Genomics

Dataset Information

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Ena-DATASET-GoT2D/T2D-GENES-08-07-2016-21:22:44:693-1130 - samples

ABSTRACT: The T2D-GENES/GoT2D 13K exome sequencing study includes ~13,000 samples, half T2D cases and half T2D controls, from five ancestries (~5K Europeans, ~2K each of African-American, East-Asian, South-Asian, and Hispanic). Samples underwent deep exome sequencing, with SNVs and INDEls called according to GATK best practices; variant sites were then filtered according to the GATK best practices, and then samples and variants underwent further filtering based on aggregate genotype quality as described in Fuchsberger et al. (e.g. low call rate, excess heterozygosity for samples, low call rate or coverage for variants). Please note that one of the samples in the T2D-GENES vcf does not have phenotype data.

PROVIDER: EGAD00001002246 | EGA |

REPOSITORIES: EGA

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Publications

The genetic architecture of type 2 diabetes.

Fuchsberger Christian C   Flannick Jason J   Teslovich Tanya M TM   Mahajan Anubha A   Agarwala Vineeta V   Gaulton Kyle J KJ   Ma Clement C   Fontanillas Pierre P   Moutsianas Loukas L   McCarthy Davis J DJ   Rivas Manuel A MA   Perry John R B JRB   Sim Xueling X   Blackwell Thomas W TW   Robertson Neil R NR   Rayner N William NW   Cingolani Pablo P   Locke Adam E AE   Tajes Juan Fernandez JF   Highland Heather M HM   Dupuis Josee J   Chines Peter S PS   Lindgren Cecilia M CM   Hartl Christopher C   Jackson Anne U AU   Chen Han H   Huyghe Jeroen R JR   van de Bunt Martijn M   Pearson Richard D RD   Kumar Ashish A   Müller-Nurasyid Martina M   Grarup Niels N   Stringham Heather M HM   Gamazon Eric R ER   Lee Jaehoon J   Chen Yuhui Y   Scott Robert A RA   Below Jennifer E JE   Chen Peng P   Huang Jinyan J   Go Min Jin MJ   Stitzel Michael L ML   Pasko Dorota D   Parker Stephen C J SCJ   Varga Tibor V TV   Green Todd T   Beer Nicola L NL   Day-Williams Aaron G AG   Ferreira Teresa T   Fingerlin Tasha T   Horikoshi Momoko M   Hu Cheng C   Huh Iksoo I   Ikram Mohammad Kamran MK   Kim Bong-Jo BJ   Kim Yongkang Y   Kim Young Jin YJ   Kwon Min-Seok MS   Lee Juyoung J   Lee Selyeong S   Lin Keng-Han KH   Maxwell Taylor J TJ   Nagai Yoshihiko Y   Wang Xu X   Welch Ryan P RP   Yoon Joon J   Zhang Weihua W   Barzilai Nir N   Voight Benjamin F BF   Han Bok-Ghee BG   Jenkinson Christopher P CP   Kuulasmaa Teemu T   Kuusisto Johanna J   Manning Alisa A   Ng Maggie C Y MCY   Palmer Nicholette D ND   Balkau Beverley B   Stančáková Alena A   Abboud Hanna E HE   Boeing Heiner H   Giedraitis Vilmantas V   Prabhakaran Dorairaj D   Gottesman Omri O   Scott James J   Carey Jason J   Kwan Phoenix P   Grant George G   Smith Joshua D JD   Neale Benjamin M BM   Purcell Shaun S   Butterworth Adam S AS   Howson Joanna M M JMM   Lee Heung Man HM   Lu Yingchang Y   Kwak Soo-Heon SH   Zhao Wei W   Danesh John J   Lam Vincent K L VKL   Park Kyong Soo KS   Saleheen Danish D   So Wing Yee WY   Tam Claudia H T CHT   Afzal Uzma U   Aguilar David D   Arya Rector R   Aung Tin T   Chan Edmund E   Navarro Carmen C   Cheng Ching-Yu CY   Palli Domenico D   Correa Adolfo A   Curran Joanne E JE   Rybin Denis D   Farook Vidya S VS   Fowler Sharon P SP   Freedman Barry I BI   Griswold Michael M   Hale Daniel Esten DE   Hicks Pamela J PJ   Khor Chiea-Chuen CC   Kumar Satish S   Lehne Benjamin B   Thuillier Dorothée D   Lim Wei Yen WY   Liu Jianjun J   van der Schouw Yvonne T YT   Loh Marie M   Musani Solomon K SK   Puppala Sobha S   Scott William R WR   Yengo Loïc L   Tan Sian-Tsung ST   Taylor Herman A HA   Thameem Farook F   Wilson Gregory G   Wong Tien Yin TY   Njølstad Pål Rasmus PR   Levy Jonathan C JC   Mangino Massimo M   Bonnycastle Lori L LL   Schwarzmayr Thomas T   Fadista João J   Surdulescu Gabriela L GL   Herder Christian C   Groves Christopher J CJ   Wieland Thomas T   Bork-Jensen Jette J   Brandslund Ivan I   Christensen Cramer C   Koistinen Heikki A HA   Doney Alex S F ASF   Kinnunen Leena L   Esko Tõnu T   Farmer Andrew J AJ   Hakaste Liisa L   Hodgkiss Dylan D   Kravic Jasmina J   Lyssenko Valeriya V   Hollensted Mette M   Jørgensen Marit E ME   Jørgensen Torben T   Ladenvall Claes C   Justesen Johanne Marie JM   Käräjämäki Annemari A   Kriebel Jennifer J   Rathmann Wolfgang W   Lannfelt Lars L   Lauritzen Torsten T   Narisu Narisu N   Linneberg Allan A   Melander Olle O   Milani Lili L   Neville Matt M   Orho-Melander Marju M   Qi Lu L   Qi Qibin Q   Roden Michael M   Rolandsson Olov O   Swift Amy A   Rosengren Anders H AH   Stirrups Kathleen K   Wood Andrew R AR   Mihailov Evelin E   Blancher Christine C   Carneiro Mauricio O MO   Maguire Jared J   Poplin Ryan R   Shakir Khalid K   Fennell Timothy T   DePristo Mark M   de Angelis Martin Hrabé MH   Deloukas Panos P   Gjesing Anette P AP   Jun Goo G   Nilsson Peter P   Murphy Jacquelyn J   Onofrio Robert R   Thorand Barbara B   Hansen Torben T   Meisinger Christa C   Hu Frank B FB   Isomaa Bo B   Karpe Fredrik F   Liang Liming L   Peters Annette A   Huth Cornelia C   O'Rahilly Stephen P SP   Palmer Colin N A CNA   Pedersen Oluf O   Rauramaa Rainer R   Tuomilehto Jaakko J   Salomaa Veikko V   Watanabe Richard M RM   Syvänen Ann-Christine AC   Bergman Richard N RN   Bharadwaj Dwaipayan D   Bottinger Erwin P EP   Cho Yoon Shin YS   Chandak Giriraj R GR   Chan Juliana C N JCN   Chia Kee Seng KS   Daly Mark J MJ   Ebrahim Shah B SB   Langenberg Claudia C   Elliott Paul P   Jablonski Kathleen A KA   Lehman Donna M DM   Jia Weiping W   Ma Ronald C W RCW   Pollin Toni I TI   Sandhu Manjinder M   Tandon Nikhil N   Froguel Philippe P   Barroso Inês I   Teo Yik Ying YY   Zeggini Eleftheria E   Loos Ruth J F RJF   Small Kerrin S KS   Ried Janina S JS   DeFronzo Ralph A RA   Grallert Harald H   Glaser Benjamin B   Metspalu Andres A   Wareham Nicholas J NJ   Walker Mark M   Banks Eric E   Gieger Christian C   Ingelsson Erik E   Im Hae Kyung HK   Illig Thomas T   Franks Paul W PW   Buck Gemma G   Trakalo Joseph J   Buck David D   Prokopenko Inga I   Mägi Reedik R   Lind Lars L   Farjoun Yossi Y   Owen Katharine R KR   Gloyn Anna L AL   Strauch Konstantin K   Tuomi Tiinamaija T   Kooner Jaspal Singh JS   Lee Jong-Young JY   Park Taesung T   Donnelly Peter P   Morris Andrew D AD   Hattersley Andrew T AT   Bowden Donald W DW   Collins Francis S FS   Atzmon Gil G   Chambers John C JC   Spector Timothy D TD   Laakso Markku M   Strom Tim M TM   Bell Graeme I GI   Blangero John J   Duggirala Ravindranath R   Tai E Shyong ES   McVean Gilean G   Hanis Craig L CL   Wilson James G JG   Seielstad Mark M   Frayling Timothy M TM   Meigs James B JB   Cox Nancy J NJ   Sladek Rob R   Lander Eric S ES   Gabriel Stacey S   Burtt Noël P NP   Mohlke Karen L KL   Meitinger Thomas T   Groop Leif L   Abecasis Goncalo G   Florez Jose C JC   Scott Laura J LJ   Morris Andrew P AP   Kang Hyun Min HM   Boehnke Michael M   Altshuler David D   McCarthy Mark I MI  

Nature 20160711 7614

The genetic architecture of common traits, including the number, frequency, and effect sizes of inherited variants that contribute to individual risk, has been long debated. Genome-wide association studies have identified scores of common variants associated with type 2 diabetes, but in aggregate, these explain only a fraction of the heritability of this disease. Here, to test the hypothesis that lower-frequency variants explain much of the remainder, the GoT2D and T2D-GENES consortia performed  ...[more]

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