Module Author: Candace Savonen (@cansavvy)
The goal of this analysis was to further classify SHH subtype medulloblastoma samples into SHH, TP53-mutated and SHH, TP53-wildtype per #247.
The notebook described below looked at any somatic TP53 mutations.
According to the Medulloblastoma WHO 2016 book chapter linked on the issue, TP53 mutations are often found in exons 4 through 8 and are germline mutations about half the time.
We do not have information regarding the presence or absence of TP53 germline mutations for this cohort.
The mutation status table in results should not be used for subtyping.
We use molecular_subtype information from the harmonized clinical file (pbta-histologies.tsv) to restrict our analysis to samples classified as SHH.
The medulloblastoma subtype classifier uses RNA-seq data, so we must identify WGS biospecimens that map to the same sample_id, if available.
We then look at the presence or absence of mutations in TP53 in the consensus mutation file (pbta-snv-consensus-mutation.maf.tsv.gz).
This analysis consists of a single R Notebook, that can be run with the following from the top directory of the project:
Rscript -e "rmarkdown::render('analyses/molecular-subtyping-SHH-tp53/SHH-tp53-molecular-subtyping-data-prep.Rmd', clean = TRUE)"
The output is a table TP53 mutation status on a per sample_id basis available as results/tp53-shh-samples-status.tsv.