TCGA Head & Neck Squamous Cell Carcinoma (HNSC) Clinical Data

Abstract:

The Cancer Genome Atlas (TCGA) was a large-scale collaborative project initiated by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI). It aimed to comprehensively characterize the genomic and molecular landscape of various cancer types. This dataset includes curated survival data from the Pan-cancer Atlas paper titled "An Integrated TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR) to drive high quality survival outcome analytics". The paper highlights four types of carefully curated survival endpoints, and recommends the use of the endpoints of OS, PFI, DFI, and DSS for each TCGA cancer type. The dataset also includes phenotypic information about HNSC. The Sample IDs are unique identifiers, which can be paired with the gene expression dataset. 

Inspiration:

This dataset was uploaded to UBRITE for GTKB project. 

Instruction:

The survival and phenotype data were merged into one file. Empty columns were removed. Columns with the same value for every sample were also removed. 

Acknowledgments:

Goldman, M.J., Craft, B., Hastie, M. et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0546-8

Liu, Jianfang, Caesar-Johnson, Samantha J. et al. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell, Volume 173, Issue 2, 400 - 416.e11. https://doi.org/10.1016/j.cell.2018.02.052

The Cancer Genome Atlas Research Network., Weinstein, J., Collisson, E. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45, 1113–1120 (2013). https://doi.org/10.1038/ng.2764

U-BRITE last update: 07/13/2023