Circulating tumor DNA (ctDNA) is increasingly employed in the screening, follow-up, and monitoring of the continuously evolving
tumor; however, most ctDNA assays validated for clinical use cannot maintain the right balance between sensitivity, coverage, sample requirements, time, and cost. Here, we report our BC-monitor, a simple, well-balanced ctDNA diagnostic approach using a gene panel significant in
breast cancer and an optimized multiplex PCR-based NGS protocol capable of identifying allele variant frequencies below 1% in cell-free plasma
DNA. We monitored a cohort of 45
breast cancer patients prospectively enrolled into our study receiving
neoadjuvant chemotherapy or endocrine
therapy or
palliative therapy for metastatic diseases. Their
tumor mutation status was examined in the archived
tumor samples and plasma samples collected before and continuously during
therapy. Traceable mutations of the used 38-plex NGS assay were found in approximately two-thirds of the patients. Importantly, we detected new pathogenic variants in follow-up plasma samples that were not detected in the primary
tumor and baseline plasma samples. We proved that the BC-monitor can pre-indicate
disease progression four-six months earlier than conventional methods. Our study highlights the need for well-designed ctDNA monitoring during treatment and follow-up, integrated into a real-time treatment assessment, which could provide information on the active
tumor DNA released into the blood.