Aggarwal et al., Small Cell Neuroendocrine Prostate Cancer, JCO 2018

[schultzn]

http://ascopubs.org/doi/suppl/10.1200/JCO.2017.77.6880

The supplemental tables have mutation data (contains copy-number calls, which have to be pulled out and converted) and expression levels.

[schultzn]

Clinical data seems to be missing - will try to get that.

[jjgao]

• [x] create a issue on datahub before curating a study (one issue per study) and copy this checklist to the issue tracker
• [ ] List information of the dataset/paper in the issue, e.g. pmid, paper link, suppl file link
• [ ] Document the curation process, e.g. how and by whom the data was transformed
• [ ] Follow the data checklist
• [ ] Create a pull request to datahub once the data is curated
• [ ] Push to triage portal
• [ ] Import into msk and public portal database
• [ ] Update cBioPortal news

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[rmadupuri]

Cohort stats: 202 patients/ 249 met samples

Data availability: RNA-seq - 119 samples analyzed - data in Supplement 3 MAF - 85 patients were targeted sequenced - data in Supplement 2 - targeted genes list in Fig4. CNA - data available in Supplement 2

Data Missing: Clinical data - only summarized table is given. Complete list of patient/sample IDs, Survival data are not available.

Status: Not curatable since the full pat/sample list is missing. Emailed author (May 26, 2021) for clinical data.

[rmadupuri]

Shared by the author: (Rahul Aggarwal - [email protected]) Clinical data was recently added to GitHub https://github.com/DavidQuigley/WCDT/blob/master/clinical_metadata/2021_03_24_JCO_2018.txt

Issue: The data here is available for only 101 patients and has only few attributes than what is summarized in the paper. Genomic files have additional patient/samples that aren't in the shared clinical data.

Status: Author has followed up internally to see if additional samples are available for uploading and has requested in the meantime to go with the 101 patients for now.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.