Abstract
IMGT, the international ImMunoGeneTics database® (http://imgt.cines.fr), is a high-quality integrated information system specializing in immunoglobulins (IG), T cell receptors (TR) and major histocompatibility complex (MHC) of human and other vertebrates, created in 1989, by LIGM, at the Université Montpellier II, CNRS, Montpellier, France. IMGT provides a common access to standardized data which include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, 2D and 3D structures. IMGT includes several databases (IMGT/LIGM-DB, IMGT/3Dstructure-DB, IMGT/HLA-DB), Web resources (‘IMGT Marie-Paule page’) and interactive tools (IMGT/V-QUEST, IMGT/JunctionAnalysis). IMGT expertly annotated data and tools described in this paper are particularly useful for the analysis of the IG and TR rearrangements in leukemia, lymphoma and myeloma, and in translocations involving the antigen receptor loci. IMGT is freely available at http://imgt.cines.fr.
This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data
Genome Medicine Open Access 20 March 2018
-
Human TRAV1-2-negative MR1-restricted T cells detect S. pyogenes and alternatives to MAIT riboflavin-based antigens
Nature Communications Open Access 16 August 2016
-
Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci
Genome Medicine Open Access 23 November 2015
Access options
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
Lefranc, M-P & Lefranc, G The Immunoglobulin FactsBook, Academic Press: London (2001).
Lefranc, M-P & Lefranc, G The T Cell Receptor FactsBook, Academic Press: London (2001).
Stoesser, G, Baker, W, Van den Broek, A, Camon, E, Garcia-Pastor, M, Kanz, C, Kulikova, T, Lombard, V, Lopez, R, Parkinson, H, Redaschi, N, Sterk, P, Stoehr, P & Tuli, M-A The EMBL nucleotide sequence database. Nucleic Acids Res, (2001). 29, 17–21.
Benson, DA, Karsch-Mizrachi, I, Lipman, D, Ostell, J, Rapp, BA & Wheeler, DL GenBank. Nucleic Acids Res, (2000). 28, 15–18.
Tateno, Y, Miyazaki, S, Ota, M, Sugawara, H & Gojobori, T DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams. Nucleic Acids Res, (2000). 28, 24–26.
Lefranc, M-P IMGT, the international ImMunoGeneTics database. Nucleic Acids Res, (2001). 29, 207–209.
Giudicelli, V, Chaume, D, Bodmer, J, Müller, W, Busin, C, Marsh, S, Bontrop, R, Lemaitre, M, Malik, & Lefranc, M-P IMGT, the international ImMunoGeneTics database. Nucleic Acids Res, (1997). 25, 206–211.
Lefranc, M-P, Giudicelli, V, Busin, C, Bodmer, J, Müller, W, Bontrop, R, Lemaitre, M, Malik, A & Chaume, D IMGT, the international ImMunoGeneTics database. Nucleic Acids Res, (1998). 26, 297–303.
Lefranc, M-P, Giudicelli, V, Ginestoux, C, Bodmer, J, Müller, W, Bontrop, R, Lemaitre, M, Malik, A, Barbié, V & Chaume, D IMGT, the international ImMunoGeneTics database. Nucleic Acids Res, (1999). 27, 209–212.
Ruiz, M, Giudicelli, V, Ginestoux, C, Stoehr, P, Robinson, J, Bodmer, J, Marsh, SG, Bontrop, R, Lemaitre, M, Lefranc, G, Chaume, D & Lefranc, M-P IMGT, the international ImMunoGeneTics database. Nucleic Acids Res, (2000). 28, 219–221.
Ruiz, M & Lefranc, M-P IMGT gene identification and Colliers de Perles of human immunoglobulin with known 3D structures. Immunogenetics DOI 10.1007/s00251-001-0408-6. Immunogenetics, (2002). 53, 857–883.
Robinson, J, Malik, A, Parham, P, Bodmer, JG & Marsh, SGE IMGT/HLA Database – a sequence database for the human major histocompatibility complex. Tissue Antigens, (2000). 55, 280–287.
Giudicelli, V & Lefranc, M-P Ontology for Immunogenetics: IMGT-ONTOLOGY. Bioinformatics, (1999). 12, 1047–1054.
Lefranc, M-P Nomenclature of the human immunoglobulin genes. Current Protocols in Immunology, J Wiley and Sons: New York (2000). Suppl. 40, A.1P.1–A.1P.37.
Lefranc, M-P Nomenclature of the human T cell Receptor genes. Current Protocols in Immunology, J Wiley and Sons: New York, USA (2000). Suppl. 40, A.1O.1–A.1O.23.
Lefranc, M-P Locus maps and genomic repertoire of the human Ig genes. Immunologist, (2000). 8, 80–87.
Lefranc, M-P Locus maps and genomic repertoire of the human T-cell receptor genes. Immunologist, (2000). 8, 72–79.
Lefranc, M-P Nomenclature of the human immunoglobulin heavy (IGH) genes. Exp Clin Immunogenet, (2001). 18, 100–116.
Lefranc, M-P Nomenclature of the human immunoglobulin kappa (IGK) genes. Exp Clin Immunogenet, (2001). 18, 161–174.
Lefranc, M-P Nomenclature of the human immunoglobulin lambda (IGL) genes. Exp Clin Immunogenet, (2001). 18, 242–254.
Lefranc, M-P IMGT (ImMunoGeneTics) Locus on Focus. A new section of experimental and clinical immunogenetics. Exp Clin Immunogenet, (1998). 15, 1–7.
Pallarès, N, Frippiat, JP, Giudicelli, V & Lefranc, M-P The human immunoglobulin lambda variable (IGLV) genes and joining (IGLJ) segments. Exp Clin Immunogenet, (1998). 15, 8–18.
Barbié, V & Lefranc, M-P The human immunoglobulin kappa variable (IGKV) genes and joining (IGKJ) segments. Exp Clin Immunogenet, (1998). 15, 171–183.
Pallarès, N, Lefebvre, S, Contet, V, Matsuda, F & Lefranc, M-P The human immunoglobulin heavy variable (IGHV) genes. Exp Clin Immunogenet, (1999). 16, 36–60.
Ruiz, M, Pallarès, N, Contet, V, Barbié, V & Lefranc, M-P The human immunoglobulin heavy diversity (IGHD) and joining (IGHJ) segments. Exp Clin Immunogenet, (1999). 16, 173–184.
Folch, G & Lefranc, M-P The human T cell receptor beta variable (TRBV) genes. Exp Clin Immunogenet, (2000). 17, 42–54.
Scaviner, D & Lefranc, M-P The human T cell receptor alpha variable (TRAV) genes. Exp Clin Immunogenet, (2000). 17, 83–96.
Scaviner, D & Lefranc, M-P The human T cell receptor alpha joining (TRAJ) genes. Exp Clin Immunogenet, (2000). 17, 97–106.
Folch, G & Lefranc, M-P The human T cell receptor beta diversity (TRBD) and beta joining (TRBJ) genes. Exp Clin Immunogenet, (2000). 17, 107–114.
Scaviner, D, Barbié, V, Ruiz, M & Lefranc, M-P Protein displays of the human immunoglobulin heavy, kappa and lambda variable and joining regions. Exp Clin Immunogenet, (1999). 16, 234–240.
Folch, G, Scaviner, D, Contet, V & Lefranc, M-P Protein displays of the human T cell receptor alpha, beta, gamma and delta variable and joining regions. Exp Clin Immunogenet, (2000). 17, 205–215.
Lefranc, M-P Unique database numbering system for immunogenetic analysis. Immunol Today, (1997). 18, 509
Lefranc, M-P The IMGT unique numbering for Immunoglobulins, T cell receptors and Ig-like domains. Immunologist, (1999). 7, 132–136.
Kabat, EA, Wu, TT, Perry, HM, Gottesman, KS & Foeller, C Sequences of Proteins of Immunological Interest, National Institute of Health Publications: Washington DC (1991). 91–3242.
Satow, Y, Cohen, GH, Padlan, EA & Davies, DR Phosphocholine binding immunoglobulin Fab McPC603. J Mol Biol, (1986). 190, 593–604.
Chothia, C & Lesk, AM Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol, (1987). 196, 901–917.
Lefranc, M-P Web sites of Interest to immunologists. Current Protocols in Immunology, J Wiley and Sons: New York (2000). A.1J.1–A.1J.33.
Giudicelli, V, Chaume, D & Lefranc, M-P IMGT/LIGM-DB: A systematized approach for ImMunoGeneTics database coherence and data distribution improvement. Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, ISBM-98. (1998). 59–68.
Giudicelli, V, Chaume, D, Mennessier, G, Althaus, HH, Mller, W, Bodmer, J, Malik, A & Lefranc, M-P IMGT, the international ImMunoGeneTics database: a new Design for Immunogenetics Data Access. In: Cesnik B et al (eds). Proceedings of the Ninth World Congress on Medical Informatics, MEDINFO’ 98, IOS Press: Amsterdam (1998). 351–355.
Lefranc, M-P IMGT, the international ImMunoGeneTics database: a high-quality information system for comparative immmunogenetics and immunology. Dev Comp Immunol, (in press)
Eckert, C, Landt, O, Taube, T, Seeger, K, Beyermann, B, Proba, J & Henze, G Potential of LightCycler technology for quantification of minimal residual disease in childhood acute lymphoblastic leukemia. Leukemia, (2000). 14, 316–323.
Delabesse, E, Burtin, ML, Millien, C, Madonik, A, Arnulf, B, Beldjord, K, Valensi, F & Macintyre, EA Rapid, multifluorescent TCRG Vgamma and Jgamma typing: application to T cell acute lymphoblastic leukemia and to the detection of minor clonal populations. Leukemia, (2000). 14, 1143–1152.
Szczepanski, T, Langerak, AW, Willemse, MJ, Wolvers-Tettero, ILM, van Wering, ER & van Dongen, JJM T cell receptor gamma (TCRG) gene rearrangements in T cell acute lymphoblastic leukemia reflect ‘end-stage’ recombinations: implications for minimal residual disease monitoring. Leukemia, (2000). 14, 1208–1214.
Bruggemann, M, Droese, J, Bolz, I, Luth, P, Pott, C, von Neuhoff, N, Scheuering, U & Kneba, M Improved assessment of minimal residual disease in B cell malignancies using fluorogenic consensus probes for real-time quantitative PCR. Leukemia, (2000). 14, 1419–1425.
Verhagen, OJHM, Willemse, MJ, Breunis, WB, Wijkhuijs, AJM, Jacobs, DCH, Joosten, SA, van Wering, ER, van Dongen, JJM & van der Schoot, CE Application of germline IGH probes in real-time quantitative PCR for the detection of minimal residual disease in acute lymphoblastic leukemia. Leukemia, (2000). 14, 1426–1435.
De Haas, V, Verhagen, OJ, von dem Borne, AE, Kroes, W, van den Berg, H & van der Schoot, CE Quantification of minimal residual disease in children with oligoclonal B-precursor acute lymphoblastic leukemia indicates that the clones that grow out during relapse already have the slowest rate of reduction during induction therapy. Leukemia, (2001). 15, 134–140.
Szczepanski, T, Willemse, MJ, van Wering, ER, Weerden, JF, Kamps, WA & van Dongen, JJM Precursor-B-ALL with DH-JH gene rearrangements have an immature immunogenotype with a high frequency of oligoclonality and hyperdiploidy of chromosome 14. Leukemia, (2001). 15, 1415–1423.
Moreira, I, Papaioannou, M, Mortuza, FY, Gameiro, P, Palmisano, GL, Harrison, CJ, Prentice, HG, Mehta, AB, Hoffbrand, AV & Foroni, L Heterogeneity of VH-JH gene rearrangement patterns: an insight into the biology of B cell precursor ALL. Leukemia, (2001). 15, 1527–1536.
Boeckx, N, Willemse, MJ, Szczepanski, T, van Der Velden, VHJ, Langerak, AW, Vandekerckhove, P & van Dongen, JJM Fusion gene transcripts and Ig/TCR gene rearrangements are complementary but infrequent targets for PCR-based detection of minimal residual disease in acute myeloid leukemia. Leukemia, (2002). 16, 368–375.
Van der Velden, VHJ, Wijkhuijs, JM, Jacobs, DCH, van Wering, ER & van Dongen, JJM T cell receptor gamma gene rearrangements as targets for detection of minimal residual disease in acute lymphoblastic leukemia by real-time quantitative PCR analysis. Leukemia, (2002). 16, (in press)
Van der Velden, VHJ, Willemse, MJ, van der Schoot, CE, van Wering, ER & van Dongen, JJM Immunoglobulin kappa deleting element rearrangements in precursor–B acute lymphoblastic leukemia are stable targets for detection of minimal residual disease by real-time quantitative PCR. Leukemia, (2002). 16, (in press)
Acknowledgements
I thank Véronique Giudicelli, Denys Chaume and Gérard Lefranc for helpful discussion, Nora Bonnet for typing the manuscript. I am deeply grateful to the IMGT team for its expertise and constant motivation. IMGT is funded by the European Union's 5th PCRDT programme (QLG2-2000-01287), the CNRS (Centre National de la Recherche Scientifique), the Ministère de l’Education Nationale, and the Ministère de la Recherche. Subventions have been received from ARC (Association pour la Recherche sur le Cancer), and the Région Languedoc-Roussillon.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Lefranc, MP. IMGT® databases, web resources and tools for immunoglobulin and T cell receptor sequence analysis, http://imgt.cines.fr. Leukemia 17, 260–266 (2003). https://doi.org/10.1038/sj.leu.2402637
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/sj.leu.2402637
Keywords
This article is cited by
-
BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data
Genome Medicine (2018)
-
Human TRAV1-2-negative MR1-restricted T cells detect S. pyogenes and alternatives to MAIT riboflavin-based antigens
Nature Communications (2016)
-
Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci
Genome Medicine (2015)
-
Artemis splice defects cause atypical SCID and can be restored in vitro by an antisense oligonucleotide
Genes & Immunity (2011)
-
Pitfalls in TCR gene clonality testing: teaching cases
Journal of Hematopathology (2008)