Longitudinal circulating tumor DNA profiling in patients with advanced endometrial cancer using an off‐the‐shelf targeted NGS panel

Intratumor heterogeneity presents a major challenge in precision oncology for endometrial cancer (EC). Circulating tumor DNA (ctDNA) offers a minimally invasive method to monitor tumor evolution and therapeutic resistance. In this retrospective study, we evaluated a tumor-agnostic NGS panel to detect and track ctDNA in 18 EC patients and directly compared its performance with a tumor-informed ddPCR approach. ctDNA was detected by NGS in over 60% of plasma samples, while ddPCR showed higher positivity rates in paired samples (71.9% vs 62.5%), with overall concordance of 65.7% and fair agreement (Cohen's kappa = 0.23). The cfDNA-NGS panel identified a broad spectrum of alterations, including relapse-specific mutations indicative of clonal evolution, but showed lower sensitivity for low-frequency variants compared with ddPCR. Discordant cases, including false-negative results in both approaches, highlight the impact of assay sensitivity, target selection, and biological factors on ctDNA detection. ctDNA dynamics correlated with disease progression and treatment response, although detection was limited in cases with brain metastases. These findings support the utility of tumor-agnostic ctDNA monitoring in advanced EC and highlight the importance of assay quality and careful interpretation to address limitations such as clonal hematopoiesis and technical sensitivity.