7316-356 has multiple extent of tumor resection

[jharenza]

What data file(s) does this issue pertain to?

histologies.tsv

What release are you using?

v11 OPC, v22 OpenPBTA

Put your question or report your issue here.

7316-356 went from having Partial resection in v21 OpenPBTA to Partial resection;Gross/Near total resection in v22. It looks like this is stemming from a concatenation of Diagnosis + 3 month update records, the latter of which @youngnm tells me should be removed from the data warehouse and CBTN all.

cc @youngnm @nicholasvk

[jharenza]

This was manually updated in the V11 histologies-base.tsv file with d3b-center/OpenPedCan-analysis#188, but can we confirm this was updated in the data warehouse/CBTN all shiny app @youngnm @nicholasvk ?

[jharenza]

@youngnm can you check this one as well?

[youngnm]

In the short term, is it possible for you to filter out the 3 month update records on your end? I'll raise this as a discussion item with the larger team because it's a major change to CBTN-All. Not sure what the timeline looks like yet.

[jharenza]

I realized I never responded @youngnm - I have already taken care of this manually!

[jharenza]

@nicholasvk - can you update this sample in the D3b warehouse?

[jharenza]

Develop a coding rule to prioritize one over the other (i.e. - use the 3 month update value because its the latest or some other rule)

Some of these are tricky and have to be done on a sample to sample basis. I had confirmed all of these with Jenn before any updates and for this sample, the coding logic here should be: For 7316-356 --> Partial resection. We do not want to use a 3 month update for tumor resection because the genomic data is for the initial visit, and at that visit, there was only partial resection. Can we add this upstream on your end if we are going to maintain 3 month updates?