Cited by 359Genetic Associations and EpidemiologyForensic and Genetic ResearchGenetic and phenotypic traits in livestock

Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies

Open access
Sohail, Mashaal, Maier, Robert M, Ganna, Andrea, Bloemendal, Alex, Martin, Alicia R, Turchin, Michael C, Chiang, Charleston WK, Hirschhorn, Joel +6 more·2019·eLife

Published version of a preprint

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).

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.7554/elife.39702

Cites

41 of 41 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • 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 measured
  • Given 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.”
  • 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.”
  • 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.”
  • 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.”

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Part of this paper’s reference list could not be split into single entries.

Flagged first, then by citations

Cited by

Sorted by citations

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)
Venue
eLife
Published
2019-03-21
Volume
8
ISSN
2050-084X (ISSN-L)
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
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review