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Updated: Jun 3, 2025
Detection and Monitoring of Tumor Associated Circulating DNA in Patient Biofluids
Published on: June 8, 2019
Ultrasensitive Detection and Monitoring of Circulating Tumor DNA Using Structural Variants in Early-Stage Breast
Mitchell J Elliott1, Karen Howarth2, Sasha Main3
1Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada.
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.
