The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource
Open accessAbstract
The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200 000 users per year from academic research, healthcare and industry. The Catalog contains variant-trait associations and supporting metadata for >45 000 published GWAS across >5000 human traits, and >40 000 full P-value summary statistics datasets. Content is curated from publications or acquired via author submission of prepublication summary statistics through a new submission portal and validation tool. GWAS data volume has vastly increased in recent years. We have updated our software to meet this scaling challenge and to enable rapid release of submitted summary statistics. The scope of the repository has expanded to include additional data types of high interest to the community, including sequencing-based GWAS, gene-based analyses and copy number variation analyses. Community outreach has increased the number of shared datasets from under-represented traits, e.g. cancer, and we continue to contribute to awareness of the lack of population diversity in GWAS. Interoperability of the Catalog has been enhanced through links to other resources including the Polygenic Score Catalog and the International Mouse Phenotyping Consortium, refinements to GWAS trait annotation, and the development of a standard format for GWAS data.
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None of the pQTLs tagging the CNV has known associations with complex traits which are not cell type or metabolite related, according to the GWAS Catalog.
“None of the pQTLs tagging the CNV has known associations with complex traits which are not cell type or metabolite related, according to the GWAS Catalog90.”
From Genetic determinants of plasma protein levels in the Estonian population (2024) · cites this paper as [90]
The Abstract identifies the GWAS Catalog as a resource containing variant–trait associations, and TRAIT ANNOTATION IMPROVEMENTS describes its coverage of protein QTLs and other traits. But the paper does not report a search of the pQTLs tagging this CNV or establish that they lack associations with traits other than cell-type or metabolite traits. (LLM, conf=0.82)
Experimental — accuracy not yet measuredLTBP4 has been found to be associated with brain volume and Duchenne muscular dystrophy.
“LTBP4, the proposed functional gene for the CLU pQTL locus on chromosome 19 (over 4 Mb from APOE), has been found to be associated with brain volume 35 and Duchenne muscular dystrophy. 36”
From A genetic and proteomic comparison of key AD biomarkers across tissues (2024) · cites this paper as [35]
The cited paper’s Trait Annotation Improvements section describes how the GWAS Catalog records trait associations, but does not report an association between LTBP4 and Duchenne muscular dystrophy. Searches for “LTBP4 Duchenne muscular dystrophy” and “brain volume CLU LTBP4” found no passage addressing either association in our copy. (LLM, conf=0.76)
Experimental — accuracy not yet measuredCCDC50 has been found to be associated with AD.
“The proposed functional gene for the novel CSF NRGN pQTL, CCDC50, has been found to be associated with AD, indicating a potential biological pathway linking CCDC50 neurogranin (NRGN), and AD. 35”
From A genetic and proteomic comparison of key AD biomarkers across tissues (2024) · cites this paper as [35]
The Increasing Data Volume and Complexity and Discussion sections describe the GWAS Catalog and its datasets, but do not report an association between CCDC50 and Alzheimer’s disease. Searches for CCDC50 and for its association with AD or neurogranin returned no passage addressing the claim. (LLM, conf=0.76)
Experimental — accuracy not yet measuredThere was a modest but not significant enrichment of protein-coding genes related to DNA damage repair in the published AD GWAS catalog (OR=1.22, 62 GWAS/DNA damage repair genes).
“we found a modest but not significant enrichment of protein-coding genes related to DNA damage repair in the published AD GWAS catalog (NHGRI-EBI, OR= 1.22, 62 GWAS/DNA damage repair genes)”
From Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration (2023) · cites this paper as [75]
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“…52], and TCGA [ 53], PathologyAtlas [ 54], and FANTOM5 [ 55]), cell-specific expressions (CellAtlas [ 56]), disease phenotypes (GAD, GWAS Catalog [ 57], Phewas [ 58], and Online Mendelian Inheritance in Man), drug–targets (PharmGKB [ 59] and DSigDB [ 60]), and miRNA–gene interactions (Microcosm…”
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- Authors
- Sollis, E., Mosaku, A., Abid, A., Buniello, A., Cerezo, M., Gil, L., Groza, T., Güneş, O., Hall, P., Hayhurst, J., Ibrahim, A., Ji, Y., John, S., Lewis, E., MacArthur, J. A. L., McMahon, A., Osumi-Sutherland, D., Panoutsopoulou, K., Pendlington, Z., Ramachandran, S., Stefancsik, R., Stewart, J., Whetzel, P., Wilson, R., Hindorff, L., Cunningham, F., Lambert, S. A., Inouye, M., Parkinson, H., & Harris, L. W.
- Affiliations
- European Bioinformatics Institute (GB)
- Open Targets (GB)
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Genome Campus , Hinxton , Cambridge CB10 1SD, UK
- University of Cambridge (GB)
- National Institutes of Health (US)
- Baker Heart and Diabetes Institute (AU)
- Corresponding author
- Parkinson, Helen
- Harris, Laura W
- ORCID
- Sollis, Elliot
- Mosaku, Abayomi
- Abid, Ala
- Buniello, Annalisa
- Cerezo, Maria
- Gil, Laurent
- Groza, Tudor
- Güneş, Osman
- Hayhurst, James
- Ibrahim, Arwa
- Ji, Yue
- John, Sajo
- Lewis, Elizabeth
- MacArthur, Jacqueline A L
- McMahon, Aoife
- Osumi-Sutherland, David
- Panoutsopoulou, Kalliope
- Pendlington, Zoë
- Ramachandran, Santhi
- Stefancsik, Ray
- Stewart, Jonathan
- Whetzel, Patricia
- Wilson, Robert
- Hindorff, Lucia
- Cunningham, Fiona
- Lambert, Samuel A
- Inouye, Michael
- Parkinson, Helen
- Harris, Laura W
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-11-09
- Volume
- 51
- Issue
- D1
- Pages
- D977-D985
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC9825413
- OpenAlex
- W4308616307
- Cited by
- 1,641
- References
- 23
- Citations by year
- 2026: 312 · 2025: 533 · 2024: 581 · 2023: 208 · 2022: 3 · 2021: 2 · 2019: 1 · 2017: 1
- FWCI
- 205.13
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Funders
- National Human Genome Research Institute of the National Institutes of Health (U41-HG007823, RM1HG010860, OTAR034, OTAR2045)
- British Heart Foundation (RG/13/13/30194, RG/18/13/33946)
- NIHR Cambridge Biomedical Research Centre (BRC-1215–20014)
- European Molecular Biology Laboratory Core Funds
- Munz Chair of Cardiovascular Prediction and Prevention and the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014)
- UK Economic and Social Research 878 Council (ES/T013192/1)
- Canadian Institutes of Health Research (MFE-171279)
- Health Data Research UK** Cambridge
- National Institutes of Health (2UM1HG006370-11)
- Monarch R24 (2R24OD011883-05A1)
- National Institute of Diabetes and Digestive and Kidney Diseases (UM1DK105554)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- GWAS Catalog, genome-wide association study, summary statistics, knowledge base, FAIR data, data interoperability, data curation, copy number variation, population diversity, polygenic risk score, data standardization
- MeSH terms
- Animals, Humans, Phenotype, Software, United States, Polymorphism, Single Nucleotide, Knowledge Bases, Mice, National Human Genome Research Institute (U.S.), Genome-Wide Association Study, DNA Copy Number Variations
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