Public Release Studies (December)

[Rima-Waleed]

Study_ID	Testing Instance Link	Sample Count
ucs_msk_2024	https://triage.cbioportal.mskcc.org/study/summary?id=ucs_msk_2024	69 Samples
ilc_msk_2023	https://private.cbioportal.mskcc.org/study/summary?id=ilc_msk_2023	25 Samples
depmap_broad_2025	https://private.cbioportal.mskcc.org/study/summary?id=depmap_broad_2025	1,981 Samples
ccrcc_sjuh_2023	https://private.cbioportal.mskcc.org/study/summary?id=ccrcc_sjuh_2023	943 Samples
aml_stjude_2024	https://private.cbioportal.mskcc.org/study/summary?id=aml_stjude_2024	887 Samples
lgg_ctf_synodos_2025	https://private.cbioportal.mskcc.org/study/summary?id=lgg_ctf_synodos_2025	31 Samples
es_dsrct_msk_2023	https://private.cbioportal.mskcc.org/study/summary?id=es_dsrct_msk_2023	290 Samples
angs_painter_2025	https://www.cbioportal.org/study/summary?id=angs_painter_2025	328 Samples
blca_iatlas_imvigor210_2017	https://www.cbioportal.org/study/summary?id=blca_iatlas_imvigor210_2017	347 Samples
brca_iatlas_anders_2022	https://www.cbioportal.org/study/summary?id=brca_iatlas_anders_2022	31 Samples
rcc_iatlas_immotion150_2018	https://www.cbioportal.org/study/summary?id=rcc_iatlas_immotion150_2018	263 Samples
mel_iatlas_liu_2019	https://www.cbioportal.org/study/summary?id=mel_iatlas_liu_2019	122 Samples
mel_iatlas_hugo_ucla_2016	https://www.cbioportal.org/study/summary?id=mel_iatlas_hugo_ucla_2016	27 Samples
crc_hta8_htan_2024	https://private.cbioportal.mskcc.org/study/summary?id=crc_hta8_htan_2024	83 Samples
	Total Samples	5,428 Samples

Notes:

Study_ID	Missing Data	Notes
lgg_ctf_synodos_2025	Missing clinical data, sample size, additional profiles	Author clarification here
ucs_msk_2024	Clinical data + treatment data	Reached out to author -> data cannot be provided for privacy concerns
ilc_msk_2023	Mutational signature data + clinical data	Reached out to author, preparing data
depmap_broad_2025		Renamed for review purposes as ccle_broad_2025 (previous release) already exists in portal
ccrcc_sjuh_2023	clinical discrepancy (supplementary files VS. tables in the paper), OS_MONTHS, and sequencing platform groups	Reached out to author, response pending
aml_stjude_2024	Arm-level CNA	Reached out to author, response pending

[rmadupuri]

Thanks, @Rima-Waleed! The studies look good overall, and I have a few questions and suggestions for improvement.

ucs_msk_2024:

• The samples were sequenced using IMPACT, so we should use DMP IDs for patient and sample identifiers, with EC IDs as display names, to maintain consistency and prevent duplicate samples with different IDs.
  *Author and collaborators wish to not use DMP IDs- author mentioned they did extensive manual curation and some patients may have diagnosis that doesn't match the msk impact study samples.
• Can we make MSI Status as MSI-H when Score >= 10 as per paper?

ilc_msk_2023:

• Update the study name to Breast Invasive Lobular Carcinoma (MSK, Nature 2024).
• Are the two samples currently listed under Invasive Breast Carcinoma also lobular carcinomas?
  *Author emailed for confirmation, pending response

depmap_broad_2025:

• Segment data doesnt look right. FGA is all close to 1. CNA shows a lot of Amplification?
  *Author confirmed seg mean values are linear and not log transformed.

• There are 94 samples without any genomic data? Is the case lists reflecting right numbers?
  *Samples were cross-checked in depmap portal to confirm they don't have genomic data
• Do we need to keep the 94 samples above? Were they sequenced at all? If sequenced, case lists need updating.
  *Confirming with author if they were sequenced at all or not- if not, samples will be removed
• The latest update includes mutation data for fewer samples compared to the previous release? 1854 vs 1970 counts.
  *Samples were cross-checked in depmap portal to confirm they don't have genomic data. Pending on author's confirmation.
• Missing gene panel matrix
• Missing TMB, Somatic Status attributes
  *Added TMB, confirming somatic status with authors.

ccrcc_sjuh_2023:

• What does 0/X in Metastasis (TNM) Stage mean? Recode as NA/Unknown?
• Rename RCC Specific (months) to RCC Specific Survival (Months)
• Chart not loading

• What is the right sequencing platform used? the description says WES/Targeted and the clinical attribute shows WGS. Can we add a gene panel matrix?
  *Authors used WGS, WES and targeted sequencing. Author emailed for clarification (cohort C2 samples are not distinguished by sequencing platform). Sequencing platforms used by cohort group:
  C1 cohort: WGS
  C2 cohort: WES + targeted (42 genes not provided)
  C3: targeted (12 genes provided)
• For the above, it appears that only the Targeted MAF from the 12 gene panel is available, based on the data mutations file and the paper's supplementary files. Please add a note to the README that only this data is shown and update the gene panel matrix from the MAF file.
• Additionally, we can remove references to other sequencing platforms to avoid confusion.

• Can the mutations for WGS and the Targeted 42 gene panel be shared by the authors? The paper seems to refer to their previous studies.
  *Authors preparing the data, pending their response.
• Recalculate TMB based on the 12 gene panel. Currently on the WES/WGS assumption, and the numbers are too low.

aml_stjude_2024:

• Normalize Male in Sex attribute
• Add TMB, Matched Normal status
• Can we add a gene panel matrix?
• I see all samples went through RNA-seq (from which only somatic mutations from 87 genes were reported Fig 1) and samples also went through WXS/WGS. How are you linking the targeted panel to the samples?
• Can we update the study name to 'Pediatric Acute Myeloid Leukemia..'?
• Missing RNA case list
• RNA data is not loaded to portal instance.
• Can we add the Tumor allele counts? See them in Supp 7.
• Was Supp Table 8 also used in SV file? It lists duplications.

lgg_ctf_synodos_2025:

• Can we make NF Open Science Initiative a hyperlink instead in the description?
• Indicate that the expression profiles are TPM based?
• Did all samples undergo WGS? The sample counts in the gene panel matrix and the mutation file don't match.

es_dsrct_msk_2023:

• Can we add “to detect EWSR1 chromoplexy-associated structural rearrangements” to the description, since this is the main focus of the study?
• What are the SV events in the data file that list only gene symbols without genomic coordinates or other details? Can these be removed as they appear to be duplicates of fully annotated events?

[ritikakundra]

angs_painter_2025:

• The description numbers and the portal numbers dont match.
• Is the genomic frequency breakdown correct? 39% mutated?
• Why are the event types in upper case
• The links in the description is not wroking
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