Hi I m working on a paediatric cancer cohort using nf core o nf-core #oncoanalyser

Hi, I’m working on a paediatric cancer cohort usin...

Chiamaka Jessica Okeke

08/12/2025, 11:29 AM

Hi, I’m working on a paediatric cancer cohort using nf-core/oncoanalyser, and I noticed that the current

isofox.hmf_3444.gene_distribution.38.csv

reference appears to be based on adult tumor datasets. Is there an existing paediatric reference database for gene expression high/low calling, or guidance on how to create one? If not, what would be the recommended approach for making a paediatric-specific reference set? Thanks in advance for your help!

Oliver Hofmann

08/12/2025, 11:28 PM

Let me check with the ITCC / ZERO team. I'd think they must have a modified version.

Oliver Hofmann

08/14/2025, 4:53 AM

Turns out no, they do not. They'll check the ITCC roadmap but their focus is on DNA for now. I don't have notes on how the reference was created, but if you do not want to wait I'd open an issue at https://github.com/hartwigmedical/hmftools/blob/master/isofox/README.md — sorry!

Joep de Ligt

08/14/2025, 7:01 AM

Hi @Chiamaka Jessica Okeke we only have adult tumors so that's why there is only that one at the moment. If you and or others have a paediatric dataset that is run with isofox and would like to create a similar file we can pick that up directly with @Peter Priestley and the Aus team to generate that resource

Joep de Ligt

08/14/2025, 7:01 AM

And +1 to the suggestion to raise on issue so we can extend the documentation for other users that might have similar requests

Chiamaka Jessica Okeke

08/14/2025, 8:18 AM

Thanks for clarifying. I’m currently working with a relatively small paediatric cohort, so it wouldn’t be large enough to create a robust reference set. If others in the community have additional paediatric RNA-seq datasets, we could pool them to build something more representative. I’ll open a GitHub issue shortly and share the link here.

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