| --- |
| license: other |
| license_name: embl-ebi |
| license_link: https://www.ebi.ac.uk/about/terms-of-use/ |
| --- |
| |
| # GWAS Catalog Samples |
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| ## Dataset Description |
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| This dataset contains sample-level metadata from the [NHGRI-EBI GWAS Catalog](https://ebi.ac.uk/gwas), describing the populations included in genome-wide association studies (GWAS). |
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| Each record represents a population sample used within a GWAS study, including information about sample size, ancestry category, and geographic origin. The dataset provides a structured representation of the participant populations contributing to published GWAS results. |
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| Unlike the [GWAS Catalog Studies dataset](https://huggingface.co/datasets/gwascatalog/studies), which focuses on publication-level metadata, and the [Associations dataset](https://huggingface.co/datasets/gwascatalog/associations), which captures SNP–trait associations, the Samples dataset describes the populations and cohorts contributing to GWAS analyses. |
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| This dataset is particularly valuable for understanding genetic ancestry representation in GWAS research, enabling analyses of population diversity, recruitment geography, and ancestry distribution across studies. |
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| Typical research uses include: |
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| * examining ancestry representation in GWAS cohorts |
| * analysing geographic recruitment patterns in genomic studies |
| * studying population diversity across GWAS datasets |
| * assessing ancestry imbalance or underrepresentation in genetic studies |
| * linking population metadata with study-level and association-level GWAS data |
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| The GWAS Catalog applies a standardised framework for representing ancestry data in genomics studies. For more details, please see: |
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| Morales, J., Welter, D., Bowler, E.H. et al. A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog. Genome Biol 19, 21 (2018). https://doi.org/10.1186/s13059-018-1396-2 |
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| ## Dataset Summary |
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| * Task categories: genomics, biomedical metadata analysis |
| * Data type: tabular |
| * Primary domain: genome-wide association studies (GWAS) |
| * Unit of observation: GWAS sample population |
| * Source: curated literature database |
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| Typical uses include: |
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| * analysing ancestry composition of GWAS cohorts |
| * evaluating population diversity in genomic research |
| * linking ancestry metadata with GWAS study results |
| * studying recruitment geography and sampling strategies in GWAS |
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| --- |
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| # Dataset Structure |
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| Each row represents a specific sample population used in a GWAS study, typically corresponding to either the discovery stage or a replication stage cohort. |
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| A single study may contain multiple sample entries representing different cohorts, recruitment locations, or ancestry groups. |
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| ## Columns |
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| | Column | Description | |
| | ------------------------------- | --------------------------------------------------------------------------------------------------------------- | |
| | STUDY ACCESSION | Accession identifier assigned to a GWAS study in the GWAS Catalog (e.g., GCST identifiers). | |
| | PUBMEDID | PubMed identifier for the publication reporting the GWAS. | |
| | FIRST AUTHOR | Last name and initials of the first author of the publication. | |
| | DATE | Publication date (online/epub date if available). | |
| | INITIAL SAMPLE DESCRIPTION | Description of the discovery-stage GWAS cohort, including sample size and ancestry information. | |
| | REPLICATION SAMPLE DESCRIPTION | Description of replication cohort(s) used to validate associations reported in the study. | |
| | STAGE | Stage of the GWAS to which the sample description applies (e.g., initial discovery stage or replication stage). | |
| | NUMBER OF INDIVIDUALS | Number of individuals included in the sample population. | |
| | BROAD ANCESTRAL CATEGORY | High-level ancestry classification assigned to place samples into broader genetic ancestry groups. | |
| | COUNTRY OF ORIGIN | Country associated with the ancestral origin of the individuals in the sample. | |
| | COUNTRY OF RECRUITMENT | Country where participants were recruited for the study. | |
| | ADDITIONAL ANCESTRY DESCRIPTION | Additional descriptors providing more detailed ancestry information for the sample population. | |
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| --- |
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| # Curation Process |
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| The GWAS Catalog is curated through a combination of automated and manual processes. |
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| ### 1. Literature identification |
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| Publications describing genome-wide association studies are identified through: |
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| * literature searches |
| * author submissions |
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| ### 2. Manual curation |
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| Expert curators review publications and extract key information including: |
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| * variant identifiers (e.g., rsIDs) |
| * associated traits or diseases |
| * statistical significance metrics |
| * effect sizes |
| * sample descriptions |
| * genomic location information |
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| ### 3. Standardisation |
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| Extracted data are normalised using standardised vocabularies and identifiers where possible, including: |
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| * controlled trait terms from the [Experimental Factor Ontology (EFO)](https://www.ebi.ac.uk/efo/) |
| * genomic coordinates |
| * gene identifiers |
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| ### 4. Annotation |
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| Variants are annotated with additional genomic information such as: |
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| * mapped genes |
| * variant context (e.g., intronic, intergenic) |
| * genomic distances to nearby genes |
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| ### 5. Quality control |
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| Curated records undergo internal quality checks to ensure: |
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| * consistency across records |
| * correct variant identifiers |
| * valid genomic annotations |
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| For more information about the curation process, please see the [GWAS Catalog documentation](https://ebi.ac.uk/gwas/docs/methods). |
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| The Hugging Face dataset mirrors the [tabular ancestry records published by the GWAS Catalog on 2026-03-17](https://www.ebi.ac.uk/gwas/docs/file-downloads). |
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| --- |
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| # Bias, Limitations, and Population Representation |
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| Genome-wide association studies have several limitations that affect analyses using this dataset. |
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| ## Population Bias |
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| A large proportion of GWAS studies have historically been conducted with individuals genetically similar to European reference populations. |
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| Please note: |
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| * genetic associations may not generalise across populations |
| * allele frequencies may differ substantially between ancestries |
| * effect sizes may vary across populations |
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| Users should exercise caution when applying results derived from GWAS to diverse populations. |
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| ## Publication Bias |
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| Because the catalog is derived from published studies, it may reflect: |
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| * overrepresentation of statistically significant findings |
| * underrepresentation of null results |
| * bias towards traits that are frequently studied |
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| ## Study Heterogeneity |
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| GWAS studies vary substantially in: |
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| * sample size |
| * cohort composition |
| * phenotype definitions |
| * genotyping platforms |
| * statistical analysis methods |
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| These factors may influence comparability across studies. |
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| --- |
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| # Credits |
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| This dataset is derived from the [NHGRI-EBI GWAS Catalog](https://ebi.ac.uk/gwas). |
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| We would like to thank: |
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| * authors who submit their data to the catalog, including full summary statistics |
| * authors of the original GWAS publications included in the catalog |
| * GWAS Catalog team members, past and present |
| * research participants who contributed data to the underlying genetic studies |
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| --- |
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| # Citation |
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| If you use this dataset in research, please cite the GWAS Catalog publication: |
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| Maria Cerezo et al. |
| *The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity.* |
| Nucleic Acids Research, 2025. |
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| ```bibtex |
| @article{cerezo2025nhgri, |
| title={The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity}, |
| author={Cerezo, Maria and Sollis, Elliot and Ji, Yue and Lewis, Elizabeth and Abid, Ala and Bircan, Karatu{\u{g}} Ozan and Hall, Peggy and Hayhurst, James and John, Sajo and Mosaku, Abayomi and others}, |
| journal={Nucleic acids research}, |
| volume={53}, |
| number={D1}, |
| pages={D998--D1005}, |
| year={2025}, |
| publisher={Oxford University Press} |
| } |
| ``` |
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| --- |
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| # Licence |
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| The NHGRI-EBI GWAS Catalog and all its contents are available under the [general Terms of Use for EMBL-EBI Services](https://ebi.ac.uk/about/terms-of-use). Summary statistics are made available under CC0 unless otherwise stated. |
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| Consumers of data hosted by the GWAS Catalog should review the licence terms of individual datasets where applicable to their specific use case. |
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