Abstract B040: OvaPrintTM – a novel cfDNA methylation liquid biopsy for cancer risk assessment in epithelial ovarian cancer
Authors: David N. Buckley, Juan Pablo Lewinger, Gerald Gooden, Monique Spillman, Monica Neuman, Mona Guo, Ben Y. Tew, Heather Miller, Varun U. Khetan, Lee P. Shulman, Lynda Roman, Bodour Salhia
Journal: Cancer Research (2024)

Abstract Epithelial ovarian cancer (EOC) is a malignancy associated with considerable morbidity and high rates of mortality, primarily due to its frequent presentation in an advanced stage. High grade serous ovarian carcinoma (HGSOC) is the most lethal gynecologic malignancy, with a 5-year survival rate of 40% or less when diagnosed at late-stage. There is currently no single effective screening tool for high risk or community-based risk assessment for HGSOC. In women with a known pelvic mass, surgery followed pathological assessment is currently the only definitive way to diagnose HGSOC. A liquid biopsy assay based on cell-free (cf)DNA methylation would enable non-invasive assessment of disease status in patients with cancer. The goal of the current study is to develop a cfDNA methylation liquid biopsy that can be used for the screening and risk assessment for EOC. Tissue and plasma samples were acquired under informed consent from multiple sources. Reduced representation bisulfite sequencing (RRBS) was performed on 35 HGSOC, 8 normal ovary, and 13 normal fallopian tube tissues. Differentially methylated regions (DMRs) were called between HGSOC and normal controls using metilene. Significant DMR calls (n = 1677) were used to generate a targeted methylation assay using the myBaits® hybrid probe capture platform. Next, targeted enrichment was performed on bisulfite converted plasma cfDNA on an independent set of 82 HGSOC (27 stage 1, 20 stage 2, 35 stage 3), 100 benign ovarian mass, 11 clear cell ovarian cancer, 12 endometroid ovarian cancer, 22 mucinous ovarian cancer, 9 EOC with mixed histology, and 26 healthy patients. Mean beta values across DMRs were used to train a novel cfDNA methylation classifier model called OvaPrintTM to discriminate HGSOC from benign masses using a repeated 10-fold cross validation approach to obtain an unbiased estimate of performance. The cross validated score for each sample was used to classify samples as high (score &amp;gt; 0.65), intermediate (0.65 &amp;gt; score &amp;gt; 0.35), or low (score &amp;lt; 0.35) risk of having HGSOC. OvaPrintTM testing in an independent cohort of 182 identified 68/182 as high risk (HGSOC N = 66, benign N = 2), 10/182 as intermediate risk (HGSOC N = 4, benign N = 6), and 104/182 as low risk samples (HGSOC N = 12, benign N = 92), (ROC AUC = 0.936). It classified 22/26 normal samples as low risk and 4 as high risk. OvaPrintTM identified 7/20 mucinous, 7/12 endometrioid, 4/11 clear cell, and 5/9 mixed EOC as high risk. Given the mixed results in non-HGSOC EOC, we are performing additional RRBS feature discovery on theses subtypes in an ongoing study. In summary, OvaPrintTM is a novel cfDNA methylation liquid biopsy that can be used for effective cancer risk assessment for HGSOC in women presenting with pelvic masses with potential screening application; prospective studies are ongoing to further validate OvaPrintTM for risk assessment of adnexal masses of HGSOC and other EOC in symptomatic and asymptomatic women. Citation Format: David N. Buckley, Juan Pablo Lewinger, Gerald Gooden, Monique Spillman, Monica Neuman, Mona Guo, Ben Y. Tew, Heather Miller, Varun U. Khetan, Lee P. Shulman, Lynda Roman, Bodour Salhia. OvaPrintTM – a novel cfDNA methylation liquid biopsy for cancer risk assessment in epithelial ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr B040.