Does anyone try to find out TCGA clinical data about response or survival after immunotherapy?
Based on this paper (Heterogeneity of tumor infltrating lymphocytes ascribed to local immune status rather than neoantigens by multiomics analysis of glioblastoma multiforme), there might be some information I mentioned above.However, I did not find out any.
The manuscript that you mention should list precisely how the clinical information was obtained. I have just checked and it states:
The raw mRNA expression data and the corresponding clinical information, which was available for 487 GBM samples, were downloaded from the Cancer Genome Atlas (TCGA) database (https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp)
The URL does not even work.
In Figure 5 of the manuscript, they relate to overall and disease-free survival, but it is not explicitly stated which parameters they used from the TCGA.
As it's not clear, I would reach out to the authors of the manuscript to find out the exact parameters that were used. The TCGA clinical data is vast and there are many different clinical variables that they could have used (multiple survival variables exist). One can normally download the clinical data from the GDC Legacy Archive.
Kevin
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