TCGA Sample barcode
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4 months ago

I have downloaded the TCGA dataset for ACC Cancer type from RNAseqV2 data. In the level 3 files for the RSEM rnaseq data, the barcodes for the samples are given as follows : "TCGA-OR-A5J1-01A-11R-A29S-07".

How to understand whether the sample is tumor or normal? In here, TCGA description for barcode , the barcode explained is given in different manner. Any help would be appreciated.

Tumor Barcode Normal TCGA • 298 views
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4 months ago
dsull ★ 2.3k

It's tumor. 01 = Primary solid tumor

https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes

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But all the samples in the dataset has “01A” in the barcode. When we search in the GDC portal, they have reported that in TCGA-ACC, there does exist Normal Tissue samples as well.

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You might be referring to blood normal samples which only undergo DNA-seq because their RNA-seq is not relevant to tissue-specific gene expression. From querying for "solid tissue normal" in TCGA ACC on GDC, I only see two cases, and they don't have RNA-seq. I can confirm the same in the legacy GDC archive.

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If you are seeking normal gene-expression in adrenal gland tissue, look into GTex instead of TCGA.

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