"Half-baked" Analysis: Using MAF files to find neo-antigens Immunotherapy is an exciting new area of research in cancer biology, and identifying neo-antigens that can illicit an immune response is an essential component. Very little work as been published on this topic, and it would be interesting to see if it is possible to identify neo-antigens in every cancer type, and if neo-antigens vary among cancers. With the advent of whole genome sequencing, it is possible to find all of the mutations in a tumor, and these mutations are typically listed in a mutation annotation format file. The Cancer Genome Atlas provides access to thousands of MAF files, but using these files to find neo-antigens requires some technical expertise and knowledge of the immune system. This post will go over what neo-antigens are, and how to find potential neo-antigens starting from MAF files. The code seen in the video is available here.