JEPEGMIX2-P108 software with default settings was used to conduct TWAS on 13 brain regions and pituitary tissue that showed significant enrichment in MAGMA/FUMA analyses using our PEC-DLPFC GReX model. JEPEGMIX2-P was applied on GWAS summary statistics to estimate gene-trait associations. This method was preferable since it relied on a covariance matrix based on 33k samples compared to other TWAS methods which use less than 3k samples109. To determine significance, a Bonferroni correction threshold for the unique number of genes tested was applied (P < 0.05/14,935). As a less conservative approach, we also applied FDR at a q-value threshold of 0.05.
