how can I understand the barcode in TCGA
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3.4 years ago
Learner ▴ 250

I am a bit confused about finding control and tumor samples in TCGA.

I have read this https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/ and many other posts but does not help much to know.

Lets have an example

TCGA_41_4097_01A

TCGA means by itself 41 is TSS? if so, then what should I understand from it? 4097 is the participant number , right? 01 is sample ? or portion? A is vial or analyte?

I am trying to find Normal and Control in data

genomics • 1.7k views
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3.4 years ago

TSS code of 41 indicates that it derives from Christiana Healthcare (source site) and is a glioblastoma multiforme sample.

The following 01 indicates that it is a tumor sample.

Take a look at my previous answer and my GitHub page:

The Code Tables will provide additional information.

Good luck, Kevin

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@Kevin Blighe thanks Kevin, so 01 is the sample !!! how one can understand that they used sample and not portion ?

do you also know how to figure out the mutation and wild type of a specific gene in sample TCGA?

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The portion is indicated by the number after the sample number:

If you obtain the Level 3 TCGA data, i.e., the Mutation Annotation Format (MAF) files, then all listed variants are somatic. There will be a column in the MAF files for 'panel of normals', I believe, which indicates that the somatic variant was additionally observed in an unrelated panel of normals (screened by Broad Institute, if my memory serves me correctly).

Only the Level 1 [protected] data has the original calls in the normal samples.

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@ Kevin Blighe so we would not be able to get normal samples?

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Normal samples will have number 10 - 19 in the Sample field. These are available for copy number, RNA-seq, and other data-types (as open access Level 3), but not DNA-seq.

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@Kevin Blighe Kevin, can you please check one of the sample for example with me? Lets look at BRCA, As an example, we pick up one of the sample TCGA-BH-A1FB-11A. So based on what you said I should see this as a normal sample, right? if I go to clinic, I can see that it is stage iib of breast cancer. Can you please comment?

ecab16bc-28d5-4c3a-8735-3c785bd047c4 TCGA-BH-A1FB TCGA-BRCA female 1940 white not hispanic or latino 2010 not reported not reported Infiltrating duct carcinoma, NOS stage iib

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Hey, yes, that is a normal tissue sample from the cancer patient. The record from the clinical data, however, just relates generally to the patient, who had 'NOS stage iib'.

So, it is normal tissue from a NOS stage iib cancer patient.