
The T-cell receptor (TCR) repertoire is continuously molded by immunological challenges, including pathogen exposure, tumor recognition, and hematological diseases: each influencing its diversity and clonality. Characterizing the structure and evolutionary dynamics of TCR repertoires provides critical insight into immune system function, persistence of antigen-specific clonotypes, and disease progression. This chapter will present foundational principles of repertoire analysis, focusing on measures of diversity (e.g., Shannon and Simpson indices), clonality (Gini index), and inter-sample overlap metrics, and their relevance for predicting disease outcomes and therapeutic responses. In addition, we will examine how antigen-specific TCR affinity shapes T-cell persistence, functionality, and promiscuity, with particular emphasis on their implications for TCR-based cell therapies. This chapter aims to bridge repertoire analytics with translational immunology, informing both fundamental understanding and clinical applications.
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