2025/01/09 by Mitchell J. Elliott, Karen Howarth, Sasha Main +24 · 1 voice · 1 citation
Biochemistry, Genetics and Molecular Biology · Medicine · #Cancer Genomics and Diagnostics #Cancer Cells and Metastasis #Genetic factors in colorectal cancer
paper · pdf · doi:10.1158/1078-0432.ccr-24-3472
openalex publication_date 2025/01/09 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31
PURPOSE: The detection of circulating tumor DNA (ctDNA) after curative-intent therapy in early-stage breast cancer is highly prognostic of disease recurrence. Current ctDNA assays, mainly targeting single-nucleotide variants, vary in sensitivity and specificity. Although increasing the number of single-nucleotide variants in tumor-informed assays improves sensitivity, structural variants (SV) 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 patients with early-stage breast cancer (n = 100, 568 timepoints) receiving neoadjuvant systemic therapy, 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 of 0.15% (range: 0.0011%-38.7%); of these, 10% (9/91) had a variant allele frequency <0.01%. ctDNA detection at cycle 2 (C2) of neoadjuvant therapy was associated with a higher likelihood of distant recurrence (log-rank P = 0.047) and enhanced residual cancer burden 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: 4-1,931 days). CONCLUSIONS: These results demonstrate the clinical validity of ultrasensitive ctDNA detection and monitoring using SVs. Prospective trials are required to evaluate ctDNA-guided treatment strategies.