5-hydroxymethylcytosines from cell-free DNA as diagnostic biomarkers for cancers

Taking advantage of a highly sensitive and selective chemical labeling technology, we report here genome-wide 5hmC profiling using circulating cell-free DNA (cfDNA) and paired tumor/adjacent tissues collected from a cohort of 53 healthy individuals and 136 patients who were recently diagnosed with colorectal, gastric, pancreatic, and thyroid cancers. 5hmC is mainly distributed in gene active regions coincident with cis-regulatory elements and active histone modifications. Consistent cancer-specific epigenetic signatures in cfDNA were identified in all cases, with 5hmC-based biomarkers demonstrating highly accurate prediction for patients with colorectal and gastric cancers versus healthy controls and superior performance to conventional biomarkers as well as the blood-based 5mC biomarkers.