This exercise is based on a specific use-case for answering some questions about head and neck cancer using the GDC TCGA data.

HPV is a virus that infects tissue and integrates itself into the human genome. Upon integration into the human genome, the viral oncogenes E6 and E7 are transcribed by the human transcriptional machinery and expressed. The resulting viral proteins then inhibit key cell cycle regulators such as TP53, which leads to cancer.

While HPV is more frequently associated with cervical cancer, it also causes head and neck cancer (HNSC). In the clinic, a colleague has noted that HNSC patients who are HPV positive seem to respond better to treatment. Our ultimate goal is to investigate the GDC TCGA data for HNSC to determine if patients that are HPV+ have better survival compared to those who don't. We are also interested in mutations in the genes TP53 and CDKN2A and if there is a survival difference between patients with and without mutations in these genes. TP53 is a commonly mutated gene in cancer, and CDKN2A produces the protein p16, which is the protein measured in the clinic to determine HPV positivity.

The first 3 activities will be walking you through the GDC Data Portal similar to what we did in the workshop, only for HNSC. The 4th activity will require you to create the survival plots to answer the questions just posed above. To do this you will need to know which patients are HPV+ and which are HPV-. I have obtained this information via analysis of the controlled access RNASeq data already, and have provided a list of HPV+ patients in the Research Guide for this workshop: https://guides.library.vcu.edu/genomic_workshop/cancer-genome