Abstract PS1-12-20: Circulating tumor DNA profiling of patients with early-line advanced luminal breast cancer

Abstract Background: Advances in the development of new endocrine treatment approaches for hormone receptor-positive (HR+)/HER2-negative (HER2-) advanced breast cancer (ABC) have significantly improved patient outcomes. However, a number of patients still have limited benefit from endocrine-based treatments, and even patients with prolonged progression-free survival (PFS) will progress at some point. To better understand the heterogeneity in treatment outcomes within the first line (1L), and between 1L and second line (2L), we performed circulating tumor DNA (ctDNA) profiling in a uniform multicenter cohort of patients with HR+/HER2- ABC in Austria. Samples were collected at defined timepoints prior to early lines of therapy. The goal of this study was to characterize ctDNA features associated with molecular and clinical heterogeneity in HR+/HER2- ABC. Methods: Patients with locally advanced or metastatic HR+/HER2– BC were included. ctDNA was analyzed using a 77-gene panel (AVENIO ctDNA Expanded Kit). Tumor fraction (TF) was estimated using two orthogonal approaches: untargeted aneuploidy assessment via mFAST-SeqS (reported as z-scores) and ichorCNA analysis of low-pass whole-genome sequencing (0.1x WGS) when available. The highest variant allele frequency (hVAF) per sample was used as an additional TF proxy. TF, hVAF, and somatic variant burden were compared between samples collected prior to 1L and 2L systemic therapy using mixed-effects models, and their associations with PFS were evaluated. Results: We analyzed 225 ctDNA samples from 184 patients with HR+/HER2– ABC (128 before start of 1L, and 76 before start of 2L), including 40 patients with paired samples. The overall TF was low (median z-score 2.49; range –0.5 to 208.3), with no significant difference between 1L and 2L samples by mFAST-SeqS (adjusted mean difference 6.33, 95%CI: -0.3-13.0; p = 0.061) or ichorCNA (adjusted mean difference -0.003, 95%CI: -0.06-0.07; p = 0.925). However, hVAF was significantly higher in 2L samples (adjusted mean difference 0.05, 95%CI: 0.01-0.09; p = 0.017). Somatic variants were detected in 84% 1L and 89% 2L samples, with pathogenic/likely pathogenic (P/LP) alterations in 63% and 70%, respectively. 2L samples harbored significantly more total (adjusted mean difference 2.58, 95%CI: 1.33-3.83; p = < 0.001) and subclonal (adjusted mean difference 2.1, 95%CI: 1.09-3.12; p = < 0.001) variants, including a higher P/LP ESR1 mutation frequency (30.2% vs. 7.8%). PI3K-pathway alterations (PIK3CA, AKT1, PTEN) were found in 41.4% 1L and 52.6% 2L samples. High TF (z-score ≥3) was associated with a shorter PFS in both 1L (17.9 vs. 50.6 months; p < 0.001) and 2L (4.6 vs. 7.3 months; p = 0.042) settings. Conclusions: Elevated ctDNA-derived TF prior to treatment was associated with significantly shorter PFS in advanced luminal BC across both 1L and 2L settings. While the spectrum and frequency of pathogenic and targetable alterations aligned with existing data, 2L samples showed higher TF (as measured by hVAF) and a greater burden of somatic variants, reflecting evolving molecular complexity. These findings underscore the utility of integrated ctDNA-based approaches for tumor burden assessment and molecular profiling. Further studies are warranted to elucidate the biological drivers of heterogeneity in early-line HR+/HER2– ABC and to optimize ctDNA-guided treatment strategies. Citation Format: N. Dobrić, S. O. Hasenleithner, C. Suppan, E. V. Klocker, D. Hlauschek, R. Graf, C. Albertini, D. Egle, A. M. Starzer, R. Bartsch, G. Rinnerthaler, P. J. Jost, E. Heitzer, N. Dandachi, M. Balic. Circulating tumor DNA profiling of patients with early-line advanced luminal breast cancer [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 PS1-12-20.