Abstract PS2-09-07: Ultra-sensitive Molecular Residual Disease Detection in Breast Cancer Using Whole-Genome Sequencing-Based Personalized ctDNA Panels: Preliminary Results from the MONSTAR-SCREEN-3 Project

Abstract Background Circulating tumor DNA (ctDNA) has emerged as a promising biomarker for detecting molecular residual disease (MRD) and is increasingly integrated into both clinical practice and translational research in breast cancer. However, whole-exome sequencing (WES)-based approaches often lack sufficient sensitivity for MRD detection, particularly in low-shedding tumors such as luminal breast cancer. To address this limitation, the MONSTAR-SCREEN-3 study is evaluating an ultra-sensitive MRD assay based on whole-genome sequencing (WGS). Methods MONSTAR-SCREEN-3 is a prospective, multicenter study enrolling 1,100 patients with solid tumors receiving curative-intent therapy in the definitive cohort. Personalized ctDNA panels are generated using the Precise MRD platform (Myriad Genetics), incorporating up to 1,000 tumor-specific alterations—including short variants and indels—identified through WGS of matched tumor tissue. Serial plasma samples are collected at baseline, after neoadjuvant chemotherapy (if applicable), 1 month post-surgery, quarterly during the first year, and biannually thereafter for up to two years. Here we report preliminary results from the breast cancer cohort. Results As of August 2025, 117 patients with resectable breast cancer had been enrolled. Clinical data were available for 89 patients, and MRD results for 92 samples from 40 patients. Median age was 52.5 years (range, 30-89). Clinical stage distribution: IA (7.9%), IIA (47.2%), IIB (22.5%), IIIA (5.6%), IIIB (7.9%), and IIIC (9.0%). Subtypes: luminal 48.2%, HER2-positive 36.5%, and triple-negative (TNBC) 14.1%. Neoadjuvant chemotherapy was given to 55% (49/89). Among these, subtype distribution was luminal 18.8%, HER2-positive 60.4%, TNBC 20.8%. Median follow-up was 4.2 months (range, 2.0-8.3). Among 40 patients with MRD results, WGS was performed on 15 biopsy and 25 surgical samples, identifying a mean of 5,394 panel-eligible alterations per patient (range: 762-40,981). Customized panel creation succeeded in 40/40 patients (100%). The assay showed 97.5% baseline sensitivity (39/40), with 28.2% (11/39) detected at an ultra-sensitive level (tumor fraction 100 ppm; minimum 4.9 ppm). Sensitivity by subtype was luminal 95.8% (23/24), HER2-positive 100% (12/12), and TNBC 100% (4/4), with ultra-sensitive detection in 39.1% (9/23), 8.3% (1/12), and 25.0% (1/4), respectively. The one ctDNA-negative case was a pT2N0 pStage IIA luminal tumor with a ctDNA tumor fraction of 2 ppm, classified as MRD-negative based on the 99.615% specificity threshold. At 1 month post-surgery, MRD positivity was 14.8% (4/27), with tumor fractions of 11.2-142 ppm. Of the four MRD-positive cases, three had 3-month data: two receiving adjuvant chemotherapy and one not receiving any adjuvant therapy. MRD positivity persisted in all three patients. Extended follow-up and longitudinal ctDNA dynamics will be reported. Conclusions The WGS-based personalized ctDNA assay achieved ultra-sensitive MRD detection across breast cancer subtypes, including detection at ppm-level tumor fractions. Updated molecular and clinical outcome data will be presented. Citation Format: Y. Naito, M. Nishimura, Y. Hisamatsu, M. Futamura, T. Toyama, T. Yamanaka, M. Tsukabe, S. Hashimoto, E. Tokunaga, M. Ishihara, R. Nakamura, H. Yasojima, T. Hashimoto, T. Shibuki, M. Imai, T. Fujisawa, H. Bando, S. Kobayashi, S. Sakashita, T. Kuwata, A. Blackler, G. Hogan, K. J. Taber, J. Jasper, D. Muzzey, E. Oki, T. Yoshino, H. Iwata. Ultra-sensitive Molecular Residual Disease Detection in Breast Cancer Using Whole-Genome Sequencing-Based Personalized ctDNA Panels: Preliminary Results from the MONSTAR-SCREEN-3 Project 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 PS2-09-07.