Question: question about TCGA survival data
1
gravatar for Johnny R
2.3 years ago by
Johnny R50
Johnny R50 wrote:

Many TCGA samples have three rows in their clinical data that may be of interest for survival analysis: days to death, days to last follow-up, and days to sample procurement. My questions are, in this data, what does day 0 refer to, and what is sample procurement?

For instance, consider SKCM patient "tcga-fs-a1zc". His days to death value is "10870", his days to last follow up value is "NA", and his days to sample procurement value is "10158". If I were plotting his information on a Kaplan Meier plot, would his survival time be 10870, or 712? (10870-10158)

Thanks!!

survival tcga clinical data • 3.2k views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Johnny R50
1
gravatar for naranoth
2.3 years ago by
naranoth20
naranoth20 wrote:

Survival time is 10870 days. As the columns vary between TCGA studies I've found http://www.cbioportal.org to be a better resource as the clinical data is in a more user-friendly format with better column names (and it is pulled directly from the latest Firehose version). Getting the info using their R package 'cgdsr' is really easy or just download it from: http://www.cbioportal.org/study?id=skcm_tcga#summary

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by naranoth20
0
gravatar for Johnny R
2.3 years ago by
Johnny R50
Johnny R50 wrote:

But... survival time since what? The sample hasn't sat in a freezer for 10,870 days. That has to be the survival time for the initial diagnosis. But if I'm doing any sort of biomarker study, it has to be from when the sample was taken... and is that 712?

ADD COMMENTlink written 2.3 years ago by Johnny R50
1

https://www.genome.gov/multimedia/slides/tcga3/25_watson.pdf

Look at slide 22. It seems likely that 712 is the survival time since sample procurement/surgical resection of the metastasis...this is supported by the difference in the disease free and overall survival as well. Tough to be certain though.

ADD REPLYlink written 2.3 years ago by naranoth20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1955 users visited in the last hour