Fig. 3

The aberrations of cfDNA fragmentation patterns at hotspots in early-stage liver cancer. a Unsupervised clustering on the z-score of IFS at the top 10,000 most variable cfDNA fragmentation hotspots called from HCC and healthy samples. Hotspots are selected based on the variance of the IFS values across all the samples. b Volcano plot of z-score differences and −log10 FDR-value (two-way Student’s t-test) for the aberration of IFS in cfDNA fragmentation hotspots between early-stage HCC and healthy. c The significant KEGG pathways for the genes associated with class I hotspots. Cistrome-GO was utilized to associate hotspots with their targeted genes. d The motifs that are significantly enriched within class I hotspots