Obtaining clinical data from the TCGA data portal

Question

[elisheva]

Hi all,

I am trying to compare different aspects of cancer genomics in smokers vs. non-smokers among lung cancer patients. For this purpose, I downloaded data from the TCGA data portal (https://portal.gdc.cancer.gov/)

However, it seems that the TCGA samples only provide information for smokers, with no explicit indication if a person is a non-smoker. I dug a little deeper and found a 2016 article where they classified patients as smokers or non-smokers (https://www.science.org/doi/10.1126/science.aag0299?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed]).

However, when I try to search for a specific patient that they defined as a non-smoker, all the information I find is:

In other words, there is no information regarding the smoking status. Is there a way to get this information?

Thank you!

Answer 1

[Zhenyu Zhang]

GDC has a dictionary viewer https://docs.gdc.cancer.gov/Data_Dictionary/viewer/

tobacco_smoking_status has enums like

  - Current Reformed Smoker, Duration Not Specified
  - Current Reformed Smoker for < or = 15 yrs
  - Current Reformed Smoker for > 15 yrs
  - Current Smoker
  - Lifelong Non-Smoker
  - Smoker at Diagnosis

[elisheva]

I know.
However, the data is miising, I somehow found it in the cBioPrtal.