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Antibody V and C Domain Sequence, Structure, and Interaction Analysis with Special Reference to IMGT®

  • Eltaf Alamyar
  • Véronique Giudicelli
  • Patrice Duroux
  • Marie-Paule Lefranc
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1131)

Abstract

IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org), created in 1989 (Centre National de la Recherche Scientifique, Montpellier University), is acknowledged as the global reference in immunogenetics and immunoinformatics. The accuracy and the consistency of the IMGT® data are based on IMGT-ONTOLOGY which bridges the gap between genes, sequences, and three-dimensional (3D) structures. Thus, receptors, chains, and domains are characterized with the same IMGT® rules and standards (IMGT standardized labels, IMGT gene and allele nomenclature, IMGT unique numbering, IMGT Collier de Perles), independently from the molecule type (genomic DNA, complementary DNA, transcript, or protein) or from the species. More particularly, IMGT® tools and databases provide a highly standardized analysis of the immunoglobulin (IG) or antibody and T cell receptor (TR) V and C domains. IMGT/V-QUEST analyzes the V domains of IG or TR rearranged nucleotide sequences, integrates the IMGT/JunctionAnalysis and IMGT/Automat tools, and provides IMGT Collier de Perles. IMGT/HighV-QUEST analyzes sequences from high-throughput sequencing (HTS) (up to 150,000 sequences per batch) and performs statistical analysis on up to 450,000 results, with the same resolution and high quality as IMGT/V-QUEST online. IMGT/DomainGapAlign analyzes amino acid sequences of V and C domains and IMGT/3Dstructure-DB and associated tools provide information on 3D structures, contact analysis, and paratope/epitope interactions. These IMGT® tools and databases, and the IMGT/mAb-DB interface with access to therapeutical antibody data, provide an invaluable help for antibody engineering and antibody humanization.

Key words

IMGT Immunoglobulin Antibody Antibody humanization High-throughput sequencing Immunogenetics Immunoinformatics IMGT-ONTOLOGY IMGT Collier de Perles IMGT unique numbering 

Notes

Acknowledgments

We are grateful to Gérard Lefranc for helpful discussion, to Souphatta Sasorith for help with the figures, and to the IMGT® team for its expertise and constant motivation. IMGT® is a registered trademark of CNRS. IMGT® is a member of the International Medical Informatics Association (IMIA). IMGT® is currently supported by CNRS, the Ministère de l’Enseignement Supérieur et de la Recherche (MESR), University Montpellier 2, the Agence Nationale de la Recherche (ANR) Labex MabImprove (ANR-10-LABX-53-01), and the Région Languedoc-Roussillon (Grand Plateau Technique pour la Recherche (GPTR)). This work was granted access to the HPC resources of CINES under the allocation 036029 (2010–2013) made by Grand Equipement National de Calcul Intensif (GENCI).

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Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  • Eltaf Alamyar
    • 1
  • Véronique Giudicelli
    • 1
  • Patrice Duroux
    • 1
  • Marie-Paule Lefranc
    • 1
  1. 1.The International ImMunoGenetics information system, Laboratoire d’ImmunoGénétique MoléculaireInstitut de Génétique Humaine IGH, Université Montpellier 2MontpellierFrance

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