A global reference for human genetic variation

Nature - Tập 526 Số 7571 - Trang 68-74 - 2015
Adam Auton1, Gonçalo R. Abecasis2, David Green3, Richard Durbin4, David Bentley5, Aravinda Chakravarti6, Andrew G. Clark7, Peter Donnelly8, Evan E. Eichler9, Paul Flicek10, Stacey Gabriel11, Richard A. Gibbs12, Eric D. Green13, Matthew E. Hurles4, Bartha Maria Knoppers14, Jan O. Korbel10, Eric S. Lander11, Charles Lee15, Hans Lehrach16, Elaine R. Mardis17, Gábor Marth18, Gil McVean8, Deborah A. Nickerson9, Jeanette P. Schmidt19, S Sherry20, Jun Wang21, Richard K. Wilson17, Eric Boerwinkle12, HarshaVardhan Doddapaneni12, Yi Han12, Viktoriya Korchina12, Christie Kovar12, Sandra Lee12, Donna M. Muzny12, Jeffrey G. Reid12, Yiming Zhu12, Yuqi Chang21, Qiang Feng21, Xiaodong Fang21, Xiaosen Guo21, Min Jian21, Hui Jiang21, Xin Jin21, Tianming Lan21, Guoqing Li21, Jingxiang Li21, Yingrui Li21, Shengmao Liu21, Xiao Liu21, Yao Lu21, Xuedi Ma21, Meifang Tang21, Bo Wang21, Guangbiao Wang21, Honglong Wu21, Renhua Wu21, Xun Xu21, Ye Yin21, Dandan Zhang21, Wenwei Zhang21, Jiao Zhao21, Meiru Zhao21, Xiaole Zheng21, Namrata Gupta11, Neda Gharani22, Lorraine Toji22, Norman P. Gerry22, Alissa Resch22, Jonathan Barker10, Laura Clarke10, Laurent Gil10, Sarah Hunt10, Gavin Kelman10, Eugene Kulesha10, Rasko Leinonen10, William McLaren10, Rajesh Radhakrishnan10, Alexandra Roa10, Dmitriy Smirnov10, Richard E. Smith10, Ian Streeter10, Anja Thormann10, Iliana Toneva10, Brendan Vaughan10, Xiangqun Zheng-Bradley10, Russell Grocock5, Sean Humphray5, Terena James5, Zoya Kingsbury5, Ralf Sudbrak23, Marcus W. Albrecht24, Vyacheslav Amstislavskiy16, Tatiana Borodina24, Matthias Lienhard16, Florian Mertes16, Marc Sultan16, Bernd Timmermann16, Marie‐Laure Yaspo16, Lucinda Fulton17, Robert S. Fulton17, Victor Ananiev20, Zinaida Belaia20, Dimitriy Beloslyudtsev20, Nathan Bouk20, Chao Chen20, Deanna M. Church25, Robert Cohen20, Charles Cook20, John Garner20, Timothy Hefferon20, Michael Kimelman20, Chunlei Liu20, John Lopez20, Peter Meric20, Chris O’Sullivan26, Yuri Ostapchuk20, Lon Phan20, Sergiy Ponomarov20, Valérie Schneider20, Eugene Shekhtman20, Karl Sirotkin20, Douglas J. Slotta20, Hua Zhang20, Senduran Balasubramaniam4, John H. Burton4, Petr Danecek4, Thomas Keane4, Anja Kolb‐Kokocinski4, Shane McCarthy4, James Stalker4, Michael A. Quail4, Christopher J. Davies19, Jeremy Gollub19, Teresa Webster19, Brant Wong19, Yiping Zhan19, Christopher Campbell1, Yu Kong1, Anthony Marcketta1, Fuli Yu12, Lilian Antunes12, Matthew N. Bainbridge12, Aniko Sabo12, Zhuoyi Huang12, Lachlan Coin21, Lin Fang21, Guoqing Li21, Qibin Li21, Zhenyu Li21, Haoxiang Lin21, Binghang Liu21, Ruibang Luo21, Haojing Shao21, Yinlong Xie21, Hongzhi Wang21, Chang Yu21, Fan Zhang21, Hancheng Zheng21, Hongmei Zhu21, Can Alkan27, Elif Dal27, Fatma Kahveci27, Erik Garrison4, Deniz Kural28, Wan-Ping Lee28, Wen Fung Leong18, Michael Strömberg29, Alistair Ward18, Jiantao Wu18, Shiqiang Zhang18, Mark J. Daly9, Mark A. DePristo30, Robert E. Handsaker11, Eric Banks11, Gaurav Bhatia11, Guillermo del Angel11, Giulio Genovese11, Heng Li11, Seva Kashin11, Steven A. McCarroll11, James Nemesh11, Ryan Poplin11, Seungtai Yoon, Jayon Lihm31, Vladimir Makarov32, Srikanth Gottipati33, Alon Keinan7, Juan L. Rodríguez-Flores34, Tobias Rausch35, Markus H. Fritz36, Adrian M. Stütz35, Kathryn Beal10, Avik Datta10, Javier Herrero37, Graham R. S. Ritchie10, Daniel R. Zerbino10, Pardis C. Sabeti11, Ilya Shlyakhter11, S. F. Schaffner11, Joseph J. Vitti11, D.N. Cooper38, Edward V. Ball39, Peter D. Stenson39, Bret Barnes29, Markus Bauer5, R. Keira Cheetham5, Anthony J. Cox5, Michael A. Eberle5, Scott D. Kahn29, Lisa Murray5, John F. Peden5, Richard J. Shaw5, Eimear E. Kenny40, Mark A. Batzer30, Miriam K. Konkel41, Jerilyn A. Walker41, Daniel G. MacArthur42, Monkol Lek43, Ralf Herwig16, Li Ding17, Daniel C. Koboldt17, David E. Larson17, Kai Ye17, Simon Gravel44, Anand Swaroop45, Emily Y. Chew45, Tuuli Lappalainen46, Yaniv Erlich47, Melissa Gymrek11, Thomas Willems48, Jared T. Simpson49, Mark D. Shriver30, Jeffrey Rosenfeld12, Carlos D. Bustamante50, Stephen B. Montgomery51, Francisco M. De La Vega51, Jake Byrnes52, Andrew Carroll53, Marianne K. DeGorter54, Phil Lacroute50, Brian K. Maples50, Alicia R. Martin50, Andrés Moreno‐Estrada50, Suyash Shringarpure50, Fouad Zakharia50, Eran Halperin55,56, Yael Baran57, Eliza Cerveira15, Jaeho Hwang15, Ankit Malhotra15, Dariusz Plewczyński15, Kamen Radew15, Mallory Romanovitch15, Chengsheng Zhang15, Fiona Hyland58, David W. Craig59, Alexis Christoforides60, Nils Homer61, Tyler Izatt60, Ahmet Kurdoglu60, Shripad Sinari60, Kevin Squire62, Chunlin Xiao20, Jonathan Sebat10, Danny Antaki63, Madhusudan Gujral63, Amina Noor63, Kenny Ye40, Esteban G. Burchard64, Ryan D. Hernandez65, Christopher R. Gignoux64, David Haussler17, Sol Katzman66, Wm. Kent66, Bryan Mowry67, Andrés Ruiz‐Linares68, Emmanouil T. Dermitzakis69,70, Scott E. Devine71, Hyun Min Kang2, Jeffrey M. Kidd72, Tom Blackwell2, Sean Caron2, Wei Chen73, Sara Bizzotto74, Lars G. Fritsche2, Christian Fuchsberger2, Goo Jun75, Bingshan Li76, Robert H. Lyons77, Chris Scheller2, Carlo Sidore78, Shiya Song79, Elżbieta Śliwerska74, Daniel Taliun2, Adrian Tan2, Ryan Welch2, Mary Kate Wing2, Xiaowei Zhan80, Philip Awadalla81,82, Alan Hodgkinson83, Yun Li84, Xinghua Shi85, Andrew Quitadamo86, Gerton Lunter87, Jonathan Marchini88, Simon Myers44, Claire Churchhouse88, Olivier Delaneau89, Anjali Gupta Hinch8, Warren W. Kretzschmar8, Zamin Iqbal8, Iain Mathieson8, Androniki Menelaou90, Andy Rimmer89, Dionysia K. Xifara88, Tarás K. Oleksyk91, Yun‐Xin Fu92, Xiaoming Liu75, Momiao Xiong75, Lynn B. Jorde59, David J. Witherspoon59, Jinchuan Xing93, Brian L. Browning94, Sharon R. Browning94, Fereydoun Hormozdiari9, Peter H. Sudmant9, Ekta Khurana95, Chris Tyler‐Smith4, Cornelis A. Albers96, Qasim Ayub4, Yuan Chen4, Vincenza Colonna97, Luke Jostins8, Klaudia Walter4, Yali Xue4, Mark Gerstein98, Alexej Abyzov99, Suganthi Balasubramanian100, Jieming Chen101, Declan Clarke102, Yao Fu101, Arif Harmanci101, Mike Jin100, Donghoon Lee101, Jeremy Liu100, Xinmeng Jasmine Mu101, Jing Zhang101, Yan Zhang101, Christopher Hartl11, Khalid Shakir11, Jeremiah D. Degenhardt7, Sascha Meiers35, Benjamin Raeder35, Francesco Paolo Casale10, Oliver Stegle10, Eric-Wubbo Lameijer103, Ira M. Hall17, Vineet Bafna104, Jacob J. Michaelson105, Eugene J. Gardner71, Ryan E. Mills11, Gargi Dayama74, Ken Chen106, Xian Fan106, Zechen Chong106, Tenghui Chen106, Mark Chaisson9, John Huddleston107, Maika Malig9, Bradley J. Nelson9, Nicholas F. Parrish76, Ben Blackburne4, Sarah Lindsay4, Zemin Ning4, Yujun Zhang4, Hugo Y. K. Lam108, Cristina Sisu101, Danny Challis12, Uday S. Evani12, James T. Lu12, Uma Nagaswamy12, Jin Yu12, Xiaosen Guo109, Wangshen Li21, Lukas Habegger101, Haiyuan Yu84, Fiona Cunningham10, Ian Dunham10, Kasper Lage110,42, Jakob Berg Jespersen111, Heiko Horn112, Donghoon Kim100, Rob DeSalle113, Apurva Narechania114, Melissa A. Wilson115, Fernando L. Méndez50, G. David Poznik116, Peter A. Underhill50, David Mittelman117, Ruby Banerjee4, María Cerezo4, Tomas Fitzgerald4, Sandra Louzada4, Andrea Massaia4, Fengtang Yang4, Dinesh Kumar12, Walker Hale12, Xu Dan21, Guoqing Li21, Kathleen C. Barnes118, Ayesha A. Motala22, Hongyu Cai21, Alexander Schönhuth109, Brenna M. Henn119, D. A. Jones33, Jane Kaye120, Alastair Kent121, Angeliki Kerasidou122, Rasika A. Mathias123, Pilar N. Ossorio124, Michael Parker122, Charles N. Rotimi125, Charmaine Royal126, Karla Sandoval50, Yeyang Su21, Zhongming Tian21, Sarah A. Tishkoff127, Marc Vía128, Yuhong Wang21, Huanming Yang129, Ling Yang21, Jiayong Zhu21, Walter F. Bodmer130, Gabriel Bedoya131, Zhiming Cai21, Yang Gao132, Jiayou Chu133, Leena Peltonen, Andrés C. García‐Montero134, Alberto Órfão134, Julie Dutil135, Juan Carlos Martínez‐Cruzado91, Luc Multigner136, Harold Watson136, Colin A. Chapman137, Firdausi Qadri138, Regina C. LaRocque138, Xiaoyan Deng139, Danny Asogun140, Onikepe Folarin141, Christian T. Happi142, Omonwunmi Omoniwa142, Matt Stremlau143, Ridhi Tariyal143, Muminatou Jallow144, Fatoumatta Sisay Joof144, Tumani Corrah144, Kirk A. Rockett144, Dominic Kwiatkowski144, Jaspal S. Kooner145, Tran Tinh Hien146, Sarah J. Dunstan147, Nguyen Thuy Hang146, Richard Fonnie148, Robert F. Garry149, Lansana Kanneh148, Lina Moses149, John S. Schieffelin149, Donald S. Grant149, Carla Gallo150, Babak Alipanahi150, Danish Saleheen151, Asif Rasheed152, Lisa Brooks153, Adam L. Felsenfeld153, Jean McEwen153, Yekaterina Vaydylevich153, Audrey Duncanson154, Michael Dunn154, Jeffery A. Schloss153
1Department of Genetics, Albert Einstein College of Medicine, Bronx, 10461, New York, USA
2Center for Statistical Genetics, Biostatistics, University of Michigan, Ann Arbor, 48109, Michigan, USA
3Vertex Pharmaceuticals, Boston, 02210, Massachusetts, USA
4Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
5Illumina United Kingdom, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, CB10 1XL, Essex, UK
6McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland, USA
7Center for Comparative and Population Genomics, Cornell University, Ithaca, 14850, New York, USA
8Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
9Department of Genome Sciences, University of Washington School of Medicine, Seattle, 98195, Washington, USA
10European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
11The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, 02142, Massachusetts, USA
12Baylor College of Medicine, Human Genome Sequencing Center, Houston, 77030, Texas, USA
13US National Institutes of Health, National Human Genome Research Institute, 31 Center Drive, Bethesda, 20892, Maryland, USA
14Centre of Genomics and Policy, McGill University, Montreal, H3A 1A4, Quebec, Canada
15The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, 06032, Connecticut, USA
16Max Planck Institute for Molecular Genetics, D-14195 Berlin-Dahlem, Germany
17McDonnell Genome Institute at Washington University, Washington University School of Medicine, St Louis, 63108, Missouri, USA
18USTAR Center for Genetic Discovery & Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, 84112, Utah, USA
19Affymetrix, Santa Clara, California 95051, USA
20US National Institutes of Health, National Center for Biotechnology Information, 45 Center Drive, Bethesda, 20892, Maryland, USA
21BGI-Shenzhen, Shenzhen 518083, China
22Coriell Institute for Medical Research, Camden, 08103, New Jersey, USA
23European Centre for Public Heath Genomics, UNU-MERIT, Maastricht University, PO Box 616, Maastricht, 6200, MD, The Netherlands
24Alacris Theranostics, D-14195 Berlin-Dahlem, Germany
25Personalis, Menlo Park, California, 94025, USA
26US National Institutes of Health, National Human Genome Research Institute, 50 South Drive, Bethesda, 20892, Maryland, USA
27Department of Computer Engineering, Bilkent University, Bilkent, TR-06800, Ankara, Turkey
28Seven Bridges Genomics, 1 Broadway, 14th floor, Cambridge, 02142, Massachusetts, USA
29Illumina, San Diego, 92122, California, USA
30SynapDx, Four Hartwell Place, Lexington, 02421, Massachusetts, USA
31Cold Spring Harbor Laboratory Cold Spring Harbor, New York, 11724 USA
32Seaver Autism Center and Department of Psychiatry, Mount Sinai School of Medicine, New York, 10029, New York, USA
33Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, 14853, New York, USA
34Department of Genetic Medicine, Weill Cornell Medical College, New York, 10044, New York, USA
35European Molecular Biology Laboratory, Genome Biology Research Unit, Meyerhofstr. 1, Heidelberg, Germany
36European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, Heidelberg, 69117, Germany
37Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, WC1E 6DD, UK
38Cardiff University, Cardiff, United Kingdom
39Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
40Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, 10461, New York, USA
41Department of Biological Sciences, Louisiana State University, Baton Rouge, 70803, Louisiana, USA
42Harvard University, Cambridge, United States
43Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, 02114, Massachusetts, USA
44McGill University and Genome Quebec Innovation Centre, 740, Avenue du Dr. Penfield, Montreal, H3A 0G1, Quebec, Canada
45National Eye Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA
46Columbia University, New York, United States
47New York Genome Center, 101 Avenue of the Americas, 7th floor, New York, 10013, New York, USA
48Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, 02142, Massachusetts, USA
49Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, M5G 0A3, Ontario, Canada
50Department of Genetics, Stanford University, Stanford, 94305, California, USA
51Stanford University, Stanford, United States
52Ancestry.com, San Francisco, 94107, California, USA
53DNAnexus, 1975 West El Camino Real STE 101, Mountain View California, 94040, USA
54Departments of Genetics and Pathology, Stanford University, Stanford, 94305-5324, California, USA
55Tel Aviv University Tel Aviv, Israel
56University of California, Berkeley, Berkeley, United States
57Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel
58Thermo Fisher Scientific, 200 Oyster Point Boulevard, South San Francisco, 94080, California, USA
59Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, 84112, Utah, USA
60The Translational Genomics Research Institute, Phoenix, 85004, Arizona, USA
61Life Technologies, Beverly, 01915, Massachusetts, USA
62Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, 90024, California, USA
63Department of Psychiatry, University of California, San Diego, La Jolla, 92093, California, USA
64Departments of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, 94158, San Francisco, USA
65University of California, San Francisco, San Francisco, United States
66Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, 95064, California, USA
67Department of Human Genetics, University of Chicago, Chicago, 60637, Illinois, USA
68Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
69SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
70University of Geneva, Geneva, Switzerland
71University of Maryland, Baltimore, Baltimore, United States
72University of Michigan–Ann Arbor, Ann Arbor, United States
73Department of Pediatrics, University of Pittsburgh, Pittsburgh, 15224, Pennsylvania, USA
74Department of Human Genetics, University of Michigan Medical School, Ann Arbor, 48109, Michigan, USA
75The University of Texas Health Science Center at Houston, Houston, 77030, Texas, USA
76Vanderbilt University School of Medicine, Nashville, 37232, Tennessee, USA
77University of Michigan Sequencing Core, University of Michigan, Ann Arbor, 48109, Michigan, USA
78Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, 09042, Cagliari, Italy
79Department of Computational Medicine and Bioinfomatics, University of Michigan, Ann Arbor, 48109, Michigan, USA
80University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, 75390, Texas, USA
81Ontario Institute for Cancer Research, Toronto, Canada
82Université de Montréal, Montreal, Canada
83Department of Pediatrics, University of Montreal, Ste. Justine Hospital Research Centre, Montreal, H3T 1C5, Quebec, Canada
84Department of Genetics, Department of Biostatistics, Department of Computer Science, University of Chapel Hill, North Carolina, 27599, USA
85Department of Genetics, Harvard Medical School, Cambridge, 02142, Massachusetts, USA
86Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, 28223, North Carolina, USA
87University of Oxford, Oxford, United Kingdom
88Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
89Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
90Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
91Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, 00680, Puerto Rico, USA
92Department of Agronomy, Kansas State University, Manhattan, 66506, Kansas, USA
93Department of Genetics, Rutgers University, Piscataway, New Jersey, 08854, USA
94University of Washington, Seattle, United States
95Cornell University, Ithaca, United States
96Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, GA Nijmegen, 6525, The Netherlands
97Institute of Genetics and Biophysics, National Research Council (CNR), Naples, 80125, Italy
98Yale University, New Haven, United States
99Department of Health Sciences Research, Mayo Clinic, Rochester, 55905, Minnesota, USA
100Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, 06520, Connecticut, USA
101Program in Computational Biology and Bioinformatics, Yale University, New Haven, 06520, Connecticut, USA
102Department of Chemistry, Yale University, New Haven, 06520, Connecticut, USA
103Department of Medical Statistics and Bioinformatics, Molecular Epidemiology Section, Leiden University Medical Center, 2333, ZA, The Netherlands
104Department of Computer Science, University of California, San Diego, La Jolla, 92093, California, USA
105Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, 92093, California, USA
106Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, 77230, Texas, USA
107Howard Hughes Medical Institute, University of Washington, Seattle, 98195, Washington, USA
108Bina Technologies, Roche Sequencing, Redwood City, 94065, California, USA
109Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, Denmark
110Broad Institute, Cambridge, United States
111Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet building 208, Lyngby, 2800, Denmark
112Department of Surgery, Massachusetts General Hospital, Boston, 02114, Massachusetts, USA
113Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, 10024, New York, USA
114Department of Invertebrate Zoology, American Museum of Natural History, New York, 10024, New York, USA
115School of Life Sciences, Arizona State University, Tempe, 85287-4701, Arizona, USA
116Program in Biomedical Informatics, Stanford University, Stanford, 94305, California, USA
117Virginia Bioinformatics Institute, 1015 Life Sciences Drive, Blacksburg, 24061, Virginia, USA
118Division of Allergy and Clinical Immunology, School of Medicine, Johns Hopkins University, Baltimore, 21205, Maryland, USA
119Department of Ecology and Evolution, Stony Brook University, Stony Brook, 11794, New York, USA
120Centre for Health, Law and Emerging Technologies, University of Oxford, Oxford, OX3 7LF, UK
121Genetic Alliance, London, N1 3QP, UK
122Nuffield Department of Population Health, The Ethox Center, University of Oxford, Old Road Campus, OX3 7LF, UK
123Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland, USA
124University of Wisconsin Law School, Madison, 53706, Wisconsin, USA
125US National Institutes of Health, Center for Research on Genomics and Global Health, National Human Genome Research Institute, 12 South Drive, Bethesda, 20892, Maryland, USA
126Department of African & African American Studies, Duke University, Durham, North, 27708, Carolina, USA
127Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, 19104, Pennsylvania, USA
128Department of Psychiatry and Clinical Psychobiology & Institute for Brain, Cognition and Behavior (IR3C), University of Barcelona, Barcelona, 08035, Spain
129James D. Watson Institute of Genome Sciences, Hangzhou, 310008, China
130Cancer and Immunogenetics Laboratory, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
131Laboratory of Molecular Genetics, Institute of Biology, University of Antioquia, Medellín, Colombia
132Peking University Shenzhen Hospital, Shenzhen 518036, China
133Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
134Instituto de Biologia Molecular y Celular del Cancer, Centro de Investigacion del Cancer/IBMCC (CSIC-USAL), Institute of Biomedical Research of Salamanca (IBSAL) & National DNA Bank Carlos III, University of Salamanca, Salamanca, 37007, Spain
135Ponce Research Institute, Ponce Health Sciences University, Ponce, 00716, Puerto Rico
136Faculty of Medical Sciences, Cave Hill Campus, The University of the West Indies,
137Tropical Metabolism Research Unit, Tropical Medicine Research Institute, Mona Campus, The University of the West Indies,
138International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
139Xishuangbanna Health School, Xishuangbanna, 666100, China
140Irrua Specialist Teaching Hospital, Edo State, Nigeria
141Redeemers University, Ogun State, Nigeria
142Harvard T. H. Chan School of Public Health, Boston, 02115, Massachusetts, USA
143Center for Systems Biology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, 02138, Massachusetts, USA
144Medical Research Council Unit, The Gambia, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia
145NHLI, Imperial College London, Hammersmith Hospital, London, SW7 2AZ, UK
146Centre for Tropical Medicine, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
147Peter Doherty Institute of Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, 3000, VIC, Australia
148Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
149Tulane University Health Sciences Center, New Orleans, 70112, Louisiana, USA
150Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Peru
151Department of Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, Pennsylvania, USA
152Center for Non-Communicable Diseases, Karachi, Pakistan
153US National Institutes of Health, National Human Genome Research Institute, 5635 Fishers Lane, Bethesda, 20892, Maryland, USA
154Wellcome Trust, Gibbs Building, 215 Euston Road, London, NW1 2BE, UK

Tóm tắt

Từ khóa


Tài liệu tham khảo

The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010)

The 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012)

Voight, B. F. et al. The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits. PLoS Genet. 8, e1002793 (2012)

Trynka, G. et al. Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nature Genet. 43, 1193–1201 (2011)

Howie, B., Fuchsberger, C., Stephens, M., Marchini, J. & Abecasis, G. R. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nature Genet. 44, 955–959 (2012)

Xue, Y. et al. Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. Am. J. Hum. Genet. 91, 1022–1032 (2012)

Jung, H., Bleazard, T., Lee, J. & Hong, D. Systematic investigation of cancer-associated somatic point mutations in SNP databases. Nature Biotechnol. 31, 787–789 (2013)

Sudmant, P. H. et al. An integrated map of structural variation in 2,504 human genomes. Nature http://dx.doi.org/10.1038/nature15394 (this issue)

The Haplotype Reference Consortium (http://www.haplotype-reference-consortium.org/)

Simons, Y. B., Turchin, M. C., Pritchard, J. K. & Sella, G. The deleterious mutation load is insensitive to recent population history. Nature Genet. 46, 220–224 (2014)

Do, R. et al. No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans. Nature Genet. 47, 126–131 (2015)

Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009)

Mathieson, I. & McVean, G. Demography and the age of rare variants. PLoS Genet. 10, e1004528 (2014)

Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011)

Moltke, I. et al. A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes. Nature 512, 190–193 (2014)

Yi, X. et al. Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329, 75–78 (2010)

Lamason, R. L. et al. SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310, 1782–1786 (2005)

Eiberg, H. et al. Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression. Hum. Genet. 123, 177–187 (2008)

Mathias, R. A. et al. Adaptive evolution of the FADS gene cluster within Africa. PLoS ONE 7, e44926 (2012)

Hernandez, R. D. et al. Classic selective sweeps were rare in recent human evolution. Science 331, 920–924 (2011)

Chen, W. et al. Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration. Proc. Natl Acad. Sci. USA 107, 7401–7406 (2010)

Wakefield, J. Bayes factors for genome-wide association studies: comparison with P-values. Genet. Epidemiol. 33, 79–86 (2009)

Wakefield, J. Commentary: genome-wide significance thresholds via Bayes factors. Int. J. Epidemiol. 41, 286–291 (2012)

Sham, P. C. & Purcell, S. M. Statistical power and significance testing in large-scale genetic studies. Nature Rev. Genet. 15, 335–346 (2014)

Gold, B. et al. Variation in factor B (BF) and complement component 2 (C2) genes is associated with age-related macular degeneration. Nature Genet. 38, 458–462 (2006)

Klein, R. J. et al. Complement factor H polymorphism in age-related macular degeneration. Science 308, 385–389 (2005)

Rivera, A. et al. Hypothetical LOC387715 is a second major susceptibility gene for age-related macular degeneration, contributing independently of complement factor H to disease risk. Hum. Mol. Genet. 14, 3227–3236 (2005)

Yates, J. R. et al. Complement C3 variant and the risk of age-related macular degeneration. N. Engl. J. Med. 357, 553–561 (2007)

Maller, J. B. et al. Bayesian refinement of association signals for 14 loci in 3 common diseases. Nature Genet. 44, 1294–1301 (2012)

Fritsche, L. G. et al. Age-related macular degeneration is associated with an unstable ARMS2 (LOC387715) mRNA. Nature Genet. 40, 892–896 (2008)

The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012)

Stranger, B. E. et al. Patterns of cis regulatory variation in diverse human populations. PLoS Genet. 8, e1002639 (2012)

Chaisson, M. J. et al. Resolving the complexity of the human genome using single-molecule sequencing. Nature 517, 608–611 (2015)

Gudbjartsson, D. F. et al. Large-scale whole-genome sequencing of the Icelandic population. Nature Genet. 47, 435–444 (2015)

The UK10K Consortium. The UK10K project identifies rare variants in health and disease. Nature http://dx.doi.org/10.1038/nature14962 (2015)

Sidore, C. et al. Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers. Nature Genet. http://dx.doi.org/10.1038/ng.3368 (2015)

Delaneau, O. & Marchini, J. The 1000 Genomes Project Consortium. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nature Commun. 5, 3934 (2014)

O’Connell, J. et al. A general approach for haplotype phasing across the full spectrum of relatedness. PLoS Genet. 10, e1004234 (2014)

Menelaou, A. & Marchini, J. Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold. Bioinformatics 29, 84–91 (2013)