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
The trans-ancestral genomic architecture of glycemic traits
Ji Chen,Ji Chen,Cassandra N. Spracklen,Cassandra N. Spracklen,Gaëlle Marenne,Gaëlle Marenne,Arushi Varshney,Laura J Corbin,Jian'an Luan,Sara M. Willems,Ying Wu,Xiaoshuai Zhang,Xiaoshuai Zhang,Momoko Horikoshi,Thibaud S. Boutin,Reedik Mägi,Johannes Waage,Ruifang Li-Gao,Kei Hang Katie Chan,Kei Hang Katie Chan,Jie Yao,Mila Desi Anasanti,Audrey Y. Chu,Annique Claringbould,Jani Heikkinen,Jaeyoung Hong,Jouke-Jan Hottenga,Jouke-Jan Hottenga,Shaofeng Huo,Marika Kaakinen,Marika Kaakinen,Tin Louie,Winfried März,Winfried März,Winfried März,Hortensia Moreno-Macías,Anne Ndungu,Sarah C. Nelson,Ilja M. Nolte,Kari E. North,Chelsea K. Raulerson,Debashree Ray,Rebecca Rohde,Denis Rybin,Claudia Schurmann,Claudia Schurmann,Xueling Sim,Xueling Sim,Lorraine Southam,Isobel D. Stewart,Carol A. Wang,Yujie Wang,Peitao Wu,Weihua Zhang,Weihua Zhang,Tarunveer S. Ahluwalia,Tarunveer S. Ahluwalia,Emil V. R. Appel,Lawrence F. Bielak,Jennifer A. Brody,Noël P. Burtt,Claudia P. Cabrera,Brian E. Cade,Brian E. Cade,Jin Fang Chai,Xiaoran Chai,Li-Ching Chang,Chien-Hsiun Chen,Brian H. Chen,Kumaraswamy Naidu Chitrala,Yen-Feng Chiu,Hugoline G. de Haan,Graciela E. Delgado,Ayse Demirkan,Ayse Demirkan,Qing Duan,Jorgen Engmann,Segun Fatumo,Javier Gayán,Franco Giulianini,Jung Ho Gong,Stefan Gustafsson,Yang Hai,Fernando Pires Hartwig,Fernando Pires Hartwig,Jing He,Yoriko Heianza,Tao Huang,Alicia Huerta-Chagoya,Mi Yeong Hwang,Richard A. Jensen,Takahisa Kawaguchi,Katherine A. Kentistou,Young-Jin Kim,Marcus E. Kleber,Ishminder K. Kooner,Shuiqing Lai,Leslie A. Lange,Carl D. Langefeld,Marie Lauzon,Man Li,Symen Ligthart,Jun Liu,Jun Liu,Marie Loh,Marie Loh,Jirong Long,Valeriya Lyssenko,Valeriya Lyssenko,Massimo Mangino,Massimo Mangino,Carola Marzi,May E. Montasser,Abhishek Nag,Masahiro Nakatochi,Damia Noce,Raymond Noordam,Giorgio Pistis,Michael Preuss,Laura M. Raffield,Laura J. Rasmussen-Torvik,Stephen S. Rich,Neil R. Robertson,Rico Rueedi,Rico Rueedi,Kathleen A. Ryan,Serena Sanna,Richa Saxena,Richa Saxena,Katharina E. Schraut,Bengt Sennblad,Kazuya Setoh,Albert V. Smith,Thomas Sparsø,Rona J. Strawbridge,Rona J. Strawbridge,Fumihiko Takeuchi,Jingyi Tan,Stella Trompet,Erik B. van den Akker,Erik B. van den Akker,Peter J. van der Most,Niek Verweij,Mandy Vogel,Heming Wang,Heming Wang,Chaolong Wang,Chaolong Wang,Nan Wang,Helen R. Warren,Wanqing Wen,Tom Wilsgaard,Andrew Wong,Andrew R. Wood,Tian Xie,Mohammad Hadi Zafarmand,Jing Hua Zhao,Wei Zhao,N. Amin,N. Amin,Zorayr Arzumanyan,Arne Astrup,Stephan J. L. Bakker,Damiano Baldassarre,Marian Beekman,Richard N. Bergman,Alain G. Bertoni,Matthias Blüher,Lori L. Bonnycastle,Stefan R. Bornstein,Donald W. Bowden,Qiuyin Cai,Archie Campbell,Archie Campbell,Harry Campbell,Yi-Cheng Chang,Yi-Cheng Chang,Eco J. C. de Geus,Eco J. C. de Geus,Abbas Dehghan,Shufa Du,Gudny Eiriksdottir,Aliki-Eleni Farmaki,Aliki-Eleni Farmaki,Mattias Frånberg,Christian Fuchsberger,Yu-Tang Gao,Anette P. Gjesing,Anuj Goel,Sohee Han,Catharina A. Hartman,Christian Herder,Andrew A. Hicks,Chang-Hsun Hsieh,Chang-Hsun Hsieh,Willa A. Hsueh,Sahoko Ichihara,Michiya Igase,M. Arfan Ikram,W. Craig Johnson,Marit E. Jørgensen,Marit E. Jørgensen,Peter K. Joshi,Rita R. Kalyani,Fouad Kandeel,Tomohiro Katsuya,Chiea Chuen Khor,Wieland Kiess,Ivana Kolcic,Teemu Kuulasmaa,Johanna Kuusisto,Kristi Läll,Kelvin Lam,Debbie A Lawlor,Nanette R. Lee,Rozenn N. Lemaitre,Honglan Li,Shih-Yi Lin,Jaana Lindström,Allan Linneberg,Allan Linneberg,Jianjun Liu,Jianjun Liu,Carlos Lorenzo,Tatsuaki Matsubara,Fumihiko Matsuda,Geltrude Mingrone,Simon P. Mooijaart,Sanghoon Moon,Toru Nabika,Girish N. Nadkarni,Jerry L. Nadler,Mari Nelis,Matt J. Neville,Jill M. Norris,Yasumasa Ohyagi,Annette Peters,Patricia A. Peyser,Ozren Polasek,Qibin Qi,Dennis Raven,Dermot F. Reilly,Alexander P. Reiner,Fernando Rivideneira,Kathryn Roll,Igor Rudan,Charumathi Sabanayagam,Kevin Sandow,Naveed Sattar,Annette Schürmann,Shi Jinxiu,Heather M. Stringham,Kent D. Taylor,Tanya M. Teslovich,Betina H. Thuesen,Paul R. H. J. Timmers,Elena Tremoli,Michael Y. Tsai,André G. Uitterlinden,Rob M. van Dam,Rob M. van Dam,Rob M. van Dam,Diana van Heemst,Astrid van Hylckama Vlieg,Jana V. van Vliet-Ostaptchouk,Jagadish Vangipurapu,Henrik Vestergaard,Tao Wang,Ko Willems van Dijk,Tatijana Zemunik,Gonçalo R. Abecasis,Linda S. Adair,Carlos A. Aguilar-Salinas,Marta E. Alarcón-Riquelme,Marta E. Alarcón-Riquelme,Ping An,M. Larissa Avilés-Santa,Diane M. Becker,Lawrence J. Beilin,Sven Bergmann,Sven Bergmann,Sven Bergmann,Hans Bisgaard,Corri Black,Michael Boehnke,Eric Boerwinkle,Eric Boerwinkle,Bernhard O. Böhm,Bernhard O. Böhm,Klaus Bønnelykke,D.I. Boomsma,D.I. Boomsma,Erwin P. Bottinger,Erwin P. Bottinger,Thomas A. Buchanan,Mickaël Canouil,Mickaël Canouil,Mark J. Caulfield,John C. Chambers,Daniel I. Chasman,Daniel I. Chasman,Yii-Der Ida Chen,Ching-Yu Cheng,Francis S. Collins,Adolfo Correa,Francesco Cucca,H. Janaka de Silva,George Dedoussis,Sölve Elmståhl,Michele K. Evans,Ele Ferrannini,Luigi Ferrucci,Jose C. Florez,Jose C. Florez,Paul W. Franks,Paul W. Franks,Timothy M. Frayling,Philippe Froguel,Philippe Froguel,Philippe Froguel,Bruna Gigante,Mark O. Goodarzi,Penny Gordon-Larsen,Harald Grallert,Niels Grarup,Sameline Grimsgaard,Leif Groop,Leif Groop,Vilmundur Gudnason,Xiuqing Guo,Anders Hamsten,Torben Hansen,Caroline Hayward,Susan R. Heckbert,Bernardo L. Horta,Wei Huang,Erik Ingelsson,Pankow S. James,Marjo-Ritta Jarvelin,Jost B. Jonas,Jost B. Jonas,J. Wouter Jukema,Pontiano Kaleebu,Robert C. Kaplan,Robert C. Kaplan,Sharon L.R. Kardia,Norihiro Kato,Sirkka Keinänen-Kiukaanniemi,Sirkka Keinänen-Kiukaanniemi,Bong-Jo Kim,Mika Kivimäki,Heikki A. Koistinen,Heikki A. Koistinen,Heikki A. Koistinen,Jaspal S. Kooner,Antje Körner,Peter Kovacs,Diana Kuh,Meena Kumari,Zoltán Kutalik,Zoltán Kutalik,Markku Laakso,Timo A. Lakka,Lenore J. Launer,Karin Leander,Huaixing Li,Xu Lin,Lars Lind,Cecilia M. Lindgren,Simin Liu,Ruth J. F. Loos,Patrik K. E. Magnusson,Anubha Mahajan,Anubha Mahajan,Andres Metspalu,Dennis O. Mook-Kanamori,Trevor A. Mori,Patricia B. Munroe,Inger Njølstad,Jeffrey R. O'Connell,Albertine J. Oldehinkel,Ken K. Ong,Sandosh Padmanabhan,Colin N. A. Palmer,Nicholette D. Palmer,Oluf Pedersen,Craig E. Pennell,David J. Porteous,David J. Porteous,Peter P. Pramstaller,Michael A. Province,Bruce M. Psaty,Lu Qi,Leslie J. Raffel,Rainer Rauramaa,Susan Redline,Susan Redline,Paul M. Ridker,Frits R. Rosendaal,Timo Saaristo,Manjinder S. Sandhu,Jouko Saramies,Neil Schneiderman,Peter E. H. Schwarz,Peter E. H. Schwarz,Laura J. Scott,Elizabeth Selvin,Peter S. Sever,Xiao-Ou Shu,P. Eline Slagboom,Kerrin S. Small,Blair H. Smith,Harold Snieder,Tamar Sofer,Tamar Sofer,Thorkild I. A. Sørensen,Tim D. Spector,Alice Stanton,Claire J. Steves,Claire J. Steves,Michael Stumvoll,Liang Sun,Yasuharu Tabara,E. Shyong Tai,E. Shyong Tai,Nicholas J. Timpson,Anke Tönjes,Jaakko Tuomilehto,Jaakko Tuomilehto,Jaakko Tuomilehto,Teresa Tusie,Matti Uusitupa,Pim van der Harst,Cornelia M. van Duijn,Cornelia M. van Duijn,Veronique Vitart,Peter Vollenweider,Tanja G. M. Vrijkotte,Lynne E. Wagenknecht,Mark Walker,Ya X. Wang,Nicholas J. Wareham,Richard M. Watanabe,Hugh Watkins,Wen B. Wei,Ananda R. Wickremasinghe,Gonneke Willemsen,Gonneke Willemsen,James F. Wilson,Tien Yin Wong,Jer-Yuarn Wu,Anny H. Xiang,Lisa R. Yanek,Loic Yengo,Mitsuhiro Yokota,Eleftheria Zeggini,Eleftheria Zeggini,Wei Zheng,Alan B. Zonderman,Jerome I. Rotter,Anna L. Gloyn,Mark I. McCarthy,Josée Dupuis,James B. Meigs,James B. Meigs,Robert A. Scott,Inga Prokopenko,Inga Prokopenko,Aaron Leong,Ching-Ti Liu,Stephen C. J. Parker,Karen L. Mohlke,Claudia Langenberg,Eleanor Wheeler,Eleanor Wheeler,Andrew P. Morris,Inês Barroso,Inês Barroso,Inês Barroso +478 more
TL;DR: This paper aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available.
Journal ArticleDOI
Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases.
M. Ryan Corces,Anna Shcherbina,Soumya Kundu,Michael J. Gloudemans,Laure Fresard,Jeffrey M. Granja,Bryan H. Louie,Tiffany Eulalio,Shadi Shams,S. Tansu Bagdatli,Maxwell R. Mumbach,Boxiang Liu,Boxiang Liu,Kathleen S. Montine,William J. Greenleaf,Anshul Kundaje,Stephen B. Montgomery,Howard Y. Chang,Thomas J. Montine +18 more
TL;DR: A machine-learning classifier is developed to integrate this multi-omic framework and predict dozens of functional single-nucleotide polymorphisms for Alzheimer's disease and Parkinson's disease, and dissected the complex inverted haplotype of the MAPT (encoding tau) PD risk locus.
Journal ArticleDOI
Genome-wide association study of 40,000 individuals identifies two novel loci associated with bipolar disorder.
Liping Hou,Sarah E. Bergen,Sarah E. Bergen,Nirmala Akula,Jie Song,Christina M. Hultman,Mikael Landén,Mikael Landén,Mazda Adli,Martin Alda,Raffaella Ardau,Bárbara Arias,Jean-Michel Aubry,Lena Backlund,Judith A. Badner,Thomas B. Barrett,Michael Bauer,Bernhard T. Baune,Frank Bellivier,Antonio Benabarre,Susanne Bengesser,Wade H. Berrettini,Abesh Kumar Bhattacharjee,Joanna M. Biernacka,Armin Birner,Cinnamon S. Bloss,Clara Brichant-Petitjean,Elise T. Bui,William Byerley,Pablo Cervantes,Caterina Chillotti,Sven Cichon,Sven Cichon,Francesc Colom,William Coryell,David Craig,Cristiana Cruceanu,Piotr M. Czerski,Tony Davis,Alexandre Dayer,Franziska Degenhardt,Maria Del Zompo,J. Raymond DePaulo,Howard J. Edenberg,Bruno Etain,Peter Falkai,Tatiana Foroud,Andreas J. Forstner,Louise Frisén,Mark A. Frye,Janice M. Fullerton,Janice M. Fullerton,Sébastien Gard,Julie Garnham,Elliot S. Gershon,Fernando S. Goes,Tiffany A. Greenwood,Maria Grigoroiu-Serbanescu,Joanna Hauser,Urs Heilbronner,Urs Heilbronner,Stefanie Heilmann-Heimbach,Stefan Herms,Stefan Herms,Maria Hipolito,Shashi Hitturlingappa,Per Hoffmann,Per Hoffmann,Andrea Hofmann,Stéphane Jamain,Esther Jiménez,Jean-Pierre Kahn,Layla Kassem,John R. Kelsoe,Sarah Kittel-Schneider,Sebastian Kliwicki,Daniel L. Koller,Barbara König,N. Lackner,Gonzalo Laje,Maren Lang,Catharina Lavebratt,William Lawson,Marion Leboyer,Susan G. Leckband,Chunyu Liu,Anna Maaser,Pamela B. Mahon,Wolfgang Maier,Mario Maj,Mirko Manchia,Mirko Manchia,Lina Martinsson,Michael McCarthy,Susan L. McElroy,Melvin G. McInnis,Rebecca McKinney,Philip B. Mitchell,Marina Mitjans,Francis M. Mondimore,Palmiero Monteleone,Palmiero Monteleone,Thomas W. Mühleisen,Caroline M. Nievergelt,Markus M. Nöthen,Tomas Novak,John I. Nurnberger,Evaristus A. Nwulia,Urban Ösby,Andrea Pfennig,James B. Potash,Peter Propping,Andreas Reif,Eva Z. Reininghaus,John P. Rice,Marcella Rietschel,Guy A. Rouleau,Janusz K. Rybakowski,Martin Schalling,William A. Scheftner,Peter R. Schofield,Peter R. Schofield,Nicholas J. Schork,Thomas G. Schulze,Johannes Schumacher,Barbara W. Schweizer,Giovanni Severino,Tatyana Shekhtman,Paul D. Shilling,Christian Simhandl,Claire Slaney,Erin N. Smith,Alessio Squassina,Thomas Stamm,Pavla Stopkova,Fabian Streit,Jana Strohmaier,Szabolcs Szelinger,Sarah K. Tighe,Alfonso Tortorella,Gustavo Turecki,Eduard Vieta,Julia Volkert,Stephanie H. Witt,Adam Wright,Peter P. Zandi,Peng Zhang,Sebastian Zöllner,Francis J. McMahon +148 more
TL;DR: A two-stage meta-analysis of GWAS of bipolar disorder patients and controls revealed genome-wide significant associations at two novel loci, adding to a growing list of common autosomal variants involved in BD and illustrating the power of comparing well-characterized cases to an excess of controls in GWAS.
Journal ArticleDOI
Avoiding dynastic, assortative mating, and population stratification biases in Mendelian randomization through within-family analyses
Ben Michael Brumpton,Ben Michael Brumpton,Eleanor Sanderson,Karl Heilbron,Fernando Pires Hartwig,Fernando Pires Hartwig,Sean Harrison,Gunnhild Åberge Vie,Yoonsu Cho,Laura D Howe,Amanda Hughes,Dorret I. Boomsma,Alexandra Havdahl,Alexandra Havdahl,John L. Hopper,Michael C. Neale,Michel G. Nivard,Nancy L. Pedersen,Chandra A. Reynolds,Elliot M. Tucker-Drob,Andrew D. Grotzinger,Laurence J. Howe,Tim T Morris,Shuai Li,Shuai Li,Adam Auton,Frank Windmeijer,Wei-Min Chen,Johan Håkon Bjørngaard,Johan Håkon Bjørngaard,Kristian Hveem,Cristen J. Willer,David M. Evans,David M. Evans,Jaakko Kaprio,George Davey Smith,Bjørn Olav Åsvold,Gibran Hemani,Neil M Davies,Neil M Davies +39 more
TL;DR: Methods for within-family Mendelian randomization analyses are described and simulation studies are used to show that family-based analyses can reduce such biases in Mendelians randomization through within- family studies.
Journal ArticleDOI
Exomic variants of an elderly cohort of Brazilians in the ABraOM database
Michel S Naslavsky,Guilherme L. Yamamoto,Tatiana F. Almeida,Suzana A. M. Ezquina,Daniele Yumi Sunaga,Nam Pho,Daniel Bozoklian,Tatiana Orli Milkewitz Sandberg,Luciano Abreu Brito,Monize Lazar,Danilo V. Bernardo,Edson Amaro,Yeda Aparecida de Oliveira Duarte,Maria Lúcia Lebrão,Maria Rita Passos-Bueno,Mayana Zatz +15 more
TL;DR: A collection of exomic variants from 609 elderly Brazilians in a census‐based cohort (SABE609) with comprehensive phenotyping is presented and incidence estimation for prevalent recessive disorders based upon heterozygous frequency is conducted and concluded that it relies on appropriate pathogenicity assertion.
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TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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BEDTools: a flexible suite of utilities for comparing genomic features
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The variant call format and VCFtools
Petr Danecek,Adam Auton,Gonçalo R. Abecasis,Cornelis A. Albers,Eric Banks,Mark A. DePristo,Robert E. Handsaker,Gerton Lunter,Gabor T. Marth,Stephen T. Sherry,Gilean McVean,Richard Durbin +11 more
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