In this study, we optimized and implemented a high-throughput-capable automated gel-extraction platform to isolate subfractions of the mononucleosomal peak in sequencing libraries of ccfDNA from patients with melanoma, colorectal adenocarcinoma, and pancreatic ductal adenocarcinoma with confirmed somatic BRAF or KRAS variants. This evidence concerns the gene BRAF and colorectal adenocarcinoma.