Add GNT back in LGAT subtyping module

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

We previously were removing GNT samples #1014 and adding them back #1017 . In this PR we will reannotate these in the LGAT subtyping module as per this discussion.

What was your approach?

The exclusion criteria was removed from json and following subsetting scripts.
At the final subtypes step we recode molecular_subtype, == GNT, subtype, instead of LGG, subtype

What GitHub issue does your pull request address?

#1086

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

Which areas should receive a particularly close look?

🔖 The issue about 7316-1985 was already discussed in #995 (comment) and was decided to keep as LGG .
Just wanted to confirm with @jharenza if it is still ok to code this sample as LGG.
7316-1985 has pathology_free_term_diagnosis == "low grade glial-glioneuronal lesion. ganglioglioma" and pathology_diagnosis == "Ganglioglioma"

Is there anything that you want to discuss further?

We will update the integrated_diagnosis in molecular_subtyping_pathology module in the next PR.

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?

6 samples were added back as GNT samples

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.

[jaclyn-taroni]

I think there are some cases where the pathology diagnosis is something other than "Low-grade glioma/astrocytoma (WHO grade I/II)" that we want to include in subtyping and recode that are not captured here. cc @jharenza

[jharenza]

🔖 The issue about 7316-1985 was already discussed in #995 (comment) and was decided to keep as LGG .
Just wanted to confirm with @jharenza if it is still ok to code this sample as LGG.
7316-1985 has pathology_free_term_diagnosis == "low grade glial-glioneuronal lesion. ganglioglioma" and pathology_diagnosis == "Ganglioglioma"

Yes - the broad histology should remain low-grade glioma/astrocytoma. Just confirmed Cassie's slack response on this from Sep 2020:

they have similar outcomes as LGG but are slightly unique entities - although GG really falls into the LGG category, DNET does not

But as per the comment above, the subtype info should capture the GNG tumor type.

About to review now.

[jharenza]

once the subtyping is updated for gangliogliomas, I think this should be good to go.

[kgaonkar6]

Last commit adds GNG, <subtype> if pathology_diagnosis=="Ganglioglioma"

[jharenza]

This looks good to me now. Thanks!