Fig. 3

The cfDNA promoter profiling shows the potential to predict ALN status. a Promoter profiling of the non-constitutive and housekeeping genes. The average promoter coverage was calculated by using the whole genome sequencing data derived from 30 breast cancer patients. The non-constitutive and housekeeping genes were obtained from the additional materials of previous study [14]. b Promoter profiling of the ALN-negative and -positive breast cancer patients. Mean promoter profiling of protein coding genes derived from15 ALN-positive and 15 ALN-negative breast cancer patients was detected using whole genome sequencing. c Uniform manifold approximation and projection (UMAP) plot representing the associations between ALN-positive and -negative groups. The genes with differential promoter coverages were used to plot UMAP. d Heat map of the z-scores of genes with differential read coverages. e Volcano plots of gene transcripts with differential read coverages at the promoter (fold change ≥ 1.5 and false discovery rate [FDR] ≤ 0.05) between 15 ALN-positive and 15 ALN-negative patients. f Analysis of Gene Ontology (GO) enrichment of genes with differential promoter coverage. TSS transcriptional start sites, Decreased genes with differentially decreased read coverage, Increased genes with differentially increased read coverage, Non genes with no differential read coverage, ALN axillary lymph node