A rare-variant analysis of FADS-related metabolites in Major Depression

Background: Genetic and observational studies have identified metabolic factors potentially contributing to the risk of Major Depression (MD). However, studies to date have concentrated on common genetic variants, many of which are in linkage disequilibrium. This makes it difficult to localise variants to a single gene. To overcome this, we used short read whole-genome sequenced datasets (srWGS) to conduct a targeted rare variant association analysis of the FADS region, which has previously been implicated in metabolic effects on MD. Methods: Using srWGS data from 740,373 individuals from All of Us (AoU) and the UK Biobank (UKB) we tested for associations between rare variants in the FADS region and MD. Additionally we conducted association tests between rare FADS variants and five blood-based metabolites implicated by previous studies of MD. Finally, we applied Mendelian randomisation to identify causal effects of metabolites on MD using rare-variants. Results: We found FADS rare variants were significantly associated with all tested metabolites, but not with MD. Using Wald-Ratio MR we found a putative causal effect of Docosahexaenoic acid (DHA) on MD using a rare-variant instrument in the FADS2 gene. Conclusion: Our study represents the largest rare-variant analysis of MD to date. However, the lack of associations between FADS rare-variants and MD suggests our analysis is underpowered, or that genetic effects on MD are conferred substantially by higher frequency variants. Rare-variant MR suggested a causal effect of DHA on MD, and implicates the FADS2 gene.