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Use of DNA methylation profiling as a molecular classification tool: a pediatric population-based study in tumors from central nervous system

ABSTRACT: Pediatric central nervous system (CNS) tumors are the second most common type of cancer in children and the leading cause of cancer-related death in this age group. Diagnosing these tumors based solely on histopathology is challenging and can lead to misdiagnosis, even among experienced pathologists. DNA methylation profiling classifies CNS tumors into molecular classes providing a more reliable diagnosis with the potential to impact patient’s management. This approach allows for faster and more accurate diagnoses combined with histopathology and other biomarkers. In this study, we performed DNA methylation analysis using the Infinium MethylationEPIC BeadChip (Illumina®) on a cohort of 182 pediatric CNS tumor samples from a reference center for pediatric cancer treatment in the countryside of São Paulo, Brazil. The data were analyzed using the DKFZ/Heidelberg CNS tumor platform (v12.8). Of the 182 tumors, excluding cases classified as control tissue, 82.8% (135 of 163) achieved a satisfactory calibrated score of ≥ 0.9 for a methylation family. Methylation profiling refined the initial diagnosis in 88 cases (65.7%) and provided a new diagnosis for 28 (20.9%) Several rare tumors only identified by methylation profile disclose the importance of analyzing full and consecutive samples, which allows the heterogeneity assessment and provide a more comprehensive insight into CNS tumors. Our work highlights the value of DNA methylation profiling as a molecular classification tool in a pediatric cohort from a middle-income country, which is often underrepresented in general databases.

ORGANISM(S): Homo sapiens

PROVIDER: GSE296487 | GEO | 2025/11/13

REPOSITORIES: GEO

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