TIRTL-seq: deep, quantitative and affordable paired TCR repertoire sequencing
Mikhail V. Pogorelyy, Allison M. Kirk, Samir Adhikari, Anastasia A. Minervina, Balaji Sundararaman, Kasi Vegesana, David C. Brice, Zachary B. Scott, SJTRC Study Team, Joshua Wolf, Aditya H. Gaur, James M. Hoffman, Tomi Mori, Li Tang, Elaine Tuomanen, Hana Hakim, Randall T. Hayden, Diego R. Hijano, Kim Allison, E. Kaitlynn Allen, Walid H. Awad, Resha Bajracharya, Brandi L. Clark, Lee-Ann Van de Velde, Taylor L. Wilson, Ronald H. Dallas, Ashleigh Gowen, Amanda Cole, Jamie Russell-Bell, Ashley Castellaw, Chun-Yang Lin, Maureen A. McGargill, Richard J. Webby, Gang Wu, Paul G. Thomas
Abstract
The specificity of T cells is determined by T cell receptor (TCR) α and β chain sequences. While bulk TCR sequencing enables cost-effective repertoire profiling without chain pairing information, single-cell approaches provide paired data but are costly and limited in throughput. Here we present throughput-intensive rapid TCR library sequencing (TIRTL-seq), an experimental and computational methodology for paired TCR repertoire sequencing (TCR-seq). TIRTL-seq is based on the parallel generation of hundreds of TCR libraries in 384-well plates at less than US$200 per plate, allowing cohort-scale paired TCR-seq studies. We benchmarked TIRTL-seq against state-of-the-art bulk TCR-seq and 10x Genomics Chromium technologies on longitudinal samples and identified severe acute respiratory syndrome coronavirus 2- and Epstein-Barr virus-specific clonal expansions after infection with distinct dynamics. TIRTL-seq offers a universal protocol scalable from a single cell to millions of T cells per sample, simultaneously delivering both precise clonal frequency estimation and accurate TCR chain pairing, combining the strengths of bulk and single-cell TCR-seq.