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VDJ-Insights: simplifying the annotation of genomic immunoglobulin and T cell receptor regions.

Susan E Ott·Giang N Le·Sayed J Mohammadi·Jesse Mittertreiner·Erica M Pasini·Ronald E Bontrop·Natasja G de Groot·Jesse Bruijnesteijn
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Abstract

MOTIVATION: Accurate annotation of germline immunoglobulin (IG) and T cell receptor (TCR) loci is critical for understanding adaptive immunity. RESULTS: VDJ-Insights provides a user-friendly software package for characterizing these complex immune regions. In addition, it assesses gene segment functionality, identifies recombination signal sequences, and annotates complementarity-determining regions 1 and 2. VDJ-Insights achieved over 99% concordance with curated annotations from multiple species, outperforming existing annotation tools. When applied to 95 haplotypes from the Human Pangenome Reference Consortium, VDJ-Insights identified 652 and 275 novel IG and TCR alleles, respectively, highlighting its scalability for large immunogenetic studies. AVAILABILITY AND IMPLEMENTATION: Datasets and software package are available in the VDJ-insights repository, https://github.com/BPRC-Bioinfo and https://doi.org/10.5281/zenodo.17588835. Additional intermediate datasets used and analyzed during the current study are available from the corresponding authors upon reasonable request.

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SoftwareHumansReceptors, Antigen, T-CellMolecular Sequence AnnotationImmunoglobulinsGenomicsAnimalsJournal ArticleResearch Support, Non-U.S. Gov't

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Susan E Ott, Giang N Le, Sayed J Mohammadi, Jesse Mittertreiner, Erica M Pasini, Ronald E Bontrop, Natasja G de Groot, Jesse Bruijnesteijn. 2026-04-07. VDJ-Insights: simplifying the annotation of genomic immunoglobulin and T cell receptor regions.. https://doi.org/10.1093/bioinformatics%2Fbtag108

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