Enhancing comparative T cell receptor repertoire analysis in small biological samples through pooling homologous cell samples from multiple mice

Motivation – Amplification and sequencing techniques for bulk-cell T cell receptor (TCR) sequencing have improved in the last decade, allowing in-depth characterization of the TCR repertoire with high accuracy. Nevertheless, tackling the diverse and complex nature of TCR repertoires remains challenging in small samples. In this study, we address this challenge by pooling homologous biological samples to collect enough input material and evaluating the effect of pooling through a set of TCR repertoire statistics.

Summary – Accurate characterization and comparison of T cell receptor (TCR) repertoires from small biological samples present significant challenges. The main challenge is the low material input, which compromises the quality of bulk sequencing and hinders the recovery of sufficient TCR sequences for robust analyses. We aimed to address this limitation by implementing a strategic approach to pool homologous biological samples. Our findings demonstrate that such pooling indeed enhances the TCR repertoire coverage, particularly for cell subsets of constrained sizes, and enables accurate comparisons of TCR repertoires at different levels of complexity across T cell subsets with different sizes. This methodology holds promise for advancing our understanding of T cell repertoires in scenarios where sample size constraints are a prevailing concern.