Genetic Differences between Five European Populations
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AIMS: We sought to examine the magnitude of the differences in SNP allele frequencies between five European populations (Scotland, Ireland, Sweden, Bulgaria and Portugal) and to identify the loci with the greatest differences. METHODS: We performed a population-based genome-wide association analysis with Affymetrix 6.0 and 5.0 arrays. We used a 4 degrees of freedom χ(2) test to determine the magnitude of stratification for each SNP. We then examined the genes within the most stratified regions, using a highly conservative cutoff of p < 10(-45). RESULTS: We found 40,593 SNPs which are genome-wide significantly (p ≤ 10(-8)) stratified between these populations. The largest differences clustered in gene ontology categories for immunity and pigmentation. Some of the top loci span genes that have already been reported as highly stratified: genes for hair color and pigmentation (HERC2, EXOC2, IRF4), the LCT gene, genes involved in NAD metabolism, and in immunity (HLA and the Toll-like receptor genes TLR10, TLR1, TLR6). However, several genes have not previously been reported as stratified within European populations, indicating that they might also have provided selective advantages: several zinc finger genes, two genes involved in glutathione synthesis or function, and most intriguingly, FOXP2, implicated in speech development. CONCLUSION: Our analysis demonstrates that many SNPs show genome-wide significant differences within European populations and the magnitude of the differences correlate with the geographical distance. At least some of these differences are due to the selective advantage of polymorphisms within these loci.
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The LCT gene is a locus well-documented as showing substantial genetic differentiation within Europe.
“The LCT gene is a locus well-documented as showing substantial genetic differentiation within Europe [29], [30].”
From Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations (2012) · cites this paper as [30]
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- Authors
- Moskvina, V., Smith, M., Ivanov, D., Blackwood, D., StClair, D., Hultman, C., Toncheva, D., Gill, M., Corvin, A., O’Dushlaine, C., Morris, D. W., Wray, N. R., Sullivan, P., Pato, C., Pato, M. T., Sklar, P., Purcell, S., Holmans, P., O’Donovan, M. C., Owen, M. J., Kirov, G., & International Schizophrenia Consortium<footref id="foot01"><sup>1</sup></footref>
- Affiliations
- Cardiff University (GB)
- University of Edinburgh (GB)
- University of Aberdeen (GB)
- Karolinska Institutet (SE)
- Alexandrovska Hospital (BG)
- Trinity College Dublin (IE)
- QIMR Berghofer Medical Research Institute (AU)
- University of North Carolina at Chapel Hill (US)
- University of Southern California (US)
- Broad Institute (US)
- ORCID
- Venue
- Human Heredity
- Publisher
- S. Karger AG
- Published
- 2010
- Volume
- 70
- Issue
- 2
- Pages
- 141-149
- ISSN
- 0001-5652 (ISSN-L)
- 1423-0062
- PMC
- PMC7077089
- OpenAlex
- W1999879135
- Cited by
- 38
- References
- 27
- Citations by year
- 2025: 2 · 2024: 3 · 2023: 2 · 2022: 3 · 2021: 4 · 2020: 2 · 2018: 3 · 2017: 1 · 2015: 1 · 2014: 3 · 2013: 5 · 2012: 3
- FWCI
- 2.52
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Human Heredity (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion)
- Funders
- Cancer Research UK (19556)
- National Institute of Mental Health (R01MH077139, R01MH080403)
- 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 › Genetic diversity and population structure
- Keywords
- population stratification, SNP allele frequencies, European populations, genetic differentiation, pigmentation genes, immunity genes, LCT gene, NAD+ metabolism, HLA, Toll-like receptors, FOXP2, zinc finger genes, glutathione synthesis, geographic distance, natural selection, Scotland, Ireland, Sweden, Bulgaria, Portugal
- MeSH terms
- Genetics, Population, Humans, Polymorphism, Single Nucleotide, Lactase, White People
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