VDJ-Insights: simplifying the annotation of genomic IG and TCR regions

Susan Ott; Ngoc Giang Le; Sayed J Mohammadi; Jesse Mittertreiner; Erica M. Pasini; Ronald E. Bontrop; Natasja G. de Groot; Jesse Bruijnesteijn

doi:10.1093/bioinformatics/btag108

GeneticsBioinformaticsMar 3, 2026

Peer-reviewed journal article

VDJ-Insights: simplifying the annotation of genomic IG and TCR regions

Susan Ott iD, Ngoc Giang Le iD, Sayed J Mohammadi, Jesse Mittertreiner, Erica M. Pasini iD, Ronald E. Bontrop iD, Natasja G. de Groot iD, Jesse Bruijnesteijn iD

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Abstract

Accurate annotation of germline immunoglobulin (IG) and T cell receptor (TCR) loci is critical for understanding adaptive immunity. 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 (RSS), and annotates complementary-determining regions 1 and 2 (CDR1, CDR2). 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.