The microarray platform has been extensively used to survey methylation in the brain. The most well-known methylation microarray is Infinium Human Methylation 450K from Illumina, which covers 99% of Refseq genes and 95% of CpG islands with additional coverage in “island shores” and the regions flanking them. Furthermore, it includes promoter regions, the 5'/3' untranslated region, first exon, gene body, and CpG islands within the intergenic region and microRNA promoter regions (Carless, 2014).With this comprehensive coverage of human genome, several studies used this microarray for epig- enome-wide association studies with brain and psychiatric diseases (Humphries et al., 2015; Kinoshita et al., 2013; Moore, McKnight, Craig, & O’Neill, 2014; Song et al., 2014). Those studies have mostly sought to reveal differences in DNA methylation between individuals that are associated with susceptibility to psychiatric illness, or to illuminate the role of DNA methylation in memory formation and maintenance. The disadvantage of using microarrays for these applications is that they only detect methylation changes in preselected regions of a specific genome. Human Methylation 450K is the only methylation microarray product currently available, and the utility of this method is thus limited to human DNA samples.
An increasing number of laboratories are choosing to avoid these issues by moving directly to whole-genome sequencing, which is increasingly affordable. Whole-genome sequencing is more flexible because it can be applied to any species and is an unbiased approach to detecting DNA modifications. More importantly, next-generation sequencing technology has increased the volume and speed of processing, and the throughput of sequencing is substantially higher than that of microarrays.