CPTAC. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer. Cell 2020.

[jjgao]

https://www.sciencedirect.com/science/article/pii/S0092867420314513?dgcid=rss_sd_all

• [ ] create an 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 the default quick select study list see https://github.com/cBioPortal/cbioportal/issues/5831 (only for studies that are not overlapping with existing ones; only for human tumors, not cell lines)
• [ ] Update cBioPortal news

[yichaoS]

S1 - clinical data S2 tab 2 - tumor purity S7 tab 3 - arm-level CNA

emailed author for mutation and RNA-seq data pei.wang@mssm.edu (Dr Wang) resnick@email.chop.edu (Dr Resnick) storm@email.chop.edu (Dr Storm) brood@childrensnational.org (Dr Rood)

[yichaoS]

Replied by Wang Pei (pei.wang@mssm.edu) on 5/11/2021

You can find the preprocessed expression, mutation and CNV data from the CPTAC DCC link:
https://cptac-data-portal.georgetown.edu/cptac/documents/GenomicData.zip

(no MAF info there tho)

replied by Adam Resnick (resnick@chop.edu) on 5/11/2021

Hi Yichao – Yuankun, Miguel, and Karthik (copied) may be able to help you in a more streamlined way as I think they have prepped the data for the pedcbio instance by and large.  Let me know if there is anything else we can do to facilitate.

Replied by Karthik(kalletlak@chop.edu) on 5/17/2021:

We already have processed files which can be directly loaded into cbio. We will create a pull request to datahub with those files.

[SRodenburg]

Hi @kalletlak, can you confirm you are working on this dataset?