Questions about TCGA Pancreatic Adenocarcinoma Clinical Records

[EOIN O'HARE]

Good morning,

I am a student at Rutgers University working on a project under the Rutgers Cancer Institute of New Jersey. For our project, we are using the clinical data of the combined study on Pancreatic Adenocarcinoma, which was combined from (TCGA, Firehose Legacy) and (TCGA, PanCancer Atlas). I had two questions about the clinical data. What is the naming convention of the patient id? Does it describe the institution or where the data was taken? For example, the 2J in TCGA-2J-AAB1-01. Also, is there a method of checking when each sample was taken? Thank you so much for your help!

Thank you so much,

Eoin O'Hare

Junior. B.S. Computer Engineering

Rutgers University Honors College

[Tali Mazor]

Hi Eoin,

The TCGA naming convention is described here: https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/

Within cBioPortal we also provide a clinical attirbute ('Tissue Source Site') which lists the site at which the sample was acquired.

In terms of when a sample was taken, it depends what you mean. As far as I know, the date of sample acquisition is not available. However, if your question relates to when a sample was taken relative to the patient disease course, that information is available for some patients, eg: https://www.cbioportal.org/patient?studyId=paad_tcga_pan_can_atlas_2018&caseId=TCGA-2J-AAB1  TCGA was primarily interested in analyzing pre-treatment tumors, so in general the samples are not post-treatment.

Finally, I advise against analyzing two different versions of the TCGA data together. This is because the Firehose Legacy and PanCancer Atlas studies contain many of the same patients/samples, which can bias your results. I suggest using just the PanCancer Atlas study, as it reflects a more recent re-analysis of all the data.

-Tali

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[EOIN O'HARE]

Good evening,

Thank you so much for the help! Hope you have a nice weekend!

Thanks again,

Eoin O'Hare

Junior. B.S. Computer Engineering

Rutgers University Honors College