Predicting Tumor Antigens Using the LENS Workflow Through RAFT.

Tumor-specific and tumor-associated antigens presented on the tumor cell surface by MHC molecules are enticing targets for personalized vaccination and T cell receptor-engineered T cell (TCR-T) therapy. Accurately predicting suitable tumor antigens is a considerable challenge and requires flexibility in both computational tools and experimental methods. Here we describe our framework for reproducible bioinformatics, RAFT, as well as our highly modular neoantigen prediction workflow, LENS. We provide step-by-step instructions for installation, running, and modifying LENS to suit different purposes.