Enrichment methods provide a feasible approach to comprehensive and adequately powered investigations of the methylome

Methylome-wide association studies (MWAS) are typically performed using microarray technologies that assay only a very small fraction of the CG methylome and entirely miss two forms of methylation that are common in brain and likely of particular relevance for neuroscience and psychiatric disorders. The alternative is the use whole genome bisulfite sequencing, but this approach is not yet practically feasible with the sample sizes required for adequate statistical power. We argue for revisiting methylation enrichment methods that, provided optimal protocols are used, enable comprehensive, adequately powered, and cost-effective genome-wide investigations of the methylome. To support our claim we use data showing that enrichment methods approximate the sensitivity obtained with the whole genome bisulfite methods with slightly better specificity. However, this performance is achieved at <5% of the reagent costs. Furthermore, because many more samples can be sequenced simultaneously, projects can be completed about 15 times faster. A potential drawback of our approach to assay CG methylation (the dominant form of methylation in the vast majority of somatic tissues). is the relatively large amount of genomic DNA (ideally >1 ug) required to obtain high quality data. Biomaterials are typically expensive to collect, provide a finite amount of DNA, and may simply not yield sufficient starting material. Thus, any possibility to use low amounts of DNA will increase the breadth and number of the studies that can be conducted. Therefore, we further adapted the enrichment step of the protocol. With this low starting material protocol, the assay performed generally equal well or better than the ample starting material protocol requiring >1 ug. Overall design: To validate the enrichment methods we calculated the sensitivity (proportion of methylated loci correctly detected by enrichment methods), specificity (proportion of non-methylated loci correctly identify by enrichment methods) and the overall agreement (proportion of times the enrichment methods arrived at the same conclusion regarding the methylation status as the bisulfite data). Please note that GSM2486673-GSM2486686 samples are discussed in the 'Nucleic Acids Res' publication and that GSM2486673-GSM2486678, GSM2593327-GSM2593338 are discussed in another manucript (pending manuscript review). Since the two papers are closely related, all samples were grouped under one Series.