Downloading triple negative breast cancer data from ICGC
I want to download RNA-seq and mutation data from the ICGC data portal at https://dcc.icgc.org/, but I'm only interested in triple negative breast cancer patients. Is there a quick and easy way to either filter the portal to get only the TNBC data, or a quick way to classify the data once downloaded from there for the three receptor statuses (ER, PGR and HER2) so that I can do the filtering myself?
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As per the TCGA cohort on the GDC, you may have to do this indirectly by looking through the clinical notes: How to download triple negative breast cancer RNA-seq fpkm data from GDC.
I can't see any global table like for the GDC, and the clinical data available for each patient does not have the information I need to filter out those who aren't TNBCs
Are you sure? I managed to configure a search on the ICGC Data Repository for breast clinical data: https://dcc.icgc.org/repositories?files=%7B%22from.... They may not store the same data-types as were stored in the TCGA, even though the TCGA data is itself listed at the ICGC Data Repo.
That data does not contain the receptor status though. The equivalent data for the TCGA data (BRCA-US project) on the GDC does have the receptor status to assess whether its TNBC or not, but the clinical data from the ICGC does not contain it.