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Update pathology feedback for BS_H1XPVS9A #1111
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added 2 commits
July 15, 2021 17:07
add pathology review note
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@jharenza @kgaonkar6 can someone on your side resolve these conflicts? I just merged #1097 and I'm not confident about doing so myself. |
- fix merge conflicts - update terms list for GNT
analyses/molecular-subtyping-pathology/04-incorporate-pathology-feedback.Rmd
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…y-feedback.Rmd Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
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@jharenza I think everything looks in order, but things need to get rerun and committed now that that typo is fixed. |
jaclyn-taroni
approved these changes
Jul 20, 2021
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Purpose/implementation Section
What scientific question is your analysis addressing?
BS_H1XPVS9A was still coded as LGG instead of PXA in the integrated diagnosis, so an update was made here.
What was your approach?
I added an additional detail from Mariarita in that she classified this as a malignant PXA after review. Given that the pathology free text diagnosis contains a grade III lesion, it is possible this could still be a high-grade lesion, but cluster with LGG given the BRAF mutational status. This has been noted in the publication here. At the time of this review, we did not have the pathology report, but just had slides. I will follow up again on this to determine whether it should really be in HGG or LGG. For now, I kept it in LGG since the remaining PXAs are all in LGG (although, they can span grades - we just don't have that level of granularity here).
What GitHub issue does your pull request address?
#1093
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
There are additional changes in this PR, presumably due to upstream subtyping tickets (TP53 CNV changes for HGAT, and pathology free text), so I think these are all expected.
Is there anything that you want to discuss further?
No
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)?
Updated table of compiled molecular subtypes
What is your summary of the results?
BS_H1XPVS9A now has an integrated diagnosis of
Pleomorphic xanthoastrocytom, BRAF V600Ebut remains with LGG histologyReproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.