"same difference": Comprehensive evaluation of four DNA methylation measurement platforms
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
Although all methods are largely consistent in terms of covered CpG loci, the commercially available capture methods result in covering nearly all CpG sites in their target regions with few off-target loci and covering similar proportions of annotated CpG loci, the restriction-based enrichment results in more off-target and unannotated CpG loci. 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 the number of samples that can be prepared is not restricted to the number of capture reactions a kit supports. However, the advantage of capture libraries is the ability to custom design areas of interest. The choice of the technique would 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.