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Antibody Sequence and Structure Analyses Using IMGT®: 30 Years of Immunoinformatics

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Computer-Aided Antibody Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2552))

Abstract

IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org, the global reference in immunogenetics and immunoinformatics, was created in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS) to manage the huge diversity of the antigen receptors, immunoglobulins (IG) or antibodies, and T cell receptors (TR) of the adaptive immune responses. The founding of IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT® standardized analysis of the IG, TR, and major histocompatibility (MH) genes and proteins bridges the gap between sequences and three-dimensional (3D) structures, for all jawed vertebrates from fish to humans. This is achieved through the IMGT Scientific chart rules, based on the IMGT-ONTOLOGY axioms, and primarily CLASSIFICATION (IMGT gene and allele nomenclature) and NUMEROTATION (IMGT unique numbering and IMGT Colliers de Perles). IMGT® comprises seven databases (IMGT/LIGM-DB for nucleotide sequences, IMGT/GENE-DB for genes and alleles, etc.), 17 tools (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/HighV-QUEST for NGS, etc.), and more than 20,000 Web resources. In this chapter, the focus is on the tools for amino acid sequences per domain (IMGT/DomainGapAlign and IMGT/Collier-de-Perles), and on the databases for receptors (IMGT/2Dstructure-DB and IMGT/3D-structure-DB) described per receptor, chain, and domain and, for 3D, with contact analysis, paratope, and epitope. The IMGT/mAb-DB is the query interface for monoclonal antibodies (mAb), fusion proteins for immune applications (FPIA), composite proteins for clinical applications (CPCA), and related proteins of interest (RPI) with links to IMGT® 2D and 3D databases and to the World Health Organization (WHO) International Nonproprietary Names (INN) program lists. The chapter includes the human IG allotypes and antibody engineered variants for effector properties used in the description of therapeutical mAb.

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Acknowledgments

We thank Karima Cherouali and Anjana Kushwaha for the biocuration of the therapeutic monoclonal antibodies in the IMGT/mAb-DB and IMGT/2Dstructure-DB, respectively. We are grateful to members of the IMGT® team for their expertise and constant motivation. We thank the many colleagues for their contribution, help, and support during these 30 years. We thank Cold Spring Harbor Protocol Press for the pdf of the IMGT Booklet available in IMGT references. IMGT® is a registered trademark of CNRS. IMGT® is a member of the International Medical Informatics Association (IMIA) and of the Global Alliance for Genomics and Health (GA4GH). IMGT® was funded in part by the BIOMED1 (BIOCT930038), Biotechnology BIOTECH2 (BIO4CT960037), fifth PCRDT Quality of Life and Management of Living Resources (QLG2-2000-01287), and sixth PCRDT Information Science and Technology (ImmunoGrid, FP6 IST-028069) programs of the European Union (EU). IMGT received financial support from the GIS IBiSA, BioCampus Montpellier, the Région Occitanie (Grand Plateau Technique pour la Recherche (GPTR)), the Agence Nationale de la Recherche (ANR), and the Labex MabImprove (ANR-10-LABX-53-01). IMGT was granted access to the HPC resources of CINES under the allocation [036029] (2010-2020) made by GENCI (Grand Equipement National de Calcul Intensif). IMGT® is currently supported by the Centre National de la Recherche Scientifique (CNRS), the Ministère de l’Enseignement Supérieur, de la Recherche et de l’Innovation (MESRI), and the Université de Montpellier.

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  1. IMGT®, the international ImMunoGeneTics information system®, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier cedex 5, France

    Marie-Paule Lefranc & Gérard Lefranc

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  1. Marie-Paule Lefranc
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Correspondence to Marie-Paule Lefranc or Gérard Lefranc .

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  1. School of Engineering, The University of Tokyo, Tokyo, Japan

    Kouhei Tsumoto

  2. School of Engineering, The University of Tokyo, Tokyo, Japan

    Daisuke Kuroda

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Lefranc, MP., Lefranc, G. (2023). Antibody Sequence and Structure Analyses Using IMGT®: 30 Years of Immunoinformatics. In: Tsumoto, K., Kuroda, D. (eds) Computer-Aided Antibody Design. Methods in Molecular Biology, vol 2552. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2609-2_1

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