Planned Analysis: Oncoprint showing landscape of genetic lesions across PBTA.

[PichaiRaman]

This figure typically focuses on a set of high frequency and cancer associated lesions (mutations / CNV) and will typically have corresponding phenotypic data so as to visualize associations. See Figure 1 (https://www.biorxiv.org/content/10.1101/656587v1.full) for an example.

[jharenza]

I imagine this analysis would make use of consensus SNV calls (#30), consensus CNV calls (#128), and filtered/prioritized fusion calls (#39 and #10) currently tied to multiple PRs. I can work on this after a grant submission Nov 15, but if anyone would like to work on this earlier, I have created some code for this for a recent manuscript that can be adapted.

[cbethell]

I imagine this analysis would make use of consensus SNV calls (#30), consensus CNV calls (#128), and filtered/prioritized fusion calls (#39 and #10) currently tied to multiple PRs. I can work on this after a grant submission Nov 15, but if anyone would like to work on this earlier, I have created some code for this for a recent manuscript that can be adapted.

I can begin working on this issue now, while keeping in mind that this analysis will need to be rerun once the aforementioned upstream issues are completed.

[jharenza]

Thanks, @cbethell !

[jaclyn-taroni]

The code in oncoprint-landscape is largely in good shape. But we will want to update the data displayed in the plots to account for the following:

• We have consensus copy number calls. GISTIC needs to be rerun with the consensus SEG file (Updated analysis: rerun GISTIC with consensus SEG file #453) and focal vs. broad losses need to be reconciled per Proposed Analysis: map from SEG file to genes (and broader segments) #186 (comment).
• We should identify recurrently altered genes that can be used to guide the display.
  • This is included as part of Proposed Analysis: chromosomal instability burden, recurrently altered genes #394 regarding amplification, deep deletion, and other SVs.
  • We have pbta-fusion-recurrently-fused-genes-byhistology.tsv now included as part of the data download that can be used to guide the display of fusions.

[jaclyn-taroni]

Closing all planned analysis tickets in favor of opening new proposed analysis/updated analysis tickets as needed.