Sequence data and association statistics from 12,940 type 2 diabetes cases and controls
Authors: Flannick Jason , Fuchsberger Christian , Mahajan Anubha , Teslovich Tanya M. , Agarwala Vineeta , Gaulton Kyle J. , Caulkins Lizz , Koesterer Ryan , Ma Clement , Moutsianas Loukas , McCarthy Davis J. , Rivas Manuel A. , Perry John R. B. , Sim Xueling , Blackwell Thomas W. , Robertson Neil R. , Rayner N William , Cingolani Pablo , Locke Adam E. , Tajes Juan Fernandez , Highland Heather M. , Dupuis Josee , Chines Peter S. , Lindgren Cecilia M. , Hartl Christopher , Jackson Anne U. , Chen Han , Huyghe Jeroen R. , van de Bunt Martijn , Pearson Richard D. , Kumar Ashish , Müller-Nurasyid Martina , Grarup Niels , Stringham Heather M. , Gamazon Eric R. , Lee Jaehoon , Chen Yuhui , Scott Robert A. , Below Jennifer E. , Chen Peng , Huang Jinyan , Go Min Jin , Stitzel Michael L. , Pasko Dorota , Parker Stephen C. J. , Varga Tibor V. , Green Todd , Beer Nicola L. , Day-Williams Aaron G. , Ferreira Teresa , Fingerlin Tasha , Horikoshi Momoko , Hu Cheng , Huh Iksoo , Ikram Mohammad Kamran , Kim Bong-Jo , Kim Yongkang , Kim Young Jin , Kwon Min-Seok , Lee Juyoung , Lee Selyeong , Lin Keng-Han , Maxwell Taylor J. , Nagai Yoshihiko , Wang Xu , Welch Ryan P. , Yoon Joon , Zhang Weihua , Barzilai Nir , Voight Benjamin F. , Han Bok-Ghee , Jenkinson Christopher P. , Kuulasmaa Teemu , Kuusisto Johanna , Manning Alisa , Ng Maggie C. Y. , Palmer Nicholette D. , Balkau Beverley , Stančáková Alena , Abboud Hanna E. , Boeing Heiner , Giedraitis Vilmantas , Prabhakaran Dorairaj , Gottesman Omri , Scott James , Carey Jason , Kwan Phoenix , Grant George , Smith Joshua D. , Neale Benjamin M. , Purcell Shaun , Butterworth Adam S. , Howson Joanna M. M. , Lee Heung Man , Lu Yingchang , Kwak Soo-Heon , Zhao Wei , Danesh John , Lam Vincent K. L. , Park Kyong Soo , Saleheen Danish , So Wing Yee , Tam Claudia H. T. , Afzal Uzma , Aguilar David , Arya Rector , Aung Tin , Chan Edmund , Navarro Carmen , Cheng Ching-Yu , Palli Domenico , Correa Adolfo , Curran Joanne E. , Rybin Dennis , Farook Vidya S. , Fowler Sharon P. , Freedman Barry I. , Griswold Michael , Hale Daniel Esten , Hicks Pamela J. , Khor Chiea-Chuen , Kumar Satish , Lehne Benjamin , Thuillier Dorothée , Lim Wei Yen , Liu Jianjun , Loh Marie , Musani Solomon K. , Puppala Sobha , Scott William R. , Yengo Loïc , Tan Sian-Tsung , Taylor Herman A. , Thameem Farook , Wilson Gregory , Wong Tien Yin , Njølstad Pål Rasmus , Levy Jonathan C. , Mangino Massimo , Bonnycastle Lori L. , Schwarzmayr Thomas , Fadista João , Surdulescu Gabriela L. , Herder Christian , Groves Christopher J. , Wieland Thomas , Bork-Jensen Jette , Brandslund Ivan , Christensen Cramer , Koistinen Heikki A. , Doney Alex S. F. , Kinnunen Leena , Esko Tõnu , Farmer Andrew J. , Hakaste Liisa , Hodgkiss Dylan , Kravic Jasmina , Lyssenko Valeri , Hollensted Mette , Jørgensen Marit E. , Jørgensen Torben , Ladenvall Claes , Justesen Johanne Marie , Käräjämäki Annemari , Kriebel Jennifer , Rathmann Wolfgang , Lannfelt Lars , Lauritzen Torsten , Narisu Narisu , Linneberg Allan , Melander Olle , Milani Lili , Neville Matt , Orho-Melander Marju , Qi Lu , Qi Qibin , Roden Michael , Rolandsson Olov , Swift Amy , Rosengren Anders H. , Stirrups Kathleen , Wood Andrew R. , Mihailov Evelin , Blancher Christine , Carneiro Mauricio O. , Maguire Jared , Poplin Ryan , Shakir Khalid , Fennell Timothy , DePristo Mark , de Angelis Martin Hrabé , Deloukas Panos , Gjesing Anette P. , Jun Goo , Nilsson Peter , Murphy Jacquelyn , Onofrio Robert , Thorand Barbara , Hansen Torben , Meisinger Christa , Hu Frank B. , Isomaa Bo , Karpe Fredrik , Liang Liming , Peters Annette , Huth Cornelia , O'Rahilly Stephen P , Palmer Colin N. A. , Pedersen Oluf , Rauramaa Rainer , Tuomilehto Jaakko , Salomaa Veikko , Watanabe Richard M. , Syvänen Ann-Christine , Bergman Richard N. , Bharadwaj Dwaipayan , Bottinger Erwin P. , Cho Yoon Shin , Chandak Giriraj R. , Chan Juliana CN , Chia Kee Seng , Daly Mark J. , Ebrahim Shah B. , Langenberg Claudia , Elliott Paul , Jablonski Kathleen A. , Lehman Donna M. , Jia Weiping , Ma Ronald C. W. , Pollin Toni I. , Sandhu Manjinder , Tandon Nikhil , Froguel Philippe , Barroso Inês , Teo Yik Ying , Zeggini Eleftheria , Loos Ruth J. F. , Small Kerrin S. , Ried Janina S. , DeFronzo Ralph A. , Grallert Harald , Glaser Benjamin , Metspalu Andres , Wareham Nicholas J. , Walker Mark , Banks Eric , Gieger Christian , Ingelsson Erik , Im Hae Kyung , Illig Thomas , Franks Paul W. , Buck Gemma , Trakalo Joseph , Buck David , Prokopenko Inga , Mägi Reedik , Lind Lars , Farjoun Yossi , Owen Katharine R. , Gloyn Anna L. , Strauch Konstantin , Tuomi Tiinamaija , Kooner Jaspal Singh , Lee Jong-Young , Park Taesung , Donnelly Peter , Morris Andrew D. , Hattersley Andrew T. , Bowden Donald W. , Collins Francis S. , Atzmon Gil , Chambers John C. , Spector Timothy D. , Laakso Markku , Strom Tim M. , Bell Graeme I. , Blangero John , Duggirala Ravindranath , Tai E. Shyong , McVean Gilean , Hanis Craig L. , Wilson James G. , Seielstad Mark , Frayling Timothy M. , Meigs James B. , Cox Nancy J. , Sladek Rob , Lander Eric S. , Gabriel Stacey , Mohlke Karen L. , Meitinger Thomas , Groop Leif , Abecasis Goncalo , Scott Laura J. , Morris Andrew P. , Kang Hyun Min , Altshuler David , Burtt Noël P. , Florez Jose C. , Boehnke Michael , McCarthy Mark I. 
Published: December 2017

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1–5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.