To determine its utility in the detection of HCC, we assessed the HCCscreen assay in the individuals who have a known diagnosis of HCC or have been excluded (non-HCC). We obtained 65 HCC cases and 70 non-HCC cases from the AFP/US-positive/suspected individuals. This HCC-positive or HCC-negative status was based on dynamic CT/MRI imaging and histologic confirmation.

These 135 cases were used as the training cohort, and the HCCscreen results were compared with the clinical diagnosis. To build a classifier integrating different types of biomarkers in the assay, we first collapsed the different types of cfDNA mutations into a region of interest (ROI) score for each gene or locus (see Methods). The ROI score was a weighted sum of the damaging effects and frequency for each point mutation within a ROI.