Integrated epigenetic biomarkers in circulating cell-free DNA as a robust classifier for pancreatic cancer

Clin Epigenetics. 2020 Jul 23;12(1):112. doi: 10.1186/s13148-020-00898-2.


Background: The high lethal rate of pancreatic cancer is partly due to a lack of efficient biomarkers for screening and early diagnosis. We attempted to develop effective and noninvasive methods using 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) markers from circulating cell-free DNA (cfDNA) for the detection of pancreatic ductal adenocarcinoma (PDAC).

Results: A 24-feature 5mC model that can accurately discriminate PDAC from healthy controls (area under the curve (AUC) = 0.977, sensitivity = 0.824, specificity = 1) and a 5hmC prediction model with 27 features demonstrated excellent detection power in two distinct validation sets (AUC = 0.992 and 0.960, sensitivity = 0.786 and 0.857, specificity = 1 and 0.993). The 51-feature model combining 5mC and 5hmC markers outperformed both of the individual models, with an AUC of 0.997 (sensitivity = 0.938, specificity = 0.955) and particularly an improvement in the prediction sensitivity of PDAC. In addition, the weighted diagnosis score (wd-score) calculated with the 5hmC model can distinguish stage I patients from stage II-IV patients.

Conclusions: Both 5mC and 5hmC biomarkers in cfDNA are effective in PDAC detection, and the 5mC-5hmC integrated model significantly improve the detection sensitivity.

Keywords: Cancer diagnosis; Cell-free 5hmC sequencing; Cell-free 5mC sequencing; Liquid biopsy; Pancreatic cancer.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5-Methylcytosine / analogs & derivatives
  • 5-Methylcytosine / blood
  • Adenocarcinoma / blood*
  • Biomarkers, Tumor / blood*
  • Carcinoma, Pancreatic Ductal / blood*
  • Cell-Free Nucleic Acids / blood*
  • Epigenesis, Genetic / physiology*
  • Female
  • Humans
  • Male
  • Middle Aged
  • Pancreatic Neoplasms / blood*
  • Reproducibility of Results
  • Sensitivity and Specificity


  • Biomarkers, Tumor
  • Cell-Free Nucleic Acids
  • 5-hydroxymethylcytosine
  • 5-Methylcytosine