A global reference for human genetic variation.
Adam Auton,Gonçalo R. Abecasis,David Altshuler,Richard Durbin,David R. Bentley,Aravinda Chakravarti,Andrew G. Clark,Peter Donnelly,Evan E. Eichler,Paul Flicek,Stacey Gabriel,Richard A. Gibbs,Eric D. Green,Matthew E. Hurles,Bartha Maria Knoppers,Jan O. Korbel,Eric S. Lander,Charles Lee,Hans Lehrach,Elaine R. Mardis,Gabor T. Marth,Gil McVean,Deborah A. Nickerson,Jeanette Schmidt,Stephen T. Sherry,Jun Wang,Richard K. Wilson,Eric Boerwinkle,Harsha Doddapaneni,Yi Han,Viktoriya Korchina,Christie Kovar,Sandra L. Lee,Donna M. Muzny,Jeffrey G. Reid,Yiming Zhu,Yuqi Chang,Qiang Feng,Qiang Feng,Xiaodong Fang,Xiaodong Fang,Xiaosen Guo,Xiaosen Guo,Min Jian,Min Jian,Hui Jiang,Hui Jiang,Xin Jin,Tianming Lan,Guoqing Li,Jingxiang Li,Yingrui Li,Shengmao Liu,Xiao 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 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 Smith,Ian Streeter,Anja Thormann,Iliana Toneva,Brendan Vaughan,Xiangqun Zheng-Bradley,Russell J. Grocock,Sean Humphray,Terena James,Zoya Kingsbury,Ralf Sudbrak,M. Albrecht,Vyacheslav Amstislavskiy,Tatiana A. Borodina,Matthias Lienhard,Florian Mertes,Marc Sultan,Bernd Timmermann,Marie-Laure Yaspo,Lucinda Fulton,Victor Ananiev,Zinaida Belaia,Dimitriy Beloslyudtsev,Nathan Bouk,Chao Chen,Deanna M. Church,Robert M. 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 A. Schneider,Eugene Shekhtman,Karl Sirotkin,Douglas J. Slotta,Hua Zhang,Senduran Balasubramaniam,John Burton,Petr Danecek,Thomas M. Keane,Anja Kolb-Kokocinski,Shane A. McCarthy,James Stalker,Michael A. Quail,Christopher Davies,Jeremy Gollub,Teresa Webster,Brant Wong,Yiping Zhan,Christopher L. Campbell,Yu Kong,Anthony Marcketta,Fuli Yu,Lilian Antunes,Matthew N. Bainbridge,Aniko Sabo,Zhuoyi Huang,Lachlan J. M. Coin,Lin Fang,Lin Fang,Qibin Li,Zhenyu Li,Haoxiang Lin,Binghang Liu,Ruibang Luo,Haojing Shao,Haojing Shao,Yinlong Xie,Chen Ye,Chang Yu,Fan Zhang,Hancheng Zheng,Zhu Hongmei,Can Alkan,Elif Dal,Fatma Kahveci,Erik Garrison,Deniz Kural,Wan-Ping Lee,Wen Fung Leong,Michael Strömberg,Alistair Ward,Jiantao Wu,Mengyao Zhang,Mark J. Daly,Mark A. DePristo,Robert E. Handsaker,Robert E. Handsaker,Eric Banks,Gaurav Bhatia,Guillermo del Angel,Giulio Genovese,Heng Li,Seva Kashin,Seva Kashin,Steven A. McCarroll,Steven A. McCarroll,James Nemesh,Ryan Poplin,Seungtai Yoon,Jayon Lihm,Vladimir Makarov,Srikanth Gottipati,Alon Keinan,Juan L. Rodriguez-Flores,Tobias Rausch,Markus Hsi-Yang Fritz,Adrian M. Stütz,Kathryn Beal,Avik Datta,Javier Herrero,Graham R. S. Ritchie,Daniel R. Zerbino,Pardis C. Sabeti,Pardis C. Sabeti,Ilya Shlyakhter,Ilya Shlyakhter,Stephen F. Schaffner,Stephen F. Schaffner,Joseph J. Vitti,Joseph J. Vitti,David Neil Cooper,Edward V. Ball,Peter D. Stenson,Bret Barnes,Markus J. Bauer,R. Keira Cheetham,Anthony J. Cox,Michael A. Eberle,Scott Kahn,Lisa Murray,John F. 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 E. Larson,Kai Ye,Simon Gravel,Anand Swaroop,Emily Y. Chew,Tuuli Lappalainen,Yaniv Erlich,Melissa Gymrek,Melissa Gymrek,Thomas Willems,Jared T. Simpson,Mark D. Shriver,Jeffrey A. Rosenfeld,Carlos Bustamante,Stephen B. Montgomery,Francisco M. De La Vega,Jake K. Byrnes,Andrew Carroll,Marianne K. DeGorter,Phil Lacroute,Brian K. Maples,Alicia R. Martin,Andrés Moreno-Estrada,Andrés Moreno-Estrada,Suyash Shringarpure,Fouad Zakharia,Eran Halperin,Eran Halperin,Yael Baran,Eliza Cerveira,Jaeho Hwang,Ankit Malhotra,Dariusz Plewczynski,Kamen Radew,Mallory Romanovitch,Chengsheng Zhang,Fiona Hyland,David Craig,Alexis Christoforides,Nils Homer,Tyler Izatt,Ahmet Kurdoglu,Shripad 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,David Haussler,Sol Katzman,W. James Kent,Bryan Howie,Andres Ruiz-Linares,Emmanouil T. Dermitzakis,Emmanouil T. Dermitzakis,Scott E. Devine,Hyun Min Kang,Jeffrey M. Kidd,Thomas W. Blackwell,Sean Caron,Wei Chen,S. Emery,Lars G. Fritsche,Christian Fuchsberger,Goo Jun,Goo Jun,Bingshan Li,Robert H. Lyons,Chris Scheller,Carlo Sidore,Carlo Sidore,Carlo Sidore,Shiya Song,Elzbieta Sliwerska,Daniel Taliun,Adrian Tan,Ryan P. Welch,Mary Kate Wing,Xiaowei Zhan,Philip Awadalla,Philip Awadalla,Alan Hodgkinson,Yun Li,Xinghua Shi,Andrew Quitadamo,Gerton Lunter,Jonathan Marchini,Simon Myers,Claire Churchhouse,Olivier Delaneau,Olivier Delaneau,Anjali Gupta-Hinch,Warren W. Kretzschmar,Zamin Iqbal,Iain Mathieson,Androniki Menelaou,Androniki Menelaou,Andy Rimmer,Dionysia Kiara Xifara,Taras K. Oleksyk,Yunxin Fu,Xiaoming Liu,Momiao Xiong,Lynn B. Jorde,David J. 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,Vincenza Colonna,Luke Jostins,Klaudia Walter,Yali Xue,Mark Gerstein,Alexej Abyzov,Suganthi Balasubramanian,Jieming Chen,Declan Clarke,Yao Fu,Arif Harmanci,Mike Jin,Dong-Hoon Lee,Jeremy Liu,Xinmeng Jasmine Mu,Xinmeng Jasmine Mu,Jing Zhang,Yan Zhang,Christopher Hartl,Khalid Shakir,Jeremiah D. Degenhardt,Sascha Meiers,Benjamin Raeder,Francesco Paolo Casale,Oliver Stegle,Eric-Wubbo Lameijer,Ira M. Hall,Vineet Bafna,Jacob J. Michaelson,Eugene J. Gardner,Ryan E. Mills,Gargi Dayama,Ken Chen,Xian Fan,Zechen Chong,Tenghui Chen,Mark Chaisson,John Huddleston,Maika Malig,Bradley J. Nelson,Nicholas F. Parrish,Ben Blackburne,Sarah J. Lindsay,Zemin Ning,Yujun Zhang,Hugo Y. K. Lam,Cristina Sisu,Danny Challis,Uday S. Evani,James T. Lu,Uma Nagaswamy,Jin Yu,Wangshen Li,Lukas Habegger,Haiyuan Yu,Fiona Cunningham,Ian Dunham,Kasper Lage,Kasper Lage,Jakob Berg Jespersen,Jakob Berg Jespersen,Jakob Berg Jespersen,Heiko Horn,Heiko Horn,Donghoon Kim,Rob DeSalle,Apurva Narechania,Melissa A. Wilson Sayres,Fernando L. Mendez,G. David Poznik,Peter A. Underhill,David Mittelman,Ruby Banerjee,Maria Cerezo,Thomas W. Fitzgerald,Sandra Louzada,Andrea Massaia,Fengtang Yang,Divya Kalra,Walker Hale,Xu Dan,Kathleen C. Barnes,Christine Beiswanger,Hongyu Cai,Hongzhi Cao,Hongzhi Cao,Brenna M. Henn,Danielle Jones,Jane Kaye,Alastair Kent,Angeliki Kerasidou,Rasika A. Mathias,Pilar N. Ossorio,Michael Parker,Charles N. Rotimi,Charmaine D.M. Royal,Karla Sandoval,Yeyang Su,Zhongming Tian,Sarah A. Tishkoff,Marc Via,Yuhong Wang,Huanming Yang,Ling Yang,Jiayong Zhu,Walter F. Bodmer,Gabriel Bedoya,Zhiming Cai,Yang Gao,Jiayou Chu,Leena Peltonen,Andrés C. García-Montero,Alberto Orfao,Julie Dutil,Juan Carlos Martínez-Cruzado,R. Mathias,Anselm Hennis,Harold Watson,Colin A. McKenzie,Firdausi Qadri,Regina C. LaRocque,Xiaoyan Deng,Danny Asogun,Onikepe A. Folarin,Christian T. Happi,Omonwunmi Omoniwa,Matt Stremlau,Matt Stremlau,Ridhi Tariyal,Ridhi Tariyal,M Jallow,M Jallow,Fatoumatta Sisay Joof,Fatoumatta Sisay Joof,Tumani Corrah,Tumani Corrah,Kirk A. Rockett,Kirk A. Rockett,Dominic P. Kwiatkowski,Dominic P. Kwiatkowski,Jaspal S. Kooner,Tran Tinh Hien,Sarah J. Dunstan,Sarah J. Dunstan,Nguyen ThuyHang,Richard Fonnie,Robert F. Garry,Lansana Kanneh,Lina M. Moses,John S. Schieffelin,Donald S. Grant,Carla Gallo,Giovanni Poletti,Danish Saleheen,Asif Rasheed,Lisa D. Brooks,Adam Felsenfeld,Jean E. McEwen,Yekaterina Vaydylevich,Audrey Duncanson,Michael Dunn,Jeffery A. Schloss +517 more
TLDR
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, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.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.read more
Citations
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A reference panel of 64,976 haplotypes for genotype imputation
Shane A. McCarthy,Sayantan Das,Warren W. Kretzschmar,Olivier Delaneau,Andrew R. Wood,Alexander Teumer,Hyun Min Kang,Christian Fuchsberger,Petr Danecek,Kevin Sharp,Yang Luo,Carlo Sidorel,Alan Kwong,Nicholas J. Timpson,Seppo Koskinen,Scott I. Vrieze,Laura J. Scott,He Zhang,Anubha Mahajan,Jan H. Veldink,Ulrike Peters,Carlos N. Pato,Cornelia M. van Duijn,Christopher E. Gillies,Ilaria Gandin,Massimo Mezzavilla,Arthur Gilly,Massimiliano Cocca,Michela Traglia,Andrea Angius,Jeffrey C. Barrett,D.I. Boomsma,Kari Branham,Gerome Breen,Chad M. Brummett,Fabio Busonero,Harry Campbell,Andrew T. Chan,Sai Che,Emily Y. Chew,Francis S. Collins,Laura J Corbin,George Davey Smith,George Dedoussis,Marcus Dörr,Aliki-Eleni Farmaki,Luigi Ferrucci,Lukas Forer,Ross M. Fraser,Stacey Gabriel,Shawn Levy,Leif Groop,Tabitha A. Harrison,Andrew T. Hattersley,Oddgeir L. Holmen,Kristian Hveem,Matthias Kretzler,James Lee,Matt McGue,Thomas Meitinger,David Melzer,Josine L. Min,Karen L. Mohlke,John B. Vincent,Matthias Nauck,Deborah A. Nickerson,Aarno Palotie,Michele T. Pato,Nicola Pirastu,Melvin G. McInnis,J. Brent Richards,Cinzia Sala,Veikko Salomaa,David Schlessinger,Sebastian Schoenherr,P. Eline Slagboom,Kerrin S. Small,Tim D. Spector,Dwight Stambolian,Marcus A. Tuke,Jaakko Tuomilehto,Leonard H. van den Berg,Wouter van Rheenen,Uwe Völker,Cisca Wijmenga,Daniela Toniolo,Eleftheria Zeggini,Paolo Gasparini,Matthew G. Sampson,James F. Wilson,Timothy M. Frayling,Paul I.W. de Bakker,Morris A. Swertz,Steven A. McCarroll,Charles Kooperberg,Annelot M. Dekker,David Altshuler,Cristen J. Willer,William G. Iacono,Samuli Ripatti,Nicole Soranzo,Klaudia Walter,Anand Swaroop,Francesco Cucca,Carl A. Anderson,Richard M. Myers,Michael Boehnke,Mark I. McCarthy,Richard Durbin,Gonçalo R. Abecasis,Jonathan Marchini +110 more
TL;DR: In this article, a reference panel of 64,976 human haplotypes at 39,235,157 SNPs constructed using whole-genome sequence data from 20 studies of predominantly European ancestry is presented.
Journal ArticleDOI
Reference-based phasing using the Haplotype Reference Consortium panel.
Po-Ru Loh,Po-Ru Loh,Petr Danecek,Pier Francesco Palamara,Pier Francesco Palamara,Christian Fuchsberger,Christian Fuchsberger,Yakir A. Reshef,Hilary K. Finucane,Hilary K. Finucane,Sebastian Schoenherr,Lukas Forer,Shane A. McCarthy,Gonçalo R. Abecasis,Richard Durbin,Alkes L. Price,Alkes L. Price +16 more
TL;DR: A new phasing algorithm, Eagle2, is introduced that attains high accuracy across a broad range of cohort sizes by efficiently leveraging information from large external reference panels (such as the Haplotype Reference Consortium; HRC) using a new data structure based on the positional Burrows-Wheeler transform.
Journal ArticleDOI
Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction.
TL;DR: The 3DEpiLoop algorithm predicts three-dimensional chromatin looping interactions within topologically associating domains (TADs) from one-dimensional epigenomics and transcription factor profiles using the statistical learning.
Journal ArticleDOI
Meta-analysis of genome-wide association studies for height and body mass index in ∼700000 individuals of European ancestry
Loic Yengo,Julia Sidorenko,Julia Sidorenko,Kathryn E. Kemper,Zhili Zheng,Andrew R. Wood,Michael N. Weedon,Timothy M. Frayling,Joel N. Hirschhorn,Jian Yang,Peter M. Visscher +10 more
TL;DR: This study demonstrates that, as previously predicted, increasing GWAS sample sizes continues to deliver, by the discovery of new loci, increasing prediction accuracy and providing additional data to achieve deeper insight into complex trait biology.
Journal ArticleDOI
Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps.
Anubha Mahajan,Daniel Taliun,Matthias Thurner,Neil R. Robertson,Jason M. Torres,N. William Rayner,N. William Rayner,Anthony Payne,Valgerdur Steinthorsdottir,Robert A. Scott,Niels Grarup,James P. Cook,Ellen M. Schmidt,Matthias Wuttke,Chloé Sarnowski,Reedik Mägi,Jana Nano,Christian Gieger,Stella Trompet,Cécile Lecoeur,Michael Preuss,Bram P. Prins,Xiuqing Guo,Lawrence F. Bielak,Jennifer E. Below,Donald W. Bowden,John C. Chambers,Young-Jin Kim,Maggie C.Y. Ng,Lauren E. Petty,Xueling Sim,Weihua Zhang,Weihua Zhang,Amanda J. Bennett,Jette Bork-Jensen,Chad M. Brummett,Mickaël Canouil,Kai-Uwe Ec Kardt,Krista Fischer,Sharon L.R. Kardia,Florian Kronenberg,Kristi Läll,Ching-Ti Liu,Adam E. Locke,Jian'an Luan,Ioanna Ntalla,Vibe Nylander,Sebastian Schönherr,Claudia Schurmann,Loic Yengo,Erwin P. Bottinger,Ivan Brandslund,Cramer Christensen,George Dedoussis,Jose C. Florez,Ian Ford,Oscar H. Franco,Timothy M. Frayling,Vilmantas Giedraitis,Sophie Hackinger,Andrew T. Hattersley,Christian Herder,M. Arfan Ikram,Martin Ingelsson,Marit E. Jørgensen,Marit E. Jørgensen,Torben Jørgensen,Torben Jørgensen,Jennifer Kriebel,Johanna Kuusisto,Symen Ligthart,Cecilia M. Lindgren,Cecilia M. Lindgren,Allan Linneberg,Allan Linneberg,Valeriya Lyssenko,Valeriya Lyssenko,Vasiliki Mamakou,Thomas Meitinger,Karen L. Mohlke,Andrew D. Morris,Andrew D. Morris,Girish N. Nadkarni,James S. Pankow,Annette Peters,Naveed Sattar,Alena Stančáková,Konstantin Strauch,Kent D. Taylor,Barbara Thorand,Gudmar Thorleifsson,Unnur Thorsteinsdottir,Unnur Thorsteinsdottir,Jaakko Tuomilehto,Daniel R. Witte,Josée Dupuis,Patricia A. Peyser,Eleftheria Zeggini,Ruth J. F. Loos,Philippe Froguel,Philippe Froguel,Erik Ingelsson,Erik Ingelsson,Lars Lind,Leif Groop,Leif Groop,Markku Laakso,Francis S. Collins,J. Wouter Jukema,Colin N. A. Palmer,Harald Grallert,Andres Metspalu,Abbas Dehghan,Abbas Dehghan,Anna Köttgen,Gonçalo R. Abecasis,James B. Meigs,Jerome I. Rotter,Jonathan Marchini,Oluf Pedersen,Torben Hansen,Torben Hansen,Claudia Langenberg,Nicholas J. Wareham,Kari Stefansson,Kari Stefansson,Anna L. Gloyn,Andrew P. Morris,Andrew P. Morris,Andrew P. Morris,Michael Boehnke,Mark I. McCarthy +131 more
TL;DR: Combining 32 genome-wide association studies with high-density imputation provides a comprehensive view of the genetic contribution to type 2 diabetes in individuals of European ancestry with respect to locus discovery, causal-variant resolution, and mechanistic insight.
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