To improve upon the current efficacy rate of cancer therapeutics, a careful approach should be taken to identify epitopes (neoantigens) capable of guiding a broad immune response against the tumour. Exploration of the alterations uniquely detected in tumour tissue leads to dense information with sparse actionability, where identification of the most relevant target epitopes is the main challenge. Building a robust neoantigen identification pipeline requires a fine balance between having a comprehensive detection approach and an optimised prioritisation strategy.
This whitepaper describes how the optimal neoantigen prediction pipeline looks like by thorough discussion of the crucial steps in the neoantigen prediction set-up. Also a comparison is made of the most commonly used prediction pipelines to define the most advanced pipeline currently available.