Massively parallel interrogation and mining of natively paired human TCR repertoires

T cells engineered to express antigen-specific T cell receptors (TCRs) are potent therapies for viral infections and cancer. However, efficient identification of clinical candidate TCRs is complicated by the size and complexity of T cell repertoires and the challenges of working with primary T cells. Here we present a high-throughput method to identify TCRs with high functional avidity from diverse human T cell repertoires. The approach used massively parallel microfluidics to generate libraries of natively paired, full-length TCR[alpha][beta] clones, from millions of primary T cells, which were then expressed in Jurkat cells. The TCR[alpha][beta]-Jurkat libraries enabled repeated screening and panning for antigen-reactive TCRs using peptide major histocompatibility complex binding and cellular activation. We captured more than 2.9 million natively paired TCR[alpha][beta] clonotypes from six healthy human donors and identified rare (