The MR-Base platform supports systematic causal inference across the human phenome
Open accessAbstract
Results from genome-wide association studies (GWAS) can be used to infer causal relationships between phenotypes, using a strategy known as 2-sample Mendelian randomization (2SMR) and bypassing the need for individual-level data. However, 2SMR methods are evolving rapidly and GWAS results are often insufficiently curated, undermining efficient implementation of the approach. We therefore developed MR-Base ( http://www.mrbase.org ): a platform that integrates a curated database of complete GWAS results (no restrictions according to statistical significance) with an application programming interface, web app and R packages that automate 2SMR. The software includes several sensitivity analyses for assessing the impact of horizontal pleiotropy and other violations of assumptions. The database currently comprises 11 billion single nucleotide polymorphism-trait associations from 1673 GWAS and is updated on a regular basis. Integrating data with software ensures more rigorous application of hypothesis-driven analyses and allows millions of potential causal relationships to be efficiently evaluated in phenome-wide association studies.
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The study performed MR and identified 17 unique proteins as putatively causal for AD (FDR-corrected P<0.05) with confirmed directionality using the Steiger test.
“We next performed MR47 and identified 17 unique proteins as putatively causal for AD (Fig. 4A, Supp. Table S40&41, FDR-corrected P<0.05) with confirmed directionality using the Steiger test52 (Supp. Table S42).”
From Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and implicates causal proteins for Alzheimer’s disease (2024) · cites this paper as [47]
Forest plots, which plot the causal estimate obtained from each genetic variant, allow for a visual inspection of heterogeneity around the overall causal estimate.
“Forest plots, which plot the causal estimate obtained from each genetic variant, allow for a visual inspection of heterogeneity around the overall causal estimate.84”
From Strengthening the Reporting of Observational Studies in Epidemiology using Mendelian Randomisation (STROBE-MR): explanation and elaboration. (2021) · cites this paper as [84]
Additional plots might also aid in the visualisation of results, assessing assumption violation, and detecting potential influential or outlier points.
“Additional plots might also aid in the visualisation of results, assessing assumption violation, and detecting potential influential or outlier points.”
From Strengthening the Reporting of Observational Studies in Epidemiology using Mendelian Randomisation (STROBE-MR): explanation and elaboration. (2021) · cites this paper as [84]
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Daghlas, I., Guo, Y., & Chasman, D. I. (2020) · European Journal of Neurology · doi:10.1111/ene.14111 · Cited by 32 · see citing works
Identifying therapeutic targets for cancer among 2074 circulating proteins and risk of nine cancers
Smith-Byrne, K., Hedman, Å., Dimitriou, M., Desai, T., Sokolov, A. V., Schioth, H. B., Koprulu, M., Pietzner, M., Langenberg, C., Atkins, J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46834-3 · Cited by 33 · see citing works
Self-citationHaworth, S., Kho, P. F., Holgerson, P. L., Hwang, L.-D., Timpson, N. J., Rentería, M. E., Johansson, I., & Cuellar-Partida, G. (2021) · European Journal of Human Genetics · doi:10.1038/s41431-020-00734-4 · Cited by 29 · see citing works
Self-citationIron status and the risk of sepsis and severe COVID-19: a two-sample Mendelian randomization study
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A selection pressure landscape for 870 human polygenic traits
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Analysis of gut microbiota and depression and anxiety: Mendelian randomization from three datasets
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- Authors
- Hemani, G., Zheng, J., Elsworth, B., Wade, K. H., Haberland, V., Baird, D., Laurin, C., Burgess, S., Bowden, J., Langdon, R., Tan, V. Y., Yarmolinsky, J., Shihab, H. A., Timpson, N. J., Evans, D. M., Relton, C., Martin, R. M., Davey Smith, G., Gaunt, T. R., & Haycock, P. C.
- Affiliations
- National Institute for Health and Care Research (GB)
- University of Cambridge (GB)
- Translational Research Institute (AU)
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Corresponding author
- Hemani, Gibran
- Zheng, Jie
- Gaunt, Tom R
- Haycock, Philip C
- ORCID
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2018-05-30
- Volume
- 7
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC5976434
- OpenAlex
- W2805983714
- Cited by
- 7,959
- References
- 81
- Citations by year
- 2026: 979 · 2025: 1671 · 2024: 2188 · 2023: 1227 · 2022: 763 · 2021: 534 · 2020: 346 · 2019: 196 · 2018: 44 · 2013: 1 · 2012: 1
- FWCI
- 176.49
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Explore Bristol Research (submittedVersion, cc-by)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- Brunel University Research Archive (BURA) (Brunel University London) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Bristol Research (University of Bristol) (submittedVersion, cc-by)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Funders
- Wellcome (208806/Z/17/Z)
- Cancer Research UK (C18281/A19169, Population Research Postdoctoral Fellowship, C52724/A20138)
- GlaxoSmithKline
- Biogen
- Medical Research Council (Methodology Research Fellowship, MR/N501906/1)
- National Institute for Health Research (NIHR Bristol BRC)
- Australian Research Council
- National Health and Medical Research Council (APP1125200, APP1137714)
- Roy Castle Lung Cancer Foundation (2013/18/Relton)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- causal inference, single nucleotide polymorphisms, horizontal pleiotropy, sensitivity analysis, phenome-wide association study, R package, web application
- MeSH terms
- Coronary Disease, Humans, Cholesterol, LDL, Models, Genetic, Phenotype, Polymorphism, Single Nucleotide, Databases, Genetic, Genome-Wide Association Study, Mendelian Randomization Analysis, Genetic Pleiotropy
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