Structural variant testing

[alisman]

Make a bookmarklet to open the same query on beta portal:

javascript:(function()%7Bwindow.open(window.location.href.replace(window.location.hostname%2C window.location.hostname.includes("sv") %3F "www.cbioportal.org" %3A "beta.cbioportal.org" ))%7D)()%3B

[tmazor]

• [x] 1) I think it'd be clearer & more consistent with other profiles to call the profile 'Structural Variants' rather than 'SV Data' https://beta.cbioportal.org/study/summary?id=lgg_tcga_pan_can_atlas_2018 NOTE: @averyniceday will handle this (6/7)

• [x] 2) SEPTIN14 is in 6 samples in prod, but none in beta: FIXED https://www.cbioportal.org/study/summary?id=lgg_tcga_pan_can_atlas_2018 https://beta.cbioportal.org/study/summary?id=lgg_tcga_pan_can_atlas_2018

• [x] 3) Probably related to the above, but EGFR fusions are showing up intragenic rather than with SEPT14 (FIXED) https://www.cbioportal.org/results/mutations?cancer_study_list=lgg_tcga_pan_can_atlas_2018&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cfusion%2Cgistic&case_set_id=lgg_tcga_pan_can_atlas_2018_cnaseq&gene_list=EGFR&geneset_list=%20&tab_index=tab_visualize&Action=Submit

https://beta.cbioportal.org/results/mutations?cancer_study_list=lgg_tcga_pan_can_atlas_2018&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Cgistic&case_set_id=lgg_tcga_pan_can_atlas_2018_cnaseq&gene_list=EGFR&geneset_list=%20&tab_index=tab_visualize&Action=Submit

• [x] 4) SV counts are different for EGFR FGFR3 TACC3 & SEPTIN14 (FIXED) https://www.cbioportal.org/study/summary?id=glioma_mskcc_2019 https://beta.cbioportal.org/study/summary?id=glioma_mskcc_2019

• [x] 5) FIXED There's a difference in driver annotations for PML & MYH11, but I think beta is actually doing it better than prod. However, the specifics of the events seem to be gone in the updated data: https://www.cbioportal.org/results?cancer_study_list=laml_tcga_pub&tab_index=tab_visualize&case_set_id=laml_tcga_pub_all&Action=Submit&gene_list=RARA%250APML%250AKMT2A%250AMYH11%250ACBFB%250ARUNX1 Whereas this is the same tooltip in beta https://beta.cbioportal.org/results?cancer_study_list=laml_tcga_pub&tab_index=tab_visualize&case_set_id=laml_tcga_pub_all&Action=Submit&gene_list=RARA%250APML%250AKMT2A%250AMYH11%250ACBFB%250ARUNX1

Link for 6-9: https://beta.cbioportal.org/results/plots?cancer_study_list=laml_tcga_pub&tab_index=tab_visualize&case_set_id=laml_tcga_pub_all&Action=Submit&gene_list=RARA%250APML%250AKMT2A%250AMYH11%250ACBFB%250ARUNX1&plots_horz_selection=%7B%22dataType%22%3A%22STRUCTURAL_VARIANT%22%7D&plots_vert_selection=%7B%7D&plots_coloring_selection=%7B%22colorBySv%22%3A%22true%22%7D

@ritikakundra I think if we fix the variantClass='NA' issue other items may be fixed

• [ ] 6) (ISSUE MADE) samples with SV are labeled 'NA' on the x-axis

• [ ] 7) (ISSUE MADE) Annotation column is blank, but these fusions are clearly drivers according to both oncoprint (previous screenshots) and the filters to the right of the lollipop plot: . SEEMS DUE TO FACT THAT WHEN WE SEND geneA and geneB, we get "unknown" result. We were formerly sending the wrong request for oncoprint (old style where we only send one gene). When we corrected this, descrepancy with oncoprint is gone. But SVs are now unkown driver status in BOTH places.

• [x] 8) SV file on download tab doesn't have any SV, eg this sample which appears in the oncoprint screenshot with a PML-RARA fusion: STUDY_ID SAMPLE_ID RARA PML KMT2A MYH11 CBFB RUNX1 laml_tcga_pub TCGA-AB-2897-03 NA NA NA NA NA NA

• [x] 9) Last table on the download tab is also missing all SV calls, eg:

• [x] 10. (FIXED) SV counts are different for TMPRSS2, ERG, KMT2C: https://www.cbioportal.org/study/summary?id=prad_cdk12_mskcc_2020 https://beta.cbioportal.org/study/summary?id=prad_cdk12_mskcc_2020

• [x] (11) I'm guessing chromosome/start pos refer to the breakpoint for the currently selected gene (ERG in this case)? I think this isn't as clear as it could be for SV (and of course it might be nice to also show the partner gene breakpoints). But maybe this is ok for now if the plan is still for an SV-specific table at some point? https://beta.cbioportal.org/results/mutations?cancer_study_list=prad_cdk12_mskcc_2020&tab_index=tab_visualize&case_set_id=prad_cdk12_mskcc_2020_all&Action=Submit&gene_list=ERG&comparison_subtab=alterations&comparison_selectedEnrichmentEventTypes=%5B%22structural_variant%22%5D @tmazor we decided we were going to punt on this for the time being

• [x] 12) Some calls in the above screenshot are missing Variant Type and Chromosome/Pos. ANUSHA: WE DON'T HAVE DATA

• [x] 13) Sample has 4 SV in prod, but 0 in beta https://www.cbioportal.org/patient?studyId=coadread_tcga_pan_can_atlas_2018&caseId=TCGA-F5-6864 https://beta.cbioportal.org/patient?studyId=coadread_tcga_pan_can_atlas_2018&caseId=TCGA-F5-6864

[tmazor]

did some more testing, continuing from my above comment

Link for 6-9: https://beta.cbioportal.org/results/plots?cancer_study_list=laml_tcga_pub&tab_index=tab_visualize&case_set_id=laml_tcga_pub_all&Action=Submit&gene_list=RARA%250APML%250AKMT2A%250AMYH11%250ACBFB%250ARUNX1&plots_horz_selection=%7B%22dataType%22%3A%22STRUCTURAL_VARIANT%22%7D&plots_vert_selection=%7B%7D&plots_coloring_selection=%7B%22colorBySv%22%3A%22true%22%7D

@ritikakundra I think if we fix the variantClass='NA' issue other items may be fixed

6. (ISSUE MADE) samples with SV are labeled 'NA' on the x-axis

7. (ISSUE MADE) Annotation column is blank, but these fusions are clearly drivers according to both oncoprint (previous screenshots) and the filters to the right of the lollipop plot:

8. SV file on download tab doesn't have any SV, eg this sample which appears in the oncoprint screenshot with a PML-RARA fusion: STUDY_ID SAMPLE_ID RARA PML KMT2A MYH11 CBFB RUNX1 laml_tcga_pub TCGA-AB-2897-03 NA NA NA NA NA NA

9. Last table on the download tab is also missing all SV calls, eg:

10. (FIXED) SV counts are different for TMPRSS2, ERG, KMT2C: https://www.cbioportal.org/study/summary?id=prad_cdk12_mskcc_2020 https://beta.cbioportal.org/study/summary?id=prad_cdk12_mskcc_2020

[ ] (11) I'm guessing chromosome/start pos refer to the breakpoint for the currently selected gene (ERG in this case)? I think this isn't as clear as it could be for SV (and of course it might be nice to also show the partner gene breakpoints). But maybe this is ok for now if the plan is still for an SV-specific table at some point? https://beta.cbioportal.org/results/mutations?cancer_study_list=prad_cdk12_mskcc_2020&tab_index=tab_visualize&case_set_id=prad_cdk12_mskcc_2020_all&Action=Submit&gene_list=ERG&comparison_subtab=alterations&comparison_selectedEnrichmentEventTypes=%5B%22structural_variant%22%5D @tmazor we decided we were going to punt on this for the time being

• [x] 12. Some calls in the above screenshot are missing Variant Type and Chromosome/Pos SV records from archer panel doesn't provide chromosome/Pos or Variant Type information and that's the reason they are being left empty.

• [x] 13. Sample has 4 SV in prod, but 0 in beta @tmazor : This issue is fixed.

https://www.cbioportal.org/patient?studyId=coadread_tcga_pan_can_atlas_2018&caseId=TCGA-F5-6864 https://beta.cbioportal.org/patient?studyId=coadread_tcga_pan_can_atlas_2018&caseId=TCGA-F5-6864

[sbabyanusha]

Thank you for your feedback. I am addressing the issues and will update you once they are fixed.

[inodb]

this is fully done as confirmed by Anusha