The largest methylome-wide study to date was the recent study of Clark and colleagues [102], examining over 600 individuals at approximately 27 million CpG sites in approximately 4 million CpG “blocks” using a novel methyl-CpG-binding domain (MBD) protein-based sequencing technology as well as a genome-wide association study using the Affymetrix 6.0 chip. Unfortunately, despite the innovative technique employed to interrogate the methylome, phenotyping was a relative weakness of the study, which employed a binary question asking if participants had ever consumed alcohol regularly versus never consumed alcohol regularly. In their discovery sample, 94% of subjects answered affirmatively, as did 93% of those in the larger replication sample of 730 subjects. Although Clark and colleagues reported significantly different methylation at 33 “blocks” or DMRs at a FDR threshold of q < 0.1, there is no overlap with these blocks and the top CpGs in the second-largest array-based study of Philibert and colleagues [101] or that of Zhao and colleagues [100].
