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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Journal ArticleDOI
Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
Biola M. Javierre,Oliver S. Burren,Steven P. Wilder,Roman Kreuzhuber,Steven M. Hill,Sven Sewitz,Jonathan Cairns,Steven W. Wingett,Csilla Várnai,Michiel J. Thiecke,Frances Burden,Samantha Farrow,Antony J. Cutler,Karola Rehnström,Kate Downes,Luigi Grassi,Myrto Kostadima,Paula Freire-Pritchett,Fan Wang,Hendrik G. Stunnenberg,John A. Todd,Daniel R. Zerbino,Oliver Stegle,Willem H. Ouwehand,Mattia Frontini,Chris Wallace,Mikhail Spivakov,Peter Fraser +27 more
TL;DR: This work uses promoter capture Hi-C to identify interacting regions of 31,253 promoters in 17 human primary hematopoietic cell types and shows that promoter interactions are highly cell type specific and enriched for links between active promoters and epigenetically marked enhancers.
Journal ArticleDOI
Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling
Ruth Pidsley,Ruth Pidsley,Elena Zotenko,Elena Zotenko,Tim J Peters,Mitchell G. Lawrence,Gail P. Risbridger,Peter L. Molloy,Susan Van Djik,Beverly S. Muhlhausler,Clare Stirzaker,Clare Stirzaker,Susan J. Clark,Susan J. Clark +13 more
TL;DR: The EPIC array is a significant improvement over the HM450 array, with increased genome coverage of regulatory regions and high reproducibility and reliability, providing a valuable tool for high-throughput human methylome analyses from diverse clinical samples.
Journal ArticleDOI
Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease
Katrina M. de Lange,Loukas Moutsianas,James Lee,Christopher A. Lamb,Yang Luo,Yang Luo,Yang Luo,Nicholas A. Kennedy,Luke Jostins,Luke Jostins,Daniel L. Rice,Javier Gutierrez-Achury,Sun-Gou Ji,Graham A. Heap,Elaine R. Nimmo,Cathryn Edwards,Paul Henderson,Paul Henderson,Craig Mowat,Jeremy D. Sanderson,Jack Satsangi,Alison Simmons,Alison Simmons,David C. Wilson,David C. Wilson,Mark Tremelling,Ailsa Hart,Christopher G. Mathew,Christopher G. Mathew,William G. Newman,William G. Newman,Miles Parkes,Charlie W. Lees,Holm H. Uhlig,Christopher J. Hawkey,Natalie J. Prescott,Tariq Ahmad,John C. Mansfield,Carl A. Anderson,Jeffrey C. Barrett +39 more
TL;DR: This work identified 25 new susceptibility loci, 3 of which contain integrin genes that encode proteins in pathways that have been identified as important therapeutic targets in inflammatory bowel disease and identified 3 associated variants that are correlated with expression changes in response to immune stimulus at two of these genes.
Journal ArticleDOI
Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program.
Daniel Taliun,Daniel N. Harris,Michael D. Kessler,Jedidiah Carlson,Jedidiah Carlson,Zachary A. Szpiech,Raul Torres,Sarah A Gagliano Taliun,André Corvelo,Stephanie M. Gogarten,Hyun Min Kang,Achilleas N. Pitsillides,Jonathon LeFaive,Seung-been Lee,Xiaowen Tian,Brian L. Browning,Sayantan Das,Anne-Katrin Emde,Wayne E. Clarke,Douglas Loesch,Amol C. Shetty,Thomas W. Blackwell,Albert V. Smith,Quenna Wong,Xiaoming Liu,Matthew P. Conomos,Dean Bobo,François Aguet,Christine M. Albert,Alvaro Alonso,Kristin G. Ardlie,Dan E. Arking,Stella Aslibekyan,Paul L. Auer,John Barnard,R. Graham Barr,Lucas Barwick,Lewis C. Becker,Rebecca L. Beer,Emelia J. Benjamin,Lawrence F. Bielak,John Blangero,Michael Boehnke,Donald W. Bowden,Jennifer A. Brody,Esteban G. Burchard,Brian E. Cade,Brian E. Cade,James F. Casella,Brandon Chalazan,Daniel I. Chasman,Daniel I. Chasman,Yii-Der Ida Chen,Michael H. Cho,Seung Hoan Choi,Mina K. Chung,Mina K. Chung,Mina K. Chung,Clary B. Clish,Adolfo Correa,Joanne E. Curran,Brian Custer,Dawood Darbar,Michelle Daya,Mariza de Andrade,Dawn L. DeMeo,Susan K. Dutcher,Patrick T. Ellinor,Leslie S. Emery,Celeste Eng,Diane Fatkin,Diane Fatkin,Diane Fatkin,Tasha E. Fingerlin,Lukas Forer,Myriam Fornage,Nora Franceschini,Christian Fuchsberger,Stephanie M. Fullerton,Soren Germer,Mark T. Gladwin,Daniel J. Gottlieb,Daniel J. Gottlieb,Xiuqing Guo,Michael E. Hall,Jiang He,Nancy L. Heard-Costa,Susan R. Heckbert,Marguerite R. Irvin,Jill M. Johnsen,Andrew D. Johnson,Robert C. Kaplan,Sharon L.R. Kardia,Tanika N. Kelly,Shannon Kelly,Eimear E. Kenny,Douglas P. Kiel,Robert Klemmer,Barbara A. Konkle,Charles Kooperberg,Anna Köttgen,Anna Köttgen,Leslie A. Lange,Jessica Lasky-Su,Daniel Levy,Daniel Levy,Xihong Lin,Keng-Han Lin,Chunyu Liu,Ruth J. F. Loos,Lori Garman,Robert E. Gerszten,Steven A. Lubitz,Kathryn L. Lunetta,Angel C.Y. Mak,Ani Manichaikul,Alisa K. Manning,Alisa K. Manning,Rasika A. Mathias,David D. McManus,Stephen T. McGarvey,James B. Meigs,Deborah A. Meyers,Julie L. Mikulla,Mollie A. Minear,Braxton D. Mitchell,Braxton D. Mitchell,Sanghamitra Mohanty,May E. Montasser,Courtney G. Montgomery,Alanna C. Morrison,Joanne M. Murabito,Andrea Natale,Pradeep Natarajan,Sarah C. Nelson,Kari E. North,Jeffrey R. O'Connell,Nicholette D. Palmer,Nathan Pankratz,Gina M. Peloso,Patricia A. Peyser,Jacob Pleiness,Wendy S. Post,Bruce M. Psaty,D. C. Rao,Susan Redline,Susan Redline,Alexander P. Reiner,Alexander P. Reiner,Dan M. Roden,Jerome I. Rotter,Ingo Ruczinski,Chloé Sarnowski,Sebastian Schoenherr,David A. Schwartz,Jeong-Sun Seo,Sudha Seshadri,Vivien A. Sheehan,Wayne Huey-Herng Sheu,M. Benjamin Shoemaker,Nicholas L. Smith,Nicholas L. Smith,Nicholas L. Smith,Jennifer A. Smith,Nona Sotoodehnia,Adrienne M. Stilp,Weihong Tang,Kent D. Taylor,Marilyn J. Telen,Timothy A. Thornton,Russell P. Tracy,David Van Den Berg,Ramachandran S. Vasan,Karine A. Viaud-Martinez,Scott I. Vrieze,Daniel E. Weeks,Bruce S. Weir,Scott T. Weiss,Lu-Chen Weng,Cristen J. Willer,Yingze Zhang,Xutong Zhao,Donna K. Arnett,Allison E. Ashley-Koch,Kathleen C. Barnes,Eric Boerwinkle,Eric Boerwinkle,Stacey Gabriel,Richard A. Gibbs,Kenneth Rice,Stephen S. Rich,Edwin K. Silverman,Pankaj Qasba,Weiniu Gan,George J. Papanicolaou,Deborah A. Nickerson,Sharon R. Browning,Michael C. Zody,Sebastian Zöllner,James G. Wilson,L. Adrienne Cupples,Cathy C. Laurie,Cashell E. Jaquish,Ryan D. Hernandez,Timothy D. O’Connor,Gonçalo R. Abecasis +205 more
TL;DR: The Trans-Omics for Precision Medicine (TOPMed) project as discussed by the authors aims to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases.
Journal ArticleDOI
A universal SNP and small-indel variant caller using deep neural networks.
Ryan Poplin,Pi-Chuan Chang,David Alexander,Scott Schwartz,Thomas Colthurst,Alexander Ku,Dan Newburger,Jojo Dijamco,Nam Nguyen,Pegah T Afshar,Sam S Gross,Lizzie Dorfman,Cory Y. McLean,Mark A. DePristo +13 more
TL;DR: A deep convolutional neural network can call genetic variation in aligned next-generation sequencing read data by learning statistical relationships between images of read pileups around putative variant and true genotype calls, outperforms existing state-of-the-art tools.
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