Abstract PS2-07-02: Tissue-free epigenomic circulating tumor DNA (ctDNA) analysis pre- and post-surgery in early breast cancer: clinical features and prognostic utility

Abstract Introduction The development of new highly sensitive assays allows for measurement of ctDNA in early breast cancer (eBC). These new tests have much lower limits of detection, which increases the potential for recurrence monitoring in the curative-intent setting. Promising applications include tracking response to neoadjuvant therapy (NAT), determining prognosis after NAT, and predicting relapse. The tissue-agnostic approach to ctDNA testing has a faster initial turnaround time (7-10 days) and is not limited by sequencing errors and tumor quantity/quality, which makes the utility of this assay type in the neoadjuvant context compelling. This study evaluates the use of a tissue-free epigenomic ctDNA assay from patients (pts) with high-risk eBC who received NAT, to determine detectability of ctDNA across subtypes and stages, and assess its use as a prognostic tool. Methods Pts with eBC consented to have serial plasma collected throughout their courses of treatment. Samples were collected at clinically relevant time points, which included prior to NAT initiation (baseline/pre-NAT), during NAT (on-NAT), after completion of NAT/prior to surgery (post-NAT/pre-op), following surgery (post-op), and throughout the surveillance period. ctDNA analysis was performed using the Guardant Reveal assay, a tissue-free, epigenomic assay, which provides a binary ctDNA detection result (present vs absent) and quantifies ctDNA via tumor fraction. Fisher’s exact test was performed to evaluate the relationship between ctDNA detectability and categorical clinical variables, and the relationship of ctDNA detection status to survival outcomes was evaluated using univariate Cox proportional hazards models and log-rank tests. Results: A total of 446 samples from 85 pts with eBC treated at the Massachusetts General Hospital were evaluable, with a 97% (446/461) quality control pass rate. Baseline ctDNA was detectable in 76% (35/46) of patients, with detection rates consistent across breast cancer subtypes and clinical stages: 70% (7/10) in ER+/HER2-, 80% (16/20) in HER2+, and 70% (12/16) in TNBC; 50% (2/4) in stage I, 79% (23/29) in stage II, and 77% (10/13) in stage III disease. There were a total of 12 recurrences (14.1%) in the evaluable cohort. At the pre-NAT time point, ctDNA was detectable in all pts who later developed distant recurrence. At a median follow-up of 51.3 months (range 2.2-99.6 months), stratification by median tumor fraction (TF) revealed a significant association between higher TF and worse D-RFI (p = 0.0052). ctDNA detection at pre-NAT (p > 0.99) or post-NAT/pre-op (p = 0.50) was not significantly associated with the likelihood of residual disease after NAT, however ctDNA detection at the post-NAT/pre-op time point was strongly associated with worse D-RFI (p < 0.0001). In the post-op setting, ctDNA detection was associated with a 15-fold increased risk of distant recurrence (p < 0.0001). Conclusion: ctDNA was detected via a tissue agnostic, methylation-based ctDNA analysis across eBC subtypes. All pts with recurrence had baseline detectable ctDNA, and detectable ctDNA post-operatively was associated with a very high risk of recurrence, with higher TF associated with poorer D-RFI. Furthermore, while post-NAT/pre-op ctDNA did not predict residual disease, detectability was strongly associated with worse D-RFI. This analysis is among the first data across all breast cancer subtypes utilizing a tissue-free assay for prognostic validation in both the NAT and post-operative setting. Additional analyses are ongoing to determine sensitivity, specificity, and lead time to recurrence, as well as the association of other clinical interventions (e.g. radiation, adjuvant therapy) on ctDNA detectability and dynamics. Updated results from these analyses will be presented at the meeting. Citation Format: A. J. Medford, J. Knape, D. Dustin, A. Dedeoglu, O. Rieur, H. Zhang, M. Shivahamy, I. Kuter, R. O. Abelman, J. M. Peppercorn, S. A. Wander, N. Vidula, S. J. Isakoff, B. Moy, L. W. Ellisen, D. Juric, L. M. Spring, A. Bardia. Tissue-free epigenomic circulating tumor DNA (ctDNA) analysis pre- and post-surgery in early breast cancer: clinical features and prognostic utility [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 PS2-07-02.