Hi All,
I am working on correlating clinical information with mutation data. I have downloaded clinical data related to Prostate Adenocarcinoma (PRAD) from TCGA firehose. But, survival times seem to be different from that of cBioPortal. For example, for TCGA-G9-6336, days_to_last_followup in TCGA is 1669, which comes to 54.87 months. But in cBioPortal, Overall Survival Time is given as 67.9 months. Any ideas which one is correct?
Thanks
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written
by
sandhya.p •
2 answers
I think, now I understand the scenario. I was taking days_to_last_followup from "PRAD.merged_only_clinical_clin_format.txt" file located in "gdac.broadinstitute.org_PRAD.Merge_Clinical.Level_1.2014101700.0.0.tar.gz". But, when I looked into "PRAD.clin.merged.picked.txt" file present in "gdac.broadinstitute.org_PRAD.Clinical_Pick_Tier1.Level_4.2014101700.0.0.tar.gz", it is same as that of given in cBioPortal. I do not know why the information given in these two files are different.
May be the survival time given by the cBioPortal is the nearest follow-up. Here(https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/) is the link of updated clinical information for all types of tumors. The follow up data is updated with the time.Anyway, you can count on the latest follow-up.
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I'm not sure those numbers disagree. The overall survival time should refer to either the survival time since admittance to the study or since first diagnosis. The "day_to_last_followup" should just be the time since the last follow-up appointment with the study. I would expect that there will be cases where the two values are equal, but there's no reason to expect them to be.
That's my quick reading of things at least.