- Design
- Paired-platform diagnostic concordance study
- Population
- 23 paediatric tumours (18 CNS, 5 non-CNS)
- Primary outcome
- Classifier agreement with integrated histology; CNV and MGMT concordance
- Effect
- Family-level agreement in all CNS cases; MGMT concordance 16/17 (94%)
Twenty-three paediatric tumours (18 CNS, 5 non-CNS) were profiled on both Illumina EPIC arrays and Oxford Nanopore, with several classifiers. One CNS outlier was excluded.
For CNS tumours, the crossNN classifier agreed with integrated histology at family level in all cases. Copy-number profiles were highly concordant, and MGMT promoter status matched in 16 of 17 (94%). The Rapid-CNS2 pipeline gave the best class-level agreement on nanopore data (16 of 17). Outside the CNS, the pan-cancer model agreed with histology in only 1 of 5.
Nanopore can give a methylation class within a day on a single sample, without batching for arrays. It needs fresh-frozen DNA and the classifiers were built on array CpG sites. For CNS tumours this looks ready to support diagnosis; for non-CNS tumours it does not.
- Keep fresh-frozen tissue for paediatric CNS tumours if nanopore is available.
- Use nanopore for rapid family-level classification; confirm class level where it changes management.
- Do not rely on the pan-cancer model for non-CNS tumours.
- Report MGMT status with the platform used.
Why it matters
It shortens the wait for methylation class from weeks of batching to a single day.
Don't overread it
Twenty-three tumours, one excluded, is a small validation set.
The statistics, in plain English
Agreement of 16 of 17 is 94%, but with so few cases the true figure could plausibly be in the 70s or 80s. One discordant result in a small series matters.
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