Pan‐cancer landscape of abnormal ctDNA methylation across human tumors

Published:September 13, 2022DOI:


      • ctDNA methylation level is abnormally high in cancer patients.
      • Methylation burden is clearly related to TMB, MSI and PD-L1.
      • ctDNA methylation is related to the type, frequency and number of mutations.



      The aim of this paper is to explore the correlation between circulating tumor DNA (ctDNA) methylation and mutations and its value in clinical early cancer screening.


      We performed target region methylation sequencing and genome sequencing on plasma samples. Methylation models to distinguish cancer from healthy individuals have been developed using hypermethylated genes in tumors and validated in training set and prediction set.


      We found that patients with cancer had higher levels of ctDNA methylation compared to healthy individuals. The level of ctDNA methylation in cell cycle, p53, Notch pathway in pan-cancer was significantly correlated with the number of mutations, and mutation frequency. Methylation burden in some tumors was significantly correlated with tumor mutational burden (TMB), microsatellite instability (MSI) and PD-L1. The ctDNA methylation differences in cancer patients were mainly concentrated in the Herpes simplex virus 1 infection pathway. The area under curve (AUC) of the training and prediction sets of the methylation model distinguishing cancer from healthy individuals were 0.93 and 0.92, respectively.


      Our study provides a landscape of methylation levels of important pathways in pan-cancer. ctDNA methylation significantly correlates with mutation type, frequency and number, providing a reference for clinical application of ctDNA methylation in early cancer screening.


      Abbreviation of cancer type:

      BRCA (breast invasive carcinoma), PRAD (prostate adenocarcinoma), OV (ovarian serous cystadenocarcinoma), HNSC (head and neck squamous cell carcinoma), UCEC (Uterine Corpus Endometrial Carcinoma), CESC (cervical squamous cell carcinoma and endocervical adenocarcinoma), READ (rectum adenocarcinoma), COAD (colon adenocarcinoma), LIHC (liver hepatocellular carcinoma), STAD (stomach adenocarcinoma), CHOL (cholangiocarcinoma), PAAD (pancreatic adenocarcinoma), NSCL (Non-Small-Cell Lung Cancer), LUAD (lung adenocarcinoma), LUSC (lung squamous cell carcinoma), ESCA (esophageal carcinoma), NASO (Nasopharyngeal Cancer)
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