update path subtyping

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

With #856 , #939 , #943 all completed, this module was out of date. Made some code updates and updated integrated dx for these samples.

What was your approach?

• Add new HGG subtypes' integrated dx, remove BRAF subtype code
• Update EPN code and integrated dx
• Add EPN, H3 K28 mutant as an integrated dx
• Update LGG BRAF tumor BS_H1XPVS9A integrated dx in script 03
• Added a table of unique subtypes and integrated dx at the end for easy spot checking
• For HGG/DMG, I left the integrated dx general since they are listed that way in the WHO 2016 guidelines (opposed to LGAT, which came from a publication). Wanted to note that here, and we can change later if this is something the clinicians want to see.

What GitHub issue does your pull request address?

NA

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

See below

Is there anything that you want to discuss further?

Q: should we remove lines 228-249 now that HGG BRAF is no longer in subtyping?

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

yes

Results

What types of results are included (e.g., table, figure)?

table

What is your summary of the results?

All new subtypes to date have corresponding integrated diagnoses.

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[jashapiro]

This all looks like it does what you say.

I was a bit confused about whether molecular_subtype == "BRAF V600E" ever occurs, and that seemed to affect the answer to your question

It took me a second to figure out which file this referred to:

Q: should we remove lines 228-249 now that HGG BRAF is no longer in subtyping?
But if it is the 03- notebook, as it appears, then yes, I would say that section should be removed if it is no longer relevant. In the rendered version of that notebook it does appear that there are no samples with molecular_subtype == "BRAF V600E" by the time that section is run.

[jashapiro]

Are these being removed because they don't occur any more in the data set? Or is there a scientific reason to remove these conditions (they will never occur)?

[jharenza]

BRAF was removed from HGG subtyping in #807 due to scientific reasons.

[jharenza]

Hi @jashapiro - thanks for reviewing and sorry for lack of context. BRAF was removed from HGG subtyping in #807 due to scientific reasons.

Of note, this is still a subtype in LGG, but all subtypes are now prefixed by the histology (eg: LGG, BRAF V600E)

I'll remove those lines of code and rerun when I get to a computer this afternoon - thanks!