Analysis of somatic hypermutations of immunoglobulin gene rearrangements in childhood acute lymphoblastic leukemia.

The current study investigated the presence, frequency, and status of somatic hypermutations as well as their role in children with B lineage ALL. The obtained sequences were analyzed using IMGT/V-QUEST. Totally, 150 IGH sequences were evaluated; 139 from the 111 patients at the time of diagnosis and 11 from 8/111 patients at the time of relapse. The findings of the current report revealed the presence of somatically mutated V genes in childhood B lineage ALL. A higher frequency of somatic hypermutations was noted in unproductive rearrangements and was generally attributed to nucleotide mutation type, region, and IGHV gene subgroup biases.

IMGT, the international ImMunoGeneTics database: a new design for immunogenetics data access.

IMGT, the international ImMunoGeneTics database is an integrated database specializing in Immunoglobulins (Ig), T-cell receptors (TcR) and MHC molecules of all vertebrate species, created by Marie-Paule Lefranc, University of Montpellier, CNRS, Montpellier, France (Nucleic Acids Research, Database issue, Vol 26, January 1998). IMGT includes three databases: LIGM-DB (for Ig and TcR), MHC/HLA-DB and IMGT/PRIMER-DB (an Ig, TcR and MHC-related primer database), the last two in development. IMGT comprises expertly annotated sequences and alignment tables. LIGM-DB contains more than 24.000 Immunoglobulin and T cell Receptor sequences from 81 different species. MHC/HLA-DB contains class I and class II Human Leucocyte Antigen alignment tables. An IMGT tool, DNAPLOT, developed for Ig, TcR and MHC sequence analysis, is also available. IMGT goals are to establish a common data access to all immunogenetics data, including nucleotide and protein sequences, oligonucleotide primers, gene maps and other genetic data of Ig, TcR and MHC molecules, from all species, and to provide a graphical user friendly data access. IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas), therapeutical approaches (antibody engineering), genome diversity and genome evolution studies. In this paper, we describe our approach for the data modelisation, the automation of the annotation procedure and control of data quality in LIGM-DB database. IMGT is freely available on the CNUSC WWW server at Montpellier: http://imgt.cnusc.fr: 8104 (contact: Denys.Chaume@cnusc.fr) and on the EBI servers: http://www.ebi.ac.uk/imgt (contact: malik@ebi.ac.uk) and ftp.ebi.ac.uk/pub/databases/imgt. LIGM-DB users are encouraged to report errors or suggestions to giudi@ligm.crbm.cnrs-mop.fr. IMGT initiator and coordinator: Marie-Paule Lefranc, lefranc@ligm.crbm.cnrs-mop.fr. (fax: +33(0)467040231).

Ontology for immunogenetics: the IMGT-ONTOLOGY.

MOTIVATION: IMGT, the international ImMunoGeneTics database (http:@imgt.cines.fr:8104), created by M.-P. Lefranc, is an integrated database specializing in antigen receptors (immunoglobulins and T-cell receptors) and major histocompatibility complex (MHC) of all vertebrate species. IMGT accurate immunogenetics data are based on the standardization of the biological knowledge provided by the 'ImMunoGeneTics' IMGT-ONTOLOGY. The IMGT-ONTOLOGY describes the classification and specification of terms needed for immunogenetics and bioinformatics. IMGT-ONTOLOGY covers four main concepts: 'IDENTIFICATION', 'DESCRIPTION', 'CLASSIFICATION' and 'OBTENTION'. These concepts allow an extensive and standardized description and characterization of immunoglobulin and T-cell receptor data. The controlled vocabulary and the annotation rules are indispensable to ensure accuracy, consistency and coherence in IMGT. IMGT-ONTOLOGY allows scientists and clinicians to use, for the first time, identical terms with the same meaning in immunogenetics. It provides a semantic repository that will improve interoperability between specialist and generalist databases.

IMGT/LIGM-DB: a systematized approach for ImMunoGeneTics database coherence and data distribution improvement.

IMGT, the international ImMunoGeneTics database (http:(/)/imgt.cnusc.fr:8104), created by Marie-Paule Lefranc, Montpellier, France, is an integrated database specializing in antigen receptors and MHC of all vertebrate species. IMGT includes LIGM-DB, developed for Immunoglobulins and T-cell-receptors. LIGM-DB distributes high quality data with an important increment value added by the LIGM expert annotations. LIGM-DB accurate immunogenetics data is based on the standardization of biological knowledge related to keywords, annotation labels and gene identification. The management of such data resulting from biological research requires an high flexible implementation to quickly reflect up-to-date results, and to integrate new knowledge. We developed a systematized approach and defined LIGM-DB systems which manage and realize the major tasks for the database survey. In this paper, we will focus on the coherence system, which became absolutely crucial to maintain data quality as the database is growing up and as the biological knowledge continues to improve, and on the distribution system which makes LIGM-DB data easy to access, download and reuse. Efforts have been done to improve the data distribution procedures and adapt them to the current bioinformatics needs. Recently, we have developed an API which allows Java programmers to remotely access and integrate LIGM-DB data in other computer environments.

The human immunoglobulin lambda variable (IGLV) genes and joining (IGLJ) segments.

The first report of the 'IMGT Locus on Focus' section comprises five tables entitled: (1) 'Number of human germline IGLV genes at 22q11.1-q11.2 and potential repertoire'; (2) 'Human germline IGLV gene table'; (3) 'Human IGLV allele table', (4) 'Human germline IGLJ table' and (5) 'Human IGLJ allele table'. These tables are available at the MariePaule page from IMGT, the international ImMunoGeneTics database (http:/(/)imgt.cnusc.fr:8104) created by Marie-Paule Lefranc, CNRS, Université Montpellier II, Montpellier, France.

Affinity purification and characterization of recombinant human galectin-1.

Galectin-1, a polypeptidic factor that can have major effects on cell growth and apoptosis, was overexpressed in E. coli. This protein was purified to homogeneity by affinity chromatography on lactose coupled to divinylsulfone-activated agarose. The recombinant galectin-1 (rGAL1) was compared with the homologous protein purified from human brain tissue using two-dimensional electrophoresis on immobilized pH gradient (IPG-DALT). rGAL1 had a major isoelectric point of 5.4 (major pI of tissular galectin-1, 5.1) and its subunit molecular mass was 14500. Addition of rGAL1 to Jurkat T-lymphoblastoid cells induced cell death in a concentration-dependent manner.

IMGT, the international ImMunoGeneTics database.

IMGT, the international ImMunoGeneTics database, is an integrated database specializing in immunoglobulins, T-cell receptors (TcR) and major histocompatibility complex (MHC) of all vertebrate species, initiated and co-ordinated by Marie-Paule Lefranc, CNRS, Montpellier II University, Montpellier, France (lefranc@ligm.crbm.cnrs-mop.fr). IMGT includes two databases: LIGM-DB (for immunoglobulins and TcR) and MHC/HLA-DB. IMGT comprises expertly annotated sequences and alignment tables. LIGM-DB contains more than 19 000 immunoglobulin and TcR sequences from 78 species. MHC/HLA-DB contains class I and class II human leukocyte antigen alignment tables. An IMGT tool, DNAPLOT, developed for immunoglobulins, TcR and MHC sequence alignments, is also available. IMGT works in close collaboration with the EMBL database. IMGT goals are to establish a common data access to all immunogenetics data, including sequences, oligonucleotide primers, gene maps and other genetic data of immunoglobulins, TcR and MHC molecules, and to provide a graphical user-friendly data access. IMGT will have important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas), therapeutical approaches (antibody engineering), genome diversity and genome evolution studies. IMGT can be accessed at http://imgt.cnusc.fr:8104 and http://www.ebi.ac.uk/IMGT

IMGT, the International ImMunoGeneTics database.

IMGT, the international ImMunoGeneTics database, is an integrated database specialising in Immunoglobulins (Ig), T cell Receptors (TcR) and Major Histocompatibility Complex (MHC) of all vertebrate species, created by Marie-Paule Lefranc, CNRS, Montpellier II University, Montpellier, France (lefranc@ligm.crbm.cnrs-mop.fr). IMGT includes three databases: LIGM-DB (for Ig and TcR), MHC/HLA-DB and PRIMER-DB (the last two in development). IMGT comprises expertly annotated sequences and alignment tables. LIGM-DB contains more than 23 000 Immunoglobulin and T cell Receptor sequences from 78 species. MHC/HLA-DB contains Class I and Class II Human Leucocyte Antigen alignment tables. An IMGT tool, DNAPLOT, developed for Ig, TcR and MHC sequence alignments, is also available. IMGT works in close collaboration with the EMBL database. IMGT goals are to establish a common data access to all immunogenetics data, including nucleotide and protein sequences, oligonucleotide primers, gene maps and other genetic data of Ig, TcR and MHC molecules, and to provide a graphical user friendly data access. IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas), therapeutical approaches (antibody engineering), genome diversity and genome evolution studies. IMGT is freely available at http://imgt.cnusc.fr:8104

IMGT, the international ImMunoGeneTics database.

IMGT, the international ImMunoGeneTics database (http://imgt.cnusc. fr:8104), is a high-quality integrated database specialising in Immunoglobulins (Ig), T cell Receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species, created in 1989 by Marie-Paule Lefranc, Université Montpellier II, CNRS, Montpellier, France (lefranc@ligm.igh.cnrs.fr). IMGT comprises three databases: LIGM-DB, a comprehensive database of Ig and TcR, MHC/HLA-DB, and PRIMER-DB (the last two in development); a tool, IMGT/DNAPLOT, developed for sequence analysis and alignments; and expertised data based on the IMGT scientific chart, the IMGT repertoire. By its high quality and its easy data distribution, IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas), therapeutic approaches (antibody engineering), genome diversity and genome evolution studies. IMGT is freely available at http://imgt.cnusc. fr:8104

IMGT, the international ImMunoGeneTics database.

IMGT, the international ImMunoGeneTics database (http://imgt.cines. fr:8104 ), is a high-quality integrated database specialising in Immunoglobulins (Ig), T cell Receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species, created in 1989 by Marie-Paule Lefranc, Université Montpellier II, CNRS, Montpellier, France (lefranc@ligm.igh.cnrs.fr ). At present, IMGT includes two databases: IMGT/LIGM-DB, a comprehensive database of Ig and TcR from human and other vertebrates, with translation for fully annotated sequences, and IMGT/HLA-DB, a database of the human MHC referred to as HLA (Human Leucocyte Antigens). The IMGT server provides a common access to expertized genomic, proteomic, structural and polymorphic data of Ig and TcR molecules of all vertebrates. By its high quality and its easy data distribution, IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas), therapeutic approaches (antibody engineering), genome diversity and genome evolution studies. IMGT is freely available at http://imgt.cines.fr:8104. The IMGT Index is provided at the IMGT Marie-Paule page (http://imgt.cines.fr:8104/textes/IMGTindex.html).