Abstract 5890: Personalized detection of circulating cell-free tumor DNA in gynecologic cancer
Authors: Andrea B. Moffitt, Jude Kendall, Joan Alexander, Asya Stepansky, Arisa Kapedani, Zihua Wang, Dan Levy, Kenny Ye, Abba M. Krieger, Marina Frimer, Gary L. Goldberg, Michael Wigler
Journal: Cancer Research (2025)

Abstract Endometrial and ovarian cancers are among the most common gynecologic malignancies in the U.S., with 5-year overall survival rates of 81% and 50% respectively. Ovarian cancer often presents late due to asymptomatic early stages and nonspecific symptoms in advanced stages. Few markers exist for early detection, and they lack the sensitivity and specificity needed for high-risk screening. Given the absence of informative protein blood biomarkers, cell-free DNA analysis has become a promising tool for early detection, treatment evaluation, and monitoring. However, previous studies of circulating tumor DNA (ctDNA) in gynecological cancers had limited sensitivity. We adapted MASQ (Multiplex Accurate Sensitive Quantitation), originally developed to measure residual cells in leukemia, to the measurement of ctDNA in solid cancers. MASQ detects patient-specific mutations simultaneously in up to 50 loci with exceptional sensitivity, below one part per million. This study uses MASQ to measure tumor-specific variants in blood (cell-free DNA) from endometrial and ovarian cancer patients, aiming to determine the range of ctDNA signals at presentation and explore correlations with clinicopathological features and patient outcomes. We analyzed samples from 46 gynecologic cancer patients (12 ovarian, 34 endometrial) treated at Northwell Health. Samples were collected in collaboration with gynecologic oncology research coordinators and the Northwell Health Biorepository. Peripheral blood was collected at diagnosis (n=46) and post-surgery (n=14), along with surgical tumor specimens. Whole genome sequencing of tumor and blood identified thousands of somatic tumor variants per patient. For each patient, 30 representative variants were selected for MASQ sequencing. MASQ libraries were generated from cell-free DNA isolated from pre- and post-surgery plasma. Ultrasensitive variant counts across 30 loci were aggregated and analyzed for clinical correlations. ctDNA signal was detected in 35 of 46 cases at presentation, with variant allele frequencies ranging from below 10^-4 to 10^-1. ctDNA signal was higher in ovarian cancer (13/13 detected) than endometrial cancer, and higher in aggressive Type II endometrial cancer (15/16) vs. Type I (5/13). ctDNA levels correlated with tumor size and copy number imbalance, but not with total cell-free DNA. Detection of ctDNA predicted worse overall survival (p=0.023) and was the strongest predictor of survival in multivariate analysis. Post-surgery follow-up in 10 of 14 patients showed significant ctDNA reduction following treatment, highlighting MASQ’s sensitivity in tracking treatment response. This study highlights the potential of sensitive ctDNA detection for early diagnosis and monitoring in gynecologic cancers. However, limited cell-free DNA abundance necessitates even more sensitive methods to enhance clinical utility. Citation Format: Andrea B. Moffitt, Jude Kendall, Joan Alexander, Asya Stepansky, Arisa Kapedani, Zihua Wang, Dan Levy, Kenny Ye, Abba M. Krieger, Marina Frimer, Gary L. Goldberg, Michael Wigler. Personalized detection of circulating cell-free tumor DNA in gynecologic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5890.