Fig. 5
From: Altered cfDNA fragmentation profile in hypomethylated regions as diagnostic markers in breast cancer
DMRs-dependent cfDNA fragmentation profiles. A Input-adjusted short fragments ratio were shown with 10 kb windows in hypermethylated and hypomethylated regions for both patients with breast cancer (purple) and healthy individuals (black). B Distribution of the cfDNA fragmentation profile mentioned above was shown across human genome. The input-adjusted short fragments ratio in each 10 kb window was calculated by dividing short fragments ratio in each 10 kb window by it in corresponding input libraries. Differentially methylated 10 kb windows were selected for representation according to the following criteria: (1) hypermethylated 10 kb windows have padj < 0.05 and log2FoldChange > 1; (2) hypomethylated 10 kb windows have padj < 0.05 and log2FoldChange < − 1; (3) the selected windows should have at least 20 deduplicated cfDNA fragments for all samples including patients with breast cancer and healthy individuals; (4) the selected windows should have input-adjusted short fragments ratio of less than 10 for any samples analyzed. Hyper, hypermethylated genomic regions; Hypo, hypomethylated genomic regions