IMGT

IMGT

Content
Description	Nucleic sequences, amino acids, annotations, and tools related to the adaptive immune system.
Organisms	Vertebrate
Release date	1989 (1989)
Access
Website	IMGT

IMGT or the international ImMunoGeneTics information system is a collection of databases and resources for immunoinformatics, particularly the V, D, J, and C gene sequences, as well as a providing other tools and data related to the adaptive immune system. IMGT/LIGM-DB, the first and still largest database hosted as part of IMGT contains reference nucleotide sequences for 360 species' T-cell receptor and immunoglobulin molecules, as of 2023. These genes encode the proteins which are the foundation of adaptive immunity, which allows highly specific recognition and memory of pathogens.

History

The logo of IMGT

IMGT was founded in June, 1989, by Marie-Paule Lefranc, an immunologist working at University of Montpellier. The project was presented to the 10th Human Genome Mapping Workshop, and resulted in the recognition of V, D, J, and C regions as genes. The first resource created was IMGT/LIGM-DB, a reference for nucleotide sequences of T-cell receptor and immunoglobulin of humans, and later vertebrate species. IMGT was created under the auspices of Laboratoire d'ImmunoGénétique Moléculaire at the University of Montpellier as well as French National Centre for Scientific Research (CNRS).

As both T-cell receptors and immunoglobulin molecules are built through a process of recombination of nucleotide sequences, the annotation of the building block regions and their role is unique within the genome. To standardize terminology and references, the IMGT-NC was created in 1992 and recognized by the International Union of Immunological Societies as a nomenclature subcommittee. Other tools include IMGT/Collier-de-Perles, a method for two dimensional representation of receptor amino acid sequences, and IMGT/mAb-DB, a database of monoclonal antibodies. Now maintained by the HLA Informatics Group, the primary reference for human HLA, IPD-IMGT/HLA Database, originated in part with IMGT. It was merged with the Immuno Polymorphism Database in 2003 to form the current reference.

Since 2015, IMGT has been headed by Sofia Kossida.

IMGT Tools

IMGT/V-QUEST

IMGT/V-QUEST is an integrated and sophisticated online tool designed for the standardized analysis of rearranged nucleotide sequences of immunoglobulins (IG) and T cell receptors (TR). It is a critical resource in immunogenetics, aiding researchers and clinicians in understanding the diverse mechanisms of antigen receptor diversity, crucial for the adaptive immune system.

Functional Capabilities

IMGT/V-QUEST includes several key functional capabilities:

1. Gene and Allele Identification: Identifies variable (V), diversity (D), and joining (J) genes and alleles in IG and TR sequences through precise alignment with the IMGT reference directory.
2. Mutation Analysis: Detects and describes mutations within the V-REGION and identifies mutation hotspots in the closest germline V gene.
3. Insertion and Deletion Detection: Uses the IMGT unique numbering system to identify insertions and deletions, ensuring accurate sequence alignment and annotation.
4. Junction Analysis: Integrates IMGT/JunctionAnalysis for detailed analysis of V-J and V-D-J junctions, providing insights into recombination events.
5. Sequence Annotation: Uses IMGT/Automat for comprehensive annotation of sequences, enhancing understanding of their structure and function.
6. Result Presentation: Results are presented in two views:
   1. *Detailed View:* Displays individual sequence results and alignments.
   2. *Synthesis View:* Shows alignments of sequences sharing the same V gene and allele for comparative analysis.
7. Customizable Analysis: Allows researchers to modify analysis parameters to suit specific research needs.

Applications and Importance

IMGT/V-QUEST is used for immunology research, offering:

• Insights into immune diversity and its genetic bases.
• Support for antibody engineering and therapeutic antibody development.
• Assistance in diagnosing and researching immunological disorders.

IMGT/HighV-QUEST

IMGT/HighV-QUEST is a high-throughput variant of IMGT/V-QUEST, specifically adapted for analyzing large datasets typically obtained through next-generation sequencing (NGS) technologies. As part of IMGT, the international ImMunoGeneTics information system, it is a globally recognized resource for immunogenetics and immunoinformatics. This tool supports extensive immune repertoire analyses and is invaluable for studies involving large-scale data, helping to explore the diversity of the adaptive immune system in health and disease, and assisting in antibody discovery and engineering.

Primary Functions

IMGT/HighV-QUEST's primary functions are comprehensive and designed to meet the needs of advanced immunological research:

1. Analysis of Nucleotide Sequences: Capable of processing and analyzing up to 500,000 IG (immunoglobulin) and TR (T cell receptor) nucleotide sequences per run, it identifies variable (V), diversity (D), and joining (J) genes and characterizes mutations, particularly those resulting from somatic hypermutations.
2. Junction Analysis: Incorporates IMGT/JunctionAnalysis for detailed characterization of the V-D-J or V-J junctions, providing insights into the molecular mechanisms underlying immune diversity.
3. Sequence Annotation: Uses IMGT/Automat for complete annotation of sequences, including the identification of insertions and deletions which may arise as errors during sequence generation (NGS errors).
4. Statistical Analysis: Performs statistical analysis on the sequence data to help identify clonotypes and understand the distribution and variation within the IG and TR repertoires.
5. High-Quality Results: Delivers results with a high degree of resolution and quality, consistent with other IMGT tools, ensuring reliable and standardized outputs for immunogenetic research.

Utility and Application

IMGT/HighV-QUEST is particularly useful in both research and clinical settings for:

• Exploring the diversity of the adaptive immune system in health and disease.
• Advancing antibody discovery and engineering.
• Supporting the diagnosis and monitoring of immunological disorders through detailed repertoire analysis. Its ability to handle large-scale data efficiently and its integration with comprehensive immunogenetics data from IMGT makes it a critical tool for advanced immunological research and practice.

Additional IMGT Websites

IMGT offers additional websites containing various information about immunogenetics. These websites offer tools and data as described above such as genome browsers, taxonomy tables, descriptions of the databases offered by IMGT and links to publications in the immunogenetics field.

IMGT Medical

The IMGT Medical page focuses on the clinical applications of immunogenetics specifically in human diseases and disorders. The page offers resources and publications to help educate medical professionals, researchers, clinicians and students study and understand the genetic bases of immune-related diseases such as autoimmune disorders, immunodeficiencies and cancer. The aim of IMGT medical is to act as a library of knowledge for a starting point rather than be a totally exhaustive encyclopedia.

IMGT Veterinary

The IMGT Verterinary page is dedicated to the study of immunogenetics in Verterinary medicine and animal health. The page serves as a website for researchers, veterinarians and breeders interested in learning more about the immune systems of various species including mammals, birds, reptiles and fish. IMGT veterinary offers data, tools and databases tailored to the specific needs of veterinary research and practices such as the study of diseases, vaccination and breeding programs.

IMGT Biotechnology

The IMGT Biotechnology focuses on the application of immunogenetics in biotechnology and pharmaceutical research. It provides resources and tools for the development of therapeutic antibodies, vaccines, and other immunotherapeutic agents. This page supports researchers and industry professionals in designing, engineering, and characterizing novel immunological products for medical and biotechnological applications. IMGT Biotechnology aims to accelerate the discovery and development of immunotherapies for various diseases, including cancer, infectious diseases, and autoimmune disorders.

IMGT Immunoinformatics

IMGT immunoinformatics specializes in the field of immunoinformatics, which involves the computational analysis and modeling of immune-related data. IMGT Immunoinformatics offers a range of bioinformatics tools, databases, and algorithms for analyzing immunoglobulin (IG) and T cell receptor (TR) sequences, predicting protein structures, studying immune repertoires, and simulating immune responses. IMGT Immunoinformatics serves as a valuable resource for researchers and bioinformaticians interested in leveraging computational methods to study the immune system and related biological processes.

IMGT/StatClonotype

Overview

IMGT/StatClonotype is a specialized tool designed for the visualization and statistical analysis of nucleotide sequences of immunoglobulins (IG) and T cell receptors (TR). It complements the capabilities of IMGT/V-QUEST by providing insights into clonal diversity, abundance, and distribution within immune repertoires, aiding researchers and clinicians in understanding the dynamics of adaptive immune responses.

Functional Capabilities

1. Clonal Analysis: Identifies and characterizes clonal populations within IG and TR sequences based on shared sequence similarity and commonality in V, D, and J gene usage.
2. Abundance Profiling: Quantifies the abundance of each clonotype within the sequenced repertoire, allowing assessment of relative frequencies of different clonal populations.
3. Diversity Metrics: Calculates various diversity metrics, such as clonal richness and evenness, providing quantitative measures of repertoire diversity.
4. Sequence Visualization: Enables exploration of sequence properties and relationships within clonal populations through interactive visualizations.
5. Statistical Analysis: Incorporates statistical algorithms for assessing the significance of observed clonal expansions or diversification events.
6. Customizable Visualization: Allows researchers to customize visualization parameters and display options according to their analytical preferences.

Applications and Importance

IMGT/StatClonotype serves as a valuable resource for researchers and clinicians engaged in various areas of immunology, including investigating immune responses to infectious diseases, monitoring clonal dynamics in cancer immunotherapy, understanding the impact of aging and environmental factors on immune repertoire diversity, and evaluating the efficacy of immunomodulatory therapies.

IMGT/JunctionAnalysis

Overview

IMGT/JunctionAnalysis is a tool tailored for the visualization and analysis of nucleotide sequences of immunoglobulins (IG) and T cell receptors (TR), focusing specifically on the detailed examination of V-J and V-D-J junction regions. It provides comprehensive insights into the recombination events that shape the diversity of antigen receptor repertoires.

Functional Capabilities

1. Junction Sequence Extraction: Identifies and extracts the junctional sequences spanning the V-J and V-D-J regions from submitted IG and TR sequences.
2. Sequence Annotation: Annotates the extracted junctional sequences with detailed information regarding nucleotide additions, deletions, and mutations.
3. Feature Visualization: Offers interactive visualizations of junctional sequences, allowing exploration of sequence characteristics and structural motifs.
4. Statistical Analysis: Incorporates statistical algorithms for quantifying the frequency and distribution of junctional motifs.
5. Comparative Analysis: Supports the comparative analysis of junctional sequences across different samples or experimental conditions.
6. Customizable Analysis: Allows researchers to customize analysis parameters and visualization settings according to their specific research needs.

Applications and Importance

IMGT/JunctionAnalysis plays a pivotal role in various areas of immunological research and clinical practice, including investigating mechanisms of antigen receptor diversity generation, characterizing junctional diversity patterns associated with immune responses, identifying diagnostic biomarkers and therapeutic targets, and monitoring clonal dynamics in cancer immunotherapy.

See also

• Open science data
• Computational immunology
• Immunomics