Downloading triple negative breast cancer data from ICGC
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3.2 years ago
graeme.thorn ▴ 60

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?

RNA-Seq icgc • 1.8k views
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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.

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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

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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.

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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.

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