TWAS was performed based on a previous MDD TWAS,79 using FUSION software with default settings. All gene expression panels were of European ancestry. Gene expression panels relating to the brain include dorsolateral prefrontal cortex (DLPFC) from PsychENCODE, differential expression and splicing in DLPFC from the CommonMind Consortium (CMC) and the 12 brain regions collected in the Genotype-Expression (GTEx) project. We also included panels capturing expression in pituitary, adrenal and thyroid tissues from GTEx, given prior evidence these tissues play a role in MDD.80,81 Finally, we included panels capturing gene expression in blood from GTEx, the Netherlands Twin Registry (NTR) and the Young Finns Study (YFS) due to their increased sample size, the moderate correlation between cis-eQTLs across tissues,82 and evidence that altered expression in blood could influence risk of MDD.83,84 To distinguish associations for a gene captured by multiple panels, we refer to each panel-gene pair as features.
