The potential of our pipeline in the investigation of somatic methylation evolution is demonstrated here for three exemplary loci: SNRPN (small nuclear ribonucleoprotein polypeptide N), an example of an imprinted gene; FGF6 (fibroblast growth factor 6) demonstrating a locus with increasing demethylation in cancer; and HS3ST2 (heparan sulfate 3-O-sulfotransferase 2) exhibiting a pattern of locus methylation in the progress of cancerogenesis. This evidence concerns the gene HS3ST2 and cancer.