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Evaluating the potential role of pleiotropy in Mendelian randomization studies
Open accessAbstract
Pleiotropy, the phenomenon of a single genetic variant influencing multiple traits, is likely widespread in the human genome. If pleiotropy arises because the single nucleotide polymorphism (SNP) influences one trait, which in turn influences another ('vertical pleiotropy'), then Mendelian randomization (MR) can be used to estimate the causal influence between the traits. Of prime focus among the many limitations to MR is the unprovable assumption that apparent pleiotropic associations are mediated by the exposure (i.e. reflect vertical pleiotropy), and do not arise due to SNPs influencing the two traits through independent pathways ('horizontal pleiotropy'). The burgeoning treasure trove of genetic associations yielded through genome wide association studies makes for a tantalizing prospect of phenome-wide causal inference. Recent years have seen substantial attention devoted to the problem of horizontal pleiotropy, and in this review we outline how newly developed methods can be used together to improve the reliability of MR.
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“This pattern is consistent with a directional influence of disease liability on longevity27,64 and is also compatible with vertical pleiotropy65.”
From Genetic trade-offs in fertility and longevity explain the maintenance of disease-associated alleles in humans (2026) · cites this paper as [65]
In the citing paper
“However, confounding of the genetic variants with the outcome in a sample can be induced by population stratification, dynastic effects and assortative mating,60 violating the second IV condition.”
From Mendelian randomization (2022) · cites this paper as [60]
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“If there are many correlated candidate variants in a gene region, then including all variants in a single analysis will typically result in numerical instability, as the analysis can be highly sensitive to small changes in the variant correlation matrix 62 .”
From Guidelines for performing Mendelian randomization investigations (2020) · cites this paper as [62]
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“Finally, MR-Egger regression was conducted to ascertain the potential directional pleiotropy via the intercept term [28].”
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“In the absence of pleiotropy, individual variants would be expected to provide homogenous estimates for outcome associations, proportional to their influence on the exposure [42].”
BackgroundGenetic Associations Between IL-6 and the Development of Autoimmune Arthritis Are Gender-Specific
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“The latter violation is commonly known as ”horizontal pleiotropy” [12], and hereafter referred to as pleiotropy for simplicity.”
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“Moreover, we particularly detected the presentence of horizontal pleiotropy through MR-Egger regression and MR-PRESSO Global test (32).”
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MethodInfluentialTime Spent Outdoors Partly Accounts for the Effect of Education on Myopia
Clark, R., Kneepkens, S. C. M., Plotnikov, D., Shah, R. L., Huang, Y., Tideman, J. W. L., Klaver, C. C. W., Atan, D., Williams, C., & Guggenheim, J. A. (2023) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.64.14.38 · Cited by 30
“For example, the existence of “horizontal pleiotropy” – the independent effects of a genetic variant on multiple traits, which is a common feature of GWAS variants 42 – would violate the third IV rule.”
BackgroundCausal relationship between immune cells and prostate cancer: a Mendelian randomization study
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“The MR Egger intercept test was used to test for directional pleiotropy (49).”
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“Because the IV exclusion restriction assumption is unprovable in practice (22), we removed the variants showing potential pleiotropic association with MS (association p value lower than the genome-wide suggestive significance level of 10), a conservative strategy allowing us to perform MR analysis with more confidence…”
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“The wide spread of pleiotropic genetic variants, which violate key IV assumptions (IV2 and especially IV3), is a particularly troublesome issue.(4,52) Many methods have been designed to improve causal effect estimation in the presence of pleiotropic effects,(38,40,46) but they do not incorporate the possibility of rev…”
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“To explore whether the MR estimates were disproportionately influenced by certain SNP alone, we performed a leave-oneout analysis by omitting instrumental SNPs one by one (23).”
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“However, since the IVW model assumes that all SNPs are valid instruments and may have directional pleiotropy, the estimates could be biased 33 .”
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“As each of these methods make different assumptions regarding horizontal pleiotropy, a consistent effect across multiple MR methods strengthens causal evidence (19).”
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“77,78 These factors hamper selection of well-de fi ned IVs in MR by increasing horizontal pleiotropy and heterogeneity, 79,80 which may cause a severe bias in MR. 79,80 Signi fi cant heterogeneity in MR also points to pleiotropy and other possible violations of the necessary IV assumptions.”
Associations between Serum Levels of Cholesterol and Survival to Age 90 in Postmenopausal Women
Maihofer, A. X., Shadyab, A. H., Wild, R. A., & LaCroix, A. Z. (2020) · Journal of the American Geriatrics Society · doi:10.1111/jgs.16306 · Cited by 25
“This study was relatively small, however, and it was based on genetic risk scores that can provide confounded results if assumptions are not met.(42) We suggest performing an MR analysis in a resource such as the UK BioBank(43) using parents’ ages at death as proxy measures of longevity for a larger, better powered an…”
Alcohol use and cognitive functioning in young adults: improving causal inference
Mahedy, L., Suddell, S. F., Skirrow, C., Fernandes, G., Field, M., Heron, J., Hickman, M., Wootton, R. E., & Munafo, M. R. (2020) · Addiction · doi:10.1111/add.15100 · Cited by 27
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Fang, S., Hemani, G., Richardson, T. G., Gaunt, T. R., & Smith, G. D. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac186 · Cited by 24
“Horizontal 516 pleiotropy could be detected through detailed examination of individual SNPs used for 517 PRS construction in each block separately, through evaluating the between-SNP 518 heterogeneity in the ratio of associations between genotype and the outcome and the 519 exposure (41, 42).”
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Liu, K., Cai, Y., Song, K., Yuan, R., & Zou, J. (2023) · The EPMA Journal · doi:10.1007/s13167-023-00321-9 · Cited by 26
“To determine heterogeneity, however, we employed Cochran’s Q test [25].”
MethodHuang, L., Ou, Y., Yang, Y., Wang, Z.-T., Tan, L., & Yu, J. (2023) · Translational Psychiatry · doi:10.1038/s41398-023-02553-9 · Cited by 28
“Mendelian randomization (MR) is a novel method that can estimate the causal effects of risk factors in observational studies by using genetic variants to provide evidence of robust associations and incorporating summary statistics from largecohort genome-wide association studies (GWASs) [10].”
MethodWard-Caviness, C. K., de Vries, P. S., Wiggins, K. L., Huffman, J. E., Huffman, J. E., Yanek, L. R., Bielak, L. F., Giulianini, F., Guo, X., Kleber, M. E., et al. (2019) · PLoS ONE · doi:10.1371/journal.pone.0216222 · Cited by 25
“We performed sensitivity analyses using four pleiotropy robust methods each of which uses a different approach to partially relax the no horizontal pleiotropy assumption of MR analyses: [63] MR-Egger [58], MR mode based estimate (MBE),[64] MR PRESSO [65], and Weighted median [66].”
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“In addition to the investigation on the general pleiotropic relationship, we emplo y ed MR to detect v ertical pleiotr opy that can assert the direction of the phenotypic relationships [ 19 ].”
Gurung, R. L., Dorajoo, R., Yiamunaa, M., Wang, L., Liu, S., Liu, J., Shao, Y. M., Chen, Y., Sim, X., Ang, K., et al. (2021) · Clinical Kidney Journal · doi:10.1093/ckj/sfab067 · Cited by 25
“This approach yields a consistent estimate of a true causal effect as long as more than 50% of SNPs are valid (29).”
BackgroundOhi, K., Takai, K., Kuramitsu, A., Sugiyama, S., Soda, M., Kitaichi, K., & Shioiri, T. (2021) · European Psychiatry · doi:10.1192/j.eurpsy.2021.2237 · Cited by 19
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“Cochran’s Q statistic was applied to assess the heterogeneity of IVW andMR-Egger (27).”
MethodLiu, Z., Peng, Z., Lin, H., Zhou, K., Liang, L., Cao, J., Huang, Z., & Mei, J. (2024) · Respiratory Research · doi:10.1186/s12931-024-02848-5 · Cited by 23
“And MR-Egger regression was used to detect potential pleiotropy in the association between the exposures and outcomes [17].”
MethodUnhealthy lifestyle factors and the risk of colorectal cancer: a Mendelian randomization study
Li, X., Chang, Z., Wang, J., Ding, K., Pan, S., Hu, H., & Tang, Q. (2024) · Scientific Reports · doi:10.1038/s41598-024-64813-y · Cited by 23
“When heterogeneity was absent, we used the fixed effects model as the primary method; when heterogeneity was present, we used the random effects model as the primary method 16 .”
MethodIntroduction to Mendelian randomization
Yeung, S. L. A., Luo, S., Iwagami, M., & Goto, A. (2024) · Annals of Clinical Epidemiology · doi:10.37737/ace.25004 · Cited by 26
“If instruments weakly associated with exposure are used (i.e. weak instrument bias, often defined as F statistics 10), the MR estimate will be biased towards the confounded observational associa‐ tion 40) .”
Qing, J., Li, Y., Soliman, K., & Cheungpasitporn, W. (2025) · Renal Failure · doi:10.1080/0886022x.2024.2445763 · Cited by 23
“• Cross-Validation: By combining the weighted median approach with MR-Egger and MR-PRESSO, researchers can cross-validate their findings, mitigating biases inherent in any single method [35,51].”
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Mendelian randomization study on atrial fibrillation and cardiovascular disease subtypes
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“Cochran’s Q statistic evaluatedheterogeneityacrossgeneticvariantswhere p 0.05 was considered statistical significance [32].”
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“However, a formal application of the MR method, along with various sensitivity analyses, are necessary as prior studies show that risk score association analyses can suffer from higher false positive rates due to horizontal pleiotropy, a violation of the MR assumptions [28, 45].”
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“The greatest concern in MR studies is the horizontal pleiotropy, which occurs when the genetic variants influence the outcome of more than one pathway (25).”
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The causal effect of obesity on diabetic retinopathy: A two-sample Mendelian randomization study
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“05 of Cochrane’s Q (30) and I(2) > 25% (31) were considered to indicate significant heterogeneity.”
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“Horizontal pleiotropy, however, undermines a key assumption of MR [6].”
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Metadata
- Authors
- Hemani, G., Bowden, J., & Davey Smith, G.
- Affiliations
- University of Bristol (GB)
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol
- Corresponding author
- Hemani, Gibran
- Venue
- Human Molecular Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-05-16
- Volume
- 27
- Issue
- R2
- Pages
- R195-R208
- ISSN
- 0964-6906 (ISSN-L)
- 1460-2083
- PMC
- PMC6061876
- OpenAlex
- W2810852503
- Cited by
- 1,496
- References
- 113
- Citations by year
- 2026: 129 · 2025: 266 · 2024: 422 · 2023: 209 · 2022: 169 · 2021: 131 · 2020: 101 · 2019: 62 · 2018: 7
- FWCI
- 10.71
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Human Molecular Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Bristol Research (University of Bristol) (submittedVersion, cc-by)
- Funders
- Wellcome Trust (208806/Z/17/Z)
- Medical Research Council (MC_UU_12013/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Physical Sciences › Mathematics › Statistics and Probability › Advanced Causal Inference Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Physical Performance
- Keywords
- pleiotropy, Mendelian randomization, horizontal pleiotropy, single nucleotide polymorphisms, causal inference, phenome-wide association study, genetic variants
- MeSH terms
- Animals, Humans, Phenotype, Genetic Variation, Reproducibility of Results, Genome, Human, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Mendelian Randomization Analysis, Genetic Pleiotropy
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