Combining information on multiple instrumental variables in Mendelian randomization: comparison of allele score and summarized data methods

Abstract

Mendelian randomization is the use of genetic instrumental variables to obtain causal inferences from observational data. Two recent developments for combining information on multiple uncorrelated instrumental variables (IVs) into a single causal estimate are as follows: (i) allele scores, in which individual-level data on the IVs are aggregated into a univariate score, which is used as a single IV, and (ii) a summary statistic method, in which causal estimates calculated from each IV using summarized data are combined in an inverse-variance weighted meta-analysis. To avoid bias from weak instruments, unweighted and externally weighted allele scores have been recommended. Here, we propose equivalent approaches using summarized data and also provide extensions of the methods for use with correlated IVs. We investigate the impact of different choices of weights on the bias and precision of estimates in simulation studies. We show that allele score estimates can be reproduced using summarized data on genetic associations with the risk factor and the outcome. Estimates from the summary statistic method using external weights are biased towards the null when the weights are imprecisely estimated; in contrast, allele score estimates are unbiased. With equal or external weights, both methods provide appropriate tests of the null hypothesis of no causal effect even with large numbers of potentially weak instruments. We illustrate these methods using summarized data on the causal effect of low-density lipoprotein cholesterol on coronary heart disease risk. It is shown that a more precise causal estimate can be obtained using multiple genetic variants from a single gene region, even if the variants are correlated.

Keywords: Mendelian randomization; aggregated data; allele score; causal inference; genetic risk score; genetic variants; instrumental variables; summarized data; weak instruments.

Figure 1

Estimated genetic associations and 95% confidence intervals with low‐density lipoprotein cholesterol (LDL‐c) and with coronary heart disease risk for 10 genetic variants in the PCSK9 gene region.