TN and TP samples in TCGA

Question

[hAjmal]

Hi, Can someone tell me, if TN samples are normal tissue samples from the 'same' human extracted from a non-tumourous site? or from another healthy human matched by age sex etc?

Answer 1

[TriS]

TN, or NT, indicate normal tissues, in order to check which one is the matched tumor you have to look at the rest of the TCGA barcode. to be more specific, the first 12 chars of the barcode.

there are wikis that you can read on the TCGA Barcode and codes here.

[hAjmal]

So what you mean to say is, that NT can be the normal tissue sample of same patient if the rest of the barcode matches a TP sample. It is a control sample (normal person) if the rest of the barcode is not present in TP samples?

[TriS]

kinda, yes. if an NT matches the first 12 characters of a TP sample then you have matched normal/tumor. I can tell you i.e. for ccRCC, breast and prostate cancer they have no normals, where normal in this case means tissue from a healthy donor. therefore you can say that i.e. if there are 100 tumor samples and 20 normal, then you have 20 matched tumor/normal and 80 non matched

[hAjmal]

Thanks TriS. Excuse me if i am wrong, but there are many breast cancer samples in TCGA data e-g. TCGA-BH-A0BJ-01A-11R-A056-07 and TCGA-BH-A0BJ-11A-23R-A089-07

These have first 12 characters same. Does that not mean they are of same patient? one healthy site (01A) and one from tumorous site (11A)? or these are TWO different people, TCGA-BH-A0BJ-01A is a breast cancer patient and TCGA-BH-A0BJ-11A is another mathced normal person?