Can anyone help me to confirm the number of matched tumor and normal samples in TCGA-BRCA?
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
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Not sure if this summary will help.
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.