Molecular and clinical features of a Japanese medulloblastoma cohort: Subgroup-specific prognostic stratification using economical/accessible diagnostic methods

Medulloblastoma (MB) is a biologically and clinically heterogeneous pediatric brain tumor. However, large-scale molecular subgrouping studies have mainly been conducted in Western populations, and comprehensive data from Asia are limited. To address this gap, we analyzed 242 MB cases collected from 39 institutions through the Japan Pediatric Molecular Neuro-Oncology Group, performing centralized molecular classification using NanoString-based gene expression profiling, DNA methylation arrays, and multiplex ligation-dependent probe amplification (MLPA)-based copy number profiling, supplemented by targeted sequencing. The subgroup distribution was 16.1% WNT, 24.8% SHH, 17.4% Group 3, and 41.7% Group 4. CTNNB1 mutations and monosomy 6 characterized all WNT cases, whereas MYCN amplification and TP53 mutations were independent adverse markers in SHH MB. Group 3 showed the worst survival, with MYC amplification and metastasis as poor prognostic factors. In Group 4, large cell/anaplastic histology predicted poor outcomes, whereas chromosome 11 loss was correlated with a favorable prognosis. Whole chromosomal aberration-defined favorable-risk patterns consistently indicate improved outcomes in non-WNT/non-SHH MBs. We also developed a simplified MLPA-based classifier targeting six loci on chromosomes 7, 8, and 11 (SEE-6-CNA), which enabled robust and clinically feasible prognostic stratification. Overall, our findings confirm that the molecular subgroup-specific features of Japanese MBs are largely concordant with global observations and that SEE-6-CNA provides a cost-effective tool to support individualized treatment planning, particularly in resource-limited settings.