About TCGA Data

[Gort, Michele]

To whom it may concern,

 

I am exporting the TCGA LUAD data from your website through the R program.

 

Upon receiving the forms, I noticed that in the term: “TOBACCO_SMOKING_HISTORY_INDICATOR” has only the values 1, 2, 3, 4; with some missing values.

 

The values specified in the clinical form with a number associated with it.  The associated numeric values for these permissible values are:

• Lifelong Non-smoker (less than 100 cigarettes smoked in Lifetime) = 1
• Current smoker (includes daily smokers and non-daily smokers or occasional smokers) = 2
• Current reformed smoker for > 15 years (greater than 15 years) = 3
• Current reformed smoker for ≤15 years (less than or equal to 15 years) = 4
• Current reformed smoker, duration not specified = 5
• Smoking History not documented = 7

 

I was told by the NCI/NIH to contact you regarding this to see if the data was changed from 1, 2, 3, 4, 5, 7 to sub-categories 1, 2, 3, 4 OR if the only variables in this dataset are truly 1-4 only. 

 

Also should the missing variables be a 7?!!?!?

 

Thanks for your help,

Michele

 

-------------------------------------------------

Michele Gort | Intern

PSM Biostatistics/Bioinformatics Department

333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503

 

[Hsiao-Wei Chen]

Hi Michele,

     The clinical data we use is from the supplementary data (Supplementary Table 7) of this TCGA publication at the link below. In their clinical data, Smoking Status (or we use "TOBACCO_SMOKING_HISTORY_INDICATOR" in cBioPortal) only has values from the first four (1-4) conditions plus [Not Available]. We didn't convert the data into any sub-categories. Please let me know if I didn't answer your question.  

http://www.nature.com/nature/journal/v534/n7605/full/nature17676.html#supplementary-information

Thanks,

Annice

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[ateo...@umich.edu]

Hi I am trying to find exactly what the numbers for this variable mean. Where can I find this or what do these numbers mean?

[Ritika Kundra]

Hi Michele,

You can fine the specifics of the values from the NCI CDE Browser:

https://cdebrowser.nci.nih.gov/CDEBrowser/

On the website under the attribute Patient Smoking History Category -> Value Domain tab you will find the table attached (screen shot)

Thanks,

Ritika

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