Detection of widespread horizontal pleiotropy in causal relationships inferred from Mendelian randomization between complex traits and diseases
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Abstract
Horizontal pleiotropy occurs when the variant has an effect on disease outside of its effect on the exposure in Mendelian randomization (MR). Violation of the 'no horizontal pleiotropy' assumption can cause severe bias in MR. We developed the Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO) test to identify horizontal pleiotropic outliers in multi-instrument summary-level MR testing. We showed using simulations that the MR-PRESSO test is best suited when horizontal pleiotropy occurs in <50% of instruments. Next we applied the MR-PRESSO test, along with several other MR tests, to complex traits and diseases and found that horizontal pleiotropy (i) was detectable in over 48% of significant causal relationships in MR; (ii) introduced distortions in the causal estimates in MR that ranged on average from -131% to 201%; (iii) induced false-positive causal relationships in up to 10% of relationships; and (iv) could be corrected in some but not all instances.
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The MR-PRESSO global test found no significant P values for horizontal pleiotropy in the four studies used in the MR meta-analysis (UKB GWAX P = 0.07, UKB GWAS P = 0.20, FinnGen P = 0.84, GR@ACE P = 0.91, unadjusted for multiple comparisons).
“We further used the MR-PRESSO global test49 to assess for horizontal pleiotropy and found no significant P values in the four studies used in the MR meta-analysis (UKB GWAX P = 0.07, UKB GWAS P = 0.20, FinnGen P = 0.84 and GR@ACE P = 0.91, all P values unadjusted for multiple comparisons).”
From Clonal hematopoiesis is associated with protection from Alzheimer’s disease (2023) · cites this paper as [49]
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Gut Microbiota and Psychiatric Disorders: A Two-Sample Mendelian Randomization Study
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Cao, Z., Wu, Y., Li, Q., Li, Y., & Wu, J. (2022) · Annals of Medicine · doi:10.1080/07853890.2022.2085883 · Cited by 183 · see citing works
Yuan, S., Gill, D., Giovannucci, E. L., & Larsson, S. C. (2021) · Clinical Gastroenterology and Hepatology · doi:10.1016/j.cgh.2020.12.034 · Cited by 177 · see citing works
Bowden, S. J., Doulgeraki, T., Bouras, E., Markozannes, G., Athanasiou, A., Grout-Smith, H., Kechagias, K. S., Ellis, L. B., Zuber, V., Chadeau‐Hyam, M., et al. (2023) · BMC Medicine · doi:10.1186/s12916-023-02965-w · Cited by 196 · see citing works
- Authors
- Verbanck, M., Chen, C.-Y., Neale, B., & Do, R.
- Affiliations
- Icahn School of Medicine at Mount Sinai (US)
- Broad Institute (US)
- Corresponding author
- Neale, Benjamin
- Do, Ron
- Venue
- Nature Genetics
- Published
- 2018-04-23
- Volume
- 50
- Issue
- 5
- Pages
- 693-698
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC6083837
- OpenAlex
- W2803072880
- Cited by
- 8,591
- References
- 77
- Citations by year
- 2026: 837 · 2025: 1873 · 2024: 2845 · 2023: 1422 · 2022: 743 · 2021: 441 · 2020: 252 · 2019: 136 · 2018: 35 · 2017: 3 · 2016: 1 · 2013: 1
- FWCI
- 134.78
- Type
- journal article
- Language
- en
- Update notices
- correction (2018-07-02)
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- American Heart Association (15CVGPSD27130014)
- National Institutes of Health
- National Heart, Lung, and Blood Institute (R01HL139865)
- National Institute of Mental Health (R01MH107649, R01MH094469)
- National Human Genome Research Institute (U01HG009088)
- National Institute of General Medical Sciences (R35GM124836)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Physical Sciences › Mathematics › Statistics and Probability › Advanced Causal Inference Techniques
- Social Sciences › Decision Sciences › Statistics, Probability and Uncertainty › Meta-analysis and systematic reviews
- Keywords
- horizontal pleiotropy, Mendelian randomization, MR-PRESSO, causal inference, complex traits, disease, summary-level data
- MeSH terms
- Disease, Humans, Genetic Variation, Genetic Predisposition to Disease, Genetic Pleiotropy
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