Unmasking human T cell receptor germline diversity: 335 novel alleles identified in 47 Pangenome reference individuals using the gAIRR Suite

Abstract

Introduction

The adaptive immune receptor repertoire (AIRR), also referred to as expressed AIRR (exprAIRR) for clarity, comprises V(D)J-recombined T cell receptors (TR) and immunoglobulins (IG), and is central to adaptive immunity. Accurate exprAIRR profiling depends on a comprehensive and population-representative germline gene set encoding AIRR (gAIRR). In addition to serving as the reference for AIRR-seq, gAIRR alleles themselves are increasingly recognized as contributors to immune-related phenotypes, including disease susceptibility, variable vaccine responsiveness, and adverse immune events.

Objectives

Current germline TR references form an essential foundation, but based on scientific inference, likely represent only a portion of true human diversity. Some alleles lack flanking genomic information, and several populations remain underrepresented—constraints rooted in earlier sequencing methodologies. This study aims to substantially expand these references by resolving full-length TR alleles and their flanking regions across ancestrally diverse individuals.

Methods

We analyzed 47 high-quality, phased diploid genomes from the Human Pangenome Reference Consortium (HPRC) using the gAIRR Suite. All novel alleles were crosschecked using two orthogonal pipelines: gAIRR-annotate (assembly-based annotation) and gAIRR-seq/gAIRR-call (targeted short-read sequencing and genotyping).

Results

We identified 335 novel TR alleles—305 TRV and 30 TRJ—representing 91.6% and 30.9% increases over IMGT records (v3.1.41; accessed 2025–04-19), respectively. Many novel alleles occurred at substantial frequencies, particularly among individuals of African ancestry. We further established a comprehensive flanking sequence database, including recombination signal sequences (RSS), and documented allele-specific variations in these regions. Functional annotation showed that several novel alleles exhibit altered coding potential, including transitions to pseudogene or open reading frames (ORFs) status.

Conclusion

This study significantly expands the known landscape of human TR germline diversity and provides a rigorously validated, population-diverse resource comprising novel alleles, flanking sequences, RSS profiles, and supporting analytical tools. These improved gAIRR references are essential for accurate germline genotyping and exprAIRR profiling, and will enable improved detection of immunogenetic associations. Our findings advance precision immunogenomics and support the development of ancestry-independent yet diversity-comprehensive genotyping, vaccines, and immunotherapies.