Abstract PS2-07-08: Longitudinal ctDNA Tracking in Early and Recurrent Breast Cancer Using an Ultrasensitive Structural Variant-Based Assay: An Updated Analysis from the TRACER Study

Abstract Background: We previously reported the performance of an ultrasensitive structural variant (SV) and digital PCR (dPCR)-based circulating tumor DNA (ctDNA) assay in a cohort of 100 patients with early breast cancer (EBC) treated with neoadjuvant therapy, demonstrating high sensitivity, specificity, and a long lead time to distant relapse. While the personalized SV ctDNA fingerprint used in this assay holds promise for monitoring ctDNA dynamics in recurrent metastatic disease, it has not yet been evaluated in this setting. Here, we report findings from an expanded EBC cohort with extended clinical follow-up and retrospective ctDNA analysis in the metastatic setting. Methods: We conducted a retrospective analysis of patients with EBC treated with neoadjuvant therapy at the Princess Margaret Cancer Centre using an ultrasensitive, SV-based, tumor-informed ctDNA assay. Plasma samples were collected at baseline, during treatment, perioperatively, and throughout follow-up. Several patients who experienced disease recurrence consented to continued prospective plasma collection following metastatic relapse. For these patients, plasma was collected at the time of metastatic recurrence (metastatic baseline) and at subsequent restaging time points during treatment. ctDNA dynamics in the metastatic setting were evaluated retrospectively and compared with clinical and radiographic response assessments. Clinical outcomes were last updated on June 1, 2025. Results: A total of 121 patients were included (36 triple-negative breast cancer TNBC, 44 HER2-positive HER2+, and 41 ER-positive/HER2-negative ER+/HER2-). Twenty-seven patients (22%) experienced recurrence (1 local, 26 distant; 11 TNBC, 3 HER2+, 13 ER+/HER2-) with a median follow-up of 3.7 years (range: 0.4-8.0). All patients with detectable ctDNA in the postoperative or adjuvant setting developed metastatic recurrence (sensitivity: 100%, specificity: 100%), including one case of isolated intracranial relapse. The median lead time from ctDNA detection to metastatic recurrence among evaluable patients was 381 days (range: 4-1931 days). Ten patients (6 TNBC, 1 HER2+, 3 ER+/HER2-) with recurrence underwent ongoing plasma collection in the metastatic setting, spanning a median of one line of therapy (range: 1-3 lines), including treatment with endocrine therapy plus a CDK4/6 inhibitor, chemotherapy, chemo-immunotherapy, and antibody-drug conjugates (ADCs). The median variant allele fraction (VAF) at metastatic baseline was 2.7% (range: 0.01-37.8%). ctDNA remained detectable in all but one patient, who had a complete radiographic response to an ADC plus immunotherapy (median VAF: 0.3%; range: 0-37.8%), with 3 of 26 timepoints falling below a VAF of 0.01%. Using radiographic response as the clinical reference standard, ctDNA monitoring, defined as any decrease for response and any subsequent rise for progression, demonstrated strong concordance with radiographic outcomes (sensitivity: 100%; negative predictive value: 100%). In all cases, a rise in ctDNA (ie. molecular progression) preceded radiographic progression. SVs identified at baseline were reproducibly detected across longitudinal timepoints in both early-stage and metastatic settings, supporting the stability of this tumor-informed approach to ctDNA detection. Conclusion: These results reaffirm the performance of an ultrasensitive ctDNA assay using an SV and dPCR-based approach. Preliminary results support the feasibility of this assay for ctDNA monitoring in the recurrent metastatic setting, across a range of standard therapies. Additional metastatic monitoring data in a larger cohort of metastatic breast cancer will be presented. Clinical Trial Information: NCT03702309 Citation Format: M. J. Elliott, J. Roh, T. Bird, M. Li, M. Nadler, E. Amir, V. Kumar, C. Yu, K. Howarth, G. Putcha, S. Woodhouse, L. Siu, P. Bedard, H. Berman, D. W. Cescon. Longitudinal ctDNA Tracking in Early and Recurrent Breast Cancer Using an Ultrasensitive Structural Variant-Based Assay: An Updated Analysis from the TRACER Study abstract. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS2-07-08.