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Cited by 221Race, Genetics, and SocietyGenetic Associations and EpidemiologyForensic and Genetic Research

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A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

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Morales, Joannella, Welter, Danielle, Bowler, Emily H., Cerezo, Maria, Harris, Laura W., McMahon, Aoife C., Hall, Peggy, Junkins, Heather A., Milano, Annalisa, Hastings, Emma, Malangone, Cinzia, Buniello, Annalisa, Burdett, Tony, Flicek, Paul, Parkinson, Helen, Cunningham, Fiona, Hindorff, Lucia A., MacArthur, Jacqueline A. L.·2018·Genome Biology
DOI 10.1186/s13059-018-1396-2PMC PMC5815218

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Abstract

The accurate description of ancestry is essential to interpret, access, and integrate human genomics data, and to ensure that these benefit individuals from all ancestral backgrounds. However, there are no established guidelines for the representation of ancestry information. Here we describe a framework for the accurate and standardized description of sample ancestry, and validate it by application to the NHGRI-EBI GWAS Catalog. We confirm known biases and gaps in diversity, and find that African and Hispanic or Latin American ancestry populations contribute a disproportionately high number of associations. It is our hope that widespread adoption of this framework will lead to improved analysis, interpretation, and integration of human genomics data.

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Fig. 1 Representation of ancestry data in the GWAS Catalog search interface (https://www.ebi.ac.uk/gwas/). Ancestry-related data are found in the Studies and Associations tables (underlined in black) when searching the Catalog. This figure shows the results of a search for PubMed Identifier 27145994. The sample description can be found in the Studies table, either by pressing “Expand all Studies” or the “+” on the study of interest (highlighted in red). Sample ancestry is captured in two forms: (1) detailed description (highlighted in blue); and (2) ancestry category (highlighted in green). The latter follows the format: sample size, category, (country of recruitment). In cases where multiple ancestries are included in a study, the ancestry associated with a particular association is found as an annotation in the p value column in the Associations table (highlighted in pink)
Fig. 1 Representation of ancestry data in the GWAS Catalog search interface (https://www.ebi.ac.uk/gwas/). Ancestry-related data are found in the Studies and Associations tables (underlined in black) when searching the Catalog. This figure shows the results of a search for PubMed Identifier 27145994. The sample description can be found in the Studies table, either by pressing “Expand all Studies” or the “+” on the study of interest (highlighted in red). Sample ancestry is captured in two forms: (1) detailed description (highlighted in blue); and (2) ancestry category (highlighted in green). The latter follows the format: sample size, category, (country of recruitment). In cases where multiple ancestries are included in a study, the ancestry associated with a particular association is found as an annotation in the p value column in the Associations table (highlighted in pink)CC BY · PubMed Central
Fig. 2 Ancestry category distribution in the GWAS Catalog. This figure summarizes the distribution of ancestry categories in percentages, of individuals (N = 110,291,046; a), individuals over time (N = 110,291,046; b), studies (N = 4,655; c), and associations (N = 60,970; d). The largest category in all panels is European (aqua). At the level of individuals (a), the largest non-European category is Asian (bright pink), with East Asian (light pink) accounting for the majority. Non-European, Non-Asian categories together (yellow) comprise 4 % of individuals, and for 6 % (white) of samples no ancestry category could be specified. b The distribution of individuals in percentages, included in the 915 studies published between 2005 and 2010 compared to the distribution of individuals included in the 2905 studies published between 2011 and 2016. d The disproportionate contribution of associations from African (blue) and Hispanic/Latin American (purple) categories, when compared to the percentage of individuals (a, blue, purple, respectively) and studies (b, blue, purple, respectively)
Fig. 2 Ancestry category distribution in the GWAS Catalog. This figure summarizes the distribution of ancestry categories in percentages, of individuals (N = 110,291,046; a), individuals over time (N = 110,291,046; b), studies (N = 4,655; c), and associations (N = 60,970; d). The largest category in all panels is European (aqua). At the level of individuals (a), the largest non-European category is Asian (bright pink), with East Asian (light pink) accounting for the majority. Non-European, Non-Asian categories together (yellow) comprise 4 % of individuals, and for 6 % (white) of samples no ancestry category could be specified. b The distribution of individuals in percentages, included in the 915 studies published between 2005 and 2010 compared to the distribution of individuals included in the 2905 studies published between 2011 and 2016. d The disproportionate contribution of associations from African (blue) and Hispanic/Latin American (purple) categories, when compared to the percentage of individuals (a, blue, purple, respectively) and studies (b, blue, purple, respectively)CC BY · PubMed Central

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Authors
Morales, J., Welter, D., Bowler, E. H., Cerezo, M., Harris, L. W., McMahon, A. C., Hall, P., Junkins, H. A., Milano, A., Hastings, E., Malangone, C., Buniello, A., Burdett, T., Flicek, P., Parkinson, H., Cunningham, F., Hindorff, L. A., & MacArthur, J. A. L.
Affiliations
  • European Bioinformatics Institute (GB)
  • National Institutes of Health (US)
Corresponding author
  • Morales, Joannella
  • MacArthur, Jacqueline A. L.
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2018-02-15
Volume
19
Issue
1
Pages
21-21
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-018-1396-2
PMC
PMC5815218
OpenAlex
W2785412624
Cited by
217
References
28
Citations by year
2026: 17 · 2025: 15 · 2024: 28 · 2023: 35 · 2022: 32 · 2021: 31 · 2020: 29 · 2019: 18 · 2018: 10
FWCI
14.08
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Genome biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • European Molecular Biology Laboratory
  • National Institutes of Health
  • National Human Genome Research Institute (U41HG006104, U41HG007823)
  • National Institute of General Medical Sciences
Topics
  • Social Sciences › Anthropology › Race, Genetics, and Society
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
Keywords
GWAS Catalog, ancestry bias, population diversity, African ancestry, genetic association studies
MeSH terms
Humans, Genetic Variation, Genomics, Racial Groups, Genome-Wide Association Study

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