Based on the methylation status and mutational/transcriptional profiles, patients were categorized into four groups (G1–G4): the G1 (normal-like) grouping included patients with certain HCC-related gene mutations such as in TP53 and CTNNB1 during the progression phase, whereas the G2 (global hypomethylation) group showed mutations in TP53 at early stages and subsequent 4q or 16q loss during the progression phase. The gene discussed is CTNNB1; the disease is hepatocellular carcinoma.