ABSTRACT Background DNA methylation in CpG context is fundamental to the epigenetic regulation of gene expression in high eukaryotes. Disorganization of methylation status is implicated in many diseases, cellular differentiation, imprinting, and other biological processes. Techniques that enrich for biologically relevant genomic regions with high CpG content are desired, since, depending on the size of an organism’s methylome, the depth of sequencing required to cover all CpGs can be prohibitively expensive. Currently, restriction enzyme based reduced representation bisulfite sequencing and its modified protocols are widely used to study methylation differences. Recently, Agilent Technologies and Roche NimbleGen have ventured to both reduce sequencing costs and capture CpGs of known biological relevance by marketing in-solution custom-capture hybridization platforms. We aimed to evaluate the similarities and differences of these three methods considering each targets approximately 10-13% of the human methylome. Results Overall, the regions covered per platform were as expected: targeted capture based methods covered &gt;95% of their designed regions whereas the restriction enzyme-based method covered &gt;70% of the expected fragments. While the total number of CpG loci shared by all methods was low, ~30% of any platform, the methylation levels of CpGs common across platforms were concordant. Annotation of CpG loci with genomic features revealed roughly the same proportions of feature annotations across the three platforms. Targeted capture methods encompass similar amounts of annotations with the restriction enzyme based method covering fewer promoters (~9%) and shores (~8%) and more unannotated loci (7-14%). Conclusions Although all methods are largely consistent in terms of covered CpG loci and cover similar proportions of annotated CpG loci, the restriction based enrichment results in more unannotated regions and the commercially available capture methods result in less off-target regions. Quality of DNA is very important for restriction based enrichment and starting material can be low. Conversely, quality of the starting material is less important for capture methods, and at least twice the amount of starting material is required. Pricing is marginally less for restriction based enrichment, and number of samples to be prepared is not restricted to the number of samples a kit supports. The one advantage of capture libraries is the ability to custom design areas of interest. The choice of the technique should be decided by the number of samples, the quality and quantity of DNA available and the biological areas of interest since comparable data are obtained from all platforms.

"Same Difference": Comprehensive evaluation of three DNA methylation measurement platforms