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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Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments
Rachel M. Gittelman,Joshua G. Schraiber,Benjamin Vernot,Carmen Mikacenic,Mark M. Wurfel,Joshua M. Akey +5 more
TL;DR: It is demonstrated that hybridization between modern and archaic hominins provided an important reservoir of advantageous alleles that enabled adaptation to out-of-Africa environments and modulation of transcript abundance was a common mechanism facilitating adaptive introgression.
Journal ArticleDOI
The Korea Biobank Array: Design and Identification of Coding Variants Associated with Blood Biochemical Traits.
Sanghoon Moon,Young-Jin Kim,Sohee Han,Mi Yeong Hwang,Dong Mun Shin,Min Young Park,Yontao Lu,Kyungheon Yoon,Hye-Mi Jang,Yun Kyoung Kim,Taejoon Park,Daesub Song,Jae Kyung Park,Jong Eun Lee,Bong-Jo Kim +14 more
TL;DR: The design and implementation of a new array, the Korea Biobank Array, optimized for the Korean population and findings from GWAS of blood biochemical traits suggest the promising utility of KoreanChip with a substantial number of damaging variants to identify new population-specific disease-associated rare/functional variants.
Journal ArticleDOI
Association analyses of East Asian individuals and trans-ancestry analyses with European individuals reveal new loci associated with cholesterol and triglyceride levels.
Cassandra N. Spracklen,Peng Chen,Peng Chen,Young-Jin Kim,Xu Wang,Hui Cai,Shengxu Li,Jirong Long,Ying Wu,Ya Xing Wang,Fumihiko Takeuchi,Jer-Yuarn Wu,Jer-Yuarn Wu,Keum Ji Jung,Cheng Hu,Koichi Akiyama,Yonghong Zhang,Sanghoon Moon,Todd A. Johnson,Huaixing Li,Rajkumar Dorajoo,Meian He,Maren E Cannon,Tamara S. Roman,Elias Salfati,Keng-Hung Lin,Xiuqing Guo,Wayne Huey-Herng Sheu,Devin Absher,Linda S. Adair,Themistocles L. Assimes,Tin Aung,Qiuyin Cai,Li-Ching Chang,Chien-Hsiun Chen,Chien-Hsiun Chen,Li-Hsin Chien,Lee-Ming Chuang,Shu-Chun Chuang,Shufa Du,Qiao Fan,Cathy S.J. Fann,Alan B. Feranil,Yechiel Friedlander,Penny Gordon-Larsen,Dongfeng Gu,Lixuan Gui,Zhirong Guo,Chew-Kiat Heng,Chew-Kiat Heng,James E. Hixson,Xuhong Hou,Chao A. Hsiung,Yao Hu,Mi Yeong Hwang,Chii-Min Hwu,Chii-Min Hwu,Masato Isono,Jyh-Ming Jimmy Juang,Chiea Chuen Khor,Chiea Chuen Khor,Yun Kyoung Kim,Woon-Puay Koh,Michiaki Kubo,I-Te Lee,I-Te Lee,Sun-Ju Lee,Wen-Jane Lee,Kae-Woei Liang,Kae-Woei Liang,Blanche Lim,Sing-Hui Lim,Jianjun Liu,Jianjun Liu,Toru Nabika,Wen-Harn Pan,Hao Peng,Thomas Quertermous,Charumathi Sabanayagam,Kevin Sandow,Shi Jinxiu,Liang Sun,Pok Chien Tan,Shu-Pei Tan,Kent D. Taylor,Yik Ying Teo,Sue-Anne Toh,Tatsuhiko Tsunoda,Rob M. van Dam,Aili Wang,Feijie Wang,Jie Wang,Wen Bin Wei,Yong-Bing Xiang,Jie Yao,Jian-Min Yuan,Rong Zhang,Wanting Zhao,Yii-Der Ida Chen,Stephen S. Rich,Jerome I. Rotter,Tzung-Dau Wang,Tangchun Wu,Xu Lin,Bok-Ghee Han,Toshihiro Tanaka,Yoon Shin Cho,Tomohiro Katsuya,Weiping Jia,Sun Ha Jee,Yuan-Tsong Chen,Norihiro Kato,Jost B. Jonas,Jost B. Jonas,Ching-Yu Cheng,Xiao-Ou Shu,Jiang He,Wei Zheng,Tien Yin Wong,Wei Huang,Bong-Jo Kim,E-Shyong Tai,Karen L. Mohlke,Xueling Sim +123 more
TL;DR: Two meta‐analyses combined results from the East Asian meta‐analysis with association results from up to 187,365 European individuals from the Global Lipids Genetics Consortium in a trans‐ancestry meta‐ analysis identified multiple novel lipid loci, providing new potential therapeutic targets.
Journal ArticleDOI
Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells
Christopher DeBoever,He Li,David Jakubosky,Paola Benaglio,Joaquin Reyna,Katrina M. Olson,Hui Huang,William H. Biggs,Efren Sandoval,Matteo D’Antonio,Kristen Jepsen,Hiroko Matsui,Angelo Arias,Bing Ren,Naoki Nariai,Erin N. Smith,Agnieszka D'Antonio-Chronowska,Emma K. Farley,Kelly A. Frazer +18 more
TL;DR: This work used whole-genome sequencing and gene expression profiling of 215 human induced pluripotent stem cell lines from different donors to identify genetic variants associated with RNA expression for 5,746 genes and predicted causal variants for these expression quantitative trait loci (eQTLs) that disrupt transcription factor binding.
Journal ArticleDOI
Quantifying the contribution of recessive coding variation to developmental disorders.
Hilary C. Martin,Wendy D Jones,Wendy D Jones,Rebecca E. McIntyre,Gabriela Sánchez-Andrade,Mark Sanderson,James Stephenson,James Stephenson,Carla P. Jones,Juliet Handsaker,Giuseppe Gallone,Michaela Bruntraeger,Jeremy F. McRae,Elena Prigmore,Patrick J. Short,Mari Niemi,Joanna Kaplanis,Elizabeth J. Radford,Elizabeth J. Radford,Nadia Akawi,Meena Balasubramanian,John Dean,Rachel Horton,Alice Hulbert,Diana S. Johnson,Katie Johnson,Dhavendra Kumar,Sally Ann Lynch,Sarju G. Mehta,Jenny Morton,Michael J. Parker,Miranda Splitt,Peter D. Turnpenny,Pradeep C. Vasudevan,Michael Wright,Andrew R. Bassett,Sebastian S. Gerety,Caroline F. Wright,David R. FitzPatrick,Helen V. Firth,Helen V. Firth,Matthew E. Hurles,Jeffrey C. Barrett +42 more
TL;DR: The results suggest that recessive coding variants account for a small fraction of currently undiagnosed nonconsanguineous individuals, and that the role of noncoding variants, incomplete penetrance, and polygenic mechanisms need further exploration.
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