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At least 19 recordsLinked to original sources
PubMed2005

IMGT, the international ImMunoGeneTics information system: a standardized approach for immunogenetics and immunoinformatics.

IMGT, the international ImMunoGeneTics information system http://imgt.cines.fr, was created in 1989 by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM) (Université Montpellier II and CNRS) at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) of any species which belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT consists of five databases, ten on-line tools and more than 8,000 HTML pages of Web resources. IMGT provides a common access to standardized data from genome, genetics, proteome and three-dimensional structures. The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY, a semantic specification of terms to be used in immunogenetics and immunoinformatics. IMGT-ONTOLOGY comprises six main concepts: IDENTIFICATION, CLASSIFICATION, DESCRIPTION, NUMEROTATION, ORIENTATION and OBTENTION. Based on these concepts, the controlled vocabulary and the annotation rules necessary for the immunogenetics data identification, classification, description and numbering and for the management of IMGT knowledge are defined in the IMGT Scientific chart. IMGT is the international reference in immunogenetics and immunoinformatics for medical research (repertoire analysis of the IG antibody sites and of the TR recognition sites in autoimmune and infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research (IG and TR repertoires in farm and wild life species), genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (single chain Fragment variable (scFv), phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (detection and follow up of residual diseases) and therapeutical approaches (grafts, immunotherapy, vaccinology). IMGT is freely available at http://imgt.cines.fr.

Journal Article↗
PubMed2002

The immunogenetics and pathogenesis of gastric cancer. Highlights of the First Sino-European Workshop on the Immunogenetics and Pathogenesis of Gastric Cancer.

Clinical scientists from eight European countries and China gathered in the ancient Chinese capital of Xi'an on April 26-28, 2001 to discuss collaboration on a modern approach to gastric cancer prevention. Participants at the First Sino-European Workshop on Immunogenetics and Pathogenesis of Gastric Cancer presented their most up-to-date research results on topics ranging from epidemiology and immune mechanisms to Helicobacter pylori and vaccine development. Researchers then formed groups with their Chinese or European counterparts to plan future research endeavors which will benefit Chinese and European populations alike. After 3 years of organization between the Institute of Digestive Diseases of the Fourth Medical University in Xi'an, China and the Laboratory of Immunogenetics, VU University Medical Center in Amsterdam, the first workshop came into being under the joint sponsorship of the Commission of the European Union, National Natural Science Foundation of China and the Institute of Digestive Diseases, Xi'an, China. As gastric cancer is the most prevalent malignant tumor in China, the workshop was of special significance to the Chinese researchers and to the Chinese population in general. During the workshop, presentations on the epidemiology of gastric cancer showed that this disease is in fact common the world over: it is the second most common cancer next to lung cancer and about 1 million new cases were diagnosed in 2000. Three-quarters of the cases of gastric cancer occur in Asia, and approximately 80% of these cases are in China and Japan. Genetic factors and environmental factors such as diet and H. pylori infection play a role in gastric carcinogenesis. As a recognized cause of gastric cancer, H. pylori was the subject of various presentations ranging from immunological studies, molecular analysis of strains and pathogenesis to vaccine development. Specific areas of discussion included bacterial-epithelial interactions in H. pylori infection, epidemiology in China, global distribution of vacA and cagA genotypes, new evidence for host factors, nonsteroidal antiinflammatory drugs and H. pylori as independent risk factor for gastric cancer, new diagnostic techniques for H. pylori using serum levels of pepsinogen I, and autoimmune processes in corpus atrophy. Vaccine development using a variety of strategies against H. pylori was the subject of an entire session of talks. Oral immunization with urease with Escherichia coli heat labile enterotoxin was shown to be safe and immunogenic in humans as a mucosal adjuvant. Results of a study using attenuated Salmonella typhimurium as a vehicle for DNA-mediated immunization in mice were also presented. A final presentation discussed an ongoing trial comparing strain variability in the vacA and cagA gene sequences and disease expression between H. pylori infection in Europe and China. Researchers also discussed the role of IL1 gene family and TNF gene polymorphisms in gastric pathology and various immune mechanisms involved in gastric cancer, such as down-regulation of NF kappa B, IL-1 and IL-1RA, cyclooxygenase signalling, and identification of MGAg antibodies. An interactive discussion followed each presentation and ideas and suggestions were provided. According to specialty, the presenters were then assigned to groups of four or five to make plans for joint research projects. A number of international and Chinese observers were present, including representatives from the European Commission, the World Health Organization and the Chinese National Center for Biotechnology Development, and offered input on the financial feasibility of such projects.

China↗
PubMed1998

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).

Amino Acid Sequence↗
PubMed2002

[Selection for disease resistance in domestic ruminants and swine by indicator traits as well as marker and causal genes--a review. Part 1: Short introduction to immunogenetics of MHC and non-MHC genes and special immunogenetics of cattle and swine].

The introduction deals with immunogenetic investigations on the field of life-stock. The main chapter is outlined as a tabular overview of current opportunities of the application of indicator traits as well as marker and causal genes in breeding for disease resistance in cattle, sheep, goats and swine. In the discussion of the second part, emphasis was layed on diseases of small ruminants in central and western Europe. Indicator traits are discussed with respect of their advantages and disadvantages. The rigorous selection of specific traits is connected with an increase of the number of homozygotes. In contrary, pathogens do undergo mutations, thus escaping the host's immune system. Out of this point of view it is advisable, to set on selection very cautiously. The role of technologies of modern immunogenetics is pointed out in respect of constructing disease resistant animals.

Animals↗
PubMed1998

IMGT (ImMunoGeneTics) locus on focus. A new section of Experimental and Clinical Immunogenetics.

IMGT, the international ImMunoGeneTics database (http:/(/)imgt.cnusc.fr:8104) 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). The new section of Experimental and Clinical Immunogenetics, 'IMGT locus on focus', will give the more updated and extensive overview of the current status of the different Ig, TcR and MHC genes in IMGT, with standardization of gene nomenclature, functionality, and allele polymorphism according to the IMGT rules and unique numbering.

Amino Acids↗
PubMed2002

IMGT, the international ImMunoGeneTics database: a high-quality information system for comparative immunogenetics and immunology.

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/HLA-DB, IMGT/3Dstructure-DB), Web resources ('IMGT Marie-Paule page') which comprise IMGT Scientific Chart, IMGT Repertoire, IMGT Bloc-notes, IMGT Education, IMGT Aide-mémoire and IMGT Index, and interactive tools (IMGT/V-QUEST, IMGT/JunctionAnalysis). These expertly annotated data on the genome, proteome, genetics and structure of the IG, TR and MHC are of high value for comparative genome evolution studies of the adaptative immune response.

Animals↗
PubMed1975

Information processing immunogenetic analysis. IV. Information amount and predictive power of different immunogenetic models.

Principles of information theory are imposed on immunogenetic information processing, whereby the 'information amount', simplicity, 'redundancy' and 'predicatability' of different encodings, models, theories or mappings can be objectively compared. As an example, the experimental observables emanating from the Rh system at its 10 reagent-8 haplotype level is shown to obtain an information amount of 140,120 and 78 bits when interpreted (encoded according to a simple-complex, complex-simple and complex-complex theory, model or program, respectively. The 'predictive' or 'accomodating' power of the simple-complex and complex-simple theories is shown to be 134, respectively 366 bits for a given set of experimental observables emanating from a S3 universe.

Computers↗
PubMed1999

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.

Animals↗
PubMed1978

Lipoprotein immunogenetics and atherosclerosis.

The discovery of the first human lipoprotein polymorphism by Allison and Blumberg [Lancet i:634-637, 1961] and the availability of alloimmune sera stimulated us to begin immunogenetic studies on swine in search of lipoprotein diversity and its relationship to biological functions. We found considerable lipoprotein polymorphism, complexity, and heterogeneity in this species. These results and the correlation between immunogenetically defined lipoprotein type and arterial lipidosis in swine, fed a high fat diet, are discussed. Immunogenetic studies of lipoproteins, initiated more recently in rhesus monkeys, will be reviewed also. Preliminary data show similarities between these two species with regard to polymorphism, complexity, phenotypic expression of lipoprotein genes and, most importantly, their serological relationship to human lipoproteins. We also note immunogenetic studies on lipoproteins done by other investigators, or in other species. Brief remarks on implications of the lipoproteins in atherosclerosis, their general classification, immunological properties, and immunological methods used in their study precede the immunogenetic presentation.

Animals↗
PubMedDate not supplied

Towards a unified theory for immunogenetic systems. Some selected properties of ABC- and AB-D reaction patterns generated by S3 and T3 universes.

The principles of a radically new unified theory and a unified but fundamentally theory-invariant classification system are described and exemplified for immunogenetic systems. The classification system permits a differentiation of immunogenetic systems into 15 qualitatively distinct classes with quantitative subsets when tested against two reagents. It can easily be expanded into a n-reagent taxonomy. The theory logically explains a set of selected and previously more or less "unexplainable" properties and their (even more unexplainable and probably previously unnoticed) associations in two main classes of immunogenetic systems, the ABC- and AB-D systems. The associated properties discussed are the presence (+) or absence (-) of: 1. antithetical alleles; 2. dosage effects; 3. inherited "strong" and "weak" antigens; 4. "silent" or "amorphous" genes. In ABC- systems, properties 1 and 2 are present while 3 and 4 are absent or extremely rare (i.e. 1+2+3-4-). In AB-D systems, properties 1 and 2 are absent while 3 and 4 are present (i.e. 1-2-3+4+). Through the design of hypothetical immunogenetic universes (HIU), these property associations are shown to be produced by the contemporary (simple-complex) framework-dependent transformations of experimental observables/matrix facts and not by any corresponding associated properties present in the input HIU in themselves.

ABO Blood-Group System↗
PubMed1983

Mathematical immunogenetics II. Antibody incidence structure.

Mathematical Immunogenetics I argued for the development of mathematics as a language for immunogenetics. A three-fold factorization of a reaction matrix was seen to be the important form of a model of a first order immunogenetic system. In the present paper, results of the authors on determining this factorization are reworked from a physical perspective and presented in an algorithmic form that can be used to compute a labeling matrix from data. Computer programs to perform these computations are in preparation.

Animals↗
PubMed1991

Subacute cutaneous lupus erythematosus-immunogenetic associations.

Thirty-two patients who fulfilled criteria for subacute cutaneous lupus erythematosus (SCLE) were examined for their immunogenetic associations. Our results confirm the previously reported association of HLA-DR3 (15/31 48% P less than 0.01) and also demonstrate an increase in HLA-DR2 (14/31, 45%, P = less than 0.05). These findings indicate there are two distinct immunogenetic (HLA) populations of Ro(SS-A) antibody-positive SCLE patients. The increased frequency of HLA-DR2 and DR3 appears to be associated with expression of the Ro(SS-A) antibody, since no HLA associations were seen in Ro(SS-A)-negative SCLE patients when compared with normal population controls. Furthermore, these data indicate that the distinctive cutaneous lesions of SCLE are not associated with one specific HLA allele, as previously suspected. These findings contrast with the relatively homogeneous immunogenetic background seen in other lupus erythematosus subsets with a high frequency of Ro(SS-A) antibody, i.e., neonatal lupus erythematosus and Sjögren's syndrome/lupus erythematosus overlap (increased frequency of HLA-DR3, DQw2 and DRW52).

Adult↗
PubMed2005

Introduction to statistical analysis of population data in immunogenetics.

We review the most classical questions addressed by the analysis of population data in immunogenetics. Basic genetics' definitions are reminded. Questions related to the population data itself (structure, missing values nomenclature, sampling) are developed first, and secondly, the population genetics questions (relevance of genetic parameters (phenotype, genotype allele and haplotype frequencies; genetic distances; linkage disequilibrium measures), methods and practical computing) are illustrated by immunogenetics polymorphisms. This article gives the essential of population immunogenetics on examples and key references. We underline the importance of population dimension in statistical analysis: structure of linkage disequilibrium and genetic diversity between populations may affect the power of the study or the interpretation of correlations between markers, genes and diseases, making population genetics both theoretical and very practical.

Data Interpretation, Statistical↗
PubMed1996

Immunogenetics in liver disease.

Recent advances in molecular biology, in particular X-ray crystallography of the purified antigens A2 and DR1 and development of PCR-based HLA genotyping techniques, has revolutionized our understanding of immunogenetics and cellular immunology. The application of molecular immunogenetics has refined our understanding of HLA-encoded susceptibility and resistance to both autoimmune and chronic viral liver disease. Recent studies of autoimmune hepatitis (AIH), primary sclerosing cholangitis (PSC) and primary biliary cirrhosis (PBC) have identified substitutions of specific amino acid residues in the HLA DR beta-polypeptide (AIH and PSC) and DP beta-polypeptide (PBC) which may determine susceptibility to and resistance from disease. Although these models of HLA-encoded susceptibility in PSC and PBC are currently controversial, the model for AIH, based on lysine residue at DR beta 71 has recently been confirmed in an independent series. Data on chronic viral liver disease are less abundant, but a number of interesting observations are beginning to emerge. In the Gambia, resistance to chronic hepatitis B infection has been associated with the HLA DRB1*1302 allele, and in studies of patients with chronic hepatitis C virus infection DQA1*03 and DQB1*05 have been identified as a possible protective factors. Clarifying these HLA associations is not simply an academic pursuit; in addition to providing useful clues to the pathogenesis of these diseases, HLA associations may be important indicators of prognosis. In AIH, patients with the DRB1*0301-DRB3*0101 haplotype appear to have more severe disease than those with DRB1*0401, while in PSC, DRB3*0101 is associated with early onset of disease and DRB1*0401 may be a marker of more rapid disease progression. To date, our knowledge of immunogenetic susceptibility in liver disease is incomplete and further work is needed.

Humans↗
PubMed1995

"The sarcoidosis map": a joint survey of clinical and immunogenetic findings in two European countries.

We pooled immunogenetic data obtained in independent studies in two European populations (Italian and Czech) of patients affected by sarcoidosis. Correspondence analysis was used to investigate the associations between clinical and immunogenetic data. Two hundred and thirty-three patients were enrolled in the study, of which 126 were from the Czech Republic and 107 from Italy. Using a common protocol, we examined each patient for sex, age of disease onset, roentgenologic stage, extrapulmonary spread, and clinical course. One thousand and ten healthy individuals, HLA typed for class I and II serologic polymorphisms, served as controls. Findings that were essentially in agreement in both populations were: (1) a positive association of sarcoidosis with HLA-A1, B8, and DR3 markers, and a negative association with HLA-B12 and DR4; (2) a prevalence of HLA-DR3 and DR4 among females and of DR5 among males; (3) a relationship of B13 and B35 with early onset and of A30, B8, DR3, and DR4 with late onset of disease; (4) an association of B27 with sarcoidosis restricted to the lungs; (5) a relationship of A1, B8, B27, and DR3 to roentgenologic stage I and of B12 and DR4 to stage III; and (6) an association of HLA-DR3 with a good outcome. Population-restricted findings essentially concerned the alleles HLA-B13 and B22, the former being associated with the disease, male sex, early onset, extrapulmonary localization and relapse only in Czechs, and the latter to disease spread only in Italians. Our results seem to support the concept that immunogenetic background may at least partly account for the clinical heterogeneity of sarcoidosis.

Adult↗
PubMed2000

Immunogenetic background of patients with autoimmune fatigue syndrome.

We have previously reported that approximately 50% of children with chronic nonspecific complaints were positive for antinuclear antibodies (ANA), and that a novel autoantibody to a 62 kD protein (anti-Sa) was found in 40% of these ANA-positive patients. Therefore, we proposed a distinct disease entity termed autoimmune fatigue syndrome (AIFS). We hypothesized that if autoimmune mechanisms did play an important role in the pathogenesis of AIFS, it is possible that it is immunogenetically regulated as observed in other autoimmune disorders. In order to examine the immunogenetic background of AIFS patients, HLA-A, -B, -C, and -DR loci were analyzed serologically in 61 AIFS patients. AIFS was found to be positively associated with the class I antigen HLA-B61 and with the class II antigen HLA-DR9, with odds ratios of 2.77 (p = 0.015, Pcorr = 0.48) and 2.60 (p= 0.012, Pcorr = 0.17), respectively. A negative association was also found between AIFS and HLA-DR2 with odds ratio of 0.25 (p = 0.029, Pcorr = 0.041). When comparing anti-Sa positive AIFS patients with healthy controls, the odds ratios associated with HLA-B61, DR9, and DR2 were 3.42 (p = 0.021, Pcorr = 0.22), 3.96 (p = 0.0011, Pcorr = 0.015), and 0.16 (p = 0.0022, Porr = 0.031), respectively. Thus, the HLA associations observed in this study suggested that immunogenetic background might play a role in AIFS.

Adolescent↗