Antonio Ahn's Blog

Introduction This document outlines the approach i took to download data level 3 TCGA data. RNA-seq, methylation 450K data and clinical information was downloaded using the RTCGAToolbox(Samur 2014) package The RTCGAToolbox package written by Samur, retreives data from the broads institutive firehose database. Detailed information on how to use this package are available in the Vignette, online courses PH525Xseries and Youtube videos. Many of the codes used here were taken from these resources.

Background and the scientific challenge For the first time in history, the word “cure” can now be used for patients with metastatic melanoma. For decades, treatment was restricted to a chemotherapy drug that do not extend patient survival. However, a major shift in treatment arose when it was found that melanoma cells frequently express a protein called PD-L1 to inhibit immune cells in order to grow undetected in the body. This was followed by discovery of novel drugs that block PD-L1 interaction which in turn reawakens the immune attack.