In order to explore the feasibility of quantitative methylation studies using 454 sequencing, a range of genomic loci was selected for in-depth analysis: tumor-suppressor genes reported to be frequently hypermethylated in hepatocellular carcinoma (p16INK4a, RASSF1A, SOCS-1, GSTπ1, [12] and references therein), classical non-protein coding CIMP loci also reported to be methylated in HCC (MINT31, [13]), and microRNA genes identified by our own group to be aberrantly methylated in HCC (mir-9-3, mir-34a, mir-596, mir-663). Here, GSTP1 is linked to neoplasm.