Fig. 1

Scheme of the three-stage EWAS. The three-stage EWAS consisted in a Discovery stage analysed with multiple linear regression with adjustment of variables known to be associated with methylation (age, sex, smoking habit, PC1 and 2), a Replication stage where the 44 nominally associated CpG sites were analysed with multiple linear regression with the same basic adjustment than in the Discovery. The replicated CpG site (cg00039070) was re-analysed in the Discovery including the specific adjustment (covariates associated with the methylation of cg00039070): PC1 and PC2. In the Discovery cohort, differentially methylation region (DMR) and block (DMB) analyses were also performed. Finally, a meta-analysis that merged the Discovery and Replication Cohorts was performed with basic EWAS adjustment. The significant CpG sites in the meta-analysis were evaluated in the pathway/features enrichment analysis, in the differentially methylated cell-type analysis and in the blood–brain correlation analysis