325O - Routine molecular subgrouping of medulloblastoma: Bridging the divide between research and the clinic using low-cost, mass spectrometry-based DNA m...

Date 07 October 2016
Event ESMO 2016 Congress
Session CNS tumours
Topics Central Nervous System Malignancies
Pathology/Molecular Biology
Basic Scientific Principles
Presenter Ed Schwalbe
Citation Annals of Oncology (2016) 27 (6): 103-113. 10.1093/annonc/mdw367
Authors E. Schwalbe1, D. Hicks1, G. Rafiee1, M. Bashton1, H. Gohlke2, A. Enshaei1, S. Potluri1, J. Matthiesen1, M. Mather1, P. Taleongpong1, R. Chaston3, S. Crosier1, A. Smith4, D. Williamson4, S. Bailey4, S. Clifford4
  • 1Paediatric Neurooncology, Northern Institute for Cancer Research University of Newcastle, NE1 4LP - Newcastle upon Tyne/GB
  • 2Agena Bioscience, Agena, D-22761 - Hamburg/DE
  • 3Genetic Diagnostics, NewGene, Newcastle upon Tyne/GB
  • 4Paediatric Neurooncology, Northern Institute for Cancer Research University of Newcastle, Newcastle upon Tyne/GB



DNA methylation patterns allow the subclassification of medulloblastoma (MB) into 4 molecular subgroups, which inform treatment and risk-stratification. Whilst microarrays to assign subgroup are suitable for research, their clinical utility is limited by expense, platform-specificity, sample quality requirements and practicality. Here, we aimed to develop a low-cost, array-independent, robust subgrouping assay suitable for routine quality-controlled subclassification, including scant, poor-quality, aged samples, and apply it to the previously unassignable PNET4 trial.


Using a cross-validated classification model, a minimal, multiply-redundant, 17-locus signature was derived to assign subgroup from 220 MBs profiled using Illumina 450k DNA-methylation arrays. We next adapted the MALDI-TOF Mass Spectometry (MassARRAY, Agena Bioscience) iPLEX assay to interrogate DNA methylation following bisulfite treatment. After in vitro validation, the assay was applied to 101 DNA extracts from fresh-frozen, FFPE and nuclear (


95/101 validation samples had high-confidence assignments which recapitulated 450k subgroup calls. Subsequently, high-confidence calls were made for 107/153 PNET4 samples. Notably, a worse survival was observed for standard-risk PNET4 Grp4 patients (EFS 80%; p = 0.01).


MBs can be routinely subgrouped using minimal DNA methylation signatures. The assay is suitable for reliable, robust testing of poor-quality, degraded samples using

Clinical trial identification

SIOP-PNET4: NCT01351870

Legal entity responsible for the study

Newcastle University


Cancer Research UK The Brain Tumour Charity Children's Cancer Run


All authors have declared no conflicts of interest.