BC-Monitor: Towards a Routinely Accessible Circulating Tumor DNA-Based Tool for Real-Time Monitoring Breast Cancer Progression and Treatment Effectiveness

SIMPLE SUMMARY: Circulating tumor DNA (ctDNA) is increasingly employed in the management of malignant diseases, though the implementation of ctDNA diagnostics in daily oncology care has limitations. Here, we report our BC-monitor, a simple, well-balanced ctDNA diagnostic approach using an optimized multiplex PCR-based NGS protocol. We monitored a cohort of 45 breast cancer patients prospectively enrolled into our study receiving neoadjuvant chemotherapy, 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 during therapy. We detected traceable mutations in approximately two-thirds of the cases, and, importantly, new pathogenic variants in follow-up plasma that were not present in the primary tumor and baseline plasma. Our results indicate that ctDNA monitoring during treatment and follow-up with the BC-monitor tool, by predicting disease progression four–six months earlier than conventional methods and supporting treatment decision, may improve the outcome significantly. ABSTRACT: 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.