Hello GLASS investigators,
Thanks again for your help.
In my study, I want to compare Platinum paired samples that are TMZ +/- radiation naive to those that have received TMZ+/- radiation.
To do this, I navigate to the clinical_surgeries table. In a prior thread, @kcjohnson informed me that these samples are "forward looking", meaning that the TmzTreatment column means this occurred **__after** the surgery and sample collection. As as example, suppose we look at patient GLSS-MD-0026:
```
SampleBarcode CaseSource Sex AgeAtDx VitalStatus TmzTreatment TmzCyclesReceived TmzConcurrence RadiotherapyReceived RadiotherapyDoseGy DoseFractionGy RadiationTreatmentDetails
GLSS-MD-0026-R1 male 77 dead 1 7 0 0 0 0 NA
GLSS-MD-0026-TP male 77 dead 1 11 1 1 60 30 IMRT
```
That would mean this patient got TMZ and radiation **AFTER **the TP sample was extracted. Then, this patient got 7 cycles of TMZ **AFTER** the R1 sample was collected. This means that this table includes no information on whether the TP samples received TMZ / radiation before the first resection, correct?
The problem is, for my study, I only want to compare samples that are TMZ/radiation naive to those that are treated. So, I want to ask, can we safely assume all TP samples **__did not receive TMZ with or without radiation BEFORE the first surgery?** Or, if not, is this data stored somewhere?
Thanks so much for all your help.
Created by Vincent Laufer LauferVA Perfect - thank you @kcjohnson - I really appreciate all your help.
VAL Hi Vincent,
Yes, that's correct that the clinical.surgeries table is forward looking.
You are also correct that there would be no specific field for whether the TP sample (a single row) received TMZ/radiation before the first resection. I am not a clinician so I cannot comment on how common such treatment for a primary brain tumor would be without a biopsy to confirm pathology. However, if there was a biopsy prior to partial/complete surgical resection, we do record this information. In this instance, I would look at whether the surgery_number = 1 and if it does not then I would incorporate that case-level information to define whether a sample did or did not receive pre-treatment.
Hope this helps,
Kevin
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Are all "TP" samples in the Platinum Pairs dataset TMZ and radiation *always* naive? page is loading…