A gene-based association analysis was conducted using fastBAT76 within GCTA version 1.94.0 beta.46 After removing SNPs with MAF < 0.01 or with imputation INFO score < 0.8, there were 6,724,173 SNPs remaining for analysis. The European subsample from phase 3 of the 1000 Genomes Project was used as the LD reference panel with the fastBAT default LD cut-off of 0.9 applied. A gene list consisting of 19,878 protein coding genes available from https://figshare.com/articles/dataset/geneMatrix/13335548 was used to map the base pair position of genes using genome build hg19. A total of 18,747 genes were analyzed for association with MDD. A Bonferroni correction (0.05/18,747) was applied, with a p-value < 2.67 ×10−6 required for an association with MDD.
