Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses

Horizontal integration of summary statistics from different GWAS traits can be used to evaluate evidence for their shared genetic causality. One popular method to do this is a Bayesian method, coloc, which is attractive in requiring only GWAS summary statistics and no linkage disequilibrium estimates and is now being used routinely to perform thousands of comparisons between traits. Here we show that while most users do not adjust default software values, misspecification of prior parameters can substantially alter posterior inference. We suggest data driven methods to derive sensible prior values, and demonstrate how sensitivity analysis can be used to assess robustness of posterior inference. The flexibility of coloc comes at the expense of an unrealistic assumption of a single causal variant per trait. This assumption can be relaxed by stepwise conditioning, but this requires external software and an LD matrix aligned to study alleles. We have now implemented conditioning within coloc, and propose a new alternative method, masking, that does not require LD and approximates conditioning when causal variants are independent. Importantly, masking can be used in combination with conditioning where allelically aligned LD estimates are available for only a single trait. We have implemented these developments in a new version of coloc which we hope will enable more informed choice of priors and overcome the restriction of the single causal variant assumptions in coloc analysis.Author summary: Determining whether two traits share a genetic cause can be helpful to identify mechanisms underlying genetically-influenced risk of disease or other traits. One method for doing this is “coloc”, which updates prior knowledge about the chance of two traits sharing a causal variant with observed genetic association data in a Bayesian statistical framework. To do this using only summary genetic association data that is commonly shared, the method makes certain assumptions, in particular about the number of genetic causal variants that may underlie each measured trait in a genomic region. We walk through several data-driven approaches to summarise the prior knowledge required for this technique, and propose sensitivity analysis as a means of checking that inference is robust to uncertainty about that prior knowledge. We also show how the assumptions about number of causal variants in a region may be relaxed, and that this improves inferential accuracy.