cis-Methylation and Gene Expression in the NIMH Brain Tissue Collection

Probes mapping all different gene variants were selected when analysing mQTL in the brain in the NIMH Brain Tissue Collection (Colantuoni et al. 2011). Raw gene expression 2-color microarray (Illumina Human 49 K Oligo array (HEEBO-7 set)) intensity data from postmortem dorsolateral prefrontal cortex (DLPFC) were downloaded (available at {"type":"entrez-geo","attrs":{"text":"GSE30272","term_id":"30272"}}GSE30272) and, among them, data from individuals free from psychiatric and/or neurologic diagnoses and substance abuse according to DSM-IV were loess-normalized as described previously (Colantuoni et al. 2011). Processed and normalized DNA methylation data generated by the Illumina HumanMethylation450 microarray on samples that had both DNA methylation and expression data were also collected as described before (Jaffe et al. 2016). Expression probes were re-annotated to the hg19 genome on these samples by using the Gemma tool (Zoubarev et al. 2012) as described previously (Jaffe et al. 2016). For methylation–expression associations, we first performed PCA using the methylation site in or ±10 kb of a gene, and the PC explaining >5% of the variance were used in association analysis with the corresponding gene expression by linear regression model.