Abstract 3360: Pre- and post-operative analysis of circulating tumor DNA in patients with breast cancer treated with neoadjuvant therapy using a tissue-free, methylation-based approach

Abstract Background: Detection of circulating tumor DNA (ctDNA) in early breast cancer (BC) is a prognostic biomarker for disease recurrence. This pilot study evaluates the performance of a tissue-free epigenomic ctDNA assay in pre-neoadjuvant therapy (NAT), on-NAT and post-op plasma samples from patients (pts) with BC. Methods: Pre-NAT, on-NAT and post-op plasma samples from 13 pts that received NAT for BC were retrospectively analyzed for ctDNA using Guardant Reveal powered by Infinity, a tissue-free assay that analyzes differentially methylated regions of DNA using an applied bioinformatics filter optimized to detect BC. It results in binary ctDNA detection calls and a quantitative estimate of tumor fraction (TF) in ctDNA+ samples. Results: A total of 27 samples from 14 pts were evaluated, with 96% (26/27) samples passing quality control and included in the analysis (10 pre-NAT, 3 on-NAT, and 13 post-op). ctDNA was detected in 42% (11/26) of samples: 70% (7/10) pre-NAT, 33% (1/3) on-NAT and 23% (3/13) post-op (Table). For post-op samples collected within one year of recurrence, sensitivity was 100% (3/3). 2/5 pts who experienced recurrence, whose post-op samples were collected during adjuvant therapy and were ctDNA-, had a recurrence >15 months after the sample collection. No pts (0%, 0/8) without recurrence were ctDNA+ post-op. A pt with a brain-only recurrence had the lowest TF fraction amongst ctDNA+ post-op samples at 0.9%, with a median post-op TF of 2.5% (range, 0.9-23%) among the 3 ctDNA+ samples. Conclusion: ctDNA was detectable in 70% of pts pre-NAT, 33% on-NAT and 23% post-op, with persistent ctDNA associated with recurrence. In the subsequent full study, ∼ 600 samples will be evaluated at these timepoints. The dataset will provide a rich clinical landscape to understand sensitivity and specificity of methylation-based ctDNA testing, optimal timing and key areas to study therapeutic interception. Citation Format: Arielle J. Medford, Justine Knape, Derek Dustin, Haiyang Zhang, Caroline Weipert, Shivahamy Maheswaran, Irene Kuter, Jeffrey Peppercorn, Seth Wander, Steven J. Isakoff, Beverly Moy, Dejan Juric, Laura M. Spring, Aditya Bardia. Pre- and post-operative analysis of circulating tumor DNA in patients with breast cancer treated with neoadjuvant therapy using a tissue-free, methylation-based approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3360.