Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes
Open accessAbstract
Genome-wide association (GWA) studies have identified multiple loci at which common variants modestly but reproducibly influence risk of type 2 diabetes (T2D). Established associations to common and rare variants explain only a small proportion of the heritability of T2D. As previously published analyses had limited power to identify variants with modest effects, we carried out meta-analysis of three T2D GWA scans comprising 10,128 individuals of European descent and approximately 2.2 million SNPs (directly genotyped and imputed), followed by replication testing in an independent sample with an effective sample size of up to 53,975. We detected at least six previously unknown loci with robust evidence for association, including the JAZF1 (P = 5.0 x 10(-14)), CDC123-CAMK1D (P = 1.2 x 10(-10)), TSPAN8-LGR5 (P = 1.1 x 10(-9)), THADA (P = 1.1 x 10(-9)), ADAMTS9 (P = 1.2 x 10(-8)) and NOTCH2 (P = 4.1 x 10(-8)) gene regions. Our results illustrate the value of large discovery and follow-up samples for gaining further insights into the inherited basis of T2D.
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Genome-wide association studies link CDKN2A, CDKN2B, CDC123 and CDKAL1 to type 2 diabetes risk.
“Strikingly, recent genome-wide association studies link the cyclin-dependent kinase inhibitors CDKN2A and CDKN2B (encoding p15Ink4b) and the cell cycle regulators CDC123 and CDKAL1 to the risk of type 2 diabetes [34–37].”
From Expansion of β-cell mass in response to pregnancy (2010) · cites this paper as [37]
The power to detect associations has been low; first-wave GWASs identified only a fraction of loci findable with larger sample sizes, and increasing power by meta-analysis and replication increased yield to more than 100 replicated loci for T2D, serum lipids, Crohn's disease, and height.
“3) The power to detect associations has been low. Given the effect sizes now known to exist, and the need to exceed stringent statistical thresholds, the first wave of GWASs provided low power to discover disease-causing loci (81, 82).”
From Genetic Mapping in Human Disease (2008) · cites this paper as [83]
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- Authors
- Wellcome Trust Case Control Consortium, Zeggini, E., Scott, L. J., Saxena, R., Voight, B. F., Marchini, J. L., Hu, T., de Bakker, P. I., Abecasis, G. R., Almgren, P., Andersen, G., Ardlie, K., Boström, K. B., Bergman, R. N., Bonnycastle, L. L., Borch-Johnsen, K., Burtt, N. P., Chen, H., Chines, P. S., Daly, M. J., Deodhar, P., Ding, C.-J., Doney, A. S. F., Duren, W. L., Elliott, K. S., Erdos, M. R., Frayling, T. M., Freathy, R. M., Gianniny, L., Grallert, H., Grarup, N., Groves, C. J., Guiducci, C., Hansen, T., Herder, C., Hitman, G. A., Hughes, T. E., Isomaa, B., Jackson, A. U., Jørgensen, T., Kong, A., Kubalanza, K., Kuruvilla, F. G., Kuusisto, J., Langenberg, C., Lango, H., Lauritzen, T., Li, Y., Lindgren, C. M., Lyssenko, V., Marvelle, A. F., Meisinger, C., Midthjell, K., Mohlke, K. L., Morken, M. A., Morris, A. D., Narisu, N., Nilsson, P., Owen, K. R., Palmer, C. N., Payne, F., Perry, J. R. B., Pettersen, E., Platou, C., Prokopenko, I., Qi, L., Qin, L., Rayner, N. W., Rees, M., Roix, J. J., Sandbæk, A., Shields, B., Sjögren, M., Steinthorsdottir, V., Stringham, H. M., Swift, A. J., Thorleifsson, G., Thorsteinsdottir, U., Timpson, N. J., Tuomi, T., Tuomilehto, J., Walker, M., Watanabe, R. M., Weedon, M. N., Willer, C. J., Illig, T., Hveem, K., Hu, F. B., Laakso, M., Stefansson, K., Pedersen, O., Wareham, N. J., Barroso, I., Hattersley, A. T., Collins, F. S., Groop, L., McCarthy, M. I., Boehnke, M., & Altshuler, D.
- Affiliations
- Centre for Human Genetics (GB)
- University of Michigan (US)
- Broad Institute (US)
- University of Oxford (GB)
- Lund University (SE)
- Steno Diabetes Center Copenhagen (DK)
- Skaraborgsinstitutet (SE)
- University of Southern California (US)
- National Human Genome Research Institute (US)
- Ninewells Hospital (GB)
- University of Exeter (GB)
- Helmholtz Munich (DE)
- Deutsches Diabetes-Zentrum e.V. (DE)
- Royal London Hospital (GB)
- Folkhälsans Forskningscentrum (FI)
- Glostrup Hospital (DK)
- deCODE Genetics (Iceland) (IS)
- Kuopio University Hospital (FI)
- Addenbrooke's Hospital (GB)
- Aarhus University (DK)
- University of North Carolina at Chapel Hill (US)
- Norwegian University of Science and Technology (NO)
- Wellcome Sanger Institute (GB)
- Brigham and Women's Hospital (US)
- University of Helsinki (FI)
- Newcastle University (GB)
- Corresponding author
- McCarthy, Mark I
- Boehnke, Michael
- Altshuler, David
- ORCID
- Zeggini, Eleftheria
- Scott, Laura J
- Saxena, Richa
- Voight, Benjamin F
- Marchini, Jonathan L
- Abecasis, Gonçalo R
- Almgren, Peter
- Andersen, Gitte
- Ardlie, Kristin
- Boström, Kristina Bengtsson
- Bergman, Richard N
- Bonnycastle, Lori L
- Burtt, Noël P
- Chen, Hong
- Daly, Mark J
- Doney, Alex S F
- Elliott, Katherine S
- Erdos, Michael R
- Frayling, Timothy M
- Freathy, Rachel M
- Grallert, Harald
- Grarup, Niels
- Groves, Christopher J
- Hansen, Torben
- Herder, Christian
- Hitman, Graham A
- Hughes, Thomas E
- Jackson, Anne U
- Jørgensen, Torben
- Kong, Augustine
- Langenberg, Claudia
- Lauritzen, Torsten
- Li, Yun
- Lindgren, Cecilia M
- Lyssenko, Valeriya
- Meisinger, Christa
- Mohlke, Karen L
- Morris, Andrew D
- Narisu, Narisu
- Nilsson, Peter
- Owen, Katharine R
- Payne, Felicity
- Perry, John R B
- Prokopenko, Inga
- Qi, Lu
- Rayner, Nigel W
- Rees, Matthew
- Shields, Beverley
- Stringham, Heather M
- Timpson, Nicholas J
- Watanabe, Richard M
- Weedon, Michael N
- Willer, Cristen J
- Hu, Frank B
- Laakso, Markku
- Pedersen, Oluf
- Wareham, Nicholas J
- Barroso, Inês
- Hattersley, Andrew T
- Collins, Francis S
- Groop, Leif
- McCarthy, Mark I
- Boehnke, Michael
- Altshuler, David
- Venue
- Nature Genetics
- Published
- 2008-03-30
- Volume
- 40
- Issue
- 5
- Pages
- 638-645
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC2672416
- OpenAlex
- W1978215768
- Cited by
- 1,864
- References
- 28
- Citations by year
- 2026: 15 · 2025: 28 · 2024: 25 · 2023: 32 · 2022: 40 · 2021: 50 · 2020: 48 · 2019: 49 · 2018: 52 · 2017: 73 · 2016: 83 · 2015: 109 · 2014: 118 · 2013: 151 · 2012: 173
- FWCI
- 25.44
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion)
- PubMed Central (acceptedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- Site cant be reached (submittedVersion)
- Explore Bristol Research (submittedVersion)
- OPUS (Augsburg University) (submittedVersion)
- Newcastle University ePrints (Newcastle Univesity)
- Funders
- Wellcome Trust (072960, GR072960, 077016, 079557, 090532, 076113)
- National Institute for Health and Care Research (DHCS/07/07/008)
- National Institutes of Health (n01hg065403-000)
- Medical Research Council (G0601261, G0600705)
- National Heart, Lung, and Blood Institute (U01HL084729, HL-084729)
- National Institute on Drug Abuse (U54DA021519)
- National Human Genome Research Institute (Z01HG000024, U01HG004399, R01HG002651, N01 HG065403, HG002651, U01HG004171)
- National Cancer Institute (CA-87969, P01CA087969)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK-072193, R01DK072193, U01DK062370, R01DK058845, R56DK062370, R01DK029867, DK-062370, DK58845, P30DK040561, R01DK062370)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Diabetes and associated disorders
- Keywords
- type 2 diabetes, genetic susceptibility loci, replication, JAZF1, THADA, ADAMTS9, Notch2, common genetic variants, heritability, European ancestry
- MeSH terms
- Diabetes Mellitus, Type 2, Humans, Genome, Human, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide
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