Query regarding change in frequency of FLCN variants

[Sriram Gubbi]

Hello,

This is Dr. Sriram Gubbi from the NIH, USA.

I was recently working on a study evaluating the presence of FLCN gene variants in all thyroid cancers combined and in anaplastic thyroid cancer. I generated oncoprints for these respective cohorts with a gene query for 'FLCN'.

However, I note that the oncoprint has changed when compared to the oncoprint that I had from about 2 months ago, and the total number of mutations has dropped from 45 down to just 1! Seems like several amplifications and deep deletions are now excluded in the revised Oncoprint. I read in your FAQs that the database keeps getting updated with novel information being available. Could you kindly suggest what have have happened to these remaining mutations of FLCN? Were they reclassified as benign variants? And where can I find the modification files on cBioPortal? I would truly appreciate your input. Thank you.

Sincerely,

Sriram

[Tali Mazor]

Hi Sriram,

Can you please share a link to the specific query you ran so we can better investigate what may have changed? If you have a download/screenshot/any other documentation of how the oncoprint looked previously, that would also be helpful for us to see.

-Tali

PS Please keep the google group cc'ed in your reply.

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[Sriram Gubbi]

Hello Tali,

Sure, here is the link for what I queried on cBioPortal website: https://www.cbioportal.org/results/oncoprint?cancer_study_list=thyroid_gatci_2024%2Cthpa_tcga_gdc%2Cthca_tcga_pub%2Cthyroid_mskcc_2016%2Cthca_tcga%2Cthca_tcga_pan_can_atlas_2018&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Cgistic%2Ccna&case_set_id=all&gene_list=FLCN&geneset_list=%20&tab_index=tab_visualize&Action=Submit 

And I have attached a figure of how the oncoprint used to look about 2 - 3 months ago.

Thank you. Please let me know if you have any further questions.

Sincerely,

Sriram

[Tali Mazor]

Hi Sriram,

Thanks for the additional information. I've raised your questions with our data curation team and they'll be in touch soon.

-Tali

[Curation Team]

Hi Sriram, 

Thank you for reaching out with your question regarding the changes in the FLCN oncoprint.After reviewing the data, we identified that one of the thyroid cancer studies had an import error in the CNA (copy number alteration) file, which affected how amplifications and deep deletions were interpreted in the portal. This issue has since been corrected, and we were able to regenerate the oncoprint you had observed from two months ago.

Please let us know if you have any further questions. 

Best,

Rima