Fig. 6

Validation of differentially methylated CGs in the discovery set and validation set by pyrosequencing. a Top row, CG sites that are differentially methylated between HCC (n = 10) and healthy controls (n = 10) in T cells (significance was measured by student t test set at a threshold of < 0.05). The primers for pyrosequencing and conditions are listed in Additional file 18: Table S17. The scattered plot shows the mean and 95% confidence intervals (C.I.). The average methylation for three CG sites in the SLFN14 differentially methylated region is shown in the left panel. Summary of statistics including CI, SD, and SEM values are presented in Additional file 16: Table S15. b Validation by pyrosequencing of DNA extracted from T cells in the validation set. ANOVA was used to compare variance between the hepatitis B (HepB) control and other groups healthy (n = 10), hepatitis B (n = 10), hepatitis C (HepC) (n = 10) group and the HCC stages 1 (n = 8), 2 (n = 12), 3 (n = 8), and 4 (n = 22). STAP1 replication presents pyrosequencing data from T cells DNA from the second replication cohort (Additional file 15: Table S14). c ROC curve measuring specificity (Y axis) and sensitivity (X axis) of STAP1 methylation as a biomarker for discriminating HCC from healthy controls in T cells first cohort (Illumina 450 K data), in first validation set (pyrosequencing) and third validation set (pyrosequencing replication). d. ROC curve for STAP1 methylation as a biomarker for distinguishing HCC from healthy persons and chronic hepatitis in PBMC (Illumina), first validation set (pyrosequencing), and third validation set (pyrosequencing, replication). Statistic code: * 0.05, ** 0.01, *** 0.001