Overall, less than half of the TWAS Bonferroni significant genes overlapped with the 76 candidate risk genes (40% of “TWAS transcript genes”; and 47% of “TWAS genes”; Supplementary Fig. 13). This was not unexpected and could be due to noise in the data and/or that TWAS models are based on expression in adult brains whereas a large proportion of individuals in the GWAS are children. Additionally, eQTLs used to derive TWAS models might not overlap GWAS identified variants as the two types of methods are systematically biased toward identification of different types of variants59.
