Fig. 4

Schematic diagram of the whole process for HCC early detection. The 10 ml peripheral blood was drawn from the individual. After cfDNA extraction, low-depth whole-genome NEEM-seq was performed on the cfDNA sample. DeepTrace model was used to predict the probability of each read within the differentially methylated regions (DMRs). The probability estimated the possibility that a read is derived from ctDNA. The individual’s HCC risk score was calculated by integrating all the reads probability, and the individual’s positive (high risk of HCC) or negative (low risk of HCC) detection result was given