The genetic architecture of type 2 diabetes
Open accessAbstract
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 whole-genome sequencing in 2,657 European individuals with and without diabetes, and exome sequencing in 12,940 individuals from five ancestry groups. To increase statistical power, we expanded the sample size via genotyping and imputation in a further 111,548 subjects. Variants associated with type 2 diabetes after sequencing were overwhelmingly common and most fell within regions previously identified by genome-wide association studies. Comprehensive enumeration of sequence variation is necessary to identify functional alleles that provide important clues to disease pathophysiology, but large-scale sequencing does not support the idea that lower-frequency variants have a major role in predisposition to type 2 diabetes.
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Increased access to exome and whole-genome sequence data has extended discovery to low-frequency and rare alleles previously inaccessible to GWAS, through direct association and imputation.
“Recently, increased access to exome and whole-genome sequence data has, through both direct association analysis45,46 and imputation3,4, extended discovery to low-frequency and rare alleles previously inaccessible to GWAS.”
From A brief history of human disease genetics (2020) · cites this paper as [45]
The collective contribution of low-frequency and rare risk alleles to overall trait variability appears modest compared with that attributable to common variants.
“Although the collective contribution of low-frequency and rare risk alleles to overall trait variability appears modest compared with that attributable to common variants45,48”
From A brief history of human disease genetics (2020) · cites this paper as [45]
The relative contributions of common and rare variants indicate that for many traits, particularly those with post-reproductive onset, purifying selection has had only limited effect.
“The relative contributions of common and rare variants indicate that, for many traits, particularly those with post-reproductive onset, purifying selection has had only limited effect45,56.”
From A brief history of human disease genetics (2020) · cites this paper as [45]
For most common diseases, polygenic inheritance involving many common variants of small effect plays a greater role than rare monogenic mutations.
“For most common diseases, polygenic inheritance, involving many common genetic variants of small effect, plays a greater role than rare monogenic mutations.2–5”
From Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations (2018) · cites this paper as [5]
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- Authors
- Fuchsberger, C., Flannick, J., Teslovich, T. M., Mahajan, A., Agarwala, V., Gaulton, K. J., Ma, C., Fontanillas, P., Moutsianas, L., McCarthy, D. J., Rivas, M. A., Perry, J. R. B., Sim, X., Blackwell, T. W., Robertson, N. R., Rayner, N. W., Cingolani, P., Locke, A. E., Tajes, J. F., Highland, H. M., Dupuis, J., Chines, P. S., Lindgren, C. M., Hartl, C., Jackson, A. U., Chen, H., Huyghe, J. R., van de Bunt, M., Pearson, R. D., Kumar, A., Müller-Nurasyid, M., Grarup, N., Stringham, H. M., Gamazon, E. R., Lee, J., Chen, Y., Scott, R. A., Below, J. E., Chen, P., Huang, J., Go, M. J., Stitzel, M. L., Pasko, D., Parker, S. C. J., Varga, T. V., Green, T., Beer, N. L., Day-Williams, A. G., Ferreira, T., Fingerlin, T., Horikoshi, M., Hu, C., Huh, I., Ikram, M. K., Kim, B.-J., Kim, Y., Kim, Y. J., Kwon, M.-S., Lee, J., Lee, S., Lin, K.-H., Maxwell, T. J., Nagai, Y., Wang, X., Welch, R. P., Yoon, J., Zhang, W., Barzilai, N., Voight, B. F., Han, B.-G., Jenkinson, C. P., Kuulasmaa, T., Kuusisto, J., Manning, A., Ng, M. C. Y., Palmer, N. D., Balkau, B., Stančáková, A., Abboud, H. E., Boeing, H., Giedraitis, V., Prabhakaran, D., Gottesman, O., Scott, J., Carey, J., Kwan, P., Grant, G., Smith, J. D., Neale, B. M., Purcell, S., Butterworth, A. S., Howson, J. M. M., Lee, H. M., Lu, Y., Kwak, S.-H., Zhao, W., Danesh, J., Lam, V. K. L., Park, K. S., Saleheen, D., So, W. Y., Tam, C. H. T., Afzal, U., Aguilar, D., Arya, R., Aung, T., Chan, E., Navarro, C., Cheng, C.-Y., Palli, D., Correa, A., Curran, J. E., Rybin, D., Farook, V. S., Fowler, S. P., Freedman, B. I., Griswold, M., Hale, D. E., Hicks, P. J., Khor, C.-C., Kumar, S., Lehne, B., Thuillier, D., Lim, W. Y., Liu, J., van der Schouw, Y. T., Loh, M., Musani, S. K., Puppala, S., Scott, W. R., Yengo, L., Tan, S.-T., Taylor, H. A., Thameem, F., Wilson, G., Wong, T. Y., Njølstad, P. R., Levy, J. C., Mangino, M., Bonnycastle, L. L., Schwarzmayr, T., Fadista, J., Surdulescu, G. L., Herder, C., Groves, C. J., Wieland, T., Bork-Jensen, J., Brandslund, I., Christensen, C., Koistinen, H. A., Doney, A. S. F., Kinnunen, L., Esko, T., Farmer, A. J., Hakaste, L., Hodgkiss, D., Kravic, J., Lyssenko, V., Hollensted, M., Jørgensen, M. E., Jørgensen, T., Ladenvall, C., Justesen, J. M., Käräjämäki, A., Kriebel, J., Rathmann, W., Lannfelt, L., Lauritzen, T., Narisu, N., Linneberg, A., Melander, O., Milani, L., Neville, M., Orho-Melander, M., Qi, L., Qi, Q., Roden, M., Rolandsson, O., Swift, A., Rosengren, A. H., Stirrups, K., Wood, A. R., Mihailov, E., Blancher, C., Carneiro, M. O., Maguire, J., Poplin, R., Shakir, K., Fennell, T., DePristo, M., Hrabé de Angelis, M., Deloukas, P., Gjesing, A. P., Jun, G., Nilsson, P., Murphy, J., Onofrio, R., Thorand, B., Hansen, T., Meisinger, C., Hu, F. B., Isomaa, B., Karpe, F., Liang, L., Peters, A., Huth, C., O’Rahilly, S. P., Palmer, C. N. A., Pedersen, O., Rauramaa, R., Tuomilehto, J., Salomaa, V., Watanabe, R. M., Syvänen, A.-C., Bergman, R. N., Bharadwaj, D., Bottinger, E. P., Cho, Y. S., Chandak, G. R., Chan, J. C. N., Chia, K. S., Daly, M. J., Ebrahim, S. B., Langenberg, C., Elliott, P., Jablonski, K. A., Lehman, D. M., Jia, W., Ma, R. C. W., Pollin, T. I., Sandhu, M., Tandon, N., Froguel, P., Barroso, I., Teo, Y. Y., Zeggini, E., Loos, R. J. F., Small, K. S., Ried, J. S., DeFronzo, R. A., Grallert, H., Glaser, B., Metspalu, A., Wareham, N. J., Walker, M., Banks, E., Gieger, C., Ingelsson, E., Im, H. K., Illig, T., Franks, P. W., Buck, G., Trakalo, J., Buck, D., Prokopenko, I., Mägi, R., Lind, L., Farjoun, Y., Owen, K. R., Gloyn, A. L., Strauch, K., Tuomi, T., Kooner, J. S., Lee, J.-Y., Park, T., Donnelly, P., Morris, A. D., Hattersley, A. T., Bowden, D. W., Collins, F. S., Atzmon, G., Chambers, J. C., Spector, T. D., Laakso, M., Strom, T. M., Bell, G. I., Blangero, J., Duggirala, R., Tai, E. S., McVean, G., Hanis, C. L., Wilson, J. G., Seielstad, M., Frayling, T. M., Meigs, J. B., Cox, N. J., Sladek, R., Lander, E. S., Gabriel, S., Burtt, N. P., Mohlke, K. L., Meitinger, T., Groop, L., Abecasis, G., Florez, J. C., Scott, L. J., Morris, A. P., Kang, H. M., Boehnke, M., Altshuler, D., & McCarthy, M. I.
- Affiliations
- Eurac Research (IT)
- Broad Institute (US)
- University of Michigan (US)
- Centre for Human Genetics (GB)
- McGill University and Génome Québec Innovation Centre (CA)
- The University of Texas Health Science Center at Houston (US)
- National Institutes of Health (US)
- Boston University (US)
- University of Copenhagen (DK)
- University of Chicago (US)
- Seoul National University (KR)
- University of Cambridge (GB)
- National University of Singapore (SG)
- Harvard University (US)
- Korea National Institute of Health (KR)
- The Jackson Laboratory for Genomic Medicine (US)
- University of Exeter (GB)
- Lund University (SE)
- University of Oxford (GB)
- Wellcome Sanger Institute (GB)
- Colorado School of Public Health (US)
- Shanghai Jiao Tong University (CN)
- Ealing Hospital NHS Trust (GB)
- Albert Einstein College of Medicine (US)
- University of Pennsylvania (US)
- The University of Texas at San Antonio Health Science Center (US)
- University of Eastern Finland (FI)
- Wake Forest University Health Sciences (US)
- Inserm (FR)
- German Institute of Human Nutrition (DE)
- Uppsala University (SE)
- Centre for Chronic Disease Control (IN)
- Icahn School of Medicine at Mount Sinai (US)
- Imperial College London (GB)
- University of Washington (US)
- Chinese University of Hong Kong (HK)
- Center for Non-Communicable Diseases (PK)
- Baylor College of Medicine (US)
- Instituto Murciano de Investigación Biosanitaria (ES)
- Istituto per lo Studio e la Prevenzione Oncologica (IT)
- University of Mississippi Medical Center (US)
- The University of Texas Rio Grande Valley (US)
- Texas Biomedical Research Institute (US)
- Agency for Science, Technology and Research (SG)
- Centre National de la Recherche Scientifique (FR)
- Jackson State University (US)
- Haukeland University Hospital (NO)
- King's College London (GB)
- Helmholtz Munich (DE)
- Deutsches Diabetes-Zentrum e.V. (DE)
- University of Southern Denmark (DK)
- Vejle Sygehus (DK)
- University of Helsinki (FI)
- Ninewells Hospital (GB)
- Finnish Institute for Health and Welfare (FI)
- Vaasa Central Hospital (FI)
- Aarhus University (DK)
- University of Tartu (EE)
- Brigham and Women's Hospital (US)
- Umeå University (SE)
- Queen Mary University of London (GB)
- Folkhälsans Forskningscentrum (FI)
- University of Dundee (GB)
- Universität für Weiterbildung Krems (AT)
- University of Southern California (US)
- Cedars-Sinai Medical Center (US)
- Institute of Genomics and Integrative Biology (IN)
- Hallym University (KR)
- Centre for Cellular and Molecular Biology (IN)
- Massachusetts General Hospital (US)
- MRC Centre for Environment and Health (GB)
- George Washington University (US)
- University of Maryland, Baltimore (US)
- All India Institute of Medical Sciences (IN)
- Newcastle University (GB)
- Imperial College Healthcare NHS Trust (GB)
- University of California, San Francisco (US)
- University of North Carolina at Chapel Hill (US)
- Corresponding author
- Boehnke, Michael
- McCarthy, Mark I.
- ORCID
- Fuchsberger, Christian
- Flannick, Jason
- Mahajan, Anubha
- Gaulton, Kyle J.
- Ma, Clement
- Fontanillas, Pierre
- Moutsianas, Loukas
- McCarthy, Davis J.
- Rivas, Manuel A.
- Perry, John R. B.
- Sim, Xueling
- Blackwell, Thomas W.
- Rayner, N. William
- Cingolani, Pablo
- Locke, Adam E.
- Highland, Heather M.
- Lindgren, Cecilia M.
- Hartl, Christopher
- Jackson, Anne U.
- Chen, Han
- Huyghe, Jeroen R.
- Pearson, Richard D.
- Kumar, Ashish
- Grarup, Niels
- Stringham, Heather M.
- Gamazon, Eric R.
- Lee, Jaehoon
- Chen, Yuhui
- Below, Jennifer E.
- Chen, Peng
- Huang, Jinyan
- Stitzel, Michael L.
- Parker, Stephen C. J.
- Varga, Tibor V.
- Beer, Nicola L.
- 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
- Wang, Xu
- Welch, Ryan P.
- Yoon, Joon
- Zhang, Weihua
- Barzilai, Nir
- Voight, Benjamin F.
- Jenkinson, Christopher P.
- Kuulasmaa, Teemu
- Manning, Alisa
- Ng, Maggie C. Y.
- Palmer, Nicholette D.
- Balkau, Beverley
- Boeing, Heiner
- Giedraitis, Vilmantas
- Prabhakaran, Dorairaj
- Scott, James
- 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
- Navarro, Carmen
- Cheng, Ching-Yu
- Palli, Domenico
- Correa, Adolfo
- Curran, Joanne E.
- Rybin, Denis
- Fowler, Sharon P.
- Freedman, Barry I.
- Griswold, Michael
- Hale, Daniel Esten
- Khor, Chiea-Chuen
- Kumar, Satish
- Liu, Jianjun
- Loh, Marie
- Puppala, Sobha
- Scott, William R.
- Yengo, Loïc
- Taylor, Herman A.
- Wilson, Gregory
- Wong, Tien Yin
- Njølstad, Pål Rasmus
- Mangino, Massimo
- Bonnycastle, Lori L.
- Fadista, João
- Herder, Christian
- Groves, Christopher J.
- Wieland, Thomas
- Brandslund, Ivan
- Koistinen, Heikki A.
- Doney, Alex S. F.
- Kinnunen, Leena
- Esko, Tõnu
- Hakaste, Liisa
- Lyssenko, Valeriya
- Hollensted, Mette
- Jørgensen, Marit E.
- Jørgensen, Torben
- Ladenvall, Claes
- Justesen, Johanne Marie
- Käräjämäki, Annemari
- Kriebel, Jennifer
- Rathmann, Wolfgang
- Lauritzen, Torsten
- Narisu, Narisu
- Linneberg, Allan
- Melander, Olle
- Milani, Lili
- Neville, Matt
- Qi, Lu
- Qi, Qibin
- Roden, Michael
- Rolandsson, Olov
- Rosengren, Anders H.
- Stirrups, Kathleen
- Wood, Andrew R.
- Blancher, Christine
- Deloukas, Panos
- Gjesing, Anette P.
- Jun, Goo
- Nilsson, Peter
- Thorand, Barbara
- Hansen, Torben
- Meisinger, Christa
- Hu, Frank B.
- Karpe, Fredrik
- Liang, Liming
- Peters, Annette
- Huth, Cornelia
- O’Rahilly, Stephen P.
- Pedersen, Oluf
- Tuomilehto, Jaakko
- Salomaa, Veikko
- Watanabe, Richard M.
- Syvänen, Ann-Christine
- Bergman, Richard N.
- Bharadwaj, Dwaipayan
- Cho, Yoon Shin
- Chandak, Giriraj R.
- Chan, Juliana C. N.
- Chia, Kee Seng
- Daly, Mark J.
- Ebrahim, Shah B.
- Langenberg, Claudia
- Elliott, Paul
- Lehman, Donna M.
- Jia, Weiping
- Pollin, Toni I.
- Sandhu, Manjinder
- Tandon, Nikhil
- Froguel, Philippe
- Barroso, Inês
- Zeggini, Eleftheria
- Loos, Ruth J. F.
- Small, Kerrin S.
- DeFronzo, Ralph A.
- Grallert, Harald
- Metspalu, Andres
- Wareham, Nicholas J.
- Walker, Mark
- Banks, Eric
- Gieger, Christian
- Ingelsson, Erik
- Im, Hae Kyung
- Franks, Paul W.
- Buck, Gemma
- Buck, David
- Prokopenko, Inga
- Mägi, Reedik
- Lind, Lars
- Farjoun, Yossi
- Owen, Katharine R.
- Gloyn, Anna L.
- Strauch, Konstantin
- 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.
- Laakso, Markku
- Blangero, John
- Duggirala, Ravindranath
- Tai, E. Shyong
- Hanis, Craig L.
- Wilson, James G.
- Seielstad, Mark
- Frayling, Timothy M.
- Meigs, James B.
- Cox, Nancy J.
- Lander, Eric S.
- Gabriel, Stacey
- Burtt, Noël P.
- Mohlke, Karen L.
- Meitinger, Thomas
- Groop, Leif
- Scott, Laura J.
- Morris, Andrew P.
- Kang, Hyun Min
- Boehnke, Michael
- Altshuler, David
- McCarthy, Mark I.
- Venue
- Nature
- Published
- 2016-07-11
- Volume
- 536
- Issue
- 7614
- Pages
- 41-47
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5034897
- OpenAlex
- W2461793432
- Cited by
- 1,051
- References
- 88
- Citations by year
- 2026: 35 · 2025: 54 · 2024: 52 · 2023: 69 · 2022: 99 · 2021: 111 · 2020: 105 · 2019: 140 · 2018: 186 · 2017: 164 · 2016: 32 · 2015: 3 · 2014: 1
- FWCI
- 139.16
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- University of Southern Denmark Research Portal (University of Southern Denmark) (publishedVersion)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- PubMed Central (acceptedVersion)
- LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
- ScholarWorks @ UTRGV (The University of Texas Rio Grande Valley) (submittedVersion)
- VBN Forskningsportal (Aalborg Universitet) (submittedVersion, other-oa)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- Discovery Research Portal (University of Dundee) (submittedVersion, other-oa)
- Lund University Publications (Lund University) (submittedVersion)
- mediaTUM (Technical University of Munich) (submittedVersion, other-oa)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion)
- Royal Devon and Exeter Research Repository (Royal Devon and Exeter) (submittedVersion)
- Spiral (Imperial College London) (submittedVersion)
- OPUS (Augsburg University) (submittedVersion)
- Open Research (University of Surrey) (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion)
- Newcastle University ePrints (Newcastle Univesity)
- Funders
- Bristol-Myers Squibb
- Wellcome Trust (095552/Z/11/Z, 084723, 100956, 092447, 090367, 098017, 085475, 098381, 095101, 064890, 086596, 095552, 090532, 098051, 100956/Z/13/Z, 200837/Z/16/Z, 083948)
- National Institute for Health and Care Research (NF-SI-0507-10228, NF-SI-0513-10109, NF-SI-0512-10077, NF-SI-0611-10136, NF-SI-0507-10380, NF-SI-0611-10099, NF-SI-0611-10219, NF-SI-0514-10027, ACF-2009-18-005)
- British Heart Foundation (SP/09/002, SP/04/002, RG/14/5/30893)
- Hungarian Scientific Research Fund
- Lundbeckfonden (R16-2007-1691)
- Novo Nordisk
- Novo Nordisk Fonden (NNF15OC0016416, NNF14OC0011039, NNF13OC0005781, NNF12OC1016167, NNF11OC1014855)
- National Institutes of Health (1s10od018522-01, 5rc2dk088389-02)
- Canadian Institutes of Health Research
- Medical Research Council (MC_UU_12015/1, MR/L01341X/1, MR/K013491/1, MC_PC_13046, G0601966, G0601261, G0800270, MR/K002414/1, MC_UU_12015/2, G0700931)
- National Institute on Aging (R01AG042188, P01AG027734, P30AG038072, R01AG046949)
- National Heart, Lung, and Blood Institute (HHSN268201300050C, HHSN268201300046C, HHSN268201300048C, HHSN268201300049C, R01HL102830, HHSN268201300047C, T32HL007055)
- National Institute of Mental Health (R01MH090937, R01MH101820)
- National Human Genome Research Institute (U01HG005773, R56HG000376, U54HG003067, R01HG000376, T32HG000040)
- National Cancer Institute (K12CA139160)
- National Institute of General Medical Sciences (T32GM007753)
- National Institute of Diabetes and Digestive and Kidney Diseases (U01DK085526, DK085526, U01DK085584, DK-072193, DK098032, U01DK085501, R01DK072193, R00DK099240, DK-085501, R00DK092251, U01DK062370, U01DK085524, R01DK066358, DK085545, RC2-DK088389, U01DK085545, K24DK110550, R01DK106236, R01DK073541, K24DK080140, R01DK101478, DK-085584, DK085524, U01DK078616, 1RC2DK088389, DK088389, DK093757, R01DK098032, P60DK020595, P30DK020572, R01DK093757, P30DK020595, R01DK062370)
- National Institute on Minority Health and Health Disparities (U54MD007588)
- 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 architecture, common genetic variants, rare variants, low-frequency variants, heritability, genetic susceptibility loci, whole genome sequencing, exome sequencing, genome-wide association study, functional alleles, disease susceptibility
- MeSH terms
- Alleles, Diabetes Mellitus, Type 2, DNA Mutational Analysis, Europe, Humans, Genetic Variation, Sample Size, Genetic Predisposition to Disease, Genome-Wide Association Study, Exome, Genotyping Techniques
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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