Sideri, I. | bioRxiv Science

bioRxiv2025

IMGT(R) at scale: FAIR, Dynamic and Automated Tools for Immune Locus Analysis

IMGT(R), the international ImMunoGeneTics information system(R), has advanced its comprehensive platform for the analysis of immunoglobulin (IG) and T cell receptor (TR) genes through the development of new automated and scalable tools. This article presents major updates aligned with IMGTs three axes of research. Axis I introduces dynamic resources such as IMGT/GeneTables, IMGT/AssemblyComparison, and IMGT/StatAssembly, enabling real-time access to annotated genomic data and quality assessment of assemblies. Axis II enhances repertoire analysis with a redesigned IMGT/GeneFrequency tool and new customization features in IMGT/V-QUEST, supporting flexible exploration of IG and TR gene expression. Axis III improves the accurate prediction of peptide-MHC thanks to IMGT/RobustpMHC. Additionally, the IMGT Knowledge Graph (IMGT-KG) and its therapeutic extension, IMGT/mAb-KG, provide semantically structured access to more than 100 million immunogenetic triplets, integrating IMGT databases and linking IMGT content to external biomedical resources. These developments promote standardization, interoperability, and integrative analysis across immunogenetics and clinical applications, reinforcing IMGTs role as a core reference in the era of FAIR data and personalized medicine.

bioinformatics↗

bioRxiv2025

Development of ferret immune repertoire reference resources and single-cell-based high-throughput profiling assays

Domestic ferrets (Mustela putorius furo) are important for modeling human respiratory diseases. However, ferret B and T cell receptors have not been completely identified or annotated, limiting immune repertoire studies. Here we performed long read transcriptome sequencing of ferret splenocyte and lymph node samples to obtain over 120,000 high-quality full-length immunoglobin (Ig) and T cell receptor (TCR) transcripts. We constructed a complete reference set of the constant regions of ferret Ig and TCR isotypes and chain types. We also systematically annotated germline Ig and TCR variable (V), diversity (D), joining (J), and constant (C) genes on a recent ferret reference genome assembly. We designed new ferret-specific immune repertoire profiling assays by targeting positions in constant regions without allelic diversity across 11 ferret genome assemblies, and experimentally validated them using a commercially compatible single-cell-based platform. These improved resources and assays will enable future studies to fully capture ferret immune repertoire diversity.

genomics↗