Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes
Open accessAbstract
Type 1 diabetes (T1D) is a common autoimmune disorder that arises from the action of multiple genetic and environmental risk factors. We report the findings of a genome-wide association study of T1D, combined in a meta-analysis with two previously published studies. The total sample set included 7,514 cases and 9,045 reference samples. Forty-one distinct genomic locations provided evidence for association with T1D in the meta-analysis (P < 10−6). After excluding previously reported associations, we further tested 27 regions in an independent set of 4,267 cases, 4,463 controls and 2,319 affected sib-pair (ASP) families. Of these, 18 regions were replicated (P < 0.01; overall P < 5 × 10−8) and 4 additional regions provided nominal evidence of replication (P < 0.05). The many new candidate genes suggested by these results include IL10, IL19, IL20, GLIS3, CD69 and IL27.
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Genome-wide association studies have confirmed a number of non-HLA genetic factors that increase the risk of a first appearing b-cell autoantibody or type 1 diabetes, both in first degree relatives of individuals with type 1 diabetes and in the general population.
“Genome-wide association studies have confirmed a number of non-HLA genetic factors that increase the risk of a first appearing b-cell autoantibody or type 1 diabetes, both in first degree relatives of individuals with type 1 diabetes and in the general population (386,387,404,405).”
From Guidelines and Recommendations for Laboratory Analysis in the Diagnosis and Management of Diabetes Mellitus (2023) · cites this paper as [386]
The Abstract (page not supplied) reports associations between multiple non-HLA loci and type 1 diabetes, tested in case-control samples and affected sib-pair families. It does not report risk of a first-appearing beta-cell autoantibody, and the affected sib-pair families do not establish the claimed finding in first-degree relatives generally. (LLM, conf=0.88)
Experimental — accuracy not yet measuredNon-HLA genetic factors include the genes for insulin (INS), PTPN22, CTLA-4, and several others.
“Non-HLA genetic factors include the genes for insulin (INS), PTPN22, CTLA-4, and several others (386,387).”
From Guidelines and Recommendations for Laboratory Analysis in the Diagnosis and Management of Diabetes Mellitus (2023) · cites this paper as [386]
Non-HLA genetic factors include INS, PTPN22, CTLA4, and several others.
“Non-HLA genetic factors include the INS (insulin), PTPN22 [protein tyrosine phosphatase, non-receptor type 22 (lymphoid)], and CTLA4 (cytotoxic T-lymphocyte-associated protein 4) genes and several others (263,265).”
From Guidelines and recommendations for laboratory analysis in the diagnosis and management of diabetes mellitus (2011) · cites this paper as [265]
Typing polymorphisms in several GWAS-identified genes may improve the precision of genetic characterization of type 1 diabetes.
“The precision in the genetic characterization of type 1 diabetes may be extended by typing for polymorphisms in several genetic factors identified in genome-wide association studies (265).”
From Guidelines and recommendations for laboratory analysis in the diagnosis and management of diabetes mellitus (2011) · cites this paper as [265]
GWAS confirm that non-HLA factors INS, VNTR, CTLA4, PTPN22, and others raise type 1 diabetes risk in first-degree relatives and the general population.
“Genomewide association studies have confirmed that the following non-HLA genetic factors increase the risk for type 1 diabetes, both in first-degree relatives of type 1 diabetic patients and in the general population: INS, VNTR, CTLA4, PTPN22, and others (263,265,282,283).”
From Guidelines and recommendations for laboratory analysis in the diagnosis and management of diabetes mellitus (2011) · cites this paper as [265]
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Histone deacetylase (HDAC) inhibition as a novel treatment for diabetes mellitus
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- Authors
- The Type 1 Diabetes Genetics Consortium, Barrett, J. C., Clayton, D. G., Concannon, P., Akolkar, B., Cooper, J. D., Erlich, H. A., Julier, C., Morahan, G., Nerup, J., Nierras, C., Plagnol, V., Pociot, F., Schuilenburg, H., Smyth, D. J., Stevens, H., Todd, J. A., Walker, N. M., & Rich, S. S.
- Affiliations
- University of Cambridge (GB)
- University of Virginia (US)
- National Institutes of Health (US)
- Inserm (FR)
- The University of Western Australia (AU)
- Breakthrough T1D (US)
- Corresponding author
- Concannon, Patrick
- ORCID
- Venue
- Nature Genetics
- Published
- 2009-05-10
- Volume
- 41
- Issue
- 6
- Pages
- 703-707
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC2889014
- OpenAlex
- W2024108088
- Semantic Scholar
- e90868a916f206554dff1baf0d49135312549a9d
- Cited by
- 1,746
- References
- 30
- Citations by year
- 2026: 23 · 2025: 49 · 2024: 65 · 2023: 57 · 2022: 70 · 2021: 107 · 2020: 84 · 2019: 82 · 2018: 90 · 2017: 110 · 2016: 116 · 2015: 126 · 2014: 153 · 2013: 152 · 2012: 149
- FWCI
- 88.99
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion)
- Zurich Open Repository and Archive (University of Zurich) (acceptedVersion, other-oa)
- PubMed Central (acceptedVersion)
- UWA Profiles and Research Repository (UWA) (submittedVersion)
- Murdoch University Research Portal (submittedVersion)
- Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
- UCL Discovery (University College London) (submittedVersion)
- UnissResearch (Università degli Studi di Sassari) (submittedVersion)
- Lithuanian University of Health Sciences (submittedVersion)
- VUBIR (Vrije Universiteit Brussel) (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion, other-oa)
- Zurich Open Repository and Archive (University of Zurich)
- Funders
- Juvenile Diabetes Research Foundation International (U01 DK062418)
- Massachusetts General Hospital
- University of Pennsylvania
- Emory University
- Northwestern University
- University of Pittsburgh
- Louisiana State University
- Wellcome Trust (061858, 076113)
- National Institute for Health and Care Research (NF-SI-0508-10274, NF-SI-0508-10275)
- Diabetes UK
- School of Medicine, Emory University
- Medical Research Council
- NIHR Cambridge Biomedical Research Centre
- National Institute of Mental Health (MH59566, MH-60870, MH-059565, MH067257, MH-061675, MH-59586, R01MH059566, R01MH059571, MH-059571, R01MH060879, R01MH059565, R01MH060870, R01MH063420, R01MH061675, R01MH059586, R01MH059588, MH63420, R01MH067257, MH-59587, MH 060879, MH-059588, R01MH059587)
- National Human Genome Research Institute
- National Institute of Allergy and Infectious Diseases
- National Institute of Diabetes and Digestive and Kidney Diseases (K08DK002876, DK46635, DK062418, U01DK062418, R01DK046635)
- National Institute of Child Health and Human Development
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Diabetes and associated disorders
- 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
- Keywords
- type 1 diabetes, genetic susceptibility loci, autoimmune disease, IL-10, GLIS3, CD69, IL-27, candidate genes, replication of genetic associations
- MeSH terms
- Interferon-Induced Helicase, IFIH1, Algorithms, Chromosome Mapping, Chromosomes, Human, Pair 1, Chromosomes, Human, Pair 17, Chromosomes, Human, Pair 2, Diabetes Mellitus, Type 1, DNA, Family, Female, Genotype, HLA Antigens, Humans, Male, Meta-Analysis as Topic, Antigens, CD, Risk Assessment, Polymorphism, Single Nucleotide, Siblings, DEAD-box RNA Helicases, Protein Tyrosine Phosphatase, Non-Receptor Type 22, Genome-Wide Association Study, CTLA-4 Antigen
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