Integrating DNA Methylation Profiling into Pediatric Brain Tumor Diagnostics: Insights from Four Cases

Background: DNA methylation profiling has become an important diagnostic tool in pediatric neuro-oncology, particularly for tumors with overlapping morphology or unusual immunophenotypes. Methods: We report four pediatric brain tumor cases evaluated by histopathology and immunohistochemistry, supplemented by targeted next-generation sequencing (NGS) and DNA methylation profiling using the DKFZ Brain Tumor Classifier (v12.8); one case also underwent DKFZ Sarcoma Classifier analysis (v13.2). Results: Methylation profiling provided clinically meaningful diagnostic insights across all cases. In two patients, methylation results supported integrated interpretation in diagnostically challenging settings without changing management. In two cases, methylation profiling prompted major diagnostic revisions with significant therapeutic consequences: (i) a tumor initially diagnosed as atypical teratoid/rhabdoid tumor was reclassified as CNS Ewing sarcoma, confirmed by an EWSR1-FLI1 fusion and immunophenotype, leading to a change to Ewing-based therapy; and (ii) a tumor interpreted as high-grade astrocytoma/glioblastoma was reclassified as a CNS tumor with BCOR internal tandem duplication, enabling a curative-intent approach and revised prognostic counseling. Conclusions: These cases illustrate that DNA methylation profiling can complement histopathology, resolve diagnostically ambiguous tumors, and in selected patients substantially alter treatment decisions and expected outcomes. Early integration of methylome profiling may improve precision diagnostics and reduce the risk of inappropriate therapy in pediatric brain tumors.