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
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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
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Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorder
Ditte Demontis,Ditte Demontis,Raymond K. Walters,Raymond K. Walters,Joanna Martin,Joanna Martin,Joanna Martin,Manuel Mattheisen,Thomas Damm Als,Thomas Damm Als,Esben Agerbo,Esben Agerbo,Gisli Baldursson,Rich Belliveau,Jonas Bybjerg-Grauholm,Jonas Bybjerg-Grauholm,Marie Bækvad-Hansen,Marie Bækvad-Hansen,Felecia Cerrato,Kimberly Chambert,Claire Churchhouse,Claire Churchhouse,Ashley Dumont,Nicholas Eriksson,Michael J. Gandal,Jacqueline I. Goldstein,Jacqueline I. Goldstein,Katrina L. Grasby,Jakob Grove,Olafur O Gudmundsson,Olafur O Gudmundsson,Christine Søholm Hansen,Christine Søholm Hansen,Christine Søholm Hansen,Mads E. Hauberg,Mads E. Hauberg,Mads V. Hollegaard,Mads V. Hollegaard,Daniel P. Howrigan,Daniel P. Howrigan,Hailiang Huang,Hailiang Huang,Julian Maller,Alicia R. Martin,Alicia R. Martin,Nicholas G. Martin,Jennifer L. Moran,Jonatan Pallesen,Jonatan Pallesen,Duncan S. Palmer,Duncan S. Palmer,Carsten Bøcker Pedersen,Carsten Bøcker Pedersen,Marianne Giørtz Pedersen,Marianne Giørtz Pedersen,Timothy Poterba,Timothy Poterba,Jesper Buchhave Poulsen,Jesper Buchhave Poulsen,Stephan Ripke,Stephan Ripke,Stephan Ripke,Elise B. Robinson,F. Kyle Satterstrom,F. Kyle Satterstrom,Hreinn Stefansson,Christine Stevens,Patrick Turley,Patrick Turley,G. Bragi Walters,G. Bragi Walters,Hyejung Won,Hyejung Won,Margaret J. Wright,Ole A. Andreassen,Philip Asherson,Christie L. Burton,Dorret I. Boomsma,Bru Cormand,Søren Dalsgaard,Barbara Franke,Joel Gelernter,Joel Gelernter,Daniel H. Geschwind,Daniel H. Geschwind,Hakon Hakonarson,Jan Haavik,Jan Haavik,Henry R. Kranzler,Henry R. Kranzler,Jonna Kuntsi,Kate Langley,Klaus-Peter Lesch,Klaus-Peter Lesch,Klaus-Peter Lesch,Christel M. Middeldorp,Christel M. Middeldorp,Andreas Reif,Luis Augusto Rohde,Panos Roussos,Russell Schachar,Pamela Sklar,Edmund J.S. Sonuga-Barke,Patrick F. Sullivan,Patrick F. Sullivan,Anita Thapar,Joyce Y. Tung,Irwin D. Waldman,Sarah E. Medland,Kari Stefansson,Kari Stefansson,Merete Nordentoft,Merete Nordentoft,David M. Hougaard,David M. Hougaard,Thomas Werge,Thomas Werge,Thomas Werge,Ole Mors,Ole Mors,Preben Bo Mortensen,Mark J. Daly,Stephen V. Faraone,Anders D. Børglum,Anders D. Børglum,Benjamin M. Neale,Benjamin M. Neale +126 more
TL;DR: A genome-wide association meta-analysis of 20,183 individuals diagnosed with ADHD and 35,191 controls identifies variants surpassing genome- wide significance in 12 independent loci and implicates neurodevelopmental pathways and conserved regions of the genome as being involved in underlying ADHD biology.
Journal ArticleDOI
Nanopore sequencing and assembly of a human genome with ultra-long reads
Miten Jain,Sergey Koren,Karen H. Miga,Josh Quick,Arthur C Rand,Thomas A Sasani,John R. Tyson,Andrew D Beggs,Alexander T. Dilthey,Ian T. Fiddes,Sunir Malla,Hannah Marriott,Tom Nieto,Justin O'Grady,Hugh E. Olsen,Brent S. Pedersen,Arang Rhie,Hollian Richardson,Aaron R. Quinlan,Terrance P. Snutch,Louise Tee,Benedict Paten,Adam M. Phillippy,Jared T. Simpson,Jared T. Simpson,Nicholas J. Loman,Matthew Loose +26 more
TL;DR: Ultra-long reads enabled assembly and phasing of the 4-Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length, and closure of gaps in the reference human genome assembly GRCh38.
Journal ArticleDOI
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.
Jason Lloyd-Price,Jason Lloyd-Price,Cesar Arze,Ashwin N. Ananthakrishnan,Melanie Schirmer,Melanie Schirmer,Julian Avila-Pacheco,Tiffany W. Poon,Elizabeth Andrews,Nadim J. Ajami,Kevin S. Bonham,Kevin S. Bonham,Colin J. Brislawn,David Casero,Holly Courtney,Antonio Gonzalez,Thomas G. Graeber,A. Brantley Hall,Kathleen Lake,Carol J. Landers,Himel Mallick,Himel Mallick,Damian R. Plichta,Mahadev Prasad,Gholamali Rahnavard,Gholamali Rahnavard,Jenny S. Sauk,Dmitry Shungin,Dmitry Shungin,Yoshiki Vázquez-Baeza,Richard A. White,Jonathan Braun,Lee A. Denson,Lee A. Denson,Janet K. Jansson,Rob Knight,Subra Kugathasan,Dermot P.B. McGovern,Joseph F. Petrosino,Thaddeus S. Stappenbeck,Harland S. Winter,Clary B. Clish,Eric A. Franzosa,Hera Vlamakis,Ramnik J. Xavier,Ramnik J. Xavier,Ramnik J. Xavier,Curtis Huttenhower,Curtis Huttenhower +48 more
TL;DR: It is demonstrated that periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts, and integrative analysis identified microbial, biochemical, and host factors central to this dysregulation.
Journal ArticleDOI
Identification of common genetic risk variants for autism spectrum disorder
TL;DR: A genome-wide association meta-analysis of 18,381 austim spectrum disorder cases and 27,969 controls identifies five risk loci and the authors find quantitative and qualitative polygenic heterogeneity across ASD subtypes.
Journal ArticleDOI
Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions
David M. Howard,Mark Adams,Toni-Kim Clarke,Jonathan D. Hafferty,Jude Gibson,Masoud Shirali,Jonathan R. I. Coleman,Jonathan R. I. Coleman,Saskia P. Hagenaars,Saskia P. Hagenaars,Joey Ward,Eleanor M. Wigmore,Clara Alloza,Xueyi Shen,Miruna C. Barbu,Eileen Y. Xu,Heather C. Whalley,Riccardo E. Marioni,David J. Porteous,Gail Davies,Ian J. Deary,Gibran Hemani,Klaus Berger,Henning Teismann,Rajesh Rawal,Volker Arolt,Bernhard T. Baune,Udo Dannlowski,Katharina Domschke,Chao Tian,David A. Hinds,Maciej Trzaskowski,Enda M. Byrne,Stephan Ripke,Stephan Ripke,Stephan Ripke,Daniel J. Smith,Patrick F. Sullivan,Patrick F. Sullivan,Naomi R. Wray,Gerome Breen,Gerome Breen,Cathryn M. Lewis,Cathryn M. Lewis,Andrew M. McIntosh,Andrew M. McIntosh +45 more
TL;DR: A genetic meta-analysis of depression found 269 associated genes that highlight several potential drug repositioning opportunities, and relationships with depression were found for neuroticism and smoking.
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