Studies for news release- Jan 2024

[Rima-Waleed]

Cancer studies updated in this pull request:

• cll_broad_2022
• mbn_sfu_2023
• brain_ccma_2023 (*Working on adding rna seq data)

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 study meta data complete? e.g. pmid, group of PUBLIC
• [ ] 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 files
• [ ] MAF is based on hg19
• [ ] MAF with 2 isoforms: uniprot and mskcc
• [ ] CNA data with meta files
• [ ] CNA segment data with meta files
• [ ] Expression data including z-scores with meta files
• [ ] Case-lists for all profiles.
• [ ] Manual checking (Niki or JJ): Triage or private Portal link here

[ritikakundra]

cll_broad_2022

• [x] Survival data needs what point zero is in the descriptions
• [x] Death (days) is computed from when?
• [x] The CTD CLL numbers and Disease Type numbers don't match
• [x] What is 0 in first Tx after sampling?