Confused vital status

[hdf87ery]

Hi,I just found a result confusing me.

> clin.query <- GDCquery(project = "TCGA-READ", data.category = "Clinical", barcode = "TCGA-F5-6702")
Accessing GDC. This might take a while...
> json  <- tryCatch(GDCdownload(clin.query), 
+                   error = function(e) GDCdownload(clin.query, method = "client"))
Of the 1 files for download 1 already exist.
All samples have been already downloaded
> clinical.patient <- GDCprepare_clinic(clin.query, clinical.info = "patient")
  |========================================================================================================================================================================================================| 100%
To get the following information please change the clinical.info argument
=> new_tumor_events: new_tumor_event 
=> drugs: drug 
=> follow_ups: follow_up 
=> radiations: radiation
Adding stage event information
  |========================================================================================================================================================================================================| 100%
> clinical.patient.followup <- GDCprepare_clinic(clin.query, clinical.info = "follow_up")
  |========================================================================================================================================================================================================| 100%
> clinical.index <- GDCquery_clinic("TCGA-READ")
> clinical.patient[,c("vital_status","days_to_death","days_to_last_followup")]
  vital_status days_to_death days_to_last_followup
1        Alive            NA                    66
> clinical.patient.followup[,c("vital_status","days_to_death","days_to_last_followup")]
  vital_status days_to_death days_to_last_followup
1         Dead           869                    NA
2        Alive            NA                   452
> clinical.index[clinical.index$submitter_id=="TCGA-F5-6702",
+                c("vital_status","days_to_death","days_to_last_follow_up")]
    vital_status days_to_death days_to_last_follow_up
159        alive           869                    452

The vital status should be "dead".

[tiagochst]

Yes, I should be dead in the indexed data. There are some inconsistencies in the indexed data. I will report it to the GDC team.

[tiagochst]

Here is the GDC answer:

Hi Tiago Chedraoui Silva, Sorry for the delay but we had to finish our investigate. You are correct, their is an issue. The logic of how the different follow up events were handled is not correct and we are in the process of fixing now.

[fabio-t]

Sorry for reviving an old issue, but this is concerning. @tiagochst did you get a further update from them? were the inconsistencies fixed?

[tiagochst]

Hello,

sorry for the delay. They told me it was fixed, but I found 9 cases that are still wrong. I just reported them.

[Lucile134]

Hello @tiagochst, Do you know if all these inconsistencies are now fixed ? Thanks

[tiagochst]

I checked last week that specific inconsistency and it was solved. I’ll try to make a script to check all cases just to be sure. But I would guess that the dead and alive seems to be fixed.