Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies
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Abstract
Genetic predictions of height differ among human populations and these differences have been interpreted as evidence of polygenic adaptation. These differences were first detected using SNPs genome-wide significantly associated with height, and shown to grow stronger when large numbers of sub-significant SNPs were included, leading to excitement about the prospect of analyzing large fractions of the genome to detect polygenic adaptation for multiple traits. Previous studies of height have been based on SNP effect size measurements in the GIANT Consortium meta-analysis. Here we repeat the analyses in the UK Biobank, a much more homogeneously designed study. We show that polygenic adaptation signals based on large numbers of SNPs below genome-wide significance are extremely sensitive to biases due to uncorrected population stratification. More generally, our results imply that typical constructions of polygenic scores are sensitive to population stratification and that population-level differences should be interpreted with caution. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Polygenic adaptation tests are sensitive to the choice of GWAS data that provide the effect sizes; effect sizes estimated from one study can generate erroneously exaggerated signatures of polygenic adaptation when assessing polygenic adaptation in a second dataset, even if two sets of effect sizes produce correlated polygenic scores.
“Recent studies of height have suggested that polygenic adaptation tests are sensitive to the choice of GWAS data that provide the effect sizes: even if two sets of effect sizes produce correlated polygenic scores, effect sizes estimated from one study can generate erroneously exaggerated signatures of polygenic adaptation when assessing polygenic adaptation in a second dataset [34, 35].”
From Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences (2019) · cites this paper as [35]
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredGiven previous concerns, we performed several sensitivity analyses for the height analysis.
“Given previous concerns26,27, we performed several sensitivity analyses for the height analysis detailed in the Supplementary Methods.”
From Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects (2022) · cites this paper as [27]
Population stratification in GWAS data likely confounded previous estimates of polygenic adaptation on height.
“However, this approach is sensitive to population stratification as illustrated by recent work using UK Biobank data which showed that population stratification in GWAS data likely confounded previous estimates of polygenic adaptation on height26,27.”
From Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects (2022) · cites this paper as [27]
Within-sibship GWAS data are robust against population stratification.
“Within-sibship GWAS data are particularly useful in this context as they are robust against population stratification26,27,29.”
From Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects (2022) · cites this paper as [27]
A previous study reporting polygenic adaptation on height in the UK population was found to be biased by population stratification in the GIANT consortium.
“A previous study reporting polygenic adaptation on height in the UK population was found to be biased by population stratification in the Genetic Investigation of ANthropometric Traits (GIANT) consortium26–28.”
From Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects (2022) · cites this paper as [27]
Even among populations with European ancestry, subtle ancestry differences between samples can lead to polygenic scores that overstate between-population differences: small biases in locus-wise effect estimates that arise from the ancestry differences can potentially accumulate across loci.
“Even among populations with European ancestry, subtle ancestry differences between samples can lead to polygenic scores that overstate between-population differences: small biases in locus-wise effect estimates that arise from the ancestry differences can potentially accumulate across loci [34, 35].”
From Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences (2019) · cites this paper as [35]
The erroneously exaggerated signatures of polygenic adaptation from using effect sizes from one study to assess a second dataset arise from subtle population differences between study samples.
“This result, which arises from subtle population differences between study samples, calls into question claims about polygenic adaptation even of traits for which it has been most extensively investigated.”
From Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences (2019) · cites this paper as [35]
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- Authors
- Sohail, M., Maier, R. M., Ganna, A., Bloemendal, A., Martin, A. R., Turchin, M. C., Chiang, C. W., Hirschhorn, J., Daly, M. J., Patterson, N., Neale, B., Mathieson, I., Reich, D., & Sunyaev, S. R.
- Affiliations
- Broad Institute (US)
- Brown University (US)
- University of Southern California (US)
- University of Pennsylvania (US)
- ORCID
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2019-03-21
- Volume
- 8
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC6428571
- OpenAlex
- W2924359406
- Cited by
- 359
- References
- 41
- Citations by year
- 2026: 28 · 2025: 30 · 2024: 35 · 2023: 36 · 2022: 59 · 2021: 63 · 2020: 58 · 2019: 42 · 2018: 7
- FWCI
- 33.49
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Työväentutkimus Vuosikirja (submittedVersion)
- Funders
- National Institutes of Health (HG009088, MH101244, GM100233, HG006399, GM127131)
- Alfred P. Sloan Foundation (Sloan Research Fellowship)
- Charles E Kaufman Foundation (New Investigator Research Grant)
- Paul Allen Foundation (Allen Discovery Center)
- Howard Hughes Medical Institute (Investigator)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- polygenic adaptation, height, population stratification, polygenic risk score, UK Biobank, genetic effect size
- MeSH terms
- Adaptation, Biological, Body Height, United Kingdom, Humans, Phylogeny, Databases, Factual, Computational Biology, Multifactorial Inheritance, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Biostatistics
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