Cited by 1,496Genetic Associations and EpidemiologyAdvanced Causal Inference TechniquesGenetics and Physical Performance

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Evaluating the potential role of pleiotropy in Mendelian randomization studies

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Hemani, Gibran, Bowden, Jack, Davey Smith, George·2018·Human Molecular Genetics

DOI 10.1093/hmg/ddy163PMC PMC6061876

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Abstract

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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Figure 1. (A) The same SNP can associate with multiple traits due to vertical pleiotropy, horizontal pleiotropy and linkage disequilibrium with distinct causal variants depending on the analytical context. To estimate the causal influence of gene expression level (Gene) 1 on Trait 1, SNP 1 is a valid instrument that acts in a vertical pleiotropic manner. But SNP 1 has a horizontal pleiotropic effect when using it to estimate the causal influence of Gene 1 on Trait 2. If SNP 1 was used to instrument Gene 1 to test its effect on Trait 3, it would exhibit a pleiotropic association through linkage disequilibrium with SNP 2. (B) A directed acyclic graph (DAG) in which four SNPs instrument an exposure. The fourth SNP has a horizontal pleiotropic effect of magnitude α. The impact of the horizontal pleiotropic effect is shown in the scatter plot in (C), where the grey slope represents the true causal effect obtained from the three valid instruments, and the red slope represents the IVW estimate when all SNPs are used as instruments.CC BY · PubMed Central

Appendix figure 1. (A) Unobserved confounding (U) makes it impossible to be fully confident that an association between risk factor X and outcome Y represents a measure of causal effect of X on Y. (B) In a perfect RCT, randomization to treatment (T) removes the possibility of confounding, enabling the causal effect of T on Y to be estimated. (C) MR uses genetic variants (G) that explain some variation in the exposure X to estimate the causal effect of X on Y. G must satisfy the instrumental variable assumptions, encoded by the solid arrows (and the strict absence of the dotted arrows) in (C). (D) Instrumental variable methods can also be used in clinical trials when randomization is imperfect because some patients do not receive the treatment they were originally assigned. This is referred to as `non-compliance’. An MR analysis is conceptually and mathematically equivalent to the analysis of RCT data in the presence of non-compliance, where the SNP (G) and exposure (X) proxy for randomization (R) and treatment (T), respectively.CC BY · PubMed Central

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“27 When horizontal pleiotropy is unbalanced, which means genetic variants are associated with the outcome through pathways other than the exposure, the MR-Egger method provides an unbiased effect estimate that could balance horizontal pleiotropy.”
Method
Prediction of causal genes at GWAS loci with pleiotropic gene regulatory effects using sets of correlated instrumental variables
Khan, M. J., Ludl, A.-A., Bankier, S., Björkegren, J., & Michoel, T. (2024) · PLoS Genetics · doi:10.1371/journal.pgen.1011473 · Cited by 2
“Hence much of the methodological development in MR has sought to address these limitations [5, 6].”
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Lehrer, S. F., & Ding, W. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-813092-6.00009-5 · Cited by 2
Finding drug targeting mechanisms with genetic evidence for Parkinson’s diseasePreprint
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“Additionally, an MR result may be driven by a locus where the SNP-exposure and SNP-outcome associations are rooted in two distinct causal SNPs (Hemani et al. 2018a).”
Background
The relationship between open angle glaucoma, optic disc morphology and Alzheimer’s Disease: a Mendelian randomization studyPreprint
Budu‐Aggrey, A., Hysi, P. G., Kehoe, P. G., Igo, R. P., Wiggs, J. L., Bailey, J. N. C., Haines, J. L., Pasquale, L. R., MacGregor, S., Biobank, U., et al. (2020) · medRxiv · doi:10.1101/2020.08.30.20184846 · Cited by 2
“provides consistent causal estimates when >50% of the information in the analysis comes from valid genetic instruments,(6) while the MBE will provide a robust causal estimate in the presence of pleiotropy when SNPs producing the most common MR estimate have no horizontally pleiotropic effects.(19) The Q-statistic was…”
BackgroundMethod
Selection of invalid instruments can improve estimation in Mendelian randomizationPreprint
Patel, A. R., DiTraglia, F. J., Zuber, V., & Burgess, S. (2021) · arXiv (Cornell University) · Cited by 2
Nature’s Curriculum: Genes Linked to Educational Attainment and Adult Socioeconomic Status in a Nordic Welfare StatePreprint
Dobewall, H., Vaalavuo, M., Böckerman, P., Viinikainen, J., Sirniö, O., Kantojärvi, K., Pehkonen, J., Raitakari, O. T., & Lehtimäki, T. J. (2024) · doi:10.31235/osf.io/g453y · Cited by 2
Causal effect of beta-blockers on the risk of lung cancer: a Mendelian randomization study
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UNVEILING THE CAUSAL ASSOCIATION BETWEEN NONINFECTIOUS RESPIRATORY DISORDERS AND SEPSIS THROUGH MENDELIAN RANDOMIZATION ANALYSIS
Liu, C., He, L., & Zheng, X. (2024) · Shock · doi:10.1097/shk.0000000000002358 · Cited by 1
Mendelian randomization evidence based on European ancestry for the causal effects of leukocyte telomere length on prostate cancer
Wu, X., Hu, C., Wu, T., Du, X., Peng, Z., Xue, W., Chen, Y., & Dong, L. (2024) · Human Genomics · doi:10.1186/s40246-024-00622-8 · Cited by 1
“…related to at least one of the multiple exposures in MVMR analysis; (2) genetic variation was not associated with confounding factors related to the association between the instruments of each exposure and PCs; (3) the impacts of genetic variation on PCs must go through each exposure [67].”
Background
Pre-school children single inhalation anesthetic exposure and neuro-psychological development: a prospective study and Mendelian randomization analysis
Zhang, J., Deng, H., Huang, X., Wang, L., Zhou, P., Zeng, J., & Yu, C. (2024) · Frontiers in Neurology · doi:10.3389/fneur.2024.1389203 · Cited by 1
“We applied MR-Egger regression testing to monitor potential horizontal pleiotropic effects (13–15).”
Method
Genetic associations between ULK3 and epilepsy: a two-sample Mendelian randomization study
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“The intercept term of MR-Egger regression was calculated to assess horizontal pleiotropy (30).”
Method
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Barry, C.-J. S., Walker, V. M., Burden, C., Havdahl, A., & Davies, N. M. (2024) · JAMA Network Open · doi:10.1001/jamanetworkopen.2024.26234 · Cited by 1
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Qi, F., & Zhang, J. (2024) · Frontiers in Psychology · doi:10.3389/fpsyg.2024.1368241 · Cited by 1
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Genetic liability to higher frailty index may increase the risk of ophthalmic disease
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Sanyaolu, A. O., Mohamed, W., Makarious, M. B., August, J. L., Kekenadze, M., Heilbron, K., Periñán, M. T., Noyce, A. J., & Bandrés‐Ciga, S. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-13550-7.00006-9 · Cited by 1
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“[25] To address the challenges of multiple testing, we applied the Bonferroni method.”
Method
High SHBG and Low Bioavailable Testosterone are Strongly Causally Associated with Increased Forearm Fracture Risk in Women: An MR Study Leveraging Novel Female-Specific Data
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“…analyses after Steiger filtering, removing genetic variants that demonstrate higher correlation with the outcome than the exposure, thus filtering instruments that are likely to be arising due to reverse cause or potentially through horizontal pleiotropy [58, 59] (Supplementary Tables S3 and S4).”
Background
New insights into the increased risk of migraines from COVID-19 infection and vaccination: a Mendelian randomization study
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“Among them, the results of IVW analysis are our focus, due to its ability to provide an unbiased estimate of causal effects in the absence of horizontal pleiotropy[13].”
Background
Unveiling therapeutic targets for spinal stenosis from genetic insights: a Mendelian randomization analysis
Fan, Z., Chen, B., Ding, L., & Guo, H. (2024) · Scientific Reports · doi:10.1038/s41598-024-80697-4 · Cited by 1
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“Finally, to distinguish whether MR estimates are influenced by a single SNP or suffer from bias, we conducted a "leave-one-out" test, examining each genetic variant one by one [37].”
Educational attainment, body mass index, and smoking as mediators in kidney disease risk: a two-step Mendelian randomization study
Zhang, L., Feng, B., Liu, Z., & Liu, Y. (2025) · Renal Failure · doi:10.1080/0886022x.2025.2476051 · Cited by 1
“(3) the genetic variants should only relate to the outcome through the exposure [18].”
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“Potential heterogeneity of IVs was assessed using Cochrane’s Q test 18 .”
Influential
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“…instrument variables and that effect estimates may be biased in the presence of directional pleiotropy supports iVW’s effective statistical ability [27]. to enhance the dependability of the results, we utilized three additional methods (MR-Egger, weighted median, and Constrained Maximum likelihood…”
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“Subsequently, MR-Egger intercepts were calculated to identify potential biases arising from directional pleiotropy and null instrument variables [13].”
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“[35,36] Ultimately, only one group of lipids showed positive results after meta-analysis and multiple corrections.”
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Habibi, D., Hamraz, I., Teymoori, F., Saeidian, A. H., Mirtavoos‐Mahyari, H., Kasnavi, Q., Taloubaghi, A. S., Masoudi, H., Azizi, F., DANESHPOUR, M. S., et al. (2025) · BMC Nutrition · doi:10.1186/s40795-025-01094-2 · Cited by 1
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“37 Furthermore, the MR-Egger intercept test was conducted.”
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Zhang, H., Cheng, J., Zheng, B., & Huang, X. (2025) · Medicine · doi:10.1097/md.0000000000043539 · Cited by 1
“…from the analysis and then conducted a 2-sample MR analysis utilizing the remaining SNPs as IVs to determine whether the overall causal effect is being disproportionately driven by a single SNP. [31] Funnel plots were created to visually examine potential directional pleiot-ropy through symmetry.”
Causal Association Between Immune Cell Traits and Risk of Multiple Malignant and Nonmalignant CNS Diseases: A Mendelian Randomization and Single‐Cell Transcriptomic Analysis
Ke, S., Yan, J., Li, B., & Feng, X. (2025) · Brain and Behavior · doi:10.1002/brb3.70632 · Cited by 1
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Influential
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“[23,24] When the outlier test indicated significant heterogeneity ( P .05), outlier variants were removed and the estimates was recalculated on the cleaned instrument set.”
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“Other possibilities that require consideration include horizontal pleiotropy missed by HEIDI [15], statistical power limitations [16], methodological choices [16,17], or allelic heterogeneity.”
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“[13] Together, the SMR and HEIDI tests enable the distinction between causal effects mediated by gene/protein expression and associations arising through alternative biological mechanisms.”
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“17 Benjamini-Hochberg correction ( 0.05) was applied as a false discovery rate (FDR)-correction.”
Influential
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“[44] To assess the robustness of the results, leave-one-out sensitivity analyses were performed, whereby influential SNPs were identified, excluded, and MR estimates were recalculated with the remaining SNPs. [47] A P value of <.05 was considered statistically significant.”
Mobile phone usage duration and male fertility: A two-sample Mendelian randomization analysis
Xiang, Y., Lan, X., Sun, Y., Hu, C., & Lv, L. (2025) · Medicine · doi:10.1097/md.0000000000044668 · Cited by 1
“[18,19] Cochran Q statistic and I 2 were used to evaluate heterogeneity.”
Exploring the causal effects of epilepsy and its subtypes on anthropometric traits: A 2-sample Mendelian randomization study
Chen, L., Hu, X., Wu, M., Zeng, Z., & Wang, Y. (2025) · Medicine · doi:10.1097/md.0000000000044619 · Cited by 1
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“[29,31] Despite the fact that up to 50% of the data utilized in the study consists of invalid IVs, the weighted median method can still generate dependable estimates of the causal effects.”
Identification of C4BPA as a genetically informed drug target in NSCLC: an integrative single-cell and multi-omics study based on the druggable genes
Xiao, Z., Liu, X., Tang, W., Lv, Y., Zhang, T., Zhan, X., Sun, Q., Omindo, W. W., Wang, Q., Zhang, R., et al. (2025) · Human Genomics · doi:10.1186/s40246-025-00829-3 · Cited by 1
“Additionally, MR-Egger regression was employed to detect potential pleiotropy in the relationship between exposures and outcomes [31].”
Influential
Association of Polygenic Risk Scores for Depression, Anxiety, and Neuroticism with Lower Urinary Tract Symptoms Among Women
Rajan, Z., Dardani, C., Burrows, K., Bastiani, O., Drake, M. J., & Joinson, C. J. (2025) · European Urology · doi:10.1016/j.eururo.2025.09.4154 · Cited by 1

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
ORCID: Hemani, Gibran
Bowden, Jack
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
DOI: 10.1093/hmg/ddy163
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: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
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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Evaluating the potential role of pleiotropy in Mendelian randomization studies

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