Physics

Phenotype

Exome sequencing

Repertoire

Biology

Gene

Antigen

Single cell sequencing

Major histocompatibility complex

Acoustics

T-cell receptor

Acquired immune system

T cell

Computational biology

Cell biology

Genetics

Immune system

Nature Methods

T cells express T cell receptors (TCRs) composed of somatically recombined TCRα and TCRβ chains, which mediate recognition of major histocompatibility complex (MHC)–antigen complexes and drive the antigen-specific adaptive immune response to pathogens and cancer. The TCR repertoire in each individual is highly diverse, which allows for recognition of a wide array of foreign antigens, but also presents a challenge in analyzing this response using conventional methods. Recent studies have developed high-throughput sequencing technologies to identify TCR sequences, analyze their antigen specificities using experimental and computational tools, and pair TCRs with transcriptional and epigenetic cell state phenotypes in single cells. In this Review, we highlight these technological advances and describe how they have been applied to discover fundamental insights into T cell-mediated immunity. This Review discusses methodological advances for high-throughput analysis of the TCR repertoire at bulk and single-cell resolution.

High-throughput and single-cell T cell receptor sequencing technologies