Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes
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Abstract
We aggregated coding variant data for 81,412 type 2 diabetes cases and 370,832 controls of diverse ancestry, identifying 40 coding variant association signals (P < 2.2 × 10−7); of these, 16 map outside known risk-associated loci. We make two important observations. First, only five of these signals are driven by low-frequency variants: even for these, effect sizes are modest (odds ratio ≤1.29). Second, when we used large-scale genome-wide association data to fine-map the associated variants in their regional context, accounting for the global enrichment of complex trait associations in coding sequence, compelling evidence for coding variant causality was obtained for only 16 signals. At 13 others, the associated coding variants clearly represent ‘false leads’ with potential to generate erroneous mechanistic inference. Coding variant associations offer a direct route to biological insight for complex diseases and identification of validated therapeutic targets; however, appropriate mechanistic inference requires careful specification of their causal contribution to disease predisposition. Trans-ethnic analyses of exome array data identify new risk loci for type 2 diabetes. Fine-mapping analyses using genome-wide association data show that the index coding variants represent the likely causal variants at only a subset of these loci.
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In several independent cohorts, subgroups have been identified that were either characterized by lower pancreatic β-cell function as described by lower HOMA2-B indices or distinct subgroups characterized by higher insulin resistance as described by higher HOMA2-IR indices.
“In several independent cohorts, subgroups have been identified that were either characterized by lower pancreatic β-cell function as described by lower HOMA2-B indices or distinct subgroups characterized by higher insulin resistance as described by higher HOMA2-IR indices (17-19).”
From Tirzepatide Improved Markers of Islet Cell Function and Insulin Sensitivity in People With T2D (SURPASS-2) (2024) · cites this paper as [19]
Split into 2 atoms — 0 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 2 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredJAKMIP1 is associated with type 2 diabetes and medications used to treat it.
“associated with type 2 diabetes and medications used to treat it82–84.”
From Genetic determinants of plasma protein levels in the Estonian population (2024) · cites this paper as [82]
The Results sections on coding-variant fine-mapping and T2D loci discuss associations for other genes, but the passages found do not mention JAKMIP1. Searches for JAKMIP1 and diabetes medications or treatment found no passage linking that gene to either T2D or its medications; the claim cannot be verified from our copy. (LLM, conf=0.72)
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Broce, I. J., Tan, C. H., Fan, C. C., Jansen, I., Savage, J. E., Witoelar, A., Wen, N., Hess, C. P., Dillon, W. P., Glastonbury, C. M., et al. (2019) · Acta Neuropathologica · doi:10.1007/s00401-018-1928-6 · Cited by 140 · see citing works
Phenotypic and genetic classification of diabetes
Deutsch, A. J., Ahlqvist, E., & Udler, M. S. (2022) · Diabetologia · doi:10.1007/s00125-022-05769-4 · Cited by 108 · see citing works
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Self-citationGenetic determinants of plasma protein levels in the Estonian population
Kalnapenkis, A., Jõeloo, M., Lepik, K., Kukuškina, V., Kals, M., Alasoo, K., Estonian Biobank Research Team, Metspalu, A., Milani, L., Nelis, M., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-57966-3 · Cited by 11 · see citing works
- Authors
- Mahajan, A., Wessel, J., Willems, S. M., Zhao, W., Robertson, N. R., Chu, A. Y., Gan, W., Kitajima, H., Taliun, D., Rayner, N. W., Guo, X., Lu, Y., Li, M., Jensen, R. A., Hu, Y., Huo, S., Lohman, K. K., Zhang, W., Cook, J. P., Prins, B. P., Flannick, J., Grarup, N., Trubetskoy, V. V., Kravic, J., Kim, Y. J., Rybin, D. V., Yaghootkar, H., Müller-Nurasyid, M., Meidtner, K., Li-Gao, R., Varga, T. V., Marten, J., Li, J., Smith, A. V., An, P., Ligthart, S., Gustafsson, S., Malerba, G., Demirkan, A., Tajes, J. F., Steinthorsdottir, V., Wuttke, M., Lecoeur, C., Preuss, M., Bielak, L. F., Graff, M., Highland, H. M., Justice, A. E., Liu, D. J., Marouli, E., Peloso, G. M., Warren, H. R., ExomeBP Consortium, MAGIC Consortium, GIANT Consortium, Afaq, S., Afzal, S., Ahlqvist, E., Almgren, P., Amin, N., Bang, L. B., Bertoni, A. G., Bombieri, C., Bork-Jensen, J., Brandslund, I., Brody, J. A., Burtt, N. P., Canouil, M., Chen, Y.-D. I., Cho, Y. S., Christensen, C., Eastwood, S. V., Eckardt, K.-U., Fischer, K., Gambaro, G., Giedraitis, V., Grove, M. L., de Haan, H. G., Hackinger, S., Hai, Y., Han, S., Tybjærg-Hansen, A., Hivert, M.-F., Isomaa, B., Jäger, S., Jørgensen, M. E., Jørgensen, T., Käräjämäki, A., Kim, B.-J., Kim, S. S., Koistinen, H. A., Kovacs, P., Kriebel, J., Kronenberg, F., Läll, K., Lange, L. A., Lee, J.-J., Lehne, B., Li, H., Lin, K.-H., Linneberg, A., Liu, C.-T., Liu, J., Loh, M., Mägi, R., Mamakou, V., McKean-Cowdin, R., Nadkarni, G., Neville, M., Nielsen, S. F., Ntalla, I., Peyser, P. A., Rathmann, W., Rice, K., Rich, S. S., Rode, L., Rolandsson, O., Schönherr, S., Selvin, E., Small, K. S., Stančáková, A., Surendran, P., Taylor, K. D., Teslovich, T. M., Thorand, B., Thorleifsson, G., Tin, A., Tönjes, A., Varbo, A., Witte, D. R., Wood, A. R., Yajnik, P., Yao, J., Yengo, L., Young, R., Amouyel, P., Boeing, H., Boerwinkle, E., Bottinger, E. P., Chowdhury, R., Collins, F. S., Dedoussis, G., Dehghan, A., Deloukas, P., Ferrario, M. M., Ferrières, J., Florez, J. C., Frossard, P., Gudnason, V., Harris, T. B., Heckbert, S. R., Howson, J. M. M., Ingelsson, M., Kathiresan, S., Kee, F., Kuusisto, J., Langenberg, C., Launer, L. J., Lindgren, C. M., Männistö, S., Meitinger, T., Melander, O., Mohlke, K. L., Moitry, M., Morris, A. D., Murray, A. D., de Mutsert, R., Orho-Melander, M., Owen, K. R., Perola, M., Peters, A., Province, M. A., Rasheed, A., Ridker, P. M., Rivadineira, F., Rosendaal, F. R., Rosengren, A. H., Salomaa, V., Sheu, W. H.-H., Sladek, R., Smith, B. H., Strauch, K., Uitterlinden, A. G., Varma, R., Willer, C. J., Blüher, M., Butterworth, A. S., Chambers, J. C., Chasman, D. I., Danesh, J., van Duijn, C., Dupuis, J., Franco, O. H., Franks, P. W., Froguel, P., Grallert, H., Groop, L., Han, B.-G., Hansen, T., Hattersley, A. T., Hayward, C., Ingelsson, E., Kardia, S. L. R., Karpe, F., Kooner, J. S., Köttgen, A., Kuulasmaa, K., Laakso, M., Lin, X., Lind, L., Liu, Y., Loos, R. J. F., Marchini, J., Metspalu, A., Mook-Kanamori, D., Nordestgaard, B. G., Palmer, C. N. A., Pankow, J. S., Pedersen, O., Psaty, B. M., Rauramaa, R., Sattar, N., Schulze, M. B., Soranzo, N., Spector, T. D., Stefansson, K., Stumvoll, M., Thorsteinsdottir, U., Tuomi, T., Tuomilehto, J., Wareham, N. J., Wilson, J. G., Zeggini, E., Scott, R. A., Barroso, I., Frayling, T. M., Goodarzi, M. O., Meigs, J. B., Boehnke, M., Saleheen, D., Morris, A. P., Rotter, J. I., & McCarthy, M. I.
- Affiliations
- Centre for Human Genetics (GB)
- Indiana University Indianapolis (US)
- University of Cambridge (GB)
- University of Pennsylvania (US)
- Brigham and Women's Hospital (US)
- University of Michigan (US)
- Harbor–UCLA Medical Center (US)
- Icahn School of Medicine at Mount Sinai (US)
- University of Washington (US)
- Chinese Academy of Sciences (CN)
- Wake Forest University Health Sciences (US)
- Ealing Hospital (GB)
- University of Liverpool (GB)
- Wellcome Sanger Institute (GB)
- Broad Institute (US)
- University of Copenhagen (DK)
- Korea National Institute of Health (KR)
- Boston University (US)
- University of Exeter (GB)
- German Center for Diabetes Research (DE)
- Lund University (SE)
- Institute of Genetics and Cancer (GB)
- Stanford Medicine (US)
- University of Iceland (IS)
- Washington University in St. Louis (US)
- Erasmus MC (NL)
- Uppsala University (SE)
- University of Verona (IT)
- University of Freiburg (DE)
- University of North Carolina at Chapel Hill (US)
- The University of Texas Health Science Center at Houston (US)
- Pennsylvania State University (US)
- Queen Mary University of London (GB)
- Imperial College London (GB)
- Copenhagen University Hospital (DK)
- University of Southern Denmark (DK)
- Centre National de la Recherche Scientifique (FR)
- Hallym University (KR)
- Vejle Sygehus (DK)
- University College London (GB)
- Charité – Universitätsmedizin Berlin (DE)
- University of Tartu (EE)
- Università Cattolica del Sacro Cuore (IT)
- Université de Sherbrooke (CA)
- Folkhälsans Forskningscentrum (FI)
- Vaasa Central Hospital (FI)
- University of Helsinki (FI)
- IFB Adiposity Diseases (DE)
- Helmholtz Munich (DE)
- Innsbruck Medical University (AT)
- University of Colorado Anschutz (US)
- Taichung Veterans General Hospital (TW)
- Agency for Science, Technology and Research (SG)
- National and Kapodistrian University of Athens (GR)
- University of Oxford (GB)
- Deutsches Diabetes-Zentrum e.V. (DE)
- University of Virginia (US)
- Herlev Hospital (DK)
- Umeå University (SE)
- Johns Hopkins University (US)
- King's College London (GB)
- University of Eastern Finland (FI)
- Leipzig University (DE)
- Aarhus University (DK)
- Inserm (FR)
- German Institute of Human Nutrition (DE)
- Baylor College of Medicine (US)
- National Institutes of Health (US)
- Harokopio University of Athens (GR)
- Center for Non-Communicable Diseases (PK)
- Queen's University Belfast (GB)
- Finnish Institute for Health and Welfare (FI)
- Hôpitaux Universitaires de Strasbourg (FR)
- University of Aberdeen (GB)
- Leiden University Medical Center (NL)
- University of Dundee (GB)
- University of Southern California (US)
- Imperial College Healthcare NHS Trust (GB)
- Harvard University (US)
- Institut für Humangenetik (DE)
- University of Minnesota (US)
- Kaiser Permanente Washington Health Research Institute (US)
- University of Glasgow (GB)
- Universität für Weiterbildung Krems (AT)
- University of Mississippi Medical Center (US)
- Cedars-Sinai Medical Center (US)
- The Lundquist Institute (US)
- Corresponding author
- Mahajan, Anubha
- Rotter, Jerome I.
- McCarthy, Mark I.
- ORCID
- Mahajan, Anubha
- Wessel, Jennifer
- Willems, Sara M.
- Zhao, Wei
- Chu, Audrey Y.
- Gan, Wei
- Kitajima, Hidetoshi
- Taliun, Daniel
- Rayner, N. William
- Guo, Xiuqing
- Lu, Yingchang
- Li, Man
- Hu, Yao
- Huo, Shaofeng
- Zhang, Weihua
- Cook, James P.
- Prins, Bram Peter
- Flannick, Jason
- Grarup, Niels
- Trubetskoy, Vassily Vladimirovich
- Kim, Young Jin
- Rybin, Denis V.
- Yaghootkar, Hanieh
- Meidtner, Karina
- Varga, Tibor V.
- Marten, Jonathan
- Smith, Albert Vernon
- An, Ping
- Gustafsson, Stefan
- Malerba, Giovanni
- Wuttke, Matthias
- Preuss, Michael
- Bielak, Lawrence F.
- Highland, Heather M.
- Justice, Anne E.
- Liu, Dajiang J.
- Marouli, Eirini
- Peloso, Gina Marie
- Warren, Helen R.
- Afzal, Shoaib
- Ahlqvist, Emma
- Almgren, Peter
- Amin, Najaf
- Bertoni, Alain G.
- Brandslund, Ivan
- Brody, Jennifer A.
- Burtt, Noël P.
- Canouil, Mickaël
- Chen, Yii-Der Ida
- Cho, Yoon Shin
- Eastwood, Sophie V.
- Eckardt, Kai-Uwe
- Fischer, Krista
- Gambaro, Giovanni
- Giedraitis, Vilmantas
- Grove, Megan L.
- Hackinger, Sophie
- Hai, Yang
- Han, Sohee
- Hivert, Marie-France
- Jäger, Susanne
- Jørgensen, Marit E.
- Jørgensen, Torben
- Käräjämäki, Annemari
- Kim, Bong-Jo
- Kim, Sung Soo
- Koistinen, Heikki A.
- Kovacs, Peter
- Kriebel, Jennifer
- Kronenberg, Florian
- Läll, Kristi
- Lee, Jung-Jin
- Lin, Keng-Hung
- Linneberg, Allan
- Liu, Jun
- Loh, Marie
- Mägi, Reedik
- Mamakou, Vasiliki
- Nadkarni, Girish
- Neville, Matt
- Nielsen, Sune F.
- Peyser, Patricia A.
- Rathmann, Wolfgang
- Rice, Kenneth
- Rich, Stephen S.
- Rode, Line
- Rolandsson, Olov
- Schönherr, Sebastian
- Selvin, Elizabeth
- Small, Kerrin S.
- Surendran, Praveen
- Taylor, Kent D.
- Thorand, Barbara
- Tin, Adrienne
- Tönjes, Anke
- Witte, Daniel R.
- Wood, Andrew R.
- Yajnik, Pranav
- Yao, Jie
- Yengo, Loïc
- Young, Robin
- Amouyel, Philippe
- Boeing, Heiner
- Boerwinkle, Eric
- Chowdhury, Rajiv
- Collins, Francis S.
- Dedoussis, George
- Dehghan, Abbas
- Deloukas, Panos
- Ferrières, Jean
- Gudnason, Vilmundur
- Harris, Tamara B.
- Heckbert, Susan R.
- Howson, Joanna M. M.
- Ingelsson, Martin
- Kathiresan, Sekar
- Kee, Frank
- Langenberg, Claudia
- Launer, Lenore J.
- Lindgren, Cecilia M.
- Männistö, Satu
- Meitinger, Thomas
- Melander, Olle
- Mohlke, Karen L.
- Moitry, Marie
- Murray, Alison D.
- Owen, Katharine R.
- Perola, Markus
- Peters, Annette
- Province, Michael A.
- Ridker, Paul M.
- Rosendaal, Frits R.
- Rosengren, Anders H.
- Salomaa, Veikko
- Sheu, Wayne H.-H.
- Smith, Blair H.
- Strauch, Konstantin
- Uitterlinden, André G.
- Varma, Rohit
- Willer, Cristen J.
- Blüher, Matthias
- Butterworth, Adam S.
- Chambers, John Campbell
- Chasman, Daniel I.
- Danesh, John
- Dupuis, Josée
- Franco, Oscar H.
- Franks, Paul W.
- Froguel, Philippe
- Grallert, Harald
- Groop, Leif
- Hansen, Torben
- Hattersley, Andrew T.
- Hayward, Caroline
- Ingelsson, Erik
- Karpe, Fredrik
- Kooner, Jaspal Singh
- Köttgen, Anna
- Kuulasmaa, Kari
- Laakso, Markku
- Lind, Lars
- Loos, Ruth J. F.
- Marchini, Jonathan
- Metspalu, Andres
- Nordestgaard, Børge G.
- Pankow, James S.
- Pedersen, Oluf
- Psaty, Bruce M.
- Sattar, Naveed
- Schulze, Matthias B.
- Soranzo, Nicole
- Tuomilehto, Jaakko
- Wareham, Nicholas J.
- Wilson, James G.
- Zeggini, Eleftheria
- Scott, Robert A.
- Barroso, Inês
- Frayling, Timothy M.
- Goodarzi, Mark O.
- Meigs, James B.
- Boehnke, Michael
- Saleheen, Danish
- Morris, Andrew P.
- Rotter, Jerome I.
- McCarthy, Mark I.
- Venue
- Nature Genetics
- Published
- 2018-04
- Volume
- 50
- Issue
- 4
- Pages
- 559-571
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC5898373
- OpenAlex
- W2619003201
- Cited by
- 442
- References
- 59
- Citations by year
- 2026: 20 · 2025: 37 · 2024: 47 · 2023: 63 · 2022: 75 · 2021: 54 · 2020: 70 · 2019: 43 · 2018: 30 · 2017: 3
- FWCI
- 30.17
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Nature Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- VBN Forskningsportal (Aalborg Universitet) (publishedVersion, other-oa)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- Edinburgh Research Explorer (University of Edinburgh) (publishedVersion, other-oa)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion, cc-by-sa)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Leiden Repository (Leiden University) (submittedVersion, other-oa)
- Aberdeen University Research Archive (Aberdeen University) (submittedVersion, cc-by-nc-nd)
- Discovery Research Portal (University of Dundee) (submittedVersion, other-oa)
- University of Southern Denmark Research Portal (University of Southern Denmark) (submittedVersion, other-oa)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- HAL (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Figshare (submittedVersion)
- IrInSubria (University of Insubria) (submittedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- Site cant be reached (submittedVersion)
- Research Explorer (The University of Manchester) (submittedVersion, other-oa)
- PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion)
- Royal Devon and Exeter Research Repository (Royal Devon and Exeter) (submittedVersion)
- Spiral (Imperial College London) (submittedVersion)
- STM:n Hallinnonalan avoin julkaisuarkisto (Julkari) (submittedVersion)
- WOS
- Funders
- Eli Lilly and Company
- Pfizer
- GlaxoSmithKline
- Sanofi
- Yale University
- Regeneron Pharmaceuticals
- Wellcome Trust (068545/Z/02), G0000934, 098395/Z/12/Z)
- Incyte
- Steno Diabetes Center Copenhagen (SDCC 3. B Epidemiology)
- National Institute for Health and Care Research (NF-SI-0617-10113, NF-SI-0512-10165, NF-SI-0507-10228, NF-SI-0611-10099, NF-SI-0611-10219, NF-SI-0616-10080, NF-SI-0514-10027, NF-SI-0512-10135, NF-SI-0617-10149, NF-SI-0617-10090)
- British Heart Foundation (RG/13/13/30194, RG/14/5/30893)
- European Commission
- National Natural Science Foundation of China (81170734, 30930081)
- ZonMw (050-060-810)
- Bundesministerium für Bildung und Forschung
- Erasmus Medisch Centrum
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (184021007, 050.060.810)
- Lundbeckfonden (R16-2007-1691)
- Novo Nordisk Fonden (NNF14OC0009819, NNF14OC0011039, NNF17OC0026828)
- Hjartavernd (N01-AG-1-2100)
- National Institutes of Health (G0000934, 271201200022C, N01-AG-1-2100, 068545/Z/02, UL1TR001881)
- Centers for Disease Control and Prevention
- Genentech
- Medical Research Council (MC_UU_12015/1, MC_PC_13040, MR/M501633/1, MR/K007017/1, MR/S003746/1, MR/K023241/1, 068545/Z/02, G0000934, MC_UU_00007/10, MR/L020149/1, MR/L003120/1)
- Korea National Institute of Health
- Korea Centers for Disease Control and Prevention
- Helmholtz Zentrum München
- Münchner Zentrum für Gesundheitswissenschaften
- NIHR Cambridge Biomedical Research Centre
- National Institute on Aging (N01-AG12100)
- National Heart, Lung, and Blood Institute (068545/Z/02, U01HL130114, R01HL119443, R00HL130580, R35HL135824, R01HL105756, G0000934, T32HL007055)
- National Institute of General Medical Sciences (P20GM121334, U54GM115428)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK072193, U01DK062370, U01DK085545, U01DK105535, R01DK078616, K24DK080140, U01DK078616, R01DK098032, P30DK020572, R01DK093757, P30DK116074, P30DK063491, R01DK062370)
- National Center for Advancing Translational Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- type 2 diabetes, coding variants, fine mapping, causal variants, low-frequency variants, genetic susceptibility loci, drug target identification, genetic association signals, complex trait genetics
- MeSH terms
- Exome Sequencing, Alleles, Chromosome Mapping, Diabetes Mellitus, Type 2, Female, Humans, Male, Genetic Variation, Genetic Predisposition to Disease, White People, Genome-Wide Association Study
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.
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