April/May Public Studies

[Rima-Waleed]

#	Study_ID	Testing Instance Link	Sample Count
1	nfib_ctf_biobank_2025	https://private.cbioportal.mskcc.org/study/summary?id=nfib_ctf_biobank_2025	68 Samples
2	hdcn_msk_2025	https://private.cbioportal.mskcc.org/study/summary?id=hdcn_msk_2025	1,270 Samples
3	rectal_radiation_msk_2024	https://private.cbioportal.mskcc.org/study/summary?id=rectal_radiation_msk_2024	48 Samples
4	pancan_metaprism_2023	https://private.cbioportal.mskcc.org/study/summary?id=pancan_metaprism_2023	1,031 Samples
5	ucec_msk_dacruzpaula_2025	https://private.cbioportal.mskcc.org/study/summary?id=ucec_msk_dacruzpaula_2025	11 Samples
6	gist_msk_2025	https://private.cbioportal.mskcc.org/study/summary?id=gist_msk_2025	183 Samples
7	pancan_pdmr_2025	https://www.cbioportal.org/study/summary?id=pancan_pdmr_2025	6,272 Samples
	Total Samples		8,883 Samples

Notes:

Study_ID	Missing Data	Notes
Hdcn_msk_2025	Missing clinical data	Pending author response
gist_msk_2025: Missing clinical data	Pending author response
Ucec_msk_dacruzpaula_2025	Missing clinical data	Author preparing data

[rmadupuri]

1. rectal_radiation_msk:

• Update study name to Secondary Rectal Cancers (MSK, JAMA Netw Open 2025)
• Update description to reflect that this is a secondary rectal cancer cohort (≥5 yr post prostate RT)
• Is the cancer type READ or COADREAD?
• Normalize Sample_Type: it should only be Primary, Metastasis, Local Recurrence. For WES Recapture samples, it should be same the corresponding impact sample?
  *Pending author response
• Normalize Sample_Class: it should only be Tumor, Cell line, and Xenograft.
  *Pending author response
• Cap Age at Rectal Cancer Diagnosis at 89.
• Gene alteration %'s are slightly different in paper vs portal (TP53:77%, APC:48.40%, KRAS:39%, SMAD4:25.80%, FBXW7:13%, PIK3CA:6%). Is this due to filtering?
  (Filtering out the WES samples and then selecting for oncogenic somatic alterations.frequencies in the paper match the frequencies reported in the public portal.)
• Mutational signatures pvalue profile not loaded to portal. profile_name is all lower case.
• No cna segment data for P-0054770-T01-IM6, P-0066749-T01-IM7?
• Does WES Recapture samples undergo SV, CNA calling? paper doesn't report CNA/SV calling and there is no CNA/SV data for WES samples. (Yes, the CNA SV from the WES/research IMPACT cases weren't included as they are processed using a different pipeline.)
• CNA, CNASeq and SV caselists includes WES samples. Need to double check if thats correct?
• 7-Mar gene in mutations file.
• Supplemental files also have the data on the primary rectal cancer cohort. Is there a reason for not including it in the portal?
• Supp eTable 10 : has additional clinical elements - OS/DFS outcome data, Neoadjuvant therapy, Timeline/treatment events, Radiation data etc, We can create a timeline, add additional elements to clinical etc

2. gist_msk_2025

• ctdna samples missing from panel matrix
  *Pending author response
• do the ACCESS samples have DMP IDs?
  *Pending author response
  *Pending author response
• mention phase II trial and trial related data in study name and description
• Serial ctDNA VAF timelines: (Figures 3A–H show ctDNA VAF over time). No timeline data file present. Possible to include in portal? There's 5 timepoints for ctDNA samples analyzed.
  *Pending author response
• Description says Targeted sequencing of 42 gastrointestinal stromal tumor samples but study contains 183 total samples (42 IMPACT + 141 ctDNA).
  *Pending author response
• meta_cna: Typo in profile_description: "MK-IMPACT" should be "MSK-IMPACT". Update stable_id from gistic to cna.
• meta_cna_hg19_seg.txt: description reads "Somatic CNA data … from TCGA." data is from MSK-IMPACT.
• Missing patients: The paper reports 42 patients enrolled and 31 patients with ctDNA data. Only 24 patient records exist in the patient clinical file. Patients whose data exists only as ctDNA (C-series IDs) have no entries in data_clinical_patient.txt
  *Author response: samples did not have suitable data for inclusion
• Patient file uses GENDER, normalize to SEX.
• Possible to get clinical data from authors? (Table1 shows the stats)
  *Pending author response
• cna, cnaseq, sv caselists: were ctdna samples profiled? no data available.
  *Pending author response
• Missing Pubmed and citation in portal link

3. pancan_pdmr_2025:

• Rename study to Patient-Derived Models Repository (NCI, 2025)
• The description says all models are Xenografts, is that correct? Can Sample Type be added to clinical, indicating whether models are PDX, PDC, PDO..
• Cancer Type Detailed for one sample is NA
• Missing mRNA zscores
• What normalization was done on mRNA (Are these really RSEMs)?
• What does Available from NCI PDMR, CTC-Derived Model attributes mean? Can we add a description?
• What does Germline Availability coorespond to? If the patients have a matched germline? or samples have germline variants?
  *Pending author response
• How were the patient and sample IDs mapped between Portal and the PDMR website
• Missing RNA case list

4. hdcn_msk_2025

• Missing Pubmed and citation in portal link
• paper mentions 498 patients, paper includes 639 patients - is it a larger registry in portal?
  *Pending author response
• meta_cna: update gistic to cna type. profile_description: Typo, "MK-IMPACT" should be "MSK-IMPACT"
• Remove sv variants in file with no gene info
• study folder has timeline files in /additional_files folder. Are they needed?
• Study description is misleading: study includes all histiocytosis subtypes (not only RAF-independent MEK mutants), also includes 500 ctDNA (MSK-ACCESS) samples
• Update citation to Diamond et al. Cancer Cell 2026
• Update GENDER -> SEX
• Add sample_class : Tumor/cfDNA
  *Pending author response
• sv case list: were ctdna samples profiled?
  *Pending author response

[ritikakundra]

review_ucec_msk_dacruzpaula_2025.html
review_pancan_metaprism_2023.html
review_nfib_ctf_biobank_2025.html

@Rima-Waleed @BabyASatravada I did a validation check using claude. Not all points will be applicable but a good report to do a check.