The authors examined single-base level DNA methylation in embryonic stem cells (H1) and fibroblasts (IMR90), utilizing MethylC-Seq/ChIP-Seq and the Genome Analyzer II. Nearly all methylcytosines in the IMR90 genome were CG; almost 25% of H1 had non-CG methylation. This was mostly lost with H1 cell differentiation. At the mCG sites IMR90 cells were less frequently methylated; methylation also differed by chromosomal location. Highly expressed genes had three times the non-CG methylation density than non-expressed genes.

Sequencing data was used to validate methyl-BEAMing results and not really for the clinical application (considered still too expensive and slow for that).

DNA methylation at CpG ‘islands’ (CGIs) may induce problematic gene expression. Current profiling investigates single nucleotides within limited regions, or whole genomes with limited resolution. The bisulfite capture method combined bisulfite conversion, hybrid selection, and deep sequencing for methylation frequencies in 324 CGIs, using Genome Analyzer II. Chip-Seq was used to investigate histone modification. In a breast cancer versus normal skin cell line there was a higher frequency of full or partial methylation, and enriched methylated sites within exons.