Fig. 3

The cell-free DNA methylation landscapes and the cfDNA methylation analysis for breast cancer diagnosis. a Gene body with ±10 kb profiles of mean sequencing coverage of cfDNA fragments using WGBS. The gene lengths were normalized to 20 kb. The cfDNA fragments were enriched in coding regions and intergenic regions compared to the loss in gene promoter regions. TSS, transcription start site; TES, transcription end site. b The amount of cfDNA in different genomic regions negatively correlating with their CpG density (r = 0.98, p < 0.0001). c Boxplots showing CpG density was significantly higher in hyper-DMRs than in hypo-DMRs (p < 0.0001). Boxplots represent the interquartile range (25–75%), with the median; whiskers correspond to 1.5 times the interquartile range. d The average amount of cfDNA fragments in hypo-DMRs is significantly higher than ones in hyper-DMRs in all of the malignant and benign samples (p < 0.0001 by Pearson’s chi-squared test). e The cfDNA malignant ratio of the top 10 optimal cfDNA hypo-DMRs markers in plasma samples from patients with breast cancer and benign breast lesions. ns, not significant; * p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001; **** p ≤ 0.0001. f and g Receiver operating characteristic (ROC) curves of the diagnostic model based on the cfMeth score. The area under the curve (AUC) of the cfMeth score obtained for the discovery (f) and validation (g) cohorts were 0.89 (95% CI, 0.84–0.94) and 0.81 (95% CI, 0.69–0.93). h and i ROC curves of the combined diagnostic model. The AUC of the cfMeth score obtained for the discovery (h) and validation (i) cohorts were 0.94 (95% CI, 0.90–0.97) and 0.93 (95% CI, 0.84–1.00)