Abstract
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.
| Originalsprog | Engelsk |
|---|---|
| Artikelnummer | 170179 |
| Tidsskrift | Scientific Data |
| Vol/bind | 4 |
| Antal sider | 20 |
| ISSN | 2052-4463 |
| DOI | |
| Status | Udgivet - 19 dec. 2017 |
Bibliografisk note
Tidsskriftet har 23.01.18 udsendt et ERRATUM: Førsteforfatteren Jason Flannick er fejlagtigt blevet registreret som Flannick Jason. Se: www.nature.com/articles/sdata20182.Fingeraftryk
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I: Scientific Data, Bind 4, 170179, 19.12.2017.
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review
TY - JOUR
T1 - Sequence data and association statistics from 12,940 type 2 diabetes cases and controls
AU - Jason, Flannick
AU - Fuchsberger, Christian
AU - Mahajan, Anubha
AU - Teslovich, Tanya M
AU - Agarwala, Vineeta
AU - Gaulton, Kyle J
AU - Caulkins, Lizz
AU - Koesterer, Ryan
AU - Ma, Clement
AU - Moutsianas, Loukas
AU - McCarthy, Davis J
AU - Rivas, Manuel A
AU - Perry, John R B
AU - Sim, Xueling
AU - Blackwell, Thomas W
AU - Robertson, Neil R
AU - Rayner, N William
AU - Cingolani, Pablo
AU - Locke, Adam E
AU - Tajes, Juan Fernandez
AU - Highland, Heather M
AU - Dupuis, Josee
AU - Chines, Peter S
AU - Lindgren, Cecilia M
AU - Hartl, Christopher
AU - Jackson, Anne U
AU - Chen, Han
AU - Huyghe, Jeroen R
AU - van de Bunt, Martijn
AU - Pearson, Richard D
AU - Kumar, Ashish
AU - Müller-Nurasyid, Martina
AU - Grarup, Niels
AU - Stringham, Heather M
AU - Gamazon, Eric R
AU - Lee, Jaehoon
AU - Chen, Yuhui
AU - Scott, Robert A
AU - Below, Jennifer E
AU - Chen, Peng
AU - Huang, Jinyan
AU - Go, Min Jin
AU - Stitzel, Michael L
AU - Pasko, Dorota
AU - Parker, Stephen C J
AU - Varga, Tibor V
AU - Green, Todd
AU - Beer, Nicola L
AU - Day-Williams, Aaron G
AU - Ferreira, Teresa
AU - Fingerlin, Tasha
AU - Horikoshi, Momoko
AU - Hu, Cheng
AU - Huh, Iksoo
AU - Ikram, Mohammad Kamran
AU - Kim, Bong-Jo
AU - Kim, Yongkang
AU - Kim, Young Jin
AU - Kwon, Min-Seok
AU - Lee, Juyoung
AU - Lee, Selyeong
AU - Lin, Keng-Han
AU - Maxwell, Taylor J
AU - Nagai, Yoshihiko
AU - Wang, Xu
AU - Welch, Ryan P
AU - Yoon, Joon
AU - Zhang, Weihua
AU - Barzilai, Nir
AU - Voight, Benjamin F
AU - Han, Bok-Ghee
AU - Jenkinson, Christopher P
AU - Kuulasmaa, Teemu
AU - Kuusisto, Johanna
AU - Manning, Alisa
AU - Ng, Maggie C Y
AU - Palmer, Nicholette D
AU - Balkau, Beverley
AU - Stančáková, Alena
AU - Abboud, Hanna E
AU - Boeing, Heiner
AU - Giedraitis, Vilmantas
AU - Prabhakaran, Dorairaj
AU - Gottesman, Omri
AU - Scott, James
AU - Carey, Jason
AU - Kwan, Phoenix
AU - Grant, George
AU - Smith, Joshua D
AU - Neale, Benjamin M
AU - Purcell, Shaun
AU - Butterworth, Adam S
AU - Howson, Joanna M M
AU - Lee, Heung Man
AU - Lu, Yingchang
AU - Kwak, Soo-Heon
AU - Zhao, Wei
AU - Danesh, John
AU - Lam, Vincent K L
AU - Park, Kyong Soo
AU - Saleheen, Danish
AU - So, Wing Yee
AU - Tam, Claudia H T
AU - Afzal, Uzma
AU - Aguilar, David
AU - Arya, Rector
AU - Aung, Tin
AU - Chan, Edmund
AU - Navarro, Carmen
AU - Cheng, Ching-Yu
AU - Palli, Domenico
AU - Correa, Adolfo
AU - Curran, Joanne E
AU - Rybin, Dennis
AU - Farook, Vidya S
AU - Fowler, Sharon P
AU - Freedman, Barry I
AU - Griswold, Michael
AU - Hale, Daniel Esten
AU - Hicks, Pamela J
AU - Khor, Chiea-Chuen
AU - Kumar, Satish
AU - Lehne, Benjamin
AU - Thuillier, Dorothée
AU - Lim, Wei Yen
AU - Liu, Jianjun
AU - Loh, Marie
AU - Musani, Solomon K
AU - Puppala, Sobha
AU - Scott, William R
AU - Yengo, Loïc
AU - Tan, Sian-Tsung
AU - Taylor, Herman A
AU - Thameem, Farook
AU - Wilson, Gregory
AU - Wong, Tien Yin
AU - Njølstad, Pål Rasmus
AU - Levy, Jonathan C
AU - Mangino, Massimo
AU - Bonnycastle, Lori L
AU - Schwarzmayr, Thomas
AU - Fadista, João
AU - Surdulescu, Gabriela L
AU - Herder, Christian
AU - Groves, Christopher J
AU - Wieland, Thomas
AU - Bork-Jensen, Jette
AU - Brandslund, Ivan
AU - Christensen, Cramer
AU - Koistinen, Heikki A
AU - Doney, Alex S F
AU - Kinnunen, Leena
AU - Esko, Tõnu
AU - Farmer, Andrew J
AU - Hakaste, Liisa
AU - Hodgkiss, Dylan
AU - Kravic, Jasmina
AU - Lyssenko, Valeri
AU - Hollensted, Mette
AU - Jørgensen, Marit E
AU - Jørgensen, Torben
AU - Ladenvall, Claes
AU - Justesen, Johanne Marie
AU - Käräjämäki, Annemari
AU - Kriebel, Jennifer
AU - Rathmann, Wolfgang
AU - Lannfelt, Lars
AU - Lauritzen, Torsten
AU - Narisu, Narisu
AU - Linneberg, Allan
AU - Melander, Olle
AU - Milani, Lili
AU - Neville, Matt
AU - Orho-Melander, Marju
AU - Qi, Lu
AU - Qi, Qibin
AU - Roden, Michael
AU - Rolandsson, Olov
AU - Swift, Amy
AU - Rosengren, Anders H
AU - Stirrups, Kathleen
AU - Wood, Andrew R
AU - Mihailov, Evelin
AU - Blancher, Christine
AU - Carneiro, Mauricio O
AU - Maguire, Jared
AU - Poplin, Ryan
AU - Shakir, Khalid
AU - Fennell, Timothy
AU - DePristo, Mark
AU - de Angelis, Martin Hrabé
AU - Deloukas, Panos
AU - Gjesing, Anette P
AU - Jun, Goo
AU - Nilsson, Peter
AU - Murphy, Jacquelyn
AU - Onofrio, Robert
AU - Thorand, Barbara
AU - Hansen, Torben
AU - Meisinger, Christa
AU - Hu, Frank B
AU - Isomaa, Bo
AU - Karpe, Fredrik
AU - Liang, Liming
AU - Peters, Annette
AU - Huth, Cornelia
AU - O'Rahilly, Stephen P
AU - Palmer, Colin N A
AU - Pedersen, Oluf
AU - Rauramaa, Rainer
AU - Tuomilehto, Jaakko
AU - Salomaa, Veikko
AU - Watanabe, Richard M
AU - Syvänen, Ann-Christine
AU - Bergman, Richard N
AU - Bharadwaj, Dwaipayan
AU - Bottinger, Erwin P
AU - Cho, Yoon Shin
AU - Chandak, Giriraj R
AU - Chan, Juliana Cn
AU - Chia, Kee Seng
AU - Daly, Mark J
AU - Ebrahim, Shah B
AU - Langenberg, Claudia
AU - Elliott, Paul
AU - Jablonski, Kathleen A
AU - Lehman, Donna M
AU - Jia, Weiping
AU - Ma, Ronald C W
AU - Pollin, Toni I
AU - Sandhu, Manjinder
AU - Tandon, Nikhil
AU - Froguel, Philippe
AU - Barroso, Inês
AU - Teo, Yik Ying
AU - Zeggini, Eleftheria
AU - Loos, Ruth J F
AU - Small, Kerrin S
AU - Ried, Janina S
AU - DeFronzo, Ralph A
AU - Grallert, Harald
AU - Glaser, Benjamin
AU - Metspalu, Andres
AU - Wareham, Nicholas J
AU - Walker, Mark
AU - Banks, Eric
AU - Gieger, Christian
AU - Ingelsson, Erik
AU - Im, Hae Kyung
AU - Illig, Thomas
AU - Franks, Paul W
AU - Buck, Gemma
AU - Trakalo, Joseph
AU - Buck, David
AU - Prokopenko, Inga
AU - Mägi, Reedik
AU - Lind, Lars
AU - Farjoun, Yossi
AU - Owen, Katharine R
AU - Gloyn, Anna L
AU - Strauch, Konstantin
AU - Tuomi, Tiinamaija
AU - Kooner, Jaspal Singh
AU - Lee, Jong-Young
AU - Park, Taesung
AU - Donnelly, Peter
AU - Morris, Andrew D
AU - Hattersley, Andrew T
AU - Bowden, Donald W
AU - Collins, Francis S
AU - Atzmon, Gil
AU - Chambers, John C
AU - Spector, Timothy D
AU - Laakso, Markku
AU - Strom, Tim M
AU - Bell, Graeme I
AU - Blangero, John
AU - Duggirala, Ravindranath
AU - Tai, E Shyong
AU - McVean, Gilean
AU - Hanis, Craig L
AU - Wilson, James G
AU - Seielstad, Mark
AU - Frayling, Timothy M
AU - Meigs, James B
AU - Cox, Nancy J
AU - Sladek, Rob
AU - Lander, Eric S
AU - Gabriel, Stacey
AU - Mohlke, Karen L
AU - Meitinger, Thomas
AU - Groop, Leif
AU - Abecasis, Goncalo
AU - Scott, Laura J
AU - Morris, Andrew P
AU - Kang, Hyun Min
AU - Altshuler, David
AU - Burtt, Noël P
AU - Florez, Jose C
AU - Boehnke, Michael
AU - McCarthy, Mark I
N1 - The journal has published an ERRATUM on 23.01.18: The first author Jason Flannick has incorrectly been registered as Flannick Jason. See: www.nature.com/articles/sdata20182.
PY - 2017/12/19
Y1 - 2017/12/19
N2 - 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.
AB - 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.
KW - Journal Article
U2 - 10.1038/sdata.2017.179
DO - 10.1038/sdata.2017.179
M3 - Journal article
C2 - 29257133
SN - 2052-4463
VL - 4
JO - Scientific Data
JF - Scientific Data
M1 - 170179
ER -