Open tmazor opened 3 years ago
Working with Tom on this
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.
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.
This issue is still relevant today. See https://bit.ly/4cMqKg5 and
There are mutations found in TERT even though the samples were not identified as being profiled for mutations for TERT. The same happens for NFIB when looking at the structural variant. It would be important to have a check for this event occurring when loading the data. Additional a decision should be made if then TERT should be added to a panel yes or no. It could be that TERT is not on the gene panel at all, or, since it’s TERT, it’s possible that the TERT promoter is covered but not the rest of the gene etc. Additionally, when having multiple panels the oncoprint also can give wrong assumptions, because the “profiled in mutations” takes a cumulative of genes. For example when I select only TERT you will see 1 sample profiled for mutations whereas if I add KMT2C more samples are profiled for mutations since KMT2C is profiled on other panels. The user most then remembers TERT was only profiled in one sample. It would be more user friendly if this track can be shown also per panel and as such make this more clear to the user. Below some suggestions to these issues:
User reported: https://groups.google.com/u/1/g/cbioportal/c/T-QlXI66WRU
Querying for TERT:DRIVER in GENIE can result in an alteration frequency >100% (see Desmoplastic Melanoma here: https://genie.cbioportal.org/results/cancerTypesSummary?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=5fa03921e4b0242bd5d29486%2C5fa036d9e4b015b63e9c7076&case_set_id=all&data_priority=0&gene_list=TERT%253A%2520DRIVER&geneset_list=%20&profileFilter=0&tab_index=tab_visualize)
The reason is that TERT mutations are called in samples where TERT is not profiled:![image](https://user-images.githubusercontent.com/10508276/97896942-c6a8f100-1d03-11eb-8fb1-f407fe45a960.png)
Can we figure out if the gene panel is wrong? Or is this is another example of calling real but off-target mutations?