Mendelian Randomisation with Proxy Exposures: Challenges and Opportunities

A key challenge in human genetics is the discovery of modifiable causal risk factors for complex traits and diseases. Mendelian randomisation (MR) using molecular traits as exposures is a particularly promising approach for identifying such risk factors. Despite early successes with low-density lipoprotein (LDL) cholesterol and C-reactive protein, recent studies have revealed a more nuanced picture, with widespread horizontal pleiotropy. Here, using data from the UK Biobank, we illustrate the issue of horizontal pleiotropy with two case studies involving glycolysis and vitamin D synthesis pathways. In both cases, we demonstrate that, although the measured metabolites (pyruvate or histidine) do not have a direct causal effect on the outcomes of interest (red blood cell count or vitamin D level), we can still use variants' effects on these metabolites to infer how they perturb protein function in different gene regions. This allows us to use variant effects on metabolite levels as proxy exposures in the cis-MR framework, thus rediscovering the causal roles of histidine ammonia lyase (HAL) in vitamin D synthesis and glycolysis pathway in red blood cell survival. We also highlight the assumptions that need to be satisfied for cis-MR with proxy exposures to yield valid inferences and discuss the practical challenges of meeting these assumptions. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement I.R., K.A, and R.T. were supported by a grant from the Estonian Research Council (grant no PSG415). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The UK Biobank study was approved by the North West Multi-Centre Research Ethics Committee. This research was conducted using the UK Biobank Resource under application numbers 91233 and 30418. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The GWAS summary statistics for the 56 metabolites are available from Zenodo (https://doi.org/10.5281/zenodo.13821209). The fine-mapped credible sets and log Bayes factors from SuSiE are available from Zenodo (https://doi.org/10.5281/zenodo.13821038). The GWAS and fine mapping Nextflow workflow is available from GitHub (https://github.com/AlasooLab/reGSusie).