The Japanese Journal of Pediatric Hematology / Oncology
Online ISSN : 2189-5384
Print ISSN : 2187-011X
ISSN-L : 2187-011X
Original Article
Application of molecular classification of central nervous system tumors using DNA methylation profiling: A single-center experience
Kohei FukuokaJun KuriharaYuki ArakawaMakiko MoriKoichi OshimaYuichi MitaniMamoru HondaYuko MatsushitaYuko HibiyaKayoko IchimuraMasashi KyushikiSatoko HondaYonehiro KanemuraSumihito NobusawaKoichi IchimuraAtsuko NakazawaKatsuyoshi Koh
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2025 Volume 62 Issue 1 Pages 52-58

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Abstract

Molecular classification using DNA methylation profiling had a great impact on the diagnosis and classification of central nervous system (CNS) tumors; however, nationwide data remain limited. Methods: We uploaded IDAT files from archived samples from the Illumina Infinium Human MethylationEPIC BeadChip array at our institution to the methylation classifier on the webpage of the German Cancer Center to obtain the molecular classification and copy number plot. Results: Sixty-one samples from 53 patients were collected. Twenty-eight samples (46%) showed calibrated scores of ≥0.9. Among them, one case suggested a diagnostic change (level of usefulness A), four were diagnosed according to the revised WHO classification (level of usefulness B), 18 obtained prognostic information from molecular classification or copy number analysis (level of usefulness C), and five supported a pathological diagnosis (level of usefulness D). Thirteen cases with calibrated scores <0.9 but ≥0.5 presented a level of usefulness of A in one case, B in one case, C in five cases, and D in six cases. Multivariate analysis showed a statistical significance in the diagnosis of medulloblastomas with a higher calibrated score (odds ratio; 12.56, p=0.004). Conclusion: Methylation classifiers can support pathological diagnosis, thereby providing additional valuable information for predicting the prognosis of childhood CNS tumors. In Japan, prospective clinical studies are underway.

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© 2025 The Japanese Society of Pediatric Hematology / Oncology
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