Lundbeck Foundation (grant R170-2014-1039, Simons Foundation (SFARI award SF51), National Science Foundation (U.S.) (Research Fellowship DGE-1147470)

Published
2015
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4. Enabling Atlas2 personal genome analysis on the cloud

Author

Danny Challis, Cristian Coarfa, Uday S. Evani, Andrew R. Jackson, Aleksandar Milosavljevic, Fuli Yu, Jin Yu, Matthew N. Bainbridge, and Sameer Paithankar

Subjects
World Wide Web, Engineering, business.industry, Software as a service, Workbench, Genomics, Cloud computing, business, Pipeline (software), Genome, Personal genomics
Abstract

Until recently, sequencing has primarily been carried out in large genome centers who also invested heavily in developing the computational infrastructure to enable post sequencing analysis. The recent advancements in sequencing technologies have lead to a wide dissemination of sequencing and we are now seeing many sequencing projects being undertaken in small laboratories. However, the limited accessibility to the computational infrastructure and high quality bioinformatic tools needed to enable analysis remains a serious road-block. The cloud computing and Software-as-a-Service (SaaS) technologies can help address this barrier. We deploy the Atlas2 Cloud Pipeline for personal genome analysis via the Genboree Workbench using software-as-a-service model. We report on a successful case study of personal genome analysis using this pipeline.

Published
2011
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5. Mapping copy number variation by population-scale genome sequencing

Author

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

Subjects
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

6. The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes

Author

Donna M. Muzny, Ryan Poplin, Danny Challis, Eric Banks, Lilian Antunes, Erik Garrison, Richard A. Gibbs, Uday S. Evani, Gabor T. Marth, and Fuli Yu

Subjects
False discovery rate, Computational biology, Biology, Distribution, Machine Learning, 03 medical and health sciences, 0302 clinical medicine, INDEL Mutation, Human Genome Project, Genetics, Humans, Exome, 1000 Genomes Project, Indel, Exome sequencing, 030304 developmental biology, 0303 health sciences, Genome, Human, Computational Biology, High-Throughput Nucleotide Sequencing, food and beverages, INDEL, Mutagenesis, Human genome, DNA microarray, 030217 neurology & neurosurgery, Research Article, Biotechnology
Abstract

Background Identifying insertion/deletion polymorphisms (INDELs) with high confidence has been intrinsically challenging in short-read sequencing data. Here we report our approach for improving INDEL calling accuracy by using a machine learning algorithm to combine call sets generated with three independent methods, and by leveraging the strengths of each individual pipeline. Utilizing this approach, we generated a consensus exome INDEL call set from a large dataset generated by the 1000 Genomes Project (1000G), maximizing both the sensitivity and the specificity of the calls. Results This consensus exome INDEL call set features 7,210 INDELs, from 1,128 individuals across 13 populations included in the 1000 Genomes Phase 1 dataset, with a false discovery rate (FDR) of about 7.0%. Conclusions In our study we further characterize the patterns and distributions of these exonic INDELs with respect to density, allele length, and site frequency spectrum, as well as the potential mutagenic mechanisms of coding INDELs in humans. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1333-7) contains supplementary material, which is available to authorized users.

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7. Atlas2 Cloud: a framework for personal genome analysis in the cloud

Author

Matthew N. Bainbridge, Sameer Paithankar, Cristian Coarfa, Aleksandar Milosavljevic, Uday S. Evani, Adinarayana Jakkamsetti, Danny Challis, Andrew R. Jackson, Fuli Yu, Jin Yu, and Peter Pham

Subjects
lcsh:QH426-470, lcsh:Biotechnology, Cloud computing, Biology, Bottleneck, User-Computer Interface, 03 medical and health sciences, 0302 clinical medicine, lcsh:TP248.13-248.65, Databases, Genetic, Genetics, Humans, 030304 developmental biology, Internet, 0303 health sciences, Variant Call Format, Genome, Human, business.industry, Research, Software as a service, Data science, Pipeline (software), Biotechnology, lcsh:Genetics, 030220 oncology & carcinogenesis, Community cloud, User interface, business, Software, Personal genomics
Abstract

Background Until recently, sequencing has primarily been carried out in large genome centers which have invested heavily in developing the computational infrastructure that enables genomic sequence analysis. The recent advancements in next generation sequencing (NGS) have led to a wide dissemination of sequencing technologies and data, to highly diverse research groups. It is expected that clinical sequencing will become part of diagnostic routines shortly. However, limited accessibility to computational infrastructure and high quality bioinformatic tools, and the demand for personnel skilled in data analysis and interpretation remains a serious bottleneck. To this end, the cloud computing and Software-as-a-Service (SaaS) technologies can help address these issues. Results We successfully enabled the Atlas2 Cloud pipeline for personal genome analysis on two different cloud service platforms: a community cloud via the Genboree Workbench, and a commercial cloud via the Amazon Web Services using Software-as-a-Service model. We report a case study of personal genome analysis using our Atlas2 Genboree pipeline. We also outline a detailed cost structure for running Atlas2 Amazon on whole exome capture data, providing cost projections in terms of storage, compute and I/O when running Atlas2 Amazon on a large data set. Conclusions We find that providing a web interface and an optimized pipeline clearly facilitates usage of cloud computing for personal genome analysis, but for it to be routinely used for large scale projects there needs to be a paradigm shift in the way we develop tools, in standard operating procedures, and in funding mechanisms.

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8. The functional spectrum of low-frequency coding variation

Author

Gabor T, Marth, Fuli, Yu, Amit R, Indap, Kiran, Garimella, Simon, Gravel, Wen Fung, Leong, Chris, Tyler-Smith, Matthew, Bainbridge, Tom, Blackwell, Xiangqun, Zheng-Bradley, Yuan, Chen, Danny, Challis, Laura, Clarke, Edward V, Ball, Kristian, Cibulskis, David N, Cooper, Bob, Fulton, Chris, Hartl, Dan, Koboldt, Donna, Muzny, Richard, Smith, Carrie, Sougnez, Chip, Stewart, Alistair, Ward, Jin, Yu, Yali, Xue, David, Altshuler, Carlos D, Bustamante, Andrew G, Clark, Mark, Daly, Mark, DePristo, Paul, Flicek, Stacey, Gabriel, Elaine, Mardis, Aarno, Palotie, Richard, Gibbs, and Reed A, Cartwright

Subjects
Genotype, Sequence analysis, Population, Human genetic variation, Biology, Polymorphism, Single Nucleotide, Sensitivity and Specificity, 03 medical and health sciences, 0302 clinical medicine, Gene Frequency, INDEL Mutation, Humans, Allele, 1000 Genomes Project, education, Allele frequency, Alleles, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, Base Sequence, Genome, Human, Research, Exons, Sequence Analysis, DNA, Genetics, Population, Sequence Alignment, Algorithms, 030217 neurology & neurosurgery
Abstract

Background Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, but because of insufficient sample size it is not clear if the same trend holds for rare variants below 1% allele frequency. Results The 1000 Genomes Exon Pilot Project has collected deep-coverage exon-capture data in roughly 1,000 human genes, for nearly 700 samples. Although medical whole-exome projects are currently afoot, this is still the deepest reported sampling of a large number of human genes with next-generation technologies. According to the goals of the 1000 Genomes Project, we created effective informatics pipelines to process and analyze the data, and discovered 12,758 exonic SNPs, 70% of them novel, and 74% below 1% allele frequency in the seven population samples we examined. Our analysis confirms that coding variants below 1% allele frequency show increased population-specificity and are enriched for functional variants. Conclusions This study represents a large step toward detecting and interpreting low frequency coding variation, clearly lays out technical steps for effective analysis of DNA capture data, and articulates functional and population properties of this important class of genetic variation.

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