Ultrasensitive Detection and Monitoring of Circulating Tumor DNA using Structural Variants in Early-Stage Breast Cancer.

Purpose: The detection of circulating tumor DNA (ctDNA) after curative-intent therapy in early breast cancer (EBC) is highly prognostic of disease recurrence. Current ctDNA assays, mainly targeting single nucleotide variants (SNVs), vary in sensitivity and specificity. While increasing the number of SNVs in tumor-informed assays improves sensitivity, structural variants (SVs) may achieve similar or better sensitivity without compromising specificity. SVs occur across all cancers, linked to genomic instability and tumorigenesis, with unique tumor- and patient-specific breakpoints occurring throughout the genome. SVs in breast cancer are underexplored, and their potential for ctDNA detection and monitoring has not been fully evaluated.

Experimental Design: We retrospectively analyzed a tumor-informed SV-based ctDNA assay in a cohort of EBC patients (n=100, 568 timepoints) receiving neoadjuvant systemic therapy (NAT), evaluating ctDNA dynamics and lead times to clinical recurrence in the postoperative period.

Results: ctDNA was detected in 96% (91/95) of participants at baseline with a median variant allele frequency (VAF) of 0.15% (range: 0.0011-38.7%); 10% (9/91) had a VAF<0.01%. ctDNA detection at cycle 2 (C2) of NAT was associated with a higher likelihood of distant recurrence (Log-rank p=0.047) and enhanced residual cancer burden (RCB) prognostication (Log-rank p=0.041). ctDNA was detected prior to distant recurrence in all cases (100% sensitivity) with a median lead time of 417 days (range: 4-1931 days).

Conclusion: These results demonstrate the clinical validity of ultrasensitive ctDNA detection and monitoring using SVs. Prospective trials are required to evaluate ctDNA-guided treatment strategies.