Abstract 3341: Preliminary clinical validation of COLO eDX, a novel plasma circulating tumor DNA methylation assay for detecting colorectal cancer
Authors: Kim Jin-Soo , Lee Yun Young , Jung Seung Yeon , Kim Mi Young , Shin Rumi , Park Jin Hyun , An Joon , Han Jinil , Heo Seung Chul , Moon Youngho 
Published: June 2023

Abstract
Introduction: Liquid biopsies with cell-free DNA (cfDNA) from plasma, are rapidly emerging as an important and minimally invasive approach for the early diagnosis of cancer. Here we present COLO eDX, as a novel methylation-specific droplet digital PCR (ddPCR)-based colorectal cancer (CRC) diagnostic tool.
Methods: During the discovery phase, we analyzed DNA methylome profiles of more than 10,000 samples from CRC, normal colorectal mucosa, and other cancer types (the TCGA and GEO public databases). Through the multi-step biomarker discovery studies, we selected 14 CRC-specific hypermethylated CpG sites. Among them, 2 candidate sites were uniquely methylated in a CRC cell line among tested cancer cell lines from various organs including CRC (HCT-15), 2 hepatocellular carcinomas (Huh7 and SK-HEP-1), 2 lung cancers (A549 and HCC827), bladder cancer (HT-1376), prostate cancer (LNCap clone FGC), and breast cancer (T-47D). Through the methylation-specific ddPCR assay of paired tissue samples from the patients with CRC, we identified that single candidate was specifically hypermethylated in the most tumor tissues regardless of cancer stage. Copy numbers of the target region (TC) were divided by the copy numbers of the internal control (IC) to normalize.
Results: We prospectively collected post-operative plasma samples from patients with CRC (N=23) who underwent surgery at Seoul National University Boramae Medical Center. According to the AJCC 8th staging system and risk groups allocation, 3 patients had standard risk and 8 patients had high risk for recurrence, among stage II patients. Among stage III patients, 3 patients had low risk and 6 patients had high risk for recurrence. 3 patients were stage IV at initial presentation. IC value in the stage IV patients (R2 resected) were significantly higher than that other groups (R0 resected), while there was no significant difference among stage II and stage III patients. Recurrence free survival for patients TC or IC value equal or higher than the median and those lower than the median were not statistically different. Since 3 patients in high risk stage III and 4 patients in high risk stage II patients did not receive the recommended adjuvant chemotherapy, comparison of RFS should be interpreted with caution.
Conclusion: We have developed and validated the qualitative detection of methylation status of the bisulfite-converted target region in cfDNA. Further studies are warranted to evaluate the impact of COLO eDx on recurrence in a larger cohort of CRC patients.
Citation Format: Jin-Soo Kim, Yun Young Lee, Seung Yeon Jung, Mi Young Kim, Rumi Shin, Jin Hyun Park, Joon An, Jinil Han, Seung Chul Heo, Youngho Moon. Preliminary clinical validation of COLO eDX, a novel plasma circulating tumor DNA methylation assay for detecting colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3341.