TCGA-PCPG Cohort

[Alkaissi, Hussam (NIH/NIDDK) [E]]

Dear all at cBioPortal,

I would like to first extend my gratitude for the immense amount of effort put in by the cBioPortal team to consolidate cancer multi-omics in one platform that is easily accessible to cancer biologists!

My main research is pheochromocytoma and paraganglioma (PCPG), and I wanted to kindly ask, if possible, to add germline annotation, as the current PCPG version in cBioPortal shows only somatic mutations, and further analysis by germline groups (e.g., germline SDHB vs germline VHL) is not available.

The original TCGA paper (Fishbein et al., Cell 2017) contains the annotation as a supplementary table (attached is a condensed version of it).

I look forward to your response, and again, thank you for your service to cancer research and biology!

Sincerely,

Hussam Alkaissi, MD MS

Endocrinology Clinical Fellow (NIH/NIDDK)

10 Center Dr, Bethesda, MD 20892

Email: hussam....@nih.gov

Phone: 929-989-5797

 

 

[Nikolaus Schultz]

Dear Hussam,

Thank you for reaching out with this excellent suggestion. I have cc’d Ritika who leads our data curation team. Ritika, can you please get this data added? 

Thanks.

Niki.

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[Alkaissi, Hussam (NIH/NIDDK) [E]]

Thank you very much for the response Niki, and nice to e-meet you Ritika, let me know if you like the data in any specific form to further help with the database. Thanks again for the great work you do for cancer research!

Best regards

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[Kundra, Ritika]

Thanks Niki.

 

Hi Hussam and nice to connect with you.

 

Thanks for sending over this recommendation. Yes, please send us the data* and we can take it from there.

 

Data*:
Hugo_Symbol

NCBI_Build

Chromosome

Start_Position

End_Position

Reference_Allele

Tumor_Seq_Allele

t_alt_count

t_ref_count

 

Thanks,

Ritika

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[Alkaissi, Hussam (NIH/NIDDK) [E]]

Hi Ritika

Unfortunately the TCGA-PCPG paper has only protein change for the germline variants. Would that disqualify such update to the database?

Best

[Nikolaus Schultz]

We could introduce the information as a clinical attribute - would that help? If we wanted to add the data as genomic data, we would have to infer the genomic change to be compatible with cBioPortal (it can be done, but won’t be perfect).

Niki.

[Alkaissi, Hussam (NIH/NIDDK) [E]]

Hi Niki,

I thought of that as well, and already made this list of available info. Let me know what you think.

[Alkaissi, Hussam (NIH/NIDDK) [E]]

Dear Niki and cBioPortal team,

I wanted to kindly follow up if you have made any progress in updating the TCGA-PCPG annotations to include germline variant. cBioPortal oncoplot is the best, but unfortunately it is unusable in its current version without germline annotation for PCPG, thus would greatly appreciate your attention to this matter. Any expected timeline to implement those changes?

Sincerely,

Hussam Alkaissi, MD MS

Endocrinology Clinical Fellow (NIH/NIDDK)

10 Center Dr, Bethesda, MD 20892

Email: hussam....@nih.gov

Phone: 929-989-5797

 

 

[Kundra, Ritika]

Hi Hussam,

 

We are currently working on this. Expected timeline is end of next week/first week of Feb.

[Alkaissi, Hussam (NIH/NIDDK) [E]]

Perfect, I look forward to it!

[Alkaissi, Hussam (NIH/NIDDK) [E]]

Dear Niki and cBioPortal team,

I wanted to kindly follow up if you have made any progress in updating the TCGA-PCPG annotations to include germline variant. I’d greatly appreciate your updates, and input

Thank you and my best regards

Hussam Alkaissi, MD MS

Endocrinology Clinical Fellow (NIH/NIDDK)

10 Center Dr, Bethesda, MD 20892

Email: hussam....@nih.gov

Phone: 929-989-5797

 

 

[Anu Vijay]

Dear Hussam,

Thank you very much for your patience, and we sincerely apologize for the delay in getting back to you.

We have now incorporated the germline information for the TCGA-PCPG cohort as clinical attributes in the portal. We appreciate you bringing this to our attention and for sharing the supporting data — it was very helpful in enabling the update.

Best regards,
Anusha

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[Alkaissi, Hussam (NIH/NIDDK) [E]]

Thank you very much! But I wanted to ask regarding how to sort the cases by those mutations, since I still don’t see the change on the oncoplot window..any suggestions?

[Anu Vijay]

The germline variant data has already been captured and added as a clinical attribute in the Summary page, as shown in your screenshot (e.g., RET Germline Mutation, NF1 Germline Mutation with their respective variant breakdowns).

If it’s not immediately visible there, please go to the Charts tab and add the corresponding clinical attributes (e.g., RET Germline Mutation, NF1 Germline Mutation) to your view. Once selected, they should visible.