Abstract 2409: Circulating differential methylation allele fraction (DMAF) strongly correlates with circulating tumor DNA (ctDNA) variant allele fraction (VAF)

Abstract Measurement of ctDNA has been established as a prognostic biomarker of cancer disease burden. Emerging evidence has demonstrated that differential methylation patterns can serve as an accurate biomarker both for cancer detection and for predicting the tissue of origin. While it is important to distinguish cancer-positive from cancer-negative patients, clinical decision making increasingly depends on the exact level of the measured biomarker. To that end, we report on the correlation between ctDNA VAF and DMAF across patients with colorectal cancer (CRC). Pre-surgical plasma samples from patients with CRC (N=70) were sourced from the prospective GALAXY, observational arm of ongoing CIRCULATE-Japan study trial (UMIN000039205). Samples classified as ctDNA-positive by a tumor-informed ctDNA assay (SignateraTM) were included in this analysis and ctDNA VAF (%) was calculated. We performed deep methylation sequencing (Illumina Novaseq) across multiple target regions using two independent target sets. DMAF was calculated computationally, which estimates the fraction of differential methylation alleles for circulating cell-free DNA across target regions. Among 70 CRC patients, 68 had positive ctDNA results. Median age at testing was 64.0 years and male individuals represented 55.9% (n=38) of the cohort. Among them, 9 (13.2%) were stage I, 24 (35.3%) were stage II, 22 (32.3%) were stage III, 8 (11.7%) were stage IV, and 5 (7.3%) had unknown staging. The correlation of DMAF with ctDNA VAF was 0.894 (Spearman’s Rank Correlation Coefficient) and was independent of disease stage, histology, age, and sex. Among MSS (micro-satellite stable; n=58) and MSI-H (micro-satellite unstable n=10) patients, the DMAF correlation was 0.9 and 0.915, respectively. The correlation between two target sets evaluating DMAF with differing numbers of targeted regions was high (0.89). These data demonstrate that abundance of differential methylation in CRC patients correlates with VAF regardless of clinicopathologic features of patients with CRC. Methylation-based assays are a promising tool for cancer detection and quantifying the disease burden. Citation Format: Preethi Srinivasan, Tzu-Chun Chen, Ehsan Haghshenas, Misagh Kordi, Ilker Tunc, Wenching Chan, Omid Shams Solari, Joshua Babiarz, Yoshiaki Nakamura, Takayuki Yoshino, Alexey Aleshin, Trupti Kawli, Johannes G. Reiter. Circulating differential methylation allele fraction (DMAF) strongly correlates with circulating tumor DNA (ctDNA) variant allele fraction (VAF) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2409.