Information regarding OS, DFI, DSS and PFI and their time points in TCGA BRCA
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I have a question regarding the determination of endpoints in case of TCGA BRCA dataset.

Can you please let me know what variable (coloumn names) should be used to determine OS (overall survival), disease-specific survival (DSS), disease-free interval (DFI), progression-free interval (PFI), relapse free survival (RFS) and time to recurrence and their respective times lines from the clinical data in case of TCGA BRCA?

For example, I have used this code for determination of OS in TCGA BRCA:

os.days <- as.integer(ifelse(clinical_brca$days_to_last_follow_up == "NA", clinical_brca$days_to_death, clinical_brca\$days_to_last_follow_up))

os.event <- case_when(vital_status == 'Alive' ~ 0, vital_status == 'Dead' ~ 1)

Can anyone please be kind to provide examples of variables (coloumn names) used from clinical data in TCGA BRCA to determine DFI, DFI.time, PFI, PFI.time and DSS, DSS.time, RFS, RFS.time, time to recurrence (lets call it RecT)?

time points can be in years/days ..

It will be helpful if you can provide the info in some R chunk/code - so it will be helpful to understand

Some reference points for endpoint data :

Disease Free Survival, Disease Free Interval Definition: The period from date of diagnosis until date of first recurrence, loco-regional or systemic. (RTOG)

Overall Survival Definition: The period from date of diagnosis until death from any cause. (RTOG)

Progression Free Survival, Progression Free Interval Definition: The period during and after treatment in which a participant is living with a disease that does not get worse. Typically it is the period from date of diagnosis until 1) loco-regional or systemic recurrence, 2) second malignancy, or 3) death from any cause; late deaths not related to cancer or its treatment are excluded. (RTOG)

Relapse Free Survival, Relapse Free Interval Definition: The period from primary disease removal by operative procedure until the detection of recurrent disease. In cancer-related studies, second primary same cancers and other primary cancers are ignored. (Adapted from DJA Punt et. al., 2007)

Time to Recurrence Definition: The period from when a participant is rendered free of evident disease until the detection of recurrent disease. In cancer-related studies, second primary same cancers and other primary cancers are ignored. (Adapted from DJA Punt et. al., 2007)

I think this will be helpful for everyone working on TCGA clinical data analysis and survival analysis and will serve as a good reference point for future users/researchers!!

R TCGA KMPlot BRCA • 1.8k views