To know the efficacy of your cancer vaccine, it is crucial to analyse the T cell response. Because of its versatility, TCR sequencing is a rising tool to monitor such immune responses. However, the full potential of TCR sequencing remains unrealised at present.
One of the major challenges is the capability to distil the relevant TCR clonotypes from the large collection of TCRs within a TCR repertoire. For example, when developing a cancer vaccine, it is useful to identify those TCR clonotypes that correlate with clinical outcomes so that these can be used as biomarkers to prove the effectiveness of the vaccine response. Furthermore, it is beneficial to pinpoint which epitopes of a multi-epitope vaccine have generated the most efficient TCR response in order to optimise vaccine design. These kinds of analyses are typically hindered by the interindividual diversity of TCR clonotypes, meaning that relevant TCRs identified in one patient can not be detected in another patient.
This white paper is directed toward researchers and developers of therapeutic cancer vaccines that want to use their TCR sequencing data to its full potential. It offers a concise overview of TCR sequencing and how it has been applied in the field of therapeutic cancer vaccination. Additionally, we highlight common challenges encountered in the data analysis and present examples of how these can be overcome with state-of-the-art data analysis techniques.