Olink proteomics data and multiplex immunofluorescence data

[Zhang,Jiexin]

Dear Sir/Madam,

 

This is Jiexin from MD Anderson Cancer Center. We are working on (1) multiplex immunofluorescence, and (2) Olink proteomics data. We would like to use cBioPortal for visualization. However, in the file formats instruction, I couldn’t find these two types of data. Can cBioPortal be used to analyze these two types of data? If so, would you please let me know file format needed so I can proceed?

 

Thanks a lot for your help,

Jiexin

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[Benjamin Gross]

Hi Jiexin,

I’m not familiar with the data types your are referring too, but if you can reduce the data to a measurement per sample & entity type pairing (where entity can be a probe or protein, etc) you can use our Generic Assay format:

https://docs.cbioportal.org/file-formats/#generic-assay

I hope this helps.  Let us know if you have any follow up questions

-Benjamin

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[de Bruijn, Ino]

Hi Jiexin,

 

Thanks for reaching out!

 

There are some options to visualize this type of data. E.g. for mpIF we have integrations with Minerva (click on the camera icon in the timeline):

 

https://www.cbioportal.org/patient?studyId=brca_hta9_htan_2022&caseId=HTA9_1#navCaseIds=brca_hta9_htan_2022:HTA9_1

 

and

 

https://www.cbioportal.org/patient/openResource_HE?studyId=msk_spectrum_tme_2022&caseId=P-0042164

 

You can also import cell type calls for each sample as we did for some of the MSK-SPECTRUM study (this uses  the generic assay format Ben mentioned):

 

https://bit.ly/3KfFEAp

 

You can look at the data files for that study on datahub for an idea of how this works:

 

https://github.com/cBioPortal/datahub/tree/master/public/msk_spectrum_tme_2022

 

We leveraged Adam Taylor’s htan-artist nextflow pipeline to set up the Minerva viewers for the mpIF images:

 

https://github.com/adamjtaylor/htan-artist/

 

I’m not super familiar with Olink proteomics data , but you can look at some of the CPTAC studies to get an idea of how to incorporate protein quantification:

 

https://github.com/cBioPortal/datahub/tree/master/public/gbm_cptac_2021

 

There is a paper describing this here:

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731080/

 

Happy to chat more via a zoom call as well, you can email me directly

 

Best wishes,

Ino

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[Zhang,Jiexin]

Dear Ino and Ben,

 

Thank you so much for all your quick reply and valuable information. These are very helpful. Glad to know that cBioPortal can handle so many different data types. I will definitely look into that.

 

Best,

Jiexin

 

From: de Bruijn, Ino <debr...@mskcc.org>
Sent: Friday, March 24, 2023 11:46 AM
To: Benjamin Gross <benjami...@gmail.com>; Zhang,Jiexin <Jiexi...@mdanderson.org>
Cc: cbiop...@googlegroups.com
Subject: [EXTERNAL] Re: [cbioportal] Olink proteomics data and multiplex immunofluorescence data

 

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