Gene-based analysis was performed for MDD, rMDD, fMDD, and mMDD using MAGMA42. The gene-based statistics were derived using the summary statistics from each meta-analysis. Genetic variants were assigned to genes based on their position according to the NCBI 37.3 build, with a gene boundary defined by an extended region between 20 kb upstream of transcript start site and 20 kb downstream of transcript end site for each of the genes. This resulted in a total of 18 111 genes for MDD, fMDD, and mMDD, and 17,225 genes for rMDD being analyzed. The European panel of the 1000 Genomes data (phase 1, release 3) was used as a reference panel to account for linkage disequilibrium43. A genome-wide significance threshold for gene-based associations was calculated using the Bonferroni method (α = 0.05/18 111; P < 2.76 × 10−6 for MDD, fMDD and mMDD; α = 0.05/17 225; P < 2.90 × 10−6 for rMDD).
