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d3b-center / OpenPedCan-analysis

The analysis repository for the Open Pediatric Cancer Project
https://d3b-center.github.io/OpenPedCan-analysis/
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BS_H1XPVS9A is malignant PXA #490

Closed jharenza closed 10 months ago

jharenza commented 10 months ago

Per the molecular subtype pathology note, BS_H1XPVS9A is malignant PXA, and should be PXA subtyped during the HGG module. I do not see this one currently pulled in - let's keep an eye during the release. I will update in #484

The relevant note from above:

  1. Pathology confirmed this HGG BRAF V600E mutant tumor, BS_H1XPVS9A - we now have a subtyping module for PXA, so this should get integrated there. to be a malignant PXA. @kgaonkar6 updated molecular_subtype here based on what it would look like, but this should come through via the LGAT subtyping ticket. The steps for LGAT subtyping are to classify LGG samples on the basis of the presence/absence of BRAF fusions and BRAF V600E mutations.

cc @zzgeng

jharenza commented 10 months ago

This came into v13 HGG subtyping, however, was subtyped WT.

jharenza commented 10 months ago

took care of this in #516

jharenza commented 10 months ago

completed in #474