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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Posted ContentDOI
Pan-cancer analysis of whole genomes
Peter J. Campbell,Peter J. Campbell,Gaddy Getz,Joshua M. Stuart,Jan O. Korbel,Lincoln Stein,Lincoln Stein +6 more
TL;DR: The integrative analysis of more than 2,600 whole cancer genomes and their matching normal tissues across 39 distinct tumour types represents the most comprehensive look at cancer whole genomes to date.
Journal ArticleDOI
Tutorial: a guide to performing polygenic risk score analyses.
TL;DR: This review presents comprehensive guidelines for performing and evaluating PRS analyses, and outlines standard quality control steps, different methods for the calculation of PRSs, and provides an introductory online tutorial that takes users through quality control and visualization steps.
Journal ArticleDOI
Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits.
Evangelos Evangelou,Evangelos Evangelou,Helen R. Warren,Helen R. Warren,David Mosen-Ansorena,Borbala Mifsud,Raha Pazoki,He Gao,Georgios Ntritsos,Niki Dimou,Claudia P. Cabrera,Claudia P. Cabrera,Ibrahim Karaman,Fu Liang Ng,Marina Evangelou,K. Witkowska,Evan Tzanis,Jacklyn N. Hellwege,Ayush Giri,Digna R. Velez Edwards,Yan V. Sun,Kelly Cho,Kelly Cho,J. Michael Gaziano,J. Michael Gaziano,Peter W.F. Wilson,Philip S. Tsao,Csaba P. Kovesdy,Tõnu Esko,Tõnu Esko,Reedik Mägi,Lili Milani,Peter Almgren,Thibaud Boutin,Stéphanie Debette,Jun Ding,Franco Giulianini,Elizabeth G. Holliday,Anne U. Jackson,Ruifang Li-Gao,Wei-Yu Lin,Jian'an Luan,Massimo Mangino,Massimo Mangino,Christopher Oldmeadow,Bram P. Prins,Yong Qian,Muralidharan Sargurupremraj,Nabi Shah,Nabi Shah,Praveen Surendran,Sébastien Thériault,Sébastien Thériault,Niek Verweij,Niek Verweij,Niek Verweij,Sara M. Willems,Jing Hua Zhao,Philippe Amouyel,John M. C. Connell,Renée de Mutsert,Alex S. F. Doney,Martin Farrall,Martin Farrall,Cristina Menni,Andrew D. Morris,Raymond Noordam,Guillaume Paré,Neil Poulter,Denis C. Shields,Alice Stanton,Simon Thom,Gonçalo R. Abecasis,Najaf Amin,Dan E. Arking,Kristin L. Ayers,Kristin L. Ayers,Caterina Barbieri,Chiara Batini,Joshua C. Bis,Tineka Blake,Murielle Bochud,Michael Boehnke,Eric Boerwinkle,Dorret I. Boomsma,Erwin P. Bottinger,Peter S. Braund,Peter S. Braund,Marco Brumat,Archie Campbell,Harry Campbell,Aravinda Chakravarti,John C. Chambers,Ganesh Chauhan,Marina Ciullo,Massimiliano Cocca,Francis S. Collins,Heather J. Cordell,Gail Davies,Martin H. de Borst,Eco J. C. de Geus,Ian J. Deary,Joris Deelen,Fabiola Del Greco M,Cumhur Y Demirkale,Marcus Dörr,Georg Ehret,Georg Ehret,Roberto Elosua,Stefan Enroth,A. Mesut Erzurumluoglu,Teresa Ferreira,Mattias Frånberg,Mattias Frånberg,Oscar H. Franco,Ilaria Gandin,Paolo Gasparini,Vilmantas Giedraitis,Christian Gieger,Giorgia Girotto,Anuj Goel,Anuj Goel,Alan J. Gow,Alan J. Gow,Vilmundur Gudnason,Xiuqing Guo,Ulf Gyllensten,Anders Hamsten,Tamara B. Harris,Sarah E. Harris,Catharina A. Hartman,Aki S. Havulinna,Aki S. Havulinna,Andrew A. Hicks,Edith Hofer,Albert Hofman,Albert Hofman,Jouke-Jan Hottenga,Jennifer E. Huffman,Jennifer E. Huffman,Shih-Jen Hwang,Erik Ingelsson,Erik Ingelsson,Alan James,Alan James,Rick Jansen,Marjo-Riitta Järvelin,Roby Joehanes,Åsa Johansson,Andrew D. Johnson,Peter K. Joshi,Pekka Jousilahti,J. Wouter Jukema,Antti Jula,Mika Kähönen,Sekar Kathiresan,Sekar Kathiresan,Sekar Kathiresan,Bernard Keavney,Bernard Keavney,Kay-Tee Khaw,Paul Knekt,Joanne Knight,Ivana Kolcic,Jaspal S. Kooner,Seppo Koskinen,Kati Kristiansson,Zoltán Kutalik,Zoltán Kutalik,Maris Laan,Marty Larson,Lenore J. Launer,Benjamin Lehne,Terho Lehtimäki,David C. Liewald,Li Lin,Lars Lind,Cecilia M. Lindgren,Cecilia M. Lindgren,Cecilia M. Lindgren,Yongmei Liu,Ruth J. F. Loos,Ruth J. F. Loos,Lorna M. Lopez,Lorna M. Lopez,Lorna M. Lopez,Yingchang Lu,Leo-Pekka Lyytikäinen,Anubha Mahajan,Chrysovalanto Mamasoula,Jaume Marrugat,Jonathan Marten,Yuri Milaneschi,Anna Morgan,Andrew P. Morris,Andrew P. Morris,Alanna C. Morrison,Peter J. Munson,Mike A. Nalls,Priyanka Nandakumar,Christopher P. Nelson,Christopher P. Nelson,Teemu J. Niiranen,Teemu J. Niiranen,Ilja M. Nolte,Teresa Nutile,Albertine J. Oldehinkel,Ben A. Oostra,Paul F. O'Reilly,Elin Org,Sandosh Padmanabhan,Sandosh Padmanabhan,Walter Palmas,Aarno Palotie,Aarno Palotie,Aarno Palotie,Alison Pattie,Brenda W.J.H. Penninx,Markus Perola,Markus Perola,Markus Perola,Annette Peters,Ozren Polasek,Peter P. Pramstaller,Quang Tri Nguyen,Olli T. Raitakari,Olli T. Raitakari,Meixia Ren,Rainer Rettig,Kenneth Rice,Paul M. Ridker,Paul M. Ridker,Janina S. Ried,Harriëtte Riese,Samuli Ripatti,Antonietta Robino,Lynda M. Rose,Jerome I. Rotter,Igor Rudan,Daniela Ruggiero,Yasaman Saba,Cinzia Sala,Veikko Salomaa,Nilesh J. Samani,Nilesh J. Samani,Antti-Pekka Sarin,Reinhold Schmidt,Helena Schmidt,Nick Shrine,David S. Siscovick,Albert V. Smith,Harold Snieder,Siim Sõber,Rossella Sorice,John M. Starr,David J. Stott,David P. Strachan,Rona J. Strawbridge,Johan Sundström,Morris A. Swertz,Kent D. Taylor,Alexander Teumer,Martin D. Tobin,Maciej Tomaszewski,Maciej Tomaszewski,Daniela Toniolo,Michela Traglia,Stella Trompet,Jaakko Tuomilehto,Christophe Tzourio,André G. Uitterlinden,Ahmad Vaez,Ahmad Vaez,Peter J. van der Most,Cornelia M. van Duijn,Anne-Claire Vergnaud,Germaine C. Verwoert,Veronique Vitart,Uwe Völker,Peter Vollenweider,Dragana Vuckovic,Dragana Vuckovic,Hugh Watkins,Hugh Watkins,Sarah H. Wild,Gonneke Willemsen,James F. Wilson,James F. Wilson,Alan F. Wright,Jie Yao,Tatijana Zemunik,Weihua Zhang,Weihua Zhang,John Attia,Adam S. Butterworth,Adam S. Butterworth,Daniel I. Chasman,Daniel I. Chasman,David Conen,David Conen,Francesco Cucca,Francesco Cucca,John Danesh,John Danesh,Caroline Hayward,Joanna M. M. Howson,Markku Laakso,Edward G. Lakatta,Claudia Langenberg,Olle Melander,Dennis O. Mook-Kanamori,Colin N. A. Palmer,Lorenz Risch,Robert A. Scott,Rodney J. Scott,Peter S. Sever,Tim D. Spector,Pim van der Harst,Nicholas J. Wareham,Eleftheria Zeggini,Daniel Levy,Patricia B. Munroe,Patricia B. Munroe,Christopher Newton-Cheh,Christopher Newton-Cheh,Morris J. Brown,Morris J. Brown,Andres Metspalu,Adriana M. Hung,Christopher J. O'Donnell,Todd L. Edwards,Bruce M. Psaty,Bruce M. Psaty,Ioanna Tzoulaki,Ioanna Tzoulaki,Michael R. Barnes,Michael R. Barnes,Louise V. Wain,Louise V. Wain,Paul Elliott,Mark J. Caulfield,Mark J. Caulfield +341 more
TL;DR: In this article, the largest genetic association study of blood pressure traits (systolic, diastolic and pulse pressure) to date in over 1 million people of European ancestry was conducted.
Journal ArticleDOI
Genome evolution across 1,011 Saccharomyces cerevisiae isolates
Jackson Peter,Matteo De Chiara,Anne Friedrich,Jia-Xing Yue,David Pflieger,Anders Bergström,Anastasie Sigwalt,Benjamin Barré,Kelle C. Freel,Agnès Llored,Corinne Cruaud,Karine Labadie,Jean-Marc Aury,Benjamin Istace,Kevin Lebrigand,Pascal Barbry,Stefan Engelen,Arnaud Lemainque,Patrick Wincker,Patrick Wincker,Gianni Liti,Joseph Schacherer +21 more
TL;DR: Whole-genome sequencing and phenotyping of 1,011 natural isolates of the yeast Saccharomyces cerevisiae reveal its evolutionary history, including a single out-of-China origin and multiple domestication events, and provides a framework for genotype–phenotype studies in this model organism.
Journal ArticleDOI
The complete sequence of a human genome
Sergey Koren,Sergey Nurk,Mikko Rautiainen,B Ren,Weijun Zhu,Richard Lawless,Саидмуродов Мамур Таирович +6 more
TL;DR: The T2T-CHM13-T2T Consortium presented a complete 3.055 billion-base pair sequence of a human genome, including gapless assemblies for all chromosomes except Y, corrected errors in the prior references, and introduced nearly 200 million base pairs of sequence containing gene predictions, 99 of which are predicted to be protein coding as discussed by the authors .
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