Fix deprecated AASTR oncotree codes based on IDH1 mutation status

[inodb]

Updated 1,757 AASTR samples across 13 studies based on IDH1 mutations:

• 241 samples with IDH1 mutations → ASTR (Astrocytoma)
• 1,516 samples with IDH1 wildtype → GB (Glioblastoma)

Updated fields for each sample:

• ONCOTREE_CODE: AASTR → ASTR or GB
• CANCER_TYPE: Updated to "Glioma"
• CANCER_TYPE_DETAILED: "Astrocytoma" (ASTR) or "Glioblastoma" (GB)

Studies modified:

• ccle_broad_2019 (1 sample)
• difg_glass (45 samples)
• difg_glass_2019 (28 samples)
• difg_msk_2023 (4 samples)
• glioma_msk_2018 (13 samples)
• glioma_mskcc_2019 (159 samples)
• lgg_tcga (130 samples)
• lgg_ucsf_2014 (11 samples)
• msk_ch_2020 (1,094 samples)
• msk_ch_2023 (168 samples)
• msk_impact_2017 (86 samples)
• pancan_mappyacts_2022 (4 samples)
• tmb_mskcc_2018 (14 samples)

AASTR (Anaplastic Astrocytoma) is deprecated in OncoTree. Modern classification splits based on IDH mutation status per WHO 2021.

🤖 Generated with Claude Code

checks

For all pull requests:

• Passes validation

For a new study (in addition to above):

• Does study name and study ID follow our convention? e.g. Tumor_Type (Institue, Journal Year); brca_mskcc_2015
• Is the study meta data complete? e.g. pmid, citation
• Were all samples profiled with WES/WGS? If not, is gene panel file curated?
• Are oncotree codes of all samples curated; Cancer Type and Cancer Type Detailed needs to be added in addition to Oncotree Code
• Clinical sample and patient data with meta files.
• Mutations data with meta file.
• Is the study based on hg38? If so, is the reference_genome: hg38 option included in meta study.
• CNA data with meta files
• CNA segment data with meta files
• Expression data including z-scores with meta files
• Other genomic profiles with meta files
• Case-lists for all profiles.
• Perform sanity checks based on the items in the checklist
• Manual checking (Niki or JJ): Triage or private Portal link here