Question: TCGA Clinical information about immunotherapy
1
gravatar for gavinym1010
2.1 years ago by
gavinym101010
gavinym101010 wrote:

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.

tcga immunotherapy • 1.1k views
ADD COMMENTlink modified 2.1 years ago by Kevin Blighe53k • written 2.1 years ago by gavinym101010
0
gravatar for Kevin Blighe
2.1 years ago by
Kevin Blighe53k
Kevin Blighe53k wrote:

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

ADD COMMENTlink written 2.1 years ago by Kevin Blighe53k
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