Multimodal analysis of ctDNA methylation and fragmentomic profiles enhances detection of nonmetastatic colorectal cancer.
Huu Thinh NguyenLe Anh Khoa HuynhTrieu Vu NguyenDuc Huy TranThuy Thi Thu TranNguyen Duy Khang LeNgoc-An Trinh LeTruong-Vinh Ngoc PhamMinh-Triet LeThi Mong Quynh PhamTrong Hieu NguyenThien Chi Van NguyenThanh Dat NguyenBui Que Tran NguyenMinh-Duy PhanHoa GiangRichard L FerreroPublished in: Future oncology (London, England) (2022)
Aims: Early detection of colorectal cancer (CRC) provides substantially better survival rates. This study aimed to develop a blood-based screening assay named SPOT-MAS ('screen for the presence of tumor by DNA methylation and size') for early CRC detection with high accuracy. Methods: Plasma cell-free DNA samples from 159 patients with nonmetastatic CRC and 158 healthy controls were simultaneously analyzed for fragment length and methylation profiles. We then employed a deep neural network with fragment length and methylation signatures to build a classification model. Results: The model achieved an area under the curve of 0.989 and a sensitivity of 96.8% at 97% specificity in detecting CRC. External validation of our model showed comparable performance, with an area under the curve of 0.96. Conclusion: SPOT-MAS based on integration of cancer-specific methylation and fragmentomic signatures could provide high accuracy for early-stage CRC detection.