Abstract 2729: Development of a targeted liquid biopsy for early gynecologic cancer detection leads to discovery of a highly prevalent genomic landscape of cancer driver gene mutations in uterine tissue from women without cancer
Authors: Pandya Deep S. , Tomita Shannon , Camacho Olga , Swierczek Sabina , Camacho Catalina , Engelman Kelsey , Polukort Stephanie , Padron Maria Mercedes , RoseFigura Jordan , Irish Jon , Chuang Linus , Andikyan Vaagn , Cohen Samantha , Fiedler Paul , Sieber Steven , Shih Ie-Ming , Billaud Jean-Noel , Reva Boris , Sebra Robert , Dottino Peter , Martignetti John A. 
Published: August 2019

Abstract
Introduction: Ovarian and endometrial cancers are, respectively, the most lethal and most frequent female reproductive tract malignancies. Currently, there are no effective screening methodologies or protocols for these cancers. We hypothesized that the use of ultra-deep, targeted gene sequencing on a highly specific and gynecologic cancer-focused analyte source, namely, uterine lavage fluid, could detect somatic mutations associated with these cancers. Using these highly sensitive NGS-based assays, we demonstrated both (1) the ability to detect tumor-specific mutations in uterine lavage from women even with microscopic stage IA ovarian and endometrial cancers and (2) the existence of highly prevalent populations of cancer driver gene mutated cells in uterine tissue from women without cancer.
Methods: In total, and following written informed consent, samples were prospectively collected and analyzed from two institutions from more than 250 women at the time of their surgery. Sequencing was performed using both Ion Torrent and Illumina-based sequencing and additional orthogonal mutation validation was performed using dPCR and Sanger sequencing.
Results: Targeted sequencing of cellular and cell free DNA isolated from uterine lavage samples was performed on all samples in a blinded fashion. Histopathologic diagnosis and sample decoding, revealed that lavage mutations were present in nearly all women with ovarian and endometrial cancer, even those with microscopic stage IA disease. These mutations were demonstrated to be tumor-specific by sequencing their respective tumors. Notably, we also identified mutations in approximately half of all women without any evidence of cancer. To define the possible origin of these mutations in normal tissue, we analyzed uterine tissue from women without cancer. Two hundred biopsy samples were obtained from 24 uterine samples following hysterectomy for non-cancerous conditions. Remarkably, sequencing revealed relatively high allele fraction cancer-associated mutations in more than half of these samples. The overwhelming majority of samples harbored low frequency mutations.
Conclusions: Our studies demonstrate the ability to detect with very high sensitivity, tumor-specific somatic mutations in women with ovarian and endometrial cancers; suggesting the future possibility of earlier diagnosis and better outcomes. At the same time, our studies again highlight caveats regarding NGS-based results for cancer screening. Finally, the identification of a previously unknown, highly prevalent, cancer-driver mutation landscape in apparently normal uterine tissue opens the door onto new areas of biologic exploration for understanding tumorigenesis and the protective mechanisms which inhibit cancer development.
Citation Format: Deep S. Pandya, Shannon Tomita, Olga Camacho, Sabina Swierczek, Catalina Camacho, Kelsey Engelman, Stephanie Polukort, Maria Mercedes Padron, Jordan RoseFigura, Jon Irish, Linus Chuang, Vaagn Andikyan, Samantha Cohen, Paul Fiedler, Steven Sieber, Ie-Ming Shih, Jean-Noel Billaud, Boris Reva, Robert Sebra, Peter Dottino, John A. Martignetti. Development of a targeted liquid biopsy for early gynecologic cancer detection leads to discovery of a highly prevalent genomic landscape of cancer driver gene mutations in uterine tissue from women without cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2729.