Open Access
A map of human genome variation from population-scale sequencing
Richard Durbin,David Altshuler,Gonçalo R. Abecasis,David R. Bentley,Aravinda Chakravarti,Andrew G. Clark,Francis S. Collins,Francisco M. De La Vega,Peter Donnelly,Michael Egholm,Paul Flicek,Stacey Gabriel,Richard A. Gibbs,Bartha Maria Knoppers,Eric S. Lander,Hans Lehrach,Elaine R. Mardis,Gil McVean,Deborah A. Nickerson,Leena Peltonen,Alan J. Schafer,Stephen T. Sherry,Jun Wang,Richard K. Wilson,David Rio Deiros,Mike Metzker,Donna M. Muzny,Jeffrey S. Reid,David C. Wheeler,Jingxiang Li,Min Jian,Guoqing Li,Ruiqiang Li,Huiqing Liang,Geng Tian,Bo Wang,Jian Wang,Wei Wang,Huanming Yang,Xiuqing Zhang,Huisong Zheng,Lauren Ambrogio,Toby Bloom,Kristian Cibulskis,Timothy Fennell,David B. Jaffe,Erica Shefler,Carrie Sougnez,Niall Anthony Gormley,Sean Humphray,Zoya Kingsbury,Paula Koko-Gonzales,Jennifer Stone,Kevin McKernan,Gina Costa,Jeffrey K. Ichikawa,Clarence Lee,Ralf Sudbrak,Tatiana A. Borodina,Andreas Dahl,Alexey N. Davydov,Peter Marquardt,Florian Mertes,Wilfiried Nietfeld,Philip Rosenstiel,Stefan Schreiber,Aleksey V. Soldatov,Bernd Timmermann,Marius Tolzmann,Jason P. Affourtit,Dana Ashworth,Said Attiya,Melissa Bachorski,Eli Buglione,Adam Burke,Amanda Caprio,Christopher Celone,Shauna Clark,David Conners,Brian Desany,Lisa Gu,Lorri Guccione,Kalvin Kao,Andrew Kebbel,Jennifer Knowlton,Matthew Labrecque,Louise McDade,Craig Elder Mealmaker,Melissa Minderman,Anne Nawrocki,Faheem Niazi,Kristen Pareja,Ramenani Ravi K,David Riches,Wanmin Song,Cynthia L. Turcotte,Shally Wang,David J. Dooling,Lucinda Fulton,Robert S. Fulton,George M. Weinstock,John Burton,David M. Carter,Carol Churcher,Alison J. Coffey,Anthony J. Cox,Aarno Palotie,Michael A. Quail,Tom Skelly,James Stalker,Harold Swerdlow,Daniel J. Turner,Anniek De Witte,Shane Giles,Matthew N. Bainbridge,Danny Challis,Aniko Sabo,Fuli Yu,Jin Yu,Xiaodong Fang,Xiaosen Guo,Yingrui Li,Ruibang Luo,Shuaishuai Tai,Honglong Wu,Hancheng Zheng,Xiaole Zheng,Yan Zhou,Gabor T. Marth,Erik Garrison,Weichun Huang,Amit Indap,Deniz Kural,Wan-Ping Lee,Wen Fung Leong,Aaron R. Quinlan,Chip Stewart,Michael Strömberg,Alistair Ward,Jiantao Wu,Charles Kai-Wu Lee,Ryan E. Mills,Xinghua Shi,Mark J. Daly,Mark A. DePristo,Aaron D. Ball,Eric Banks,Brian L. Browning,Kiran V. Garimella,Sharon R. Grossman,Robert E. Handsaker,Matt Hanna,Christopher Hartl,Andrew Kernytsky,Joshua M. Korn,Heng Li,Jared Maguire,Steven A. McCarroll,Aaron McKenna,James Nemesh,Anthony A. Philippakis,Ryan Poplin,Alkes L. Price,Manuel A. Rivas,Pardis C. Sabeti,Stephen F. Schaffner,Ilya Shlyakhter,David Neil Cooper,Edward V. Ball,Matthew Mort,Andrew David Phillips,Peter D. Stenson,Jonathan Sebat,Vladimir Makarov,Kenny Ye,Seungtai Yoon,Carlos Bustamante,Adam R. Boyko,Jeremiah D. Degenhardt,Simon Gravel,Ryan N. Gutenkunst,Mark Kaganovich,Alon Keinan,Phil Lacroute,Xin Ma,Andrew R. Reynolds,Laura Clarke,Fiona Cunningham,Javier Herrero,Stephen Keenen,Eugene Kulesha,Rasko Leinonen,William M. McLaren,Rajesh Radhakrishnan,Richard Smith,Vadim Zalunin,Xiangqun Zheng-Bradley,Jan O. Korbel,Adrian M. Stütz,Markus J. Bauer,R. Keira Cheetham,Tony Cox,Michael A. Eberle,Terena James,Scott Kahn,Lisa Murray,Kai Ye,Yutao Fu,Fiona Hyland,Jonathan M. Manning,Stephen F. McLaughlin,Heather E. Peckham,Onur Sakarya,Yongming A. Sun,Eric F. Tsung,Mark A. Batzer,Miriam K. Konkel,Jerilyn A. Walker,M. Albrecht,Vyacheslav Amstislavskiy,Ralf Herwig,Dimitri V. Parkhomchuk,Richa Agarwala,Hoda M. Khouri,Aleksandr Morgulis,Justin Paschall,Lon Phan,Kirill Rotmistrovsky,Robert Sanders,Martin Shumway,Chunlin Xiao,Adam Auton,Zamin Iqbal,Gerton Lunter,Jonathan Marchini,Loukas Moutsianas,Simon Myers,Afidalina Tumian,James R. Knight,Roger Winer,David Craig,Steve M. Beckstrom-Sternberg,Alexis Christoforides,Ahmet Kurdoglu,John V. Pearson,Shripad Sinari,Waibhav Tembe,David Haussler,Angie S. Hinrichs,Sol Katzman,Andrew D. Kern,Robert M. Kuhn,Molly Przeworski,Ryan D. Hernandez,Bryan Howie,Joanna L. Kelley,S. Cord Melton,Yun Li,Paul Anderson,Thomas W. Blackwell,Wei Chen,William O.C.M. Cookson,Jun Ding,Hyun Min Kang,Mark Lathrop,Liming Liang,Miriam F. Moffatt,Paul Scheet,Carlo Sidore,Matthew W. Snyder,Xiaowei Zhan,Sebastian Zöllner,Philip Awadalla,Ferran Casals,Youssef Idaghdour,John Keebler,Eric A. Stone,Martine Zilversmit,Lynn B. Jorde,Jinchuan Xing,Evan E. Eichler,Gozde Aksay,Can Alkan,Iman Hajirasouliha,Fereydoun Hormozdiari,Jeffrey M. Kidd,S. Cenk Sahinalp,Peter H. Sudmant,Ken Chen,Asif T. Chinwalla,Li Ding,Daniel C. Koboldt,Michael D. McLellan,John W. Wallis,Michael C. Wendl,Qunyuan Zhang,Cornelis A. Albers,Qasim Ayub,Senduran Balasubramaniam,Jeffrey C. Barrett,Yuan Chen,Donald F. Conrad,Petr Danecek,Emmanouil T. Dermitzakis,Min Hu,Ni Huang,Matthew E. Hurles,Han-Jun Jin,Luke Jostins,Thomas M. Keane,Si Quang Le,Sarah J. Lindsay,Quan Long,Daniel G. MacArthur,Stephen B. Montgomery,Leopold Parts,Chris Tyler-Smith,Klaudia Walter,Yujun Zhang,Mark Gerstein,Michael Snyder,Alexej Abyzov,Suganthi Balasubramanian,Robert D. Bjornson,Jiang Du,Fabian Grubert,Lukas Habegger,Rajini R Haraksingh,Justin Jee,Ekta Khurana,Hugo Y. K. Lam,Jing Leng,Xinmeng Jasmine Mu,Alexander E. Urban,Zhengdong D. Zhang,Cristian Coafra,Huyen Dinh,Christie Kovar,Sandy Lee,Lynne V. Nazareth,Jane E. Wilkinson,Allison Coffey,Carol Scott,Neda Gharani,Jane Kaye,Alastair Kent,Taosha Li,Amy L. McGuire,Pilar N. Ossorio,Charles N. Rotimi,Yeyang Su,Lorraine Toji,Lisa D. Brooks,Adam Felsenfeld,Jean E. McEwen,Assya Abdallah,Christopher R. Juenger,Nicholas C. Clemm,Audrey Duncanson,Eric D. Green,Mark S. Guyer,Jane Peterson +361 more
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TLDR
The pilot phase of the 1000 Genomes Project is presented, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms, and the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants are described.About:
The article was published on 2010-10-01 and is currently open access. It has received 599 citations till now. The article focuses on the topics: Cancer genome sequencing & Reference genome.read more
Citations
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Differential expression in RNA-seq: A matter of depth
TL;DR: This work analyzed how sequencing depth affects the detection of transcripts and their identification as differentially expressed, and proposed a novel approach--NOISeq--that differs from existing methods in that it is data-adaptive and nonparametric.
Journal ArticleDOI
A high-resolution map of human evolutionary constraint using 29 mammals.
Kerstin Lindblad-Toh,Manuel Garber,Or Zuk,Michael F. Lin,Michael F. Lin,Brian J. Parker,Stefan Washietl,Pouya Kheradpour,Pouya Kheradpour,Jason Ernst,Jason Ernst,Gregory E. Jordan,Evan Mauceli,Lucas D. Ward,Lucas D. Ward,Craig B. Lowe,Craig B. Lowe,Craig B. Lowe,Alisha K. Holloway,Michele Clamp,Sante Gnerre,Jessica Alföldi,Kathryn Beal,Jean Chang,Hiram Clawson,James Cuff,Federica Di Palma,Stephen Fitzgerald,Paul Flicek,Mitchell Guttman,Melissa J. Hubisz,David B. Jaffe,Irwin Jungreis,W. James Kent,Dennis Kostka,Marcia Lara,André L. Martins,Tim Massingham,Ida Moltke,Brian J. Raney,Matthew D. Rasmussen,James Robinson,Alexander Stark,Albert J. Vilella,Jiayu Wen,Xiaohui Xie,Michael C. Zody,Kim C. Worley,Christie Kovar,Donna M. Muzny,Richard A. Gibbs,Wesley C. Warren,Elaine R. Mardis,George M. Weinstock,George M. Weinstock,Richard K. Wilson,Ewan Birney,Elliott H. Margulies,Javier Herrero,Eric D. Green,David Haussler,David Haussler,Adam Siepel,Nick Goldman,Katherine S. Pollard,Jakob Skou Pedersen,Jakob Skou Pedersen,Eric S. Lander,Manolis Kellis,Manolis Kellis +69 more
TL;DR: The comparison of related genomes has emerged as a powerful lens for genome interpretation and sequencing and comparative analysis of 29 eutherian genomes confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2%" of the genome.
Journal ArticleDOI
Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies
Xiaolei Liu,Xiaolei Liu,Meng Huang,Bin Fan,Edward S. Buckler,Edward S. Buckler,Zhiwu Zhang,Zhiwu Zhang +7 more
TL;DR: A new method is named as Fixed and random model Circulating Probability Unification (FarmCPU) that improves statistical power compared to current methods and avoids model over-fitting problem in FEM.
Journal ArticleDOI
Trimethylamine-N-Oxide, a Metabolite Associated with Atherosclerosis, Exhibits Complex Genetic and Dietary Regulation
Brian J. Bennett,Thomas Q. de Aguiar Vallim,Zeneng Wang,Diana M. Shih,Yonghong Meng,Jill C. Gregory,Hooman Allayee,Richard G. Lee,Mark J. Graham,Rosanne M. Crooke,Peter A. Edwards,Stanley L. Hazen,Aldons J. Lusis +12 more
TL;DR: It is demonstrated that two flavin mono-oxygenase family members, FMO1 and FMO3, oxidize trimethylamine (TMA), derived from gut flora metabolism of choline, to TMAO, and it is shown that F MO3 exhibits 10-fold higher specific activity than F MO1.
Journal ArticleDOI
Integrative functional genomic analysis of human brain development and neuropsychiatric risks
Mingfeng Li,Gabriel Santpere,Yuka Imamura Kawasawa,Yuka Imamura Kawasawa,Oleg V. Evgrafov,Forrest O. Gulden,Sirisha Pochareddy,Susan M. Sunkin,Zhen Li,Yurae Shin,Yurae Shin,Ying Zhu,André M. M. Sousa,Donna M. Werling,Robert R. Kitchen,Hyo Jung Kang,Hyo Jung Kang,Mihovil Pletikos,Mihovil Pletikos,Jinmyung Choi,Sydney Muchnik,Xuming Xu,Daifeng Wang,Belen Lorente-Galdos,Shuang Liu,Paola Giusti-Rodríguez,Hyejung Won,Christiaan de Leeuw,Antonio F. Pardiñas,PsychENCODE Developmental Subgroup,Ming Hu,Fulai Jin,Yun Li,Michael John Owen,Michael Conlon O'Donovan,James T.R. Walters,Danielle Posthuma,Mark Reimers,Pat Levitt,Pat Levitt,Daniel R. Weinberger,Thomas M. Hyde,Joel E. Kleinman,Daniel H. Geschwind,Michael Hawrylycz,Matthew W. State,Stephen Sanders,Patrick F. Sullivan,Mark Gerstein,Ed S. Lein,James A. Knowles,Nenad Sestan +51 more
TL;DR: The generation and analysis of a variety of genomic data modalities at the tissue and single-cell levels, including transcriptome, DNA methylation, and histone modifications across multiple brain regions ranging in age from embryonic development through adulthood, reveal insights into neurodevelopment and the genomic basis of neuropsychiatric risks.
References
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Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
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Accurate whole human genome sequencing using reversible terminator chemistry
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TL;DR: An approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost is reported, effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.
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A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
Ravi Sachidanandam,David Weissman,Steven Schmidt,Jerzy M. Kakol,Lincoln Stein,Gabor T. Marth,Steve Sherry,James C. Mullikin,Beverley J. Mortimore,David Willey,Sarah E. Hunt,Charlotte G. Cole,Penny Coggill,Catherine M. Rice,Zemin Ning,Jane Rogers,David R. Bentley,Pui-Yan Kwok,Elaine R. Mardis,Raymond T. Yeh,Brian Schultz,Lisa Cook,Ruth Davenport,Michael Dante,Lucinda Fulton,LaDeana W. Hillier,Robert H. Waterston,John Douglas Mcpherson,Brian Gilman,Stephen F. Schaffner,William J. Van Etten,David Reich,John M. Higgins,Mark J. Daly,Brendan Blumenstiel,Jennifer Baldwin,Nicole Stange-Thomann,Michael C. Zody,Lauren Linton,Eric S. Lander,David Altshuler +40 more
TL;DR: This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.
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Sequence Variations in PCSK9, Low LDL, and Protection against Coronary Heart Disease
TL;DR: It is indicated that moderate lifelong reduction in the plasma level of LDL cholesterol is associated with a substantial Reduction in the incidence of coronary events, even in populations with a high prevalence of non-lipid-related cardiovascular risk factors.
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