Fig. 3
Landscape of plasma cfDNA in healthy individuals and hepatitis, cirrhosis, and HCC patients. a The distribution of cfDNA fragment size in the group of healthy, hepatitis, cirrhosis, early-stage HCC, advanced HCC, and HCC after surgery. The vertical dashed lines indicate the median values in all groups. b The enrichment scores of CpGs at different genomic elements and regions surrounding HBV integration sites of all the 54 cfDNA samples at low-pass WGBS. HBVi represents for HBV integration site. c The enrichment scores of CpGs at different genomic elements of cfDNA and tissue samples by randomly resampling 10 M reads from published dataset. P values between cfDNA samples and tissue samples at CpG island, promoter, exon, intron, intergenic, repeat region, HBV integration site, HBVi ±100 bp, and HBVi ±5 kb are 4.1 × 10−12, 7.6 × 10−12, 1.5 × 10−13, 4.9 × 10−8, 4.7 × 10−13, 2.1 × 10−12, 1.3 × 10−11, 9.2 × 10−12, and 1.9 × 10−11, respectively. d Long-range methylation around HBV integration sites (MethylHBV5k) in all the 54 samples. The black dot represents for AFP level (log10) for the corresponding individual. e The correlation between AFP (log10) and MethylHBV5k