From Cancer Sequencing Data to Neoantigen Prediction: A reusable pipeline using Snakemake

RNA-Sequencing (RNA-Seq) is a sequencing technique to profile the expression levels of genes in a sample. Whole Exome Sequencing (WES) is a sequencing technique that targets only the protein-coding regions of a sample. By detecting genetic variants using both WES and RNA-Seq data, we can identify expressed somatic mutations, which can give rise to new cancer-induced antigens (neoantigens). Because neoantigens are unique to cancer cells, they can be used to target cancerous cells with immunotherapy. Predicting neoantigens using sequencing data can thus lead to personalized cancer immunotherapeutics.

College of Natural Sciences, University of Texas at Austin – LiveSTRONG Cancer Institute