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Immunogenetics pp 605-633 | Cite as

IMGT/DomainGapAlign: The IMGT® Tool for the Analysis of IG, TR, MH, IgSF, and MhSF Domain Amino Acid Polymorphism

  • François Ehrenmann
  • Marie-Paule Lefranc
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 882)

Abstract

IMGT/DomainGapAlign is the online tool of IMGT®, the international ImMunoGeneTics information system®, for the analysis of amino acid sequences and two-dimensional (2D) structures of domains. IMGT/DomainGapAlign allows the analysis of the closest variable (V) and constant (C) domains of immunoglobulins (IG) or antibodies, T cell receptors (TR), and immunoglobulin superfamily (IgSF) proteins, and of the groove (G) domains of major histocompatibility (MH; in humans, HLA for human leukocyte antigen) and MH superfamily proteins. IMGT/DomainGapAlign aligns the user own sequences against the IMGT domain reference directory, displays amino acid changes, creates IMGT gaps, and delimits the domain strands and loops (and helix for G domain) according to the IMGT unique numbering. IMGT/DomainGapAlign is coupled to the IMGT/Collier-de-Perles tool that draws standardized IMGT Colliers de Perles. The analysis is based on the IMGT-ONTOLOGY concepts of identification, classification, description, and numerotation generated from the axioms of the Formal IMGT-ONTOLOGY or IMGT-Kaleidoscope. IMGT/DomainGapAlign provides an invaluable help for antibody engineering and antibody humanization as it precisely defines the standardized framework regions (FR-IMGT) and complementarity determining regions (CDR-IMGT) to be grafted. IMGT/DomainGapAlign is freely available at http://www.imgt.org.

Key words

IMGT Immunoglobulin Antibody T cell receptor IMGT-ONTOLOGY Immuno­globulin superfamily Major histocompatibility HLA MH superfamily Antibody humanization 

References

  1. 1.
    Lefranc M-P, Giudicelli V, Ginestoux C, Jabado-Michaloud J, Folch G, Bellahcene F, Wu Y, Gemrot E, Brochet X, Lane J, Regnier L, Ehrenmann F, Lefranc G, Duroux P (2009) IMGT®, the international ImMunoGeneTics information system®. Nucleic Acids Res 37:D1006–D1012PubMedCrossRefGoogle Scholar
  2. 2.
    Ehrenmann F, Kaas Q, Lefranc M-P (2010) IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. Nucleic Acids Res 38:D301–D307PubMedCrossRefGoogle Scholar
  3. 3.
    Giudicelli V, Lefranc M-P (1999) Ontology for immunogenetics: IMGT-ONTOLOGY. Bioinformatics 15:1047–1054PubMedCrossRefGoogle Scholar
  4. 4.
    Lefranc M-P, Giudicelli V, Ginestoux C, Bosc N, Folch G, Guiraudou D, Jabado-Michaloud J, Magris S, Scaviner D, Thouvenin V, Combres K, Girod D, Jeanjean S, Protat C, Yousfi Monod M, Duprat E, Kaas Q, Pommié C, Chaume D, Lefranc G (2004) IMGT-ONTOLOGY for Immunogenetics and Immunoinformatics. In Silico Biol 4:17–29. http://www.imgt.org
  5. 5.
    Lefranc M-P (2004) IMGT-ONTOLOGY and IMGT databases, tools and web resources for immunogenetics and immunoinformatics. Mol Immunol 40:647–660PubMedCrossRefGoogle Scholar
  6. 6.
    Duroux P, Kaas Q, Brochet X, Lane J, Ginestoux C, Lefranc M-P, Giudicelli V (2008) IMGT-Kaleidoscope, the formal IMGT-ONTOLOGY paradigm. Biochimie 90:570–583PubMedCrossRefGoogle Scholar
  7. 7.
    Lefranc M-P (1997) Unique database numbering system for immunogenetic analysis. Immunol Today 18:509PubMedCrossRefGoogle Scholar
  8. 8.
    Lefranc M-P (1999) The IMGT unique ­numbering for immunoglobulins, T cell ­receptors and Ig-like domains. Immunologist 7:132–136Google Scholar
  9. 9.
    Lefranc M-P, Pommié C, Ruiz M, Giudicelli V, Foulquier E, Truong L, Thouvenin-Contet V, Lefranc G (2003) IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol 27:55–77PubMedCrossRefGoogle Scholar
  10. 10.
    Lefranc M-P, Pommié C, Kaas Q, Duprat E, Bosc N, Guiraudou D, Jean C, Ruiz M, Da Piedade I, Rouard M, Foulquier E, Thouvenin V, Lefranc G (2005) IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev Comp Immunol 29:185–203PubMedCrossRefGoogle Scholar
  11. 11.
    Lefranc M-P, Duprat E, Kaas Q, Tranne M, Thiriot A, Lefranc G (2005) IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MhcSF) G-LIKE-DOMAIN. Dev Comp Immunol 29:917–938PubMedCrossRefGoogle Scholar
  12. 12.
    Lefranc M-P, Lefranc G (2001) The immunoglobulin FactsBook. Academic Press, London, UK, pp 1–458Google Scholar
  13. 13.
    Lefranc M-P, Lefranc G (2001) The T cell receptor FactsBook. Academic Press, London, UK, pp 1–398Google Scholar
  14. 14.
    Giudicelli V, Chaume D, Lefranc M-P (2005) IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res 33:D256–D261PubMedCrossRefGoogle Scholar
  15. 15.
    Ruiz M, Lefranc M-P (2002) IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures. Immunogenetics 53:857–883PubMedCrossRefGoogle Scholar
  16. 16.
    Kaas Q, Lefranc M-P (2007) IMGT Colliers de Perles: standardized sequence-structure representations of the IgSF and MhcSF superfamily domains. Curr Bioinform 2:21–30CrossRefGoogle Scholar
  17. 17.
    Kaas Q, Ehrenmann F, Lefranc M-P (2007) IG, TR and IgSf, MHC and MhcSF: what do we learn from the IMGT Colliers de Perles? Brief Funct Genomic Proteomic 6:253–264PubMedCrossRefGoogle Scholar
  18. 18.
    Pommié C, Levadoux S, Sabatier R, Lefranc M-P (2004) IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties. J Mol Recognit 17:17–32PubMedCrossRefGoogle Scholar
  19. 19.
    Duprat E, Kaas Q, Garelle V, Lefranc G, Lefranc M-P (2004) IMGT standardization for alleles and mutations of the V-LIKE-DOMAINs and C-LIKE-DOMAINs of the immunoglobulin superfamily. In: Pandalai SG (ed) Recent research developments in human genetics Research Signpost, Trivandram, Kerala, vol 2. pp 111–136Google Scholar
  20. 20.
    Garapati VP, Lefranc M-P (2007) IMGT Colliers de Perles and IgSF domain standardization for T cell costimulatory activatory (CD28, ICOS) and inhibitory (CTLA4, PDCD1 and BTLA) receptors. Dev Comp Immunol 31:1050–1072PubMedCrossRefGoogle Scholar
  21. 21.
    Bernard D, Hansen JD, du Pasquier L, Lefranc M-P, Benmansour A, Boudinot P (2005) Costimulatory receptors in jawed vertebrates: conserved CD28, odd CTLA4 and multiple BTLAs. Dev Comp Immunol 31:255–271CrossRefGoogle Scholar
  22. 22.
    Duprat E, Lefranc M-P, Gascuel O (2006) A simple method to predict protein binding from aligned sequences-application to MHC superfamily and beta2-microglobulin. Bioinformatics 22:453–459PubMedCrossRefGoogle Scholar
  23. 23.
    Bertrand G, Duprat E, Lefranc M-P, Marti J, Coste J (2004) Characterization of human FCGR3B*02 (HNA-1b, NA2) cDNAs and IMGT standardized description of FCGR3B alleles. Tissue Antigens Cover 64:119–131CrossRefGoogle Scholar
  24. 24.
    Frigoul A, Lefranc M-P (2005) MICA: standardized IMGT allele nomenclature, polymorphisms and diseases. In: Pandalai SG (ed) Recent research developments in human genetics, vol 3. Research Signpost, Trivandrum, Kerala, pp 95–145Google Scholar
  25. 25.
    Brochet X, Lefranc M-P, Giudicelli V (2008) IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res 36:W503–W508PubMedCrossRefGoogle Scholar
  26. 26.
    Lefranc M-P, Giudicelli V, Regnier L, Duroux P (2008) IMGT®, a system and an ontology that bridge biological and computational spheres in bioinformatics. Brief Bioinform 9:263–275PubMedCrossRefGoogle Scholar
  27. 27.
    Lefranc M-P (2009) Antibody databases and tools: The IMGT® experience. In: Zhiqiang An (ed) Therapeutic monoclonal antibodies: from bench to clinic (chapter 4). John Wiley & Sons, Inc., Hoboken, NJ, USA, pp 91–114PubMedCrossRefGoogle Scholar
  28. 28.
    Ehrenmann F, Duroux P, Giudicelli V, Lefranc M-P (2010) Standardized sequence and structure analysis of antibody using IMGT®. In: Kontermann R, and Dübel S (eds) Antibody engineering (chapter 2), vol 2, Springer-Verlab, Berlin, Heidelberg, pp 11–31PubMedCrossRefGoogle Scholar
  29. 29.
    Kaas Q, Ruiz M, Lefranc M-P (2004) IMGT/3Dstructure-DB and IMGT/Structural­Query, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Res 32:D208–D210PubMedCrossRefGoogle Scholar
  30. 30.
    Kaas Q, Lefranc M-P (2005) T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/3Dstructure-DB. In Silico Biol 5:505–528PubMedGoogle Scholar
  31. 31.
    Kaas Q, Duprat E, Tourneur G, Lefranc M-P (2008) IMGT standardization for molecular characterization of the T cell receptor/peptide/MHC complexes. In: Schoenbach C, Ranganathan S, Brusic V (eds) Immunoin­formatics. Immunomics Reviews, Series of Springer Science and Business Media LLC (chapter 2). Springer, New York, USA, pp 19–49Google Scholar
  32. 32.
    Lefranc M-P (2009) Antibody databases: IMGT®, a French platform of world-wide interest. Bases de données anticorps: IMGT®, une plate-forme française d’intérêt mondial “Anticorps monoclonaux en thérapeutique”. Med Sci 25:1020–1023Google Scholar
  33. 33.
    Lefranc M-P (2011) Antibody nomenclature: from IMGT-ONTOLOGY to INN definition. MAbs 3:1–2PubMedCrossRefGoogle Scholar
  34. 34.
    Jefferis R, Lefranc M-P (2009) Human immunoglobulin allotypes: possible implications for immunogenicity. MAbs 1(4):332–338PubMedCrossRefGoogle Scholar
  35. 35.
    Lefranc M-P, Lefranc G (2012) Human Gm, Km and Am allotypes and their molecular characterization: a remarkable demonstration of polymorphism. In: Tait B, Christiansen F (eds) Methods in Molecular Biology – Immunogenetics, Chapter 34PubMedCrossRefGoogle Scholar
  36. 36.
    Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147(1):195–197PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.IMGT®, The International ImMunoGeneTics Information System®Université Montpellier 2, Laboratoire d’ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UPR CNRS 1142MontpellierFrance
  2. 2.IMGT®, The International ImMunoGeneTics Information System®Université Montpellier 2, Laboratoire d’ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UPR CNRS1142MontpellierFrance

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