We examined expression in brain tissue of the genes flanking the GWS intergenic locus on chromosome 2 to determine whether either of these genes is functionally related to AD. A probe (ILMN_1811050) mapping to the 3′-UTR region of CCDC88A was consistently downregulated in the brain regions of alcoholics: CNA: P = 0.05; BLA: P = 0.03 and CTX: P = 0.04. MTIF2 did not exhibit differential expression in any of the three brain regions. Thus, only CCDC88A appeared to be differentially expressed in AD, supporting possible involvement of the protein product of that locus in risk for the trait. Among expression probes mapping to other genes containing GWS SNPs, probe ILMN_1673069, mapping to the 3′-UTR of DPP9, was significantly differentially expressed (P = 0.0024) in BLA (Supplementary Table S3).
