A robust method to estimate regional polygenic correlation identifies heterogeneity in the shared heritability between complex traits

Background Complex traits can share a substantial proportion of their polygenic heritability. However, genome-wide polygenic correlations between pairs of traits can mask heterogeneity in their shared polygenic effects across loci. We propose a novel method (WML-RPC) to evaluate polygenic correlation between two complex traits in small genomic regions using summary association statistics. Our method tests for evidence that the polygenic effect at a given region affects two traits concurrently. Results We show through simulations that our method is well calibrated, powerful and more robust to misspecification of linkage disequilibrium than other methods under a polygenic model. As small genomic regions are more likely to harbour specific genetic effects, our method is ideal to identify heterogeneity in shared polygenic correlation across regions. We illustrate the usefulness of our method by addressing two questions related to cardio-metabolic traits. First, we explored how regional polygenic correlation can inform on the strong epidemiological association between HDL cholesterol and coronary artery disease (CAD), suggesting a key role for triglycerides metabolism. Second, we investigated the potential role of PPARγ activators in the prevention of CAD. Conclusions Our results provide a compelling argument that shared heritability between complex traits is highly heterogeneous across loci.