PS4-05-14: Integrated NGS-Based Tissue and Plasma Profiling to Advance Precision Oncology in Breast Cancer

Abstract Introduction: The integration of broad genomic testing has become increasingly vital for personalized treatment planning in breast cancer patients. In this study, we evaluated the analytical performance and clinical relevance of a certified for in vitro diagnostics (CE-IVD), 1021-gene comprehensive genomic profiling panel in detecting actionable tumor biomarkers across a diverse cohort of breast cancer cases. The study aimed to validate the robustness of the assay in both tissue and liquid biopsy formats, and to explore its clinical utility in real-world patients with advanced breast cancer. Methods: Tumor and blood samples from 353 patients were analyzed, including 197 FFPE tumor and 156 plasma cfDNA. Concurrent molecular profiling of tissue and plasma was conducted in 23 cases to evaluate the efficacy of liquid biopsy although tissue samples may have originated from prior procedures. DNA extracted from leukocytes was used as a control to prevent the detection of false-positive results due to clonal hematopoiesis mutations. Targeted-capture sequencing was performed using the Oncology Multi-Gene Variant Assay (GenePlus) which is a qualitative in vitro diagnostic test for detection of variants in 1021 tumor-related genes, and gene fusions in 38 genes. Sequencing was carried out on the MGI DNBSEQ-G400 platform. NGS data were analyzed via a dedicated bioinformatics pipeline on the Gene Box platform (GenePlus), enabling detection of all major genomic alterations, including gene fusions, as well as assessment of tumor mutational burden (TMB) and microsatellite instability (MSI). Results: Regarding the analysis of 197 FFPE samples, at least one on-label actionable biomarker was identified in 54.8% of cases. Among these samples, PIK3CA mutations were the most frequently detected in 27.4% of biomarker-positivethe cases. ESR1 mutations were present in 16.2% Mutations in PTEN and AKT1 genes were also observed in 7.6% and 3% of cases, respectively. Additionally, 20% of patients harbored a suspected germline variant in BRCA1/2, PTEN and CDH1 genes. In the analysis of 156 plasma samples, 46% were positive for an on label-biomarker. Among these, PIK3CA alterations were identified in 17.9% and ESR1 mutations were present in 17.3% of the cases. At lower frequency, variants were also observed in BRCA1/2 (3.8%), PTEN (3.2%), AKT1(1.3%) genes. ERBB2 (1.3%) amplification and an NTRK fusion (0.6%) were also detected. Approximately 20% of plasma samples harbored verified germline variants, most frequently in BRCA1/2 and CHEK2 genes. In a subset of 23 mBC patients, concurrent analysis of tissue and liquid biopsy demonstrated a 70% overall concordance rate on on-label biomarker analysis. In two cases, FFPE analysis identified additional on-label mutations not detected in plasma, whereas in one case plasma analysis revealed a second ESR1 mutation not detected in the FFPE sample. In two patients, plasma analysis was negative, while tissue profiling identified alterations in ESR1 and PIK3CA genes. Importantly, in two cases, liquid biopsy surpassed tissue analysis by detecting an ESR1 variant and an NTRK fusion. Conclusions: This study demonstrates the clinical utility of comprehensive multigene NGS profiling in both tissue and plasma samples from patients with breast cancer by revealing a high rate of actionable variants. Parallel analysis of matched tissue and plasma samples revealed a high concordance rate, indicating complementary role of both approaches in genomic profiling. In conclusion, integrated NGS analysis of tissue and liquid biopsies provides a powerful platform for precision oncology in breast cancer, supporting therapeutic decisions, resistance monitoring, and hereditary cancer risk assessment. The combined use of both sample types maximizes diagnostic yield and clinical impact, especially in the context of advanced disease. Citation Format: D. Mavroudis, D. Jinga, E. Razis, S. Giassas, N. Touroutoglou, C. Bilir, M. Ozdogan, I. Ökten, S. Karageorgopoulou, E. Galani, G. El Hachem, D. Tzanninis, T. Floros, G. Lazaridis, P. Vlachostergios, I. Hacibekiroglu, E. Maragkouli, I. Gioulbasanis, A. Tsantikidi, S. Maxouri, C. Florou-Chatzigiannidou, V. Metaxa-Mariatou, E. Papadopoulou, D. Grigoriadis, A. Papathanasiou, G. Nasioulas. Integrated NGS-Based Tissue and Plasma Profiling to Advance Precision Oncology in 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 PS4-05-14.