Question: How to do Disease-Free survival analysis with TCGA data ??
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gravatar for miky.zo
11 weeks ago by
miky.zo20
Italy / Busto Arsizio / University of Insubria
miky.zo20 wrote:

Hi everybody! I am trying to do survival analysis with TCGA-PRAD data. I learned how to do overall survival, KM plots and cox regression following this tutorial: https://bioconnector.github.io/workshops/r-survival.html , in which you learn how to use R packages "survival", "survminer" and TCGA data using the package "RTCGA".

My aim now is to do disease-free survival, but looking at the clinical data that i can download with RTCGA, I can't understand which columns I have to use, I can't see a clear indication of dfs. Also, checking here on biostars it seems that there are no other questions related specifically to it.

Can someone please help me to find a way to do this? Some example code will be really appreciated! Thank you a lot!!

ADD COMMENTlink modified 11 weeks ago by MatthewP660 • written 11 weeks ago by miky.zo20

Hi @miky.zo ! Have you solved your problem?I now met the same question with you.I downloaded BLCA clinical data via TCGA-Assembler but I don't know how to get DFS(disease-free survival). I only know the OS(overall survival) is merge days_to_last_followup and days_to_death but have no idea about anything like progress/recurrent. Besides, after I read @MatthewP 's reply I am confused why the DFS in TCGA and cbioportor are different?

ADD REPLYlink written 9 weeks ago by weiqiao10290
0
gravatar for MatthewP
11 weeks ago by
MatthewP660
China
MatthewP660 wrote:

Hello, I don't know RTCGA.
The events of DFS is progress/recurrent so you need to find which column contains this information. I personally suggest you download clinical data from cBioportal, and you will get 2 columns Disease Free (Months) and Disease Free Status.
BTY, I did DFS for TCGA-PRAD before and it seems too little event cases. You can try.

ADD COMMENTlink written 11 weeks ago by MatthewP660

Hi, thank you for your answer! The problem is that in PRAD, there are very few death events (like 10 in 500 cases) so I don't think that doing overall survival will give good results with this dataset, so I thought that DFS might be better.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by miky.zo20
1

DFS also too few events in TCGA-PRAD. PFS(Progress Free Survival) has many more events in clinical data from cBioportal.

ADD REPLYlink written 11 weeks ago by MatthewP660

Ok, I'll try pfs, thank you!

ADD REPLYlink written 11 weeks ago by miky.zo20

why the DFS is different in TCGA and cbioportal?

ADD REPLYlink written 9 weeks ago by weiqiao10290
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