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 Harbor Protocols

Volumn 6, Issue 6, 2011, Pages 716-725

  Giudicelli, Véronique ^a   Lefranc, Marie Paule ^a  

^a CNRS and University Montpellier II   (France)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN; T LYMPHOCYTE RECEPTOR;

ANALYTIC METHOD; ARTICLE; DIVERSITY GENE; GENE; GENE REARRANGEMENT; GENETIC VARIABILITY; INFORMATION SYSTEM; INTERNATIOMAL IMMUNOGENETICS INFORMATION SYSTEM; JOINING GENE; MOLECULAR MECHANICS; SOMATIC HYPERMUTATION; VARIABLE GENE;

EID: 79958026088     PISSN: None     EISSN: 15596095     Source Type: Journal    
DOI: 10.1101/pdb.prot5634     Document Type: Article

References (44)

1. Alamyar E, Giudicelli V, Duroux P, Lefranc M-P. 2010. IMGT/HighVQUEST: A high-throughput system and Web portal for the analysis of rearranged nucleotide sequences of antigen receptors - Highthroughput version of IMGT/V-QUEST. JOBIM 2010 Poster 60. http://www.jobim2010.fr/?q=fr/node/55.
2. Alamyar E, Duroux D, Lefranc M-P, Giudicelli V. 2011. 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. Methods Mol Biol (in press).
3. Bleakley K, Giudicelli V, Wu Y, Lefranc M-P, Biau G. 2006. IMGT standardization for statistical analyses of T cell receptor junctions: The TRAV-TRAJ example. In Silico Biol 6: 573-588.
4. Bleakley K, Lefranc M-P, Biau G. 2008. Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools. BMC Bioinformatics 9: 408. doi: 10.1186/1471-2105-9-408.
5. 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. Nucl Acids Res 36: W503-W508.
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: 570-583.
7. Ehrenmann F, Lefranc M-P. 2011a. IMGT/DomainGapAlign: IMGT standardized analysis of amino acid sequences of variable, constant and groove domains (IG, TR, MH, IgSF, MhSF). Cold Spring Harb Protoc doi: 10.1101/pdb.prot5636.
8. Ehrenmann F, Lefranc M-P. 2011b. 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 doi: 10.1101/pdb.prot5637.
9. Ehrenmann F, Duroux P, Giudicelli V, Lefranc M-P. 2010. Standardized sequence and structure analysis of antibody using IMGT. In Antibody engineering 2nd ed. (ed. R Kontermann, S Dübel), Vol 2, pp. 11-31. Springer-Verlag, Berlin/Heidelberg, Germany.
10. Ehrenmann F, Giudicelli V, Brochet X, Lefranc M-P. 2011. 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 doi: 10.1101/pdb. prot5635.
11. Giudicelli V, Lefranc M-P. 1999. Ontology for immunogenetics: IMGT-ONTOLOGY. Bioinformatics 15: 1047-1054.
12. Giudicelli V, Lefranc M-P. 2005. Interactive IMGT on-line tools for the analysis of immunoglobulin and T cell receptor repertoires. In New Research on Immunology (ed. BA Veskler), pp. 77-105. Nova Science, Hauppauge, NY.
13. Giudicelli V, Lefranc M-P. 2008. IMGT standardized analysis of immunoglobulin rearranged sequences. In Immunoglobulin gene analysis in Chronic Lymphocytic Leukemia (ed. P Ghia, R Rosenquist, F Davi), pp. 33-52. Wolters Kluwer Health Italy, Italy.
14. Giudicelli V, Protat C, Lefranc M-P. 2003. The IMGT strategy for the automatic annotation of IG and TR cDNA sequences: IMGT/ Automat. In Proceedings of the European Conference on Computational Biology, pp. 103-104. Paris, France.
15. Giudicelli V, Chaume D, Lefranc M-P. 2005a. IMGT/GENE-DB: A comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res 33: D256-D261.
16. Giudicelli V, Chaume D, Jabado-Michaloud J, Lefranc M-P. 2005b. Immunogenetics sequence annotation: The strategy of IMGT based on IMGT-ONTOLOGY. Stud Health Technol Inform 116: 3-8.
17. Giudicelli V, Duroux P, Ginestoux C, Folch G, Jabado-Michaloud J, Chaume D, Lefranc M-P. 2006. IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. Nucl Acids Res 34: D781-D784.
18. Giudicelli V, Brochet X, Lefranc M-P. 2011. IMGT/V-QUEST: IMGT standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences. Cold Spring Harb Protoc doi: 10.1101/pdb.prot5633.
19. Lefranc M-P. 1997. Unique database numbering system for immunogenetic analysis. Immunol Today 18: 509. doi: 10.1016/ S0167-5699(97)01163-8.
20. Lefranc M-P. 1999. The IMGT unique numbering for Immunoglobulins, T cell receptors and Ig-like domains. The Immunologist 7: 132-136.
21. Lefranc M-P. 2000a. Nomenclature of the human immunoglobulin genes. In Current Protocols in Immunology (ed. JE Coligan et al.), pp. A.1P.1-A.1P.37. John Wiley and Sons, Hoboken, NJ.
22. Lefranc M-P. 2000b. Nomenclature of the human T cell receptor genes. In Current Protocols in Immunology (ed. JE Coligan et al.), pp. A.1O.1-A.1O.23. John Wiley and Sons, Hoboken, NJ.
23. Lefranc M-P. 2004. IMGT, the International ImMunoGenetics Information System. In Antibody engineering methods and protocols 2nd ed. (ed. BKC Lo), Vol 248, pp. 27-49. Methods in Molecular Biology, Humana Press, Totowa, NJ.
24. Lefranc M-P. 2007. WHO-IUIS Nomenclature Subcommittee for Immunoglobulins and T cell receptors report. Immunogenetics 59: 899-902.
25. Lefranc M-P. 2008. 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 32: 461-463.
26. Lefranc M-P. 2009. Antibody database and tools: The IMGT experience. In Therapeutic monoclonal antibodies: From bench to clinic (ed. A Zhiqiang), pp. 91-114. John Wiley and Sons, Hoboken, NJ.
27. Lefranc M-P. 2011a. IMGT, the International ImMunoGeneTics Information System. Cold Spring Harb Protoc doi: 10.1101/pdb. top115.
28. Lefranc M-P. 2011b. From IMGT-ONTOLOGY IDENTIFICATION axiom to IMGT standardized keywords: For immunoglobulins (IG), T cell receptors (TR), and conventional genes. Cold Spring Harb Protoc doi: 10.1101/pdb.ip82.
29. Lefranc M-P. 2011c. From IMGT-ONTOLOGY DESCRIPTION axiom to IMGT standardized labels: For immunoglobulin (IG) and T cell receptor (TR) sequences and structures. Cold Spring Harb Protoc doi: 10.1101/pdb.ip83.
30. Lefranc M-P. 2011d. From IMGT-ONTOLOGY CLASSIFICATION axiom to IMGT standardized gene and allele nomenclature: For immunoglobulins (IG) and T cell receptors (TR). Cold Spring Harb Protoc doi: 10.1101/pdb.ip84.
31. Lefranc M-P. 2011e. IMGT unique numbering for the variable (V), constant (C), and groove (G) domains of IG, TR, MH, IgSF, and MhSF. Cold Spring Harb Protoc doi: 10.1101/pdb.ip85.
32. Lefranc M-P. 2011f. 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 doi: 10.1101/pdb.ip86.
33. Lefranc M-P, Lefranc G. 2001a. The Immunoglobulin FactsBook, 1-458. Academic Press, London, UK.
34. Lefranc M-P, Lefranc G. 2001b. The T cell receptor FactsBook, 1-398. Academic Press, London, UK.
35. 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: 55-77.
36. Lefranc M-P, Giudicelli V, Ginestoux C, Bosc N, Folch G, Guiraudou D, Jabado-Michaloud J, Magris S, Scaviner D, Thouvenin V, et al. 2004. IMGT-ONTOLOGY for Immunogenetics and Immunoinformatics. In Silico Biology 4: 17-29.
37. Lefranc M-P, Clément O, Kaas Q, Duprat E, Chastellan P, Coelho I, Combres K, Ginestoux C, Giudicelli V, Chaume D, et al. 2005a. IMGT-Choreography for Immunogenetics and Immunoinformatics. In Silico Biology 5: 45-60.
38. Lefranc M-P, Pommié C, Kaas Q, Duprat E, Bosc N, Guiraudou D, Jean C, Ruiz M, Da Piedade I, Rouard M, et al. 2005b. IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev Comp Immunol 29: 185-203.
39. Lefranc M-P, Duprat E, Kaas Q, Tranne M, Thiriot A, Lefranc G. 2005c. IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MhcSF) G-LIKE-DOMAIN. Dev Comp Immunol 29: 917-938.
40. 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: 263-275.
41. Lefranc M-P, Giudicelli V, Ginestoux C, Jabado-Michaloud J, Folch G, Bellahcene F, Wu Y, Gemrot E, Brochet X, Lane J, et al. 2009. IMGT, the international ImMunoGeneTics information system. Nucl Acids Res 37: D1006-D1012.
42. 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: 17-32.
43. Stamatopoulos K, Belessi C, Moreno C, Boudjograh M, Guida G, Smilevska T, Belhoul L, Stella S, Stavroyianni N, Crespo M, et al. 2007. Over 20% of patients with chronic lymphocytic leukemia carry stereotyped receptors: Pathogenetic implications and clinical correlations. Blood 109: 259-270.
44. Yousfi Monod M, Giudicelli V, Chaume D, Lefranc M-P. 2004. IMGT/ JunctionAnalysis: The first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics 20: i379-i385.