Fig. 6

By MeD-seq analysis, DNA methylation patterns of cfDNA are similar between cirrhotic HCC and cirrhosis, but distinct from those of healthy individuals. A MeD-seq was conducted on samples from patients with ALD-related cirrhotic HCC (n = 20), ALD-related cirrhosis (n = 10), and healthy individuals (n = 10). No DMRs were observed when comparing cirrhotic HCC and cirrhosis. However, distinct DNA methylation patterns were identified in both cirrhotic HCC and cirrhosis when compared to healthy individuals. B PCA analysis was conducted using cirrhotic HCC tissue-specific DMMs, with a total of 3842, 4417, and 5154 DMRs selected for this analysis in the transcription start sites (TSS), CpG islands (CpG), and gene bodies (GB), respectively. DNA methylation patterns were similar among cirrhosis (n = 12), early-stage cirrhotic HCC (n = 10), and late-stage cirrhotic HCC (n = 10). DMRs located on the X- and Y-chromosome were removed to avoid gender-related effects