Genomic Profiling in Patients with Endometrial Cancer by Deep Sequencing of Vaginal Swabs and Plasma

Abstract Introduction: Endometrial cancer is a common gynecologic malignancy lacks effective non-invasive screening tools, as traditional approaches rely on invasive biopsies. In this large prospective study, we evaluated a novel approach combining vaginal swab DNA and plasma-based circulating tumor DNA (ctDNA) for genomic profiling to provide a comprehensive framework for diagnosis, prognosis, and disease monitoring. Materials and Methods: Adult patients with diverse stages of endometrial cancer, pre-neoplastic disease, and benign endometrial conditions were prospectively recruited over two years. Paired vaginal swab DNA and plasma-based ctDNA were collected pre-operatively, and additional plasma samples were obtained multiple time points post-operatively. Deep next-generation sequencing targeting 101 genes was performed, achieving an average depth exceeding 40,000x. Results: A total of 191 patients contributed 388 samples. Vaginal swab DNA demonstrated 77.7% sensitivity and 96.6% specificity. PTEN mutations were associated with favorable prognosis (hazard ratio: 0.27; 95% CI: 0.092-0.77) and TP53 mutations were associated with poor prognosis (hazard ratio: 3.7; 95% CI: 1.4-10). A novel classification system based on the mutational profile of PTEN/TP53 identified distinct prognostic groups. Plasma-based ctDNA was significantly associated with stage, lymphovascular invasion, and prognosis (p < 0.01 for all). Patients with pre-operative positive plasma-based ctDNA results exhibited poorer outcomes (p < 0.01), whereas post-operative positive ctDNA enabled early detection of recurrence. Discussion: These two non-invasive methods have distinct, complementary roles in the management of endometrial cancer. Vaginal swab DNA and novel PTEN/TP53-based classification have distinct prognostic advantages over existing frameworks. Plasma-based ctDNA provides dynamic insights into recurrence risk and disease progression.