TIRTL-seq: deep, quantitative and affordable paired TCR repertoire sequencing.

Area of Science:

• Immunology
• Genomics
• Bioinformatics

Background:

• T cell receptor (TCR) α and β chain sequences dictate T cell specificity.
• Bulk TCR sequencing is cost-effective but lacks chain pairing data.
• Single-cell TCR sequencing provides paired data but is expensive and has low throughput.

Purpose of the Study:

• To introduce throughput-intensive rapid TCR library sequencing (TIRTL-seq), a novel method for paired TCR repertoire sequencing.
• To enable cost-effective, cohort-scale paired TCR sequencing.
• To combine the strengths of bulk and single-cell TCR sequencing.

Main Methods:

• TIRTL-seq utilizes parallel generation of hundreds of TCR libraries in 384-well plates.
• The method achieves a cost of less than US$200 per plate.
• It integrates experimental and computational approaches for paired TCR repertoire sequencing.

Main Results:

• TIRTL-seq was benchmarked against bulk TCR-seq and 10x Genomics Chromium technologies.
• The study identified severe acute respiratory syndrome coronavirus 2- and Epstein-Barr virus-specific clonal expansions.
• Distinct dynamics of clonal expansions were observed in longitudinal samples.

Conclusions:

• TIRTL-seq offers a universal protocol scalable from single cells to millions of T cells.
• The method provides precise clonal frequency estimation and accurate TCR chain pairing.
• TIRTL-seq overcomes limitations of existing TCR sequencing methods, enabling comprehensive repertoire analysis.