I need to validate my findings from my microarray data with TCGA RNA-Seq. However, I cant figure out where I could get the PAM50, IHC Receptor Status (for classification of TNBC) and samples from TCGA-BRCA. Could anyone guide me? Thank you!
1 answer
The IHC data are available through cBioPortal. Go to the cBioPortal site, select Breast as the cancer type and scroll down to find the TCGA samples. The data have been analysed several different times, but I recommend the "firehose legacy" set, as this definately has the IHC data. Select "Explore Selected Studies". Then go to the Clinical data tab, and use the "Columns" drop down to select the IHC data you are interested in.
There is a link at the top to the raw data for expression data. You want the RNAseq_V2 files. Unforunately the analysis is old. The same data can be obtained from GDC with a more modern analysis pipeline, but might be more of a faff to download and link to the clinical data.
I've only seen PAM50 analysis of the TCGA set for the inital 2012 publication. That can be found here: https://gdc.cancer.gov/about-data/publications/brca_2012, but i think it covers on a pretty small subset of the data.
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