Updated analysis: update Ependymoma subtyping to add K28M --> PFA

[jharenza]

What analysis module should be updated and why?

https://github.com/PediatricOpenTargets/OpenPedCan-analysis/tree/dev/analyses/molecular-subtyping-EPN

We previously had detected an H3 mutation in an EPN sample - turns out this is found in a small subset of PFA tumors. So, we should subtype this one as PFA.

What changes need to be made? Please provide enough detail for another participant to make the update.

Add a conditional requirement of PFA tumors to be:

• posterior fossa location + presence of H3 K28M mutation

See this JSON file for the genes and mutation designation for H3 (histone 3) genes to select: https://github.com/PediatricOpenTargets/OpenPedCan-analysis/blob/cd4e379a7f835160284a65b5d7a6c62a5bc125c4/analyses/molecular-subtyping-LGAT/input/snvOI_list.json#L74-L117

These should be added to the https://github.com/PediatricOpenTargets/OpenPedCan-analysis/blob/dev/analyses/molecular-subtyping-EPN/results/EPN_all_data.tsv file, either separate or in one combined column as "K28_mutant" with yes/no or 0,1 for example.

What input data should be used? Which data were used in the version being updated?

snv-consensus-plus-hotspots.maf.tsv.gz

Note: use data.table::fread() to load the maf

When do you expect the revised analysis will be completed?

< 1 week

Who will complete the updated analysis?