Update nfosi jhu dataset

[anngvu]

What?

Fix #2034

Cancer studies updated in this pull request:

• ntap_nfosi_ntap

checks

For all pull requests:

• Passes validation

For a new study (in addition to above):

• Does study name and study ID follow our convention? e.g. Tumor_Type (Institue, Journal Year); brca_mskcc_2015
• is study meta data complete? e.g. pmid, group of PUBLIC
• were all samples profiled with WES/WGS? If not, is gene panel file curated?
• are oncotree codes of all samples curated; Cancer Type and Cancer Type Detailed needs to be added in addition to Oncotree Code
• clinical sample and patient data with meta files
• mutations data with meta files
• MAF is based on hg19
• MAF with 2 isoforms: uniprot and mskcc
• CNA data with meta files
• CNA segment data with meta files
• Expression data including z-scores with meta files
• Case-lists for all profiles.
• Manual checking (Niki or JJ): Triage or private Portal link here

[anngvu]

@ritikakundra Help with this?

[ritikakundra]

@anngvu is this for private access?

[jaybee84]

@ritikakundra I am chiming in here on behalf of @anngvu, This is for the public portal. This is the original study which needs to be updated.

We are hoping to highlight this update/new submission in a conference in June, 2024. Would it be possible to add these updates before mid June?

[Rima-Waleed]

Hi @jaybee84 @anngvu,

Thank you for the study update and PR! The data looks good but I have a couple of fixes before we can merge:

1. The paper mentions 55 samples from 23 patients, while the study files have 134 samples from 54 patients. Can you clarify the difference in patient/sample count?
2. Do all the samples have matched normals? Can this info be added to the sample file? The attribute we use is SOMATIC_STATUS (Matched/Unmatched).
3. The mrna expression files have to be renamed to the recommended file names: I assume data_mrna_seq_rpkm and data_mrna_seq_tpm, correct?
4. It would be helpful if you add a README file to outline how the data was curated.

I added some attributes required by cBioPortal to the clinical files such as ONCOTREE_CODE, CANCER_TYPE, CANCER_TYPE_DETAILED, & TMB_NONSYNONYMOUS.

Looking forward to update the study!
Thanks!

[jaybee84]

@Rima-Waleed Thanks for the review.

The paper mentions 55 samples from 23 patients, while the study files have 134 samples from 54 patients. Can you clarify the difference in patient/sample count?

This submission updates the previous cohort by adding additional batches of samples. The new preprint that describes the full cohort is here: https://www.biorxiv.org/content/10.1101/2024.01.23.576977v1. Please add this preprint along with the original publication for reference.

I am tagging @anngvu to address the points 2,3, and 4.

[anngvu]

@Rima-Waleed Thanks for the notes, we'll update these. I think the SOMATIC_STATUS is new (at least it wasn't pointed out last time).

[anngvu]

Hmm, I am unable to update the last thing because I get this:

It sounds as if cBioPortal account rather than ours needs to purchase bandwidth for LFS?

• According to:GH docs https://docs.github.com/en/repositories/working-with-files/managing-large-files/about-storage-and-bandwidth-usage, it sounds as if cBioPortal account rather than ours needs to purchase bandwidth for LFS?
• Also because of this issue I see here Error when pulling file: "repository is over its data quota." #1990

UPDATE: Actually, it looks like we are the ones who need to update storage according to this:

• Can't access data over LFS due to data quota limit #1738**
  

[Rima-Waleed]

Hi @anngvu,
Apologies about that, we have hit the datahub LFS limit this month and it will reset itself on the 12th. This is why you're not able to push the study files to datahub. Should work on the 12th, I'll review the files as soon as it's updated.
Thanks!

[anngvu]

@Rima-Waleed No worries, I confirmed side of the bandwidth issue a couple of days ago. Maybe we can find a way to donate bandwidth through GitHub sponsorship? Just an idea -- I'll talk to Ino and Ritika. Anyway, made suggested updates with somatic status (and we're only going to keep TPM). Thanks!

[anngvu]

@Rima-Waleed All files are updated.

[Rima-Waleed]

Thank you @anngvu! Doing a final review of the study and sending you the study link soon.

[jaybee84]

@Rima-Waleed @ritikakundra Just wanted to follow up here to see if it would be possible to update the study on the public portal by today or tomorrow. We are hoping to showcase the study and cBioPortal functionalities in an upcoming international conference (on Friday) if possible. :)

[ritikakundra]

@jaybee84 We are just wrapping up it up. We will have the link ready by tomorrow morning.

[jaybee84]

Super! Thanks to the whole cBioPortal team and specially to @Rima-Waleed and @ritikakundra for pushing this through ! Really appreciate the help.

[Rima-Waleed]

Hi @jaybee84, thank you for your patience and collaboration! We have the public link ready and you can access the study using this link: https://www.cbioportal.org/study/summary?id=nst_jhusm_2020

I had to make some edits to make sure the study complies with cBioPortal formats, so please let me know if you have any questions.

Also, this is an easy fix but I just wanted to make sure which paper you want linked to the study: just the preprint, or the original study, or both?

[jaybee84]

@Rima-Waleed Thanks for making this ready so quickly. Couple of thoughts:

We have the public link ready and you can access the study using this link: https://www.cbioportal.org/study/summary?id=nst_jhusm_2020

Is it possible to update the original study link: https://www.cbioportal.org/study/summary?id=nst_nfosi_ntap instead of making a new one? This is an ongoing project with additional samples from the same biobank. Also, can we add the description that has been included in the Readme of this PR?

this is an easy fix but I just wanted to make sure which paper you want linked to the study: just the preprint, or the original study, or both?

We should include both.

[Rima-Waleed]

@jaybee84 thanks for the feedback.

Of course! This link was a test link just to get your approval before updating the original study link. I have added the original description along with the preprint and citation in the description. The study should be imported to public portal after midnight and you'll be able to see the updated study here: https://www.cbioportal.org/study/summary?id=nst_nfosi_ntap

[jaybee84]

Thanks @Rima-Waleed. The updated study looks great. Thanks again for all the help!

[jaybee84]

Oh! actually one more request:
Could we make the title of the study "Nerve Sheath Tumors (Johns Hopkins NF1 Biospecimen Repository, 2024)" instead of "Nerve Sheath Tumors (Johns Hopkins, Sci Data 2020)". The data currently exceeds the samples described in Sci Data 2020 paper.