Immunoglobulins: 25 years of immunoinformatics and imgt-ontology

Biomolecules

Volumn 4, Issue 4, 2014, Pages 1102-1139

  Lefranc, Marie Paule ^a  

^a UNIV MONTPELLIER   (France)

Author keywords

Antibody humanization; IMGT; IMGT collier de perles; IMGT unique numbering; IMGT ONTOLOGY; Immune repertoire; Immunogenetics; Immunoglobulin; Immunoinformatics; Next generation sequencing

Indexed keywords

EPITOPE; HELIX LOOP HELIX PROTEIN; IMMUNOGLOBULIN; IMMUNOGLOBULIN ALLOTYPE; IMMUNOGLOBULIN ANTIBODY; IMMUNOGLOBULIN HEAVY CHAIN; IMMUNOGLOBULIN KAPPA CHAIN; IMMUNOGLOBULIN LAMBDA CHAIN; IMMUNOGLOBULIN LIGHT CHAIN; LYMPHOCYTE ANTIGEN RECEPTOR; MAJOR HISTOCOMPATIBILITY ANTIGEN; MONOCLONAL ANTIBODY; T LYMPHOCYTE RECEPTOR; CARRIER PROTEIN; PROLACTIN-BINDING PROTEIN;

ALLELE; AMINO ACID SEQUENCE; ANTIBODY COMBINING SITE; ANTIBODY ENGINEERING; ANTIGEN BINDING; BIOINFORMATICS; COMPUTER ANALYSIS; DATA ANALYSIS SOFTWARE; DNA BINDING MOTIF; GENE MAPPING; GENE NUMBER; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; GLYCOSYLATION; HIGH THROUGHPUT SEQUENCING; HINGE REGION; HUMAN; IMMUNOGENETICS; IMMUNOGENETICS INFORMATION SYSTEM; IMMUNOGENICITY; IMMUNOGLOBULIN CONSTANT REGION; IMMUNOGLOBULIN STRUCTURE, FUNCTION AND VARIABILITY; IMMUNOGLOBULIN VARIABLE REGION; NUCLEOTIDE SEQUENCE; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEIN TERTIARY STRUCTURE; REVIEW; BIOLOGY; GENETICS; IMMUNOGLOBULIN GENE; IMMUNOLOGY; PROCEDURES; PROTEIN DATABASE; PROTEIN ENGINEERING;

ALLELES; ANTIBODIES, MONOCLONAL, HUMANIZED; CARRIER PROTEINS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; GENES, IMMUNOGLOBULIN; GLYCOSYLATION; HUMANS; IMMUNOGENETICS; PROTEIN ENGINEERING;

EID: 84964315189     PISSN: None     EISSN: 2218273X     Source Type: Journal    
DOI: 10.3390/biom4041102     Document Type: Review

References (99)

1. IMGT®, the international ImMunoGeneTics information system®. Available online: http://www.imgt.org/ (accessed on 4 November 2014).
2. Lefranc, M.-P.; Giudicelli, V.; Duroux, P.; Jabado-Michaloud, J.; Folch, G.; Aouinti, S.; Carillon, E.; Duvergey, H.; Houles, A.; Paysan-Lafosse, T. et al. IMGT®, the international ImMunoGeneTics information system® 25 years on. Nucleic Acids Res. 2014, doi:10.1093/nar/gku1056.
3. Lefranc, M.-P.; Lefranc, G. The Immunoglobulin FactsBook; Academic Press: London, UK, 2001; pp. 1–458.
4. Lefranc, M.-P.; Lefranc, G. The T Cell Receptor FactsBook; Academic Press: London, UK, 2001; pp. 1–398.
5. Lefranc, M.-P. Nomenclature of the human immunoglobulin genes. In Current Protocols in Immunology; Coligan, J.E., Bierer, B.E., Margulies, D.E., Shevach, E.M., Strober, W., Eds.; John Wiley and Sons: Hoboken, NJ, USA, 2000; pp. 1–37.
6. Lefranc, M.-P. Nomenclature of the human T cell Receptor genes. In Current Protocols in Immunology; Coligan, J.E., Bierer, B.E., Margulies, D.E., Shevach, E.M., Strober, W., Eds.; John Wiley and Sons: Hoboken, NJ, USA, 2000; pp. 1–23.
7. Giudicelli, V.; Duroux, P.; Ginestoux, C.; Folch, G.; Jabado-Michaloud, J.; Chaume, D.; Lefranc, M.-P. IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. Nucleic Acids Res. 2006, 34, D781–D784.
8. Giudicelli, V.; Chaume, D.; Lefranc, M.-P. IMGT/GENE-DB: A comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res. 2005, 33, D256–D261.
9. Kaas, Q.; Ruiz, M.; Lefranc, M.-P. IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Res. 2004, 32, D208–D210.
10. Ehrenmann, F.; Kaas, Q.; Lefranc, M.-P. 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. 2010, 38, D301–D307.
11. Ehrenmann, F.; Lefranc, M-P. IMGT/3Dstructure-DB: Querying the IMGT Database for 3D Structures in Immunology and Immunoinformatics (IG or Antibodies, TR, MH, RPI, and FPIA). Cold Spring Harb. Protoc.2011, 6, 750–761.
12. Poiron, C.; Wu, Y.; Ginestoux, C.; Ehrenmann, F.; Duroux, P.; Lefranc, M.-P. IMGT/mAb-DB: the IMGT® database for therapeutic monoclonal antibodies. In proceedings of the 11èmes Journées Ouvertes de Biologie, Informatique et Mathématiques (JOBIM), Montpellier, France, 7–9 September 2010.
13. Giudicelli, V.; Chaume, D.; Lefranc, M.-P. IMGT/V-QUEST, an integrated software for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis. Nucleic Acids Res. 2004, 32, W435–W440.
14. Giudicelli, V.; Lefranc, M.-P. Interactive IMGT on-line tools for the analysis of immunoglobulin and T cell receptor repertoires. In New Research on Immunology; Veskler, B.A., Ed.; Nova Science Publishers Inc.: New York, NY, USA, 2005; pp. 77–105.
15. Brochet, X.; Lefranc, M.-P.; Giudicelli, V. 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. 2008, 36, W503–W508.
16. Giudicelli, V.; Lefranc, M.-P. IMGT® standardized analysis of immunoglobulin rearranged sequences. In Immunoglobulin Gene Analysis in Chronic Lymphocytic Leukemia; Ghia, P., Rosenquist, R., Davi, F., Eds.; Wolters Kluwer Health Italy Ltd: Milan, Italy, 2008; Chapter 2, pp. 33–52.
17. Giudicelli, V.; Brochet, X.; Lefranc, M.-P. IMGT/V-QUEST: IMGT Standardized Analysis of the Immunoglobulin (IG) and T Cell Receptor (TR) Nucleotide Sequences. Cold Spring Harb. Protoc.2011, 6, 695–715.
18. Alamyar, E.; Duroux, P.; Lefranc, M.-P.; Giudicelli, V. IMGT® tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. In Immunogenetics: Methods and Applications in Clinical Practice; Christiansen F.T., Tait, B.D., Eds.; Humana Press, Springer Science + Business Media: New York, NY, USA, 2012; Chapter 32, pp. 569–604.
19. Yousfi Monod, M.; Giudicelli, V.; Chaume, D.; Lefranc, M.-P. IMGT/JunctionAnalysis: The first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics2004, 20, i379–i385.
20. Giudicelli, V.; Lefranc, M.-P. IMGT/JunctionAnalysis: IMGT standardized analysis of the V-J and V-D-J junctions of the rearranged immunoglobulins (IG) and T cell receptors (TR). Cold Spring Harb. Protoc.2011, 6, 716–725.
21. Giudicelli, V.; Protat, C.; Lefranc, M.-P. The IMGT strategy for the automatic annotation of IG and TR cDNA sequences: IMGT/Automat. In Proceedings of the European Conference on Computational Biology (ECCB 2003), Data and Knowledge Bases, ECCB 2003, Paris, France, 27–30 September 2003; Institut National de Recherche en Informatique et en Automatique: Paris, France, 2003; pp. 103–104.
22. Giudicelli, V.; Chaume, D.; Jabado-Michaloud, J.; Lefranc, M.-P. Immunogenetics Sequence Annotation: the Strategy of IMGT based on IMGT-ONTOLOGY. Stud. Health Technol. Inform.2005, 116, 3–8.
23. Alamyar, E.; Giudicelli, V.; Shuo, L.; Duroux, P.; Lefranc, M.-P. IMGT/HighV-QUEST: The IMGT® web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. Immunome Res. 2012, 8, 1–15.
24. Li, S.; Lefranc, M.-P.; Miles, J.J.; Alamyar, E.; Giudicelli, V.; Duroux, P.; Freeman, J.D.; Corbin, V.; Scheerlinck, J.-P.; Frohman, M.A. et al. IMGT/HighV-QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nat. Commun.2013, 4, 1–13.
25. Ehrenmann, F.; Lefranc, M.-P. IMGT/DomainGapAlign: IMGT standardized analysis of amino acid sequences of Variable, Constant, and Groove domains (IG, TR, MH, IgSF, MhSF). Cold Spring Harb. Protoc.2011, 6, 737–749.
26. Ehrenmann, F.; Lefranc, M.-P. IMGT/DomainGapAlign: The IMGT® tool for the analysis of IG, TR, MHC, IgSF and MhcSF domain amino acid polymorphism. In Immunogenetics: Methods and Applications in Clinical Practice; Christiansen, F.T., Tait, B.D., Eds.; Humana Press, Springer Science + Business Media: New York, NY, USA, 2012; Chapter 33, pp. 605–633.
27. Ehrenmann, F.; Giudicelli, V.; Duroux, P.; Lefranc, M.-P. IMGT/Collier de Perles: IMGT Standardized Representation of Domains (IG, TR, and IgSF Variable and Constant Domains, MH and MhSF Groove Domains). Cold Spring Harb. Protoc.2011, 6, 726–736.
28. Lane, J.; Duroux, P.; Lefranc, M.-P. From IMGT-ONTOLOGY to IMGT/LIGMotif: The IMGT® standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences. BMC Bioinform. 2010, 11, 1–16.
29. Pommié, C.; Levadoux, S.; Sabatier, R.; Lefranc, G.; Lefranc, M.-P. IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties. J. Mol. Recognit.2004, 17, 17–32.
30. Lefranc, M.-P. IMGT, the international ImMunoGeneTics information system. In Immunoinformatics: Bioinformatic Strategies for Better Understanding of Immune Function; Bock G., Goode, J., Eds.; Novartis Foundation Symposium, John Wiley and Sons: Chichester, UK, 2003; Volume 254, pp. 126–142.
31. Lefranc, M.-P.; Giudicelli, V.; Ginestoux, C.; Chaume, D. IMGT, the international ImMunoGeneTics information system: the reference in immunoinformatics. Stud. Health Technol. Inform.2003, 95, 74–79.
32. Lefranc, M.-P. IMGT databases, web resources and tools for immunoglobulin and T cell receptor sequence analysis. Leukemia2003, 17, 260–266.
33. Lefranc, M.-P. IMGT, the international ImMunoGenetics information system®. In Antibody Engineering Methods and Protocols, 2nd ed.; Lo, B.K.C., Ed.; Humana Press: Totowa, NJ, USA, 2004; pp. 27–49.
34. Lefranc, M.-P. IMGT-ONTOLOGY and IMGT databases, tools and Web resources for immunogenetics and immunoinformatics. Mol. Immunol.2004, 40, 647–660.
35. Lefranc, M.-P. IMGT, the international ImMunoGeneTics information system: A standardized approach for immunogenetics and immunoinformatics. Immunome Res. 2005, 1, 1–11.
36. Lefranc, M.-P. IMGT®, the international ImMunoGeneTics information system® for immunoinformatics. Methods for querying IMGT® databases, tools and Web resources in the context of immunoinformatics. In Immunoinformatics: Predicting Immunogenicity in Silico; Flower, D.R., Ed.; Humana Press, Springer: Totowa, NJ, USA, 2007; Chapter 2; pp. 19–42.
37. Lefranc, M.-P. IMGT-ONTOLOGY, IMGT® databases, tools and Web resources for Immunoinformatics. In Immunoinformatics; Schoenbach, C., Ranganathan, S., Brusic, V., Eds.; Immunomics Reviews, Series of Springer Science and Business Media LLC; Springer: New York, NY, USA, 2008; Volume 1, Chapter 1, pp. 1–18.
38. Lefranc, M.-P.; Giudicelli, V.; Regnier, L.; Duroux, P. IMGT®, a system and an ontology that bridge biological and computational spheres in bioinformatics. Brief Bioinform. 2008, 9, 263–275.
39. Lefranc, M.-P. IMGT®, the international ImMunoGeneTics information system® for immunoinformatics. Methods for querying IMGT® databases, tools and Web resources in the context of immunoinformatics. Mol. Biotechnol. 2008, 40, 101–111.
40. Lefranc, M.-P. Antibody databases and tools: The IMGT® experience. In Therapeutic Monoclonal Antibodies: From Bench to Clinic; An, Z., Ed.; John Wiley and Sons: Hoboken, NJ, USA, 2009; Chapter 4, pp. 91–114.
41. Lefranc, M.-P. Antibody databases: IMGT®, a French platform of world-wide interest (in French). Bases de données anticorps: IMGT®, une plate-forme française d’intérêt mondial. Med. Sci. 2009, 25, 1020–1023.
42. Ehrenmann, F.; Duroux, P.; Giudicelli, V.; Lefranc, M.-P. Standardized sequence and structure analysis of antibody using IMGT®. In Antibody Engineering; Kontermann, R., Dübel, S., Eds.; Springer-Verlab: Berlin, Heidelberg, Germany, 2010; Volume 2, Chapter 2, pp. 11–31.
43. Lefranc, M-P. IMGT, the international ImMunoGeneTics information system. Cold Spring Harb. Protoc.2011, 6, 595–603.
44. Lefranc, M.-P. IMGT® Information System. In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science + Business Media, LLC012: New York, NY, USA, 2013; pp. 959–964.
45. Lefranc, M.-P. Immunoglobulin (IG) and T cell receptor genes (TR): IMGT® and the birth and rise of immunoinformatics. Front. Immunol. 2014, 5, 1–22.
46. Lefranc, M.-P. WHO-IUIS Nomenclature Subcommittee for immunoglobulins and T cell receptors report. Immunogenetics2007, 59, 899–902.
47. Lefranc, M.-P. WHO-IUIS Nomenclature Subcommittee for immunoglobulins and T cell receptors report August 2007, 13th International Congress of Immunology, Rio de Janeiro, Brazil. Dev. Comp. Immunol. 2008, 32, 461–463.
48. World Health Organization. International Nonproprietary Names (INN) for Biological and Biotechnological Substances (a Review). Available online: http://www.who.int/medicines/services/inn/BioRev2012.pdf (accessed on 4 November 2014).
49. Lefranc, M-P. Antibody nomenclature: From IMGT-ONTOLOGY to INN definition. MAbs 2011, 3, 1–2.
50. Giudicelli, V.; Lefranc, M.-P. Ontology for immunogenetics: IMGT-ONTOLOGY. Bioinformatics1999, 15, 1047–1054.
51. Giudicelli, V.; Lefranc, M.-P. IMGT-ONTOLOGY 2012. Frontiers in Bioinformatics and Computational Biology. Front. Genet. 2012, 3, 1–16.
52. Giudicelli, V.; Lefranc, M.-P. IMGT-ONTOLOGY. In Encyclopedia of Systems Biology; Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Eds.; Springer Science + Business Media, LLC012: New York, NY, USA, 2013; pp. 964–972.
53. Giudicelli, V.; Lefranc, M.-P. IMGT-ONTOLOGY: Gestion et découverte de connaissances au sein d’IMGT (in French). In Extraction et Gestion des Connaissances (EGC’2003); Hacid, M.-S., Kodratoff, Y., Boulanger, D., Eds.; Hermès Science Publications, Lavoisier: Cachan, Paris, France, 2003; pp. 13–23.
54. Lefranc, M.-P.; Giudicelli, V.; Ginestoux C.; Bosc, N.; Folch, G.; Guiraudou, D.; Jabado-Michaloud, J.; Magris, S.; Scaviner, D.; Thouvenin, V. et al. IMGT-ONTOLOGY for immunogenetics and immunoinformatics. Silico Biol. 2004, 4, 17–29.
55. Lefranc, M.-P.; Clément, O.; Kaas, Q.; Duprat, E.; Chastellan, P.; Coelho, I.; Combres, K.; Ginestoux, C.; Giudicelli, V.; Chaume, D. et al. IMGT-Choreography for Immunogenetics and Immunoinformatics. Silico Biol. 2005, 5, 45–60.
56. Duroux, P.; Kaas, Q.; Brochet, X.; Lane, J.; Ginestoux, C.; Lefranc, M.-P.; Giudicelli, V. IMGT-Kaleidoscope, the formal IMGT-ONTOLOGY paradigm. Biochimie2008, 90, 570–583.
57. Lefranc, M.-P. From IMGT-ONTOLOGY IDENTIFICATION axiom to IMGT standardized keywords: For immunoglobulins (IG), T cell receptors (TR), and conventional genes. Cold Spring Harb. Protoc. 2011, 6, 604–613.
58. Lefranc, M.-P. From IMGT-ONTOLOGY DESCRIPTION axiom to IMGT standardized labels: For immunoglobulin (IG) and T cell receptor (TR) sequences and structures. Cold Spring Harb. Protoc. 2011, 6, 614–626.
59. Lefranc, M.-P. From IMGT-ONTOLOGY CLASSIFICATION axiom to IMGT standardized gene and allele nomenclature: For immunoglobulins (IG) and T cell receptors (TR). Cold Spring Harb. Protoc.2011, 6, 627-632.
60. Lefranc, M.-P. Unique database numbering system for immunogenetic analysis. Immunol. Today1997, 18, 509.
61. Lefranc, M.-P. The IMGT unique numbering for Immunoglobulins, T cell receptors and Ig-like domains. Immunologist1999, 7, 132-136.
62. Lefranc, M.-P.; Pommié, C; Ruiz, M.; Giudicelli, V.; Foulquier, E.; Truong, L.; Thouvenin-Contet, V.; Lefranc, G. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev. Comp. Immunol. 2003, 27, 55–77.
63. Lefranc, M.-P.; Pommié, C; Kaas, Q.; Duprat, E.; Bosc, N.; Guiraudou, D.; Jean, C; Ruiz, M.; da Piedade, I.; Rouard, M. et al.IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev. Comp. Immunol.2005, 29, 185-203.
64. Lefranc, M.-P.; Duprat, E.; Kaas, Q.; Tranne, M.; Thiriot, A.; Lefranc, G. IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MhcSF) G-LIKE-DOMAIN. Dev. Comp. Immunol.2005, 29, 917-938.
65. Lefranc, M-P. IMGT unique numbering for the variable (V), constant (C), and groove (G) domains of IG, TR, MH, IgSF, and MhSF. Cold Spring Harb. Protoc. 2011, 6, 633-642.
66. Ruiz, M.; Lefranc, M.-P. IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures. Immunogenetics2002, 53, 857-883.
67. Kaas, Q.; Lefranc, M.-P. IMGT Colliers de Perles: Standardized sequence-structure representations of the IgSF and MhcSF superfamily domains. Curr. Bioinform.2007, 2, 21-30.
68. Kaas, Q.; Ehrenmann, F.; Lefranc, M.-P. IG, TR and IgSf, MHC and MhcSF: What do we learn from the IMGT Colliers de Perles? Brief Funct. Genomic Proteomic 2007, 6, 253-264.
69. Lefranc, M-P. IMGT Collier de Perles for the variable (V), constant (C), and groove (G) domains of IG, TR, MH, IgSF, and MhSF. Cold Spring Harb. Protoc. 2011, 6, 643-651.
70. Lefranc, M.-P. IMGT® immunoglobulin repertoire analysis and antibody humanization. In Molecular Biology of B Cells, 2nd ed.; Alt, F., Honjo, T., Radbruch, A., Reth, M., Eds.; Elsevier Ltd.: London, UK, 2014; Volume 1, Chapter 27, pp. 481-514.
71. Robert, R.; Lefranc, M.-P.; Ghochikyan, A.; Agadjanyan, M.G; Cribbs, D.H.; van Nostrand, W.E.; Wark, K.L.; Dolezal, O. Restricted V gene usage and VH/VL pairing of mouse humoral response against the N-terminal immunodominant epitope of the amyloid p peptide. Mol. Immunol.2010, 48, 59-72.
72. Ghia, P.; Stamatopoulos, K; Belessi, C; Moreno, C; Stilgenbauer, S.; Stevenson, F.I.; Davi, F.; Rosenquist, R. ERIC recommendations on IGHV gene mutational status analysis in chronic lymphocytic leukemia. Leukemia2007, 21, 1-3.
73. Agathangelidis, A.; Darzentas, N.; Hadzidimitriou, A.; Brochet, X.; Murray, F.; Yan, X.J.; Davis, Z.; van Gastel-Mol, E.J.; Tresoldi, C; Chu, C.C. et al.Stereotyped B-cell receptors in one third of chronic lymphocytic leukemia: Towards a molecular classification with implications for targeted therapeutic interventions. Blood2012, 119, 4467-4475.
74. Kostareli, E.; Gounari, M.; Janus, A.; Murray, F.; Brochet, X.; Giudicelli, V.; Pospisilova, S.; Oscier, D.; Foroni, L.; di Celle, P.F. et al. Antigen receptor stereotypy across B-cell lymphoproliferations: the case of IGHV4–59/IGKV3–20 receptors with rheumatoid factor activity. Leukemia2012, 26, 1127–1131.
75. Xochelli, A.; Agathangelidis, A.; Kavakiotis, I.; Minga, E.; Sutton, L.A.; Baliakas, P.; Chouvarda, I.; Giudicelli, V.; Vlahavas, I.; Maglaveras, N. et al. Immunoglobulin heavy variable (IGHV) genes and alleles: New entities, new names and implications for research and prognostication in chronic lymphocytic leukemia. Immunogenetics2014, doi:10.1007/s00251-014-0812-3.
76. Jefferis, R.; Lefranc, M.-P Human immunoglobulin allotypes: Possible implications for immunogenicity. MAbs2009, 1, 332–338.
77. Lefranc, M.-P.; Lefranc, G. Human Gm, Km and Am allotypes and their molecular characterization: A remarkable demonstration of polymorphism. In Immunogenetics: Methods and Applications in Clinical Practice; Christiansen, F.T., Tait, B.D., Eds.; Humana Press, Springer: New York, NY, USA, 2012; Chapter 34; pp. 635–680.
78. Dechavanne, C.; Guillonneau, F.; Chiappetta, G.; Sago, L.; Lévy, P.; Salnot, V.; Guitard, E.; Ehrenmann, F.; Broussard, C.; Chafey, P. et al. Mass spectrometry detection of G3m and IGHG3 alleles and follow-up of differential mother and neonate IgG3. PLoS One2012, 7, e46097.
79. Magdelaine-Beuzelin, C.; Kaas, Q.; Wehbi, V.; Ohresser, M.; Jefferis, R.; Lefranc, M.-P.; Watier, H. Structure-function relationships of the variable domains of monoclonal antibodies approved for cancer treatment. Crit. Rev. Oncol. Hematol.2007, 64, 210–225.
80. Pelat, T.; Bedouelle, H.; Rees, A.R.; Crennell, S.J.; Lefranc, M.-P.; Thullier, P. Germline humanization of a non-human Primate antibody that neutralizes the anthrax toxin, by in vitro and in silico engineering. J. Mol. Biol.2008, 384, 1400–1407.
81. Pelat, T.; Hust, M.; Hale, M.; Lefranc, M.-P.; Dübel, S.; Thullier, P. Isolation of a human-like antibody fragment (scFv) that neutralizes ricin biological activity. BMC Biotechnol. 2009, 9, 1–13.
82. Lefranc, M.-P.; Ehrenmann, F.; Ginestoux, C.; Duroux, P.; Giudicelli, V. Use of IMGT® databases and tools for antibody engineering and humanization. In Antibody Engineering, 2nd ed.; Chames, P., Ed.; Humana Press, Springer Science + Business Media LLC: New York, NY, USA, 2012; Chapter 1; pp. 3–37.
83. Alamyar, E.; Giudicelli, V.; Duroux, P.; Lefranc, M.-P. Antibody V and C domain sequence, structure and interaction analysis with special reference to IMGT®. In Monoclonal Antibodies: Methods and Protocols, 2nd ed.; Ossipow, V., Fisher, A., Eds.; Humana Press, Springer Science + Business Media LLC: New York, NY, USA, 2013; Chapter 21; pp. 337–381.
84. Lefranc, M.-P. Immunoinformatics of the V, C and G domains: IMGT® definitive system for IG, TR and IgSF, MH and MhSF. In Immunoinformatics: From Biology to Informatics, 2nd ed.; de, R.K., Tomar, N., Eds.; Humana Press, Springer Science + Business Media LLC: New York, NY, USA, 2013; Chapter 4; pp. 59–107.
85. Lefranc, M.-P. How to use IMGT® for therapeutic antibody engineering. In Handbook of Therapeutic Antibodies, 2nd ed.; Dübel, S., Reichert, J., Eds.; Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, Germany, 2014; Volume 1, Chapter 10, pp. 229–263.
86. Shirai, H.; Prades, C.; Vita, R.; Marcatili, P.; Popovic, B.; Xu, J.; Overington, J.P.; Hirayama, K.; Soga, S.; Tsunoyama, K. et al. Biochim. Biophys. Acta2014, 1844, 2002–2015.
87. BioPortal. Available online: http://bioportal.bioontology.org/ontologies/IMGT-ONTOLOGY/ (accessed on 4 November 2014).
88. Wain, H.M.; Bruford, E.A.; Lovering, R.C.; Lush, M.J.; Wright, M.W.; Povey S. Guidelines for human gene nomenclature. Genomics 2002, 79, 464–470.
89. Bruford, E.A.; Lush, M.J.; Wright, M.W.; Sneddon, T.P.; Povey, S.; Birney, E. The HGNC database in 2008: A resource for the human genome. Nucleic Acids Res. 2008, 36, D445–D448.
90. Letovsky, S.I.; Cottingham, R.W.; Porter, C.J.; Li, P.W. GDB: The human Genome Database. Nucleic Acids Res. 1998, 26, 94–99.
91. Maglott, D.R.; Katz, K.S.; Sicotte, H.; Pruitt, K.D. NCBI’s LocusLink and RefSeq. Nucleic Acids Res. 2000, 28, 126–128.
92. Maglott, D.; Ostell, J.; Pruitt, K.D.; Tatusova, T. Entrez Gene: Gene-centered information at NCBI. Nucleic Acids Res. 2007, 35, D26–D31.
93. Stabenau, A.; McVicker, G.; Melsopp, C.; Proctor, G.; Clamp, M.; Birney, E. The Ensembl core software libraries. Genome Res. 2004, 14, 929–933.
94. Wilming, L.G.; Gilbert, J.G.; Howe, K.; Trevanion, S.; Hubbard, T.; Harrow, J.L. The vertebrate genome annotation (Vega) database. Nucleic Acids Res. 2008, 36, D753–D760.
95. Kabat, E.A.; Wu, T.T.; Perry, H.M.; Gottesman K.S.; Foeller C. Sequences of Proteins of Immunological Interest; Department of Health and Human Services (USDHHS), National Institute of Health NIH Publication: Washington, DC, USA, 1991; pp. 91–3242.
96. Chothia, C.; Lesk, A.M. Canonical structures for the hypervariable regions of immunoglobulins. Mol. Biol.1987, 196, 901–917.
97. PyMOL. Available online: http://www.pymol.org/ (accessed on 4 November 2014).
98. Rose, P.W.; Beran, B.; Bi, C.; Bluhm, W.F.; Dimitropoulos, D.; Goodsell, D.S.; Prlic, A.; Quesada, M.; Quinn, G.B.; Westbrook, J.D. et al. The RCSB Protein Data Bank: Redesigned web site and web services. Nucleic Acids Res. 2011, 39, D392–D401.
99. Riechmann, L.; Clark, M.; Waldmann, H.; Winter, G. Reshaping human antibodies for therapy. Nature 1988, 332, 323–327.