Treatment Type

[Joseph Celidonio]

Hello Tali,

I hope all has been well with you.  I am looking to determine the type of treatment each patient had in 3 head & neck cancer studies (screenshot attached).  I don't see an option for treatment type in the clinical data tab - is there a way to determine what type of treatment each patient received in these studies (e.g. chemoradiation therapy alone vs. surgery with postoperative chemoradiation?)

Thank you for your help.

Sincerely,

Joe Celidonio 

[Priti Kumari]

Hi Joe,

I believe the screenshot did not come through. Can you attach them again?

Also currently, we only have limited functionality to visualize longitudinal data in the study view (Treatment name per patient/sample). You can visualize the treatment data in the patient view. If you want summary counts, you can download the data.

Hope this helps,

Priti

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[Joseph Celidonio]

Good morning Priti,

Thank you for your reply.  Can you explain where I can find treatment data in the patient view from the following link?  https://www.cbioportal.org/study/summary?id=hnsc_broad%2Chnsc_jhu%2Chnsc_tcga

In the link above I've selected the studies and filters that I would like to use.  I am interested in seeing which treatments were pursued in all 117 patients in this cohort with the goal of exporting this data into an excel sheet for statistical analysis.  Please advise on how it would be best to collect the treatment data for this cohort.

Thank you for your time.

Sincerely,

Joe Celidonio

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From: Priti Kumari <prit...@gmail.com>
Sent: Wednesday, February 12, 2025 5:31 PM
To: Joseph Celidonio <jc2...@njms.rutgers.edu>
Cc: Tali Mazor <tma...@ds.dfci.harvard.edu>; cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] Treatment Type

 

[Priti Kumari]

Hi Joe,

I dont think these studies have any treatment data. I would recommend you look at the publications associated with these studies to see if you can find additional info.

Best,

Priti

[Joseph Celidonio]

Hi Priti,

Thank you for your response.  If a study did have treatment data, would I be able to see this under the clinical data tab?  If there are other places to check for this data please let me know.  I would be open to using other studies instead if they contained treatment data. 

Sincerely,

Joe Celidonio

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From: Priti Kumari <prit...@gmail.com>
Sent: Thursday, February 13, 2025 4:56:27 PM

[Joseph Celidonio]

Good morning,

I just wanted to follow up on my previous inquiry.  Can you please confirm that none of the above studies have treatment data available?  I did my own search and there does not seem to be treatment data in any of the studies.  I'm reaching out to confirm that I am correct, because if this is the case then I will be calling off a planned research project.  Please let me know if any of these studies have treatment data available in cBioPortal.

Thank you for all of your help.

Sincerely,

Joe Celidonio

---

From: Joseph Celidonio <jc2...@njms.rutgers.edu>
Sent: Thursday, February 13, 2025 5:30 PM
To: Priti Kumari <prit...@gmail.com>

[Priti Kumari]

Hi Joseph,

If the study has treatment data, it would show up in the study view as timeline events availability table. You may have to click on add Charts to pull this table. Here is an example: https://www.cbioportal.org/study/summary?id=msk_chord_2024
You will also see tables for Treatment per patient and sample. Also attached screenshot

Hope this helps.

Best,

Priti

[Priti Kumari]

Hi Joe,

It looks like there is a clinical field called "ICD10 classification" and based on a quick google search it seems code C32.9 codes for Malignant neoplasm: Larynx, unspecified.

I would recommend you go through each clinical data type in a study for your research. Alternatively, try looking at the publication for further details.

Hope this helps,

Priti

On Mon, Feb 17, 2025 at 3:24 PM Joseph Celidonio <jc2...@njms.rutgers.edu> wrote:

Hi Priti,

Thank you for that information.  I was able to find this study which seems to have treatment data available: https://www.cbioportal.org/study/summary?id=hnsc_tcga_pan_can_atlas_2018

cBioPortal for Cancer Genomics mRNA expression z-scores relative to all samples (log RNA Seq V2 RSEM) www.cbioportal.org

Do you know if there is a way to determine which patients have cancer of the larynx?  It seems that the only primary tumor site listed is "head and neck," but I need to be more specific than this for my research purposes.  Please let me know if there is a way to identify which patients had laryngeal cancer.

Sincerely,

Joe Celidonio

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From: Priti Kumari <prit...@gmail.com>
Sent: Monday, February 17, 2025 11:43 AM
To: Joseph Celidonio <jc2...@njms.rutgers.edu>

Subject: Re: [cbioportal] Treatment Type

Hi Joseph,

If the study has treatment data, it would show up in the study view as timeline events availability table. You may have to click on add Charts to pull this table. Here is an example: https://www.cbioportal.org/study/summary?id=msk_chord_2024
You will also see tables for Treatment per patient and sample. Also attached screenshot

Hope this helps.

Best,

Priti