IMGT JunctionAnalysis

IMGT JunctionAnalysis analyzes nucleotide sequences of V-J and V-D-J junctions in the variable domains of immunoglobulins (IG) and T cell receptors (TR) to characterize junctional composition, P- and N-region diversity, and somatic hypermutation for adaptive immune repertoire studies.

Key Features:

• Detailed Junction Analysis: Performs automated, detailed examination of IG and TR junctions following the IMGT Scientific Chart rules and IMGT-ONTOLOGY concepts for precise annotation.
• Combinatorial Diversity Delimitation: Delimits V, D, and J gene segments at the nucleotide level to identify segments involved in junction formation.
• Identification of N-Diversity Regions: Identifies palindromic P-REGION(s) and N-REGION(s) resulting from non-templated nucleotide additions (N-diversity).
• Somatic Hypermutation Evaluation: Evaluates the number and distribution of somatic hypermutations within each gene segment at the junction.
• Scalability and species/locus support: Processes an unlimited number of junctions in a single run for specified species (human and mouse) and loci.

Scientific Applications:

• Basic immunogenetics: Characterizes junctional diversity and composition in studies of adaptive immune repertoires.
• Veterinary science: Applies junctional analyses to non-human immunogenetic investigations in veterinary contexts.
• Medical and clinical research: Supports clinical investigations and research into immune receptor variation.
• Mutation analysis in leukemia and lymphoma: Enables analysis of junctional mutations relevant to hematologic malignancies.
• Antibody engineering and humanization: Informs antibody design and humanization by defining junctional composition and variability.
• High-throughput repertoire analysis: Handles next-generation sequencing (NGS) high-throughput data for genomic and expressed IG and TR repertoire analyses.

Methodology:

Analysis is grounded in the IMGT-ONTOLOGY framework and follows the IMGT Scientific Chart, employing standardized keywords, labels, nomenclature, unique numbering and Colliers de Perles (numerotation) to link genes, sequences and 3D structures.