EDIT: V22 rerun all tables

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

Rerun Tables 1, S1 as QC for the new v22 histologies file.

Rerun all tables for manuscript with the following updates:

• Remove duplicates from Table 1 #1459
• Add new hypermutator to Table 2 #1481
• Add missing Key Resources #1407

What was your approach?

Reran only tables 1 and S1 from the Rmd of output_tables.Rmd. This probably can be kept as a draft until we get the remaining analysis updated for v22, then rerun this entire notebook.

Made the above updates and reran all tables

What GitHub issue does your pull request address?

1510

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

Which areas should receive a particularly close look?

Code updates

Is there anything that you want to discuss further?

Looks like this checks out to me.

Note: Since we added [BS_F0GNWEJJ](https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1448/commits/e5739b97cd16c3f1c66b1b6c9ec5b6da0fd14fe8) to the hypermutator table and this sample is a metastatic NBL, not a HGG and therefore not subtyped, I added a small notebook to assess the same (as HGG) TP53 status and additionally, MYCN status. NBLs are most broadly categorized as MYCN amp or non-amp. This sample was found to not have any TP53 alterations, although it does have a high TP53 score. It is not MYCN-amplified via consensus CNV analysis, and additional manual inspection shows no amplification at 2p. (attached below).

I further asked, and Sharon Diskin's germline lab team has shared their germline annotation and pathogenicity analysis for these six patients. Therefore, I added a column specifically for germline pathogenic variant (this was previously pulled from pathology report manual review by me). Here, we add one more pathogenic variant than was previously described via pathology reports. I will create an issue in the manuscript repository to add a short method for germline annotation/pathogenicity and add them as authors.

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

yes, for Tables 1, S1

Yes

Results

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

Updated tables

What is your summary of the results?

NA

Reproducibility Checklist

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

Documentation Checklist

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

[jashapiro]

Suggesting updating the code here to add a distinct() statement as below from a separate branch:

This will allow closing #1459 with this same PR

https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/fc873572b724f27234be7bf5cba40fa282d835f0/tables/output_tables.Rmd#L78-L88

[sjspielman]

Noting this closes #1510

[jharenza]

Also closes #1409

[jharenza]

Hi @sjspielman - updated based on your comments, and reran.

UPDATE: I actually marked this as blocked, pending #1525

[jharenza]

@sjspielman we decided in #1525 to remove cell lines from the subtyping table (Table 1), which I did in the lastest commit, so this can be re-reviewed.