PBTA Histologies v19 Part 8 of N: Run molecular subtyping

[kgaonkar6]

🚨 🚨 🚨 merge #1039, #1040, #1041, #1042, #1043, #1044, #1045 before this PR.
I checked out each module as a different PR so that it can be reviewed and then this PR can be specifically for molecular-subtyping-* modules which might have fewer ( then 124) files to review.

Purpose/implementation Section

What scientific question is your analysis addressing?

Run molecular subtyping for v19 release

What was your approach?

I re-ran https://github.com/kgaonkar6/OpenPBTA-analysis/blob/v19-release/scripts/run-for-subtyping.sh with an addition in code to run tp53_nf1_score module to add TP53 alteration status for HGG samples and newly Ok-ed chordoma subtyping.

What GitHub issue does your pull request address?

#867

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

Which areas should receive a particularly close look?

Changes in results per subtyping modules would be of most interest, please read my summary of the changes below.

Is there anything that you want to discuss further?

Update embryonal molecular 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)?

tables

What is your summary of the results?

• BS_JXF8A2A6: is removed as per Data: BS_JXF8A2A6 likely needs removal from dataset #862
• BS_F8K4VQMF and BS_GG9W3J9Y: is added to HGG subset because the pathology free text is updated in v19 release.

Kids_First_Biospecimen_ID	pathology_free_text_diagnosis_latest	pathology_free_text_diagnosis_previous
BS_F8K4VQMF	glioblastoma, idh-1 negative, who grade iv	gliomatosis cerebri
BS_GG9W3J9Y	High-grade glioma/astrocytoma (WHO grade III/IV)	Gliomatosis Cerebri

In v18 because #972, the sample was removed in previous hgg subset using v18 because of updated exclusion if Gliomatosis Cerebri without grad 3or 4 in pathology free text diagnosis

• BS_D7XRFE0R and BS_KABQQA0T are now updated to the correct sample_id to match to it's DNA sample so the subtyping results is matched correctly

Kids_First_Biospecimen_ID	sample_id_latest	sample_id_previous
BS_D7XRFE0R	A18777	7316-5812
BS_KABQQA0T	A16915	7316-5003

• BS_4GKH983E and BS_MQCKXD60 are being removed because of Updated analysis: molecular subtyping LGAT: remove non LGG tumors #995

Kids_First_Biospecimen_ID	broad_histology_latest	broad_histology_previous
BS_4GKH983E	Neuronal and mixed neuronal-glial tumor	Low-grade astrocytic tumor
BS_MQCKXD60	Neuronal and mixed neuronal-glial tumor	Low-grade astrocytic tumor

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]

Most of the changes here are as expected and in line with the PR description. There are a few places where there were some apparent changes that were not described, which I have noted and asked about.

The biggest change that concerns me is the apparent loss of all BRAF V600E mutations in the HGG module (visible most easily in the plot molecular-subtyping-HGG/plots/HGG_stranded.png).

Other changes seem more minor and in line with expectations.

[migbro]

Ok, the updated mafs have been uploaded!

[kgaonkar6]

Thanks for the update @migbro, the BRAF V600E in HGG_cleaned_mutation.tsv are now in! 🎉

[jashapiro]

I think this looks fine, though it is obviously hard to check everything. There are now a number of conflicts, however, including in pbta-histologies.tsv, that need to be resolved before this is ready to merge.

[kgaonkar6]

I just fixed the conflicts. Thank you for the reviews @jashapiro @jharenza

[jashapiro]

I think this should be ready.