update histologies file information/molecular subtype methods #86
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- in methods, change `disease_type_old` to `pathology_diagnosis` and `disease_type_new` to `integrated_diagnosis` - add missing `parent_aliquot_id` field to table
add HGG and some embryonal subtyping information
fix italic
fix spacing
add additional embryonal subtypes, even those we did not have in our dataset
add references
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@jaclyn-taroni I think this is ready now - let me know if this is OK how I have it set up or if you prefer we describe these a bit differently. Of note, I added all of the subtypes we attempted, even if we did not have samples fitting those. |
| Medulloblastoma (MB) subtypes SHH, MYC, Group 3, and Group 4 were predicted using an [RNA expression classifier](https://github.com/d3b-center/medullo-classifier-package) on the RSEM FPKM data. | ||
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| High-grade glioma (HGG) subtypes were derived using the criteria below (additional details in the analysis [README](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/molecular-subtyping-HGG)): | ||
| 1. If any sample contained an H3F3A K28M, HIST1H3B K28M, HIST1H3C K28M, or HIST2H3C K28M mutation and no BRAF V600E mutation, it was subtyped as `DMG, H3K28`. |
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There may be some nomenclature nuance I'm missing here, but I would expect these gene symbols to be italicized...although I guess the K28M means it is referring to the protein? A link with guidance would be helpful.
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Hmm, yeah, since they are describing protein, they would be in non-italicized caps. Here, I wrote out each gene to be very specific, but we could opt for saying H3 K28M etc, like in this paper. Even in this paper, though, they seem to bounce back and forth with italicizing and not. I would suggest we just adhere to the human gene/protein naming standards of cap/italic for gene names/RNA, and caps for protein. (I thought there was another official website, but couldn't find quickly - could find fly, mouse, zebrafish, ha!).
add @jaclyn-taroni suggestion Co-Authored-By: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
fix typo per @jaclyn-taroni suggestion Co-Authored-By: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
fix typo per @jaclyn-taroni suggestion Co-Authored-By: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
update per @jaclyn-taroni suggestion Co-Authored-By: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
italicize FOXR2
italicize CIC
fix CIC fusion sentence
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thanks @jashapiro ! |
…-subtyping This build is based on 1e71105. This commit was created by the following Travis CI build and job: https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/builds/153323829 https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/jobs/298143803 [ci skip] The full commit message that triggered this build is copied below: Merge pull request #86 from AlexsLemonade/update-methods-disease-type-subtyping update histologies file information/molecular subtype methods
…-subtyping This build is based on 1e71105. This commit was created by the following Travis CI build and job: https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/builds/153323829 https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/jobs/298143803 [ci skip] The full commit message that triggered this build is copied below: Merge pull request #86 from AlexsLemonade/update-methods-disease-type-subtyping update histologies file information/molecular subtype methods
Purpose
Briefly describe your changes here.
disease_type_oldtopathology_diagnosisanddisease_type_newtointegrated_diagnosisparent_aliquot_idfield to tableIssue
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#82
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