add TERT promoter mutations to TCGA studies

[tmazor]

Some TCGA studies have called TERT promoter mutation but we don't have that data in cBioPortal. This is likely because the mutations may not come from the standard exome sequencing pipeline but from an independent sequencing assay specifically targeted at the TERT promoter.

We need to identify which studies have TERT mutation data and add that data to cBioPortal.

Below is an incomplete list of studies with TERT promoter mutation data:

• [ ] LGG/GBM https://www.ncbi.nlm.nih.gov/pubmed/26824661
• [ ] LGG https://www.ncbi.nlm.nih.gov/pubmed/26061751
• [ ] Cutaneous Melanoma https://www.ncbi.nlm.nih.gov/pubmed/26091043
• [ ] Hepatocellular Carcinoma https://www.ncbi.nlm.nih.gov/pubmed/28622513

[tmazor]

A user has requested the Cutaneous Melanoma data specifically: https://groups.google.com/forum/#!topic/cbioportal/jdRjXLsnlzk

[tmazor]

@jjgao @ritikakundra @yichaoS any update on when this data will be made available? I just received another user request about this data, specifically for LGG and GBM.

[kojix2]

Hello.

I use cBioPortal every day. The service is really great.

https://www.ncbi.nlm.nih.gov/pubmed/28622513

TERT promoter mutations were the most common somatic mutation, found in 87 of 196 (44%) HCCs analyzed in the TERT promoter region (Figure S1A, Table S3).

I would like to access the most frequent mutations in liver cancer through the cBioPortal.

Thanks!

[laveniyas]

CBioPortal is an excellent resource, thank you. Just wondering, has TERT promoter status been added to cBioPortal, especially for GBM?

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[tmazor]

we should still do this

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[ritikakundra]

@sbabyanusha @rmadupuri need to prioritize this cared

[rmadupuri]

@tmazor we looked into the TCGA publications for TERT promoter mutations. Only two studies had data readily available. Few studies have sequenced for TERTp but the data is not available. Will reach out to the authors. Below is the current status

Study	TERTp Sequencing Status
blca_tcga_pub	No
blca_tcga_pub_2017	No
brca_tcga_pub	No
brca_tcga_pub2015	No
coadread_tcga_pub	No
gbm_tcga_pub	No
gbm_tcga_pub2013	Yes https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910500/. (From Fig 4C. 25 samples analysed for TERTp. 21 C228T, 6 C250T, 4 WT - but no data available)
hnsc_tcga_pub	No
kich_tcga_pub	No
kirc_tcga_pub	No
laml_tcga_pub	No
lgggbm_tcga_pub	Yes but data not available
lusc_tcga_pub	No
luad_tcga_pub	No
ov_tcga_pub	No
pcpg_tcga_pub	No
prad_tcga_pub	19 samples were high pass whole genome sequenced for TERTp. No TERTp variants found. No info on which 19 samples were sequenced.
sarc_tcga_pub	TERTp validation was done. But no data available. Portal has 1 TERTp variant for the study. Looks like the data was already included in the MAF.
skcm_tcga_pub_2015	Yes. Data added to portal
stad_tcga_pub	No
stes_tcga_pub	No
thca_tcga_pub	Yes. Data added to portal
ucec_tcga_pub	No
Hepatocellular Carcinoma	Yes. Has TERTp data. Study not curated to portal yet. https://pubmed.ncbi.nlm.nih.gov/28622513/

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Issue: The number of samples profiles for WES and TERT promoters is different (344 and 115 in this case). Adding TERT promoter variants to the WES MAF shows wrong percentages on the Oncoprint.

Should be 74/115.

Since we do not support this yet, the TERTp variant data is captured in clinical.

[santiago-es]

Hi, thanks for adding this data to CBIO portal. I noticed some of the studies above had classified TERTp but had not posted the data in portal. I had spent some time tthree years ago annotating the patient IDs per study by hand for papers that had published this info, attached. Just in case it's useful, may be redundant.

TCGA TERTp Patient IDs.xlsx