We are interested in using the data available through The Cancer Genome Atlas (TCGA) to look at pharmacogenomic outcomes. Essentially, we want to look at how patients with a type of cancer (e.g. breast cancer) responded, or failed to respond, to medication used. There are 3 levels of data available for SNP and CNV genotype data. The clinical treatment data is apparently sparse with a lot of missing variables or incorrectly annotated. I wonder if anyone has experience with this or could comment on the correctness or completeness of this dataset and the feasibility of examining pharmacogenomic outcomes.
I have had less luck getting a straight answer to this question from the source and the application process is a bit of a pain. Is there someplace this information can be found? Or do any of you know?