Fig. 3: Recalling and analyzing the copy number variant events in cell-free DNA whole-genome bisulfite sequencing data.

a A whole-genome bisulfite sequencing (WGBS)-based approach for recalling recurrent copy number variants (CNVs) in WGBS data from tissues and cfDNA. b Take Patient 002 in the ECGEA cohort as an example, the amplifications in chr. 3 and chr.5 and deletions in chr. 3, 4, 9, 10, 11, 13, 16,18, and 21 were identified in whole-genome sequencing data and recalled in paired WGBS data. c Compared to the CNV events in 150 healthy controls (HCs), 153 regions had significantly higher CNV event rates in 150 patients with esophageal squamous cell carcinoma (ESCC). The amplifications (red) and deletions (blue) were shown with the corresponding adjusted p value (false discovery rate, FDR) of the difference in ESCCs vs. HCs (two-sided t test; ns, gray; FDR <  0.05, yellow; FDR <  0.01, orange; FDR <  0.001, dark red). d The CNV-positive rates were significantly higher in patients with ESCC and intraepithelial neoplasia (IEN) than the HCs in the discovery cohort and the validation cohorts and positively correlated with the stages and grades. ESCC esophageal squamous cell carcinoma, IEN intraepithelial neoplasia, LGIEN low-grade IEN, HGIEN high-grade IEN, HC healthy control, WGS whole-genome sequencing, WGBS whole-genome bisulfite sequencing, GMM Gaussian Mixture Model, HMM Hidden Markov Model, CNV copy number variant, AMPL amplification, DELE deletion, ns no significance, G grade. Source data are provided as a Source Data file.