Improved circulating tumor DNA identification for detection of esophageal squamous cell carcinoma by enzymatic methyl sequencing and hybrid neural network.

ABSTRACT: Detection of cancer at early stage can significantly improve the five-year survival rate of patients. Bisulfite-based methylation detection can cause DNA damage, especially in high GC content regions which was associated with the development of cancers. Loss of aberrant methylated CpG sites in cfDNA will lead to the undetectability of certain circulating tumor DNA (ctDNA), consequently may affect the cancer detection. Our study uses enzymatic method to detect whole genome abnormal methylation regions in esophageal squamous cell carcinoma (ESCC). We also provide a pretrained neural network, hybrid of BERT and CNN (BCNN), to identify ctDNA robustly. Maximum posterior probability is utilized to estimate the fraction of ESCC-derived ctDNA in plasma for predicting the risk of ESCC cancer. Our r

SUBMITTER: Shen J 

PROVIDER: S-EPMC12475058 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature