Enabling sensitive and precise detection of ctDNA through somatic copy number aberrations in breast cancer

Cell-free DNA (cfDNA) extracted from peripheral blood has emerged as a crucial biomarker source in oncology research. To enhance the detection of somatic copy number alterations (SCNAs) and circulating tumor DNA (ctDNA), we developed eSENSES, a 2 Mb breast cancer-targeted NGS panel. It includes 15,000 genome-wide SNPs, 500 focal SNPs in breast cancer driver regions, and exons from 81 commonly altered genes, alongside a custom computational approach. We assessed the performance of eSENSES using both synthetic and clinical samples showing that eSENSES can detect ctDNA levels below 1%, exhibiting high sensitivity and specificity at 2-3% ctDNA levels. In patients with metastatic breast cancer, ctDNA estimations correlated with disease progression. When compared with other technologies and state-of-the-art approaches, eSENSES demonstrated enhanced performance. eSENSES provides a reliable, powerful and cost-effective tool for monitoring disease progression and guiding therapeutic decisions in breast cancer patients.