Question: Can anyone help me to confirm the number of matched tumor and normal samples in TCGA-BRCA?
0
gravatar for Wen Wang
14 months ago by
Wen Wang0
USA/Minneapolis/University of Minnesota
Wen Wang0 wrote:

Hi all,

I was looking at the somatic mutation summary at GDC data portal. It seems there are 986 samples with matched tumor and normal SNV data available. For example, # Affected Cases in Cohort for mutation "chr3:g.179234297A>G" is " 121 / 986". However, I only find 356 samples in dbGaP Study Accession: phs000178.v9.p8.

Is there a way to find out the actual number of matched tumor and normal samples in TCGA-BRCA? Your help is greatly appreciated.

Wen

snp genome • 424 views
ADD COMMENTlink written 14 months ago by Wen Wang0
1

Not sure if this summary will help.

ADD REPLYlink written 14 months ago by genomax65k

The link genomax provided should be relatively updated. From the summary, download the TCGA barcodes (TCGA-XX-XX-##X and match them. Same patient will have the same TCGA-XX-XX, tumor is 01 and normal is 11. If you want to the most updated list, download all the UUIDs of TCGA-BRCA from GDC, convert them to TCGA barcodes, and match them.

ADD REPLYlink written 14 months ago by Eric Lim1.3k
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