GENIE BPC post release bugs list

[inodb]

https://genie-private.cbioportal.org/study/summary?id=nsclc_genie_bpc

Study view fixes:

• [x] Sample Treatments and Patient Treatments should show up by default - instead they show up with 0.1% data availability in the Charts Menu (added separate issue: https://github.com/cBioPortal/cbioportal/issues/8288)
• [x] The "Distant Mets: xxx" charts seem off: we are missing data for 57.1% of samples
• [x] We could rename two charts:
  • [x] GENIE Sequence Year - rename to "Year of Next Generation Sequencing"
  • [x] ~"Is the patient dead at time of curation" (YES/NO) should be changed to "Patient vital status at time of curation" (ALIVE/DECEASED)~ (seems like this attribute is removed)

Timeline data questions:

• [ ] In GENIE-DFCI-011116, why is there a 1 month delay between sample acquisition and sequencing, but the therapy (use of erlotinib for EGFR L858R, use of osimertinib for EGFR T790M) starts right after sample acquisition and seems to anticipate the sequencing result? Similarly for GENIE-DFCI-011355
• [ ] GENIE-DFCI-015198 has two distinct lung cancers, >5 years apart. Same for GENIE-MSK-P-0002996. In each case, one is the index cancer, the other isn't. We really need to introduce a new level between patient and sample for cancer incidence

Timeline fixes here: https://github.com/cBioPortal/cbioportal/issues/7066

[alisman]

@inodb samples are ordered like so: // sort samples based on event, clinical data and id // 1. based on sample collection data (timeline event) // 2. if all cases have derived normalized case types, put primary first // 3. natural sort of sample ids

I believe this means that if a primary was collected after a metast, it would still be (1)

My thought is that samples should always be ordered sequentially in the TOP track. It would be confusing if they are out of order there. I think this is same as saying, always order by collection date. That seems intuitive to me. The sequencing date seems secondary. If you were surprised to find out that a sample was collected long before it was sequenced, that would be a big deal. But if you found out that it was sequenced long after it was collected, it wouldn't be that big a deal (right?)

[inodb]

@alisman sorry i just moved that bit to the timeline prissmm enhancements epic. But agree order sequentially by top track makes sense. So yes order by collection date first

[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.