Differential methylation of 29 out of 78 CG probes associated with PD1 in the 450K array strongly correlated with HCC progression (R < − 0.7, Q < 1 × 10−8), a highly significant enrichment (hypergeometric test, p = 4.3 × 10−238) (Additional file 12: Table S11). This evidence concerns the gene PDCD1 and hepatocellular carcinoma.