Celiac Disease GWAS summary statistics

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Alam, Mohammad Sayeef; Thomas, Laurent F.; Brumpton, Ben M.; Hveem, Kristian; Lundin, Knut E. A.; Withoff, Sebo; Jonkers, Iris H.; Sollid, Ludvig M.; Hjort, Rebecka; Ness-Jensen, Eivind, 2025, "Celiac Disease GWAS summary statistics", https://doi.org/10.18710/8LC9EA, DataverseNO, V1

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Description	Previous studies have uncovered genetic loci associated with celiac disease (CeD) within both the human leukocyte antigen (HLA) and non-HLA regions. However, half of the heritability remains unexplained. This study aimed to identify novel loci associated with CeD in a general adult population screened for the disease, mitigating the likely selection bias observed in previous case-control studies. The study utilized data from the fourth Trøndelag Health Study (HUNT4) in Norway, where 52,358 adults were screened for CeD using serology, identifying 465 previously undiagnosed biopsy-confirmed cases. Additionally, 377 previously diagnosed cases were identified through hospital journal searches and registry data. Genotyping of 373,185 single nucleotide polymorphisms was performed on all participant using four Illumina HumanCoreExome arrays. Imputation, using the Haplotype Reference Consortium panel, resulted in approximately 24.9 million variants, post quality control. A genome-wide association study was performed using SAIGE, and functional mapping and pathway enrichment analysis was conducted using FUMA. All except one of the 42 known autosomal loci were present in the data, of which seven reached the suggestive significance threshold (P ≤ 5 × 10−6). Thirteen independent novel associations were observed (P ≤ 5× 10−8), with the 5p15.33 locus showing the highest potential for a true association with CeD, warranting further studies to validate the findings. Notably, the IRX1 gene, located close to the 5p15.33 locus has also been associated with rheumatoid arthritis, suggesting a new shared autoimmune locus. (2024-12-12)
Subject	Medicine, Health and Life Sciences
Keyword	celiac disease, gwas, non-HLA, gluten
Related Publication	Alam, M.S., Thomas, L., Brumpton, B. et al. Population screening of adults identifies novel genetic variants associated with celiac disease. Sci Rep 15, 19764 (2025). doi: 10.1038/s41598-025-04421-6
License/Data Use Agreement	CC0 1.0

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Citation Metadata

Persistent Identifier	doi:10.18710/8LC9EA
Publication Date	2025-08-29
Title	Celiac Disease GWAS summary statistics
Author	Alam, Mohammad Sayeef (NTNU – Norwegian University of Science and Technology) - ORCID: https://orcid.org/0000-0002-1478-5975 Thomas, Laurent F. (NTNU – Norwegian University of Science and Technology) Brumpton, Ben M. (NTNU – Norwegian University of Science and Technology) Hveem, Kristian (NTNU – Norwegian University of Science and Technology) Lundin, Knut E. A. (UiO - University in Oslo) Withoff, Sebo (UMCG - University Medical Center Groningen) Jonkers, Iris H. (UMCG - University Medical Center Groningen) Sollid, Ludvig M. (UiO - University in Oslo) Hjort, Rebecka (NTNU – Norwegian University of Science and Technology) Ness-Jensen, Eivind (NTNU – Norwegian University of Science and Technology)
Point of Contact	Use email button above to contact. Alam, Mohammad Sayeef (NTNU – Norwegian University of Science and Technology)
Description	Previous studies have uncovered genetic loci associated with celiac disease (CeD) within both the human leukocyte antigen (HLA) and non-HLA regions. However, half of the heritability remains unexplained. This study aimed to identify novel loci associated with CeD in a general adult population screened for the disease, mitigating the likely selection bias observed in previous case-control studies. The study utilized data from the fourth Trøndelag Health Study (HUNT4) in Norway, where 52,358 adults were screened for CeD using serology, identifying 465 previously undiagnosed biopsy-confirmed cases. Additionally, 377 previously diagnosed cases were identified through hospital journal searches and registry data. Genotyping of 373,185 single nucleotide polymorphisms was performed on all participant using four Illumina HumanCoreExome arrays. Imputation, using the Haplotype Reference Consortium panel, resulted in approximately 24.9 million variants, post quality control. A genome-wide association study was performed using SAIGE, and functional mapping and pathway enrichment analysis was conducted using FUMA. All except one of the 42 known autosomal loci were present in the data, of which seven reached the suggestive significance threshold (P ≤ 5 × 10−6). Thirteen independent novel associations were observed (P ≤ 5× 10−8), with the 5p15.33 locus showing the highest potential for a true association with CeD, warranting further studies to validate the findings. Notably, the IRX1 gene, located close to the 5p15.33 locus has also been associated with rheumatoid arthritis, suggesting a new shared autoimmune locus. (2024-12-12)
Subject	Medicine, Health and Life Sciences
Keyword	celiac disease gwas non-HLA gluten
Related Publication	Alam, M.S., Thomas, L., Brumpton, B. et al. Population screening of adults identifies novel genetic variants associated with celiac disease. Sci Rep 15, 19764 (2025). doi: 10.1038/s41598-025-04421-6 https://doi.org/10.1038/s41598-025-04421-6
Language	English
Producer	NTNU – Norwegian University of Science and Technology (NTNU) https://www.ntnu.edu/
Production Location	Trondheim
Contributor	Data Curator : Alam, Mohammad Sayeef Project Leader : Ness-Jensen, Eivind Supervisor : Hjort, Rebecka Supervisor : Sollid, Ludvig M. Supervisor : Lundin, Knut E. A. Supervisor : Jonkers, Iris H. Supervisor : Withoff, Sebo
Funding Information	Research Council of Norway: #288308 Liaison Committee between NTNU and the Central Norway Regional Health Authority: #17/38297 Liaison Committee between NTNU and the Central Norway Regional Health Authority: #18/42795 Liaison Committee between NTNU and the Central Norway Regional Health Authority: #23/32925 NIH - National Institutes of Health: NIH R35 HL135824-03
Distributor	NTNU – Norwegian University of Science and Technology (NTNU) https://dataverse.no/dataverse/ntnu
Depositor	Alam, Mohammad Sayeef
Deposit Date	2025-02-11
Software	R, Version: 4.1.2 Plink, Version: 1.9
Documentation and Access to Sources	The Trøndelag Health Study (HUNT) has invited individuals aged 13-100 years to four surveys between 1984 and 2019. Comprehensive data from more than 140,000 individuals having participated at least once and biological material from 78,000 individual are collected. The data are stored in HUNT databank and biological material in HUNT biobank. HUNT Research Centre has permission from the Norwegian Data Inspectorate to store and handle these data. The key identification in the database is the personal identification number given to all Norwegians at birth or immigration, whilst de-identified data are sent to researchers upon approval of a research protocol by the Regional Ethical Committee and HUNT Research Centre. To protect participants’ privacy, HUNT Research Centre aims to limit storage of data outside HUNT databank and cannot deposit data in open repositories. HUNT databank has precise information on all data exported to different projects and are able to reproduce these on request. There are no restrictions regarding data export given approval of applications to HUNT Research Centre. For more information see: http://www.ntnu.edu/hunt/data

Geospatial Metadata

Geographic Coverage	Norway, Nord Trøndelag

Social Science and Humanities Metadata

Unit of Analysis	Single Nucleotide Polymorphism
Universe	All adults over 19 years.
Time Method	Cross-sectional
Data Collector	HUNT
Response Rate	54%

Life Sciences Metadata

Design Type	Case Control; Cross Sectional
Factor Type	Genetic Characteristics
Organism	Homo sapiens
Measurement Type	SNP analysis
Technology Type	Other
Technology Platform	Illumina; Other

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