Journal Article

A robust and efficient method for Mendelian randomization with hundreds of genetic variants

Foley, Christopher N, Staley, James R, Allara, Elias, Burgess, Stephen, Howson, Joanna M. M.

2020

Overview

Mendelian randomization (MR) is an epidemiological technique that uses genetic variants to distinguish correlation from causation in observational data. The reliability of a MR investigation depends on the validity of the genetic variants as instrumental variables (IVs). We develop the contamination mixture method, a method for MR with two modalities. First, it identifies groups of genetic variants with similar causal estimates, which may represent distinct mechanisms by which the risk factor influences the outcome. Second, it performs MR robustly and efficiently in the presence of invalid IVs. Compared to other robust methods, it has the lowest mean squared error across a range of realistic scenarios. The method identifies 11 variants associated with increased high-density lipoprotein-cholesterol, decreased triglyceride levels, and decreased coronary heart disease risk that have the same directions of associations with various blood cell traits, suggesting a shared mechanism linking lipids and coronary heart disease risk mediated via platelet aggregation. Mendelian randomization (MR) is a method for inferring causal relationships between risk factors and outcomes via associated genetic variants. Here, Burgess et al. develop the contamination mixture method which yields robust MR results in the presence of invalid instrumental variables and groups variants by their effect estimates.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 631/208/205 / 631/443/592/2727 / 692/308/174 / 692/53/2422 / Blood cells / Body Mass Index / Cardiovascular disease / Cardiovascular diseases / Causation / Cholesterol / Cholesterol, HDL - blood / Cholesterol, HDL - genetics / Cholesterol, LDL - blood / Cholesterol, LDL - genetics / Contamination / Coronary artery disease / Coronary Disease - blood / Coronary Disease - epidemiology / Coronary Disease - genetics / Diabetes Mellitus, Type 2 - genetics / Epidemiology / Genetic Association Studies / Genetic diversity / Genetic Pleiotropy / Genetic Predisposition to Disease - genetics / Genetic variance / Genetic Variation / Health risk assessment / Health risks / Heart diseases / Humanities and Social Sciences / Humans / Lipids / Mendelian Randomization Analysis - methods / Models, Genetic / Molecular Epidemiology - methods / multidisciplinary / Phenotype / Platelet aggregation / Randomization / Reproducibility of Results / Research Design / Risk analysis / Risk Factors / Robustness / Science / Science (multidisciplinary) / Triglycerides / Triglycerides - blood / Triglycerides - genetics