Possible errant SV data

[alisman]

We see here that only a tiny fraction of genie data is profiled for SV. This seems like a data issue? Then there's that one SV alteration on a sample which is NOT profiled for SV. Is this just junk data?

https://genie.cbioportal.org/results/oncoprint?cancer_study_list=genie_public&tab_index=tab_visualize&case_set_id=genie_public_all&Action=Submit&gene_list=AAGAB&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=structural_variants&geneset_list=%20

[ritikakundra]

@alisman for this issue, 81% of samples were profiled for SV. The only center with this gene on their profiles did not have any SV detected for this particular gene. However, for the 2 MSK cases that do show the SV, the partner gene, SMAD3 is in the panel, AAGAB is not. Therefore it shows up as not profiled. But if you query for SMAD3, you will see it as profiled:

https://genie.cbioportal.org/results?cancer_study_list=genie_public&tab_index=tab_visualize&case_set_id=-1&case_ids=genie_public%3AGENIE-MSK-P-0035586-T01-IM6%2Bgenie_public%3AGENIE-MSK-P-0042310-T01-IM6&Action=Submit&gene_list=SMAD3