Question: TCGA barcode for SNP sample
0
gravatar for mms140130
2.5 years ago by
mms14013060
mms14013060 wrote:

I have a sample header as TCGA-AC-A7VB-01A-11D-A350-01

I'm not sure what does it mean, I searched TCGA barcode and I found different format

TCGA-02-0001-01C-01D-0182-01

any help?

snp • 1.4k views
ADD COMMENTlink modified 2.5 years ago by dyollluap300 • written 2.5 years ago by mms14013060
3
gravatar for dyollluap
2.5 years ago by
dyollluap300
USA, California, Bay Area
dyollluap300 wrote:

The TCGA barcode component format is {project name}-{tissue source site}-{study participant number}-{sample}-{sample vial/aliquot}-{portion of sample and analyte}-{sample plate}-{center}

Sometimes the disease name abbreviation is used to also identify the center from which the sample was derived.

Your example: TCGA-AC-A7VB-01A-11D-A350-01 TCGA project Breast Invasive Carcinoma - International Genomics Consortium Patient ID A7VB Solid Primary tumor, vial or aliquot A 11 DNA Plate ID A350 Broad Institute

The GDC has a fragmented description for each of the barcode components at this page: https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables

This older TCGA link contains the barcode component breakdown https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode

ADD COMMENTlink written 2.5 years ago by dyollluap300

Does the barcode tells anything about the race of the patient ??

ADD REPLYlink written 2.5 years ago by mms14013060
1

No, if you want patient clinical information you'll need to download the associated clinical metadata files.

ADD REPLYlink written 2.5 years ago by dyollluap300

could you please if you don't mind have a look at my question https://www.biostars.org/p/238939/

ADD REPLYlink written 2.5 years ago by mms14013060
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