Cell-free DNA Methylation Analysis, a Noninvasive Biomarker for Detection,Prediction, Classification, and Treatment Monitoring for Brain Tumors

Background and Objective: Brain tumors represent a major clinical challenge due to difficulties in early detection and precise molecular characterization. Recent advances in liquid biopsy have highlighted cellfree DNA (cfDNA) methylation profiling as a promising non-invasive approach for the detection, classification, prognostication, and longitudinal monitoring of brain tumors. Methods: A literature search was performed using the PubMed database covering studies published up to July 2025. The search terms “cell-free DNA methylation” and “brain tumors” were applied. Eligible studies investigated cfDNA methylation for early diagnosis, molecular classification, prognostic assessment, or treatment monitoring, with a particular focus on gliomas and medulloblastomas. Key findings were qualitatively summarized. Results: cfDNA methylation profiling consistently demonstrated high diagnostic accuracy, with reported sensitivities and specificities frequently exceeding 97%. This approach enables early tumor identification, detection of brain metastases, and accurate classification of central nervous system tumors in both adult and pediatric cohorts. Furthermore, cfDNA methylation dynamics provide valuable insights into treatment response and the emergence of therapeutic resistance, including resistance to CDK4/6 inhibitors. Cerebrospinal fluid generally outperforms plasma in sensitivity due to its closer proximity to the tumor microenvironment. Advanced methodologies such as cfMeDIP-seq, enzymatic methylation sequencing, and nanopore sequencing have further improved performance with low-input cfDNA. Conclusion: cfDNA methylation analysis is a highly sensitive and minimally invasive tool with substantial potential to improve early diagnosis, molecular stratification, and real-time monitoring of brain tumors. Despite existing technical and pre-analytical challenges, large-scale prospective studies are warranted to enable clinical translation and standardization.