Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary Statistics
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Abstract
MOTIVATION: Measuring genetic diversity is an important problem because increasing genetic diversity is a key to making new genetic discoveries, while also being a major source of confounding to be aware of in genetics studies. RESULTS: Using the UK Biobank data, a prospective cohort study with deep genetic and phenotypic data collected on almost 500 000 individuals from across the UK, we carefully define 21 distinct ancestry groups from all four corners of the world. These ancestry groups can serve as a global reference of worldwide populations, with a handful of applications. Here, we develop a method that uses allele frequencies and principal components derived from these ancestry groups to effectively measure ancestry proportions from allele frequencies of any genetic dataset. AVAILABILITY AND IMPLEMENTATION: This method is implemented in function snp_ancestry_summary of R package bigsnpr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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The UK Biobank, a prospective cohort of 500,000 patients, has only 6% of the cohort of non-European ancestry.
“Even large repositories like the UK Biobank that represents a prospective cohort of 500,000 patients are limited for some patient groups: only 6% of the cohort are of non-European ancestry. 24”
From AI pitfalls and what not to do: mitigating bias in AI (2023) · cites this paper as [24]
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AI pitfalls and what not to do: mitigating bias in AI
Gichoya, J. W., Thomas, K., Celi, L. A., Safdar, N., Banerjee, I., Banja, J. D., Seyyed-Kalantari, L., Trivedi, H., & Purkayastha, S. (2023) · The British Journal of Radiology · doi:10.1259/bjr.20230023 · Cited by 277 · see citing works
“24 Presently, it would be difficult to further evaluate model bias on these data sets.”
- Authors
- Privé, F.
- Affiliations
- Aarhus University (DK)
- Corresponding author
- Privé, Florian
- ORCID
- Privé, Florian
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-05-23
- Volume
- 38
- Issue
- 13
- Pages
- 3477-3480
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC9237724
- OpenAlex
- W4281297248
- Cited by
- 33
- References
- 30
- Citations by year
- 2026: 6 · 2025: 8 · 2024: 11 · 2023: 6 · 2022: 2
- FWCI
- 4.06
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Danish National Research Foundation
- Lundbeck Foundation Fellowship (R335-2019-2339)
- Bjarni J. Vilhjálmsson
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Race, Genetics, and Society
- Keywords
- ancestry diversity, genetic ancestry estimation, UK Biobank, allele frequency, principal components, ancestry proportions, genetic diversity, GWAS summary statistics, population stratification
- MeSH terms
- Genotype, United Kingdom, Humans, Prospective Studies, Biological Specimen Banks, Polymorphism, Single Nucleotide, Genome-Wide Association Study
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