A clinically and genomically annotated nerve sheath tumor biospecimen repository. Pollard et al. Sci Data 2020

[anngvu]

This is a proposed new public study. Raw genomics data was generated for this study in 2020 and is stored on Synapse: JHU Biobank project. In 2022, the lab had contract support for NF-OSI team at Sage to process the data and submit a very small subset to the public cBioPortal (because we're excluding a lot of germline data). Processing pipelines are described here: NPD-Nextflow Data Processing & Configuration-161122-155435.pdf.

• 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
  • doi: https://www.nature.com/articles/s41597-020-0508-5
• 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 options for selecting tcga + non-tcga studies cbioportal#5831 (only for studies that are not overlapping with existing ones; only for human tumors, not cell lines)
• Update cBioPortal news

[anngvu]

@inodb @ritikakundra Question about the public cBioPortal requring GRCh37 -- I was told Thomas Yu had a meeting (with Ino, I think) and said the public portal will be moving to/accepting GRCh38 soon? Currently the checklist and validation still requires GRCh37.

[allaway]

Hello all, I was wondering if there was any update on this data deposit? Thanks!

[rmadupuri]

Hi @allaway @anngvu @jaybee84! The study is now released to the public cBioPortal at https://www.cbioportal.org/study/summary?id=nst_nfosi_ntap. Could you review the data to make sure everything looks right?

Thanks so much!

[allaway]

Hi @rmadupuri, thanks so much for this! I have opened a PR to make some minor wording changes in the description. I'll leave the review of the actual data to @jaybee84 as she is much more familiar with it than I.

[jaybee84]

The initial spot checks with the data looks good. There are some differences in the variants identified in this submission compared to the original publication. Most likely the difference has arisen due to differences in reprocessing parameters as well as the reference genome build. I added a sentence in the study description to make that explicit.

[jaybee84]

@rmadupuri just wanted to attract your attention to a more recent PR that helps avoid code jargon in the description (that I had added earlier). Thanks again for the review and addition.

[jaybee84]

@rmadupuri I was looking through the genes reported as having variants in these samples on cbioportal and found a gene called FOCAD with variant in one sample. But I could not find this gene in the original mutation MAF file on my end. Do you have a guess what may be happening here?

[rmadupuri]

@jaybee84 thanks for the corrections. The changes are now public.

I do see one FOCAD Splice variant in the original submission here https://github.com/nf-osi/datahub/blob/d929f69a212861b4cb14ef97240d0e9e06ca0122/public/mixed_nfosi_2022/data_mutations.txt from PR #1736. Let us know if there's any issues.

[jaybee84]

@rmadupuri Sorry for my delayed response, I was out of office. I am following up on the noted difference and will report back soon.

[jaybee84]

It looks like I was missing the above mentioned variant because I was seeing only a subset of the variants on my end. This was because I was using an analytical package function to read the original MAF file that filters out the silent variants. So this variant was being filtered out.

This issue is resolved from my end. The updated mutations.txt file and the original maf file are concurrent in terms of reported variants.

[stale]

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.