Non-invasive diagnosis of colorectal cancer via targeted high-throughput DNA methylation sequencing of circulating tumor DNA (ctDNA)

Colorectal cancer (CRC) commonly develops from precancerous polyps. Most polyps are benign. The current screening method involves stool tests and colonoscopy, which is an unpleasant procedure. Even though stool DNA-based approach has been developed, it is still a clinical challenge to differentiate benign complications and malignant CRC. We took the approach of high-throughput DNA bisulfide sequencing of tissue samples to identify cancer-specific methylation signatures. We learned methylation patterns by in-depth data mining and then applied pattern recognition approach to classify plasma samples. From a cohort of 70 pairs of tumor-normal matched tissue samples, we identified 1062 differential methylation markers. Next, we applied a greedy optimization algorithm to build a malignancy classification model using a training set of 118 plasma samples (malignant CRC: 56, benign complications: 23, healthy subjects: 39). In the training set, we achieved an AUC of 91.9% (95%CI: 87.3-96.5%). In an independent test set of 150 plasma samples (malignant CRC: 56, benign complications: 23, healthy subjects: 71), we achieved an AUC of 92.9% (95%CI: 88.3%~97.5%). Specifically, the model had a sensitivity of 91.1% for the identification of malignant CRC, and a specificity of 84.5% and 78.3% for healthy subjects and benign complications respectively. Our assay was demonstrated to be very sensitive towards early-stage CRC detection, with a sensitivity of 76.5% and 95% for stage I and II CRC respectively. The performance of this assay still awaits further validation in a large-scale clinical trial. In summary, we have developed a highly sensitive blood-based non-invasive diagnostic assay for the identification of malignant CRC, which can aid clinical decisions for doctors. This approach can also be extended to non-invasive early screening for various other cancer types. Citation Format: Xianrui Wu, Jiacheng Chuan, Tuo Hu, Tingting Peng, Meng Yang, Hui Shen, Peter Laird, Yangbin Gao, Xuyu Cai, Weihong Xu, Jian-bing Fan, Ping Lan. Non-invasive diagnosis of colorectal cancer via targeted high-throughput DNA methylation sequencing of circulating tumor DNA (ctDNA) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3310.