Using Bioinformatics Tools for the Sequence Analysis of Immunoglobulins and T Cell Receptors

Abstract

The huge potential repertoire of 10(12) immunoglobulins and 10(12) T cell receptors per individual results from complex mechanisms of combinatorial diversity between the variable (V), diversity (D), and junction (J) genes, nucleotide deletions and insertions (N-diversity) at the junctions and, for the immunoglobulins, somatic hypermutations. The accurate analysis of rearranged immunoglobulin and T cell receptor sequences, and the annotation of the junctions, therefore represent a huge challenge. The IMGT Scientific chart rules, based on the IMGT-ONTOLOGY concepts, were the prerequisites for the implementation of the IMGT/V-QUEST and IMGT/JunctionAnalysis tools. IMGT/V-QUEST analyzes germline V and rearranged V-J or V-D-J nucleotide sequences. IMGT/JunctionAnalysis is the first tool that automatically analyzes the complex junctions in detail. These interactive tools are easy to use and freely available on the Web (http://imgt.cines.fr), either separately or integrated.

An Efficient Single-Cell RNA-Seq Approach to Identify Neoantigen-Specific T Cell Receptors

“…To isolate paired TCRa/b sequences, the conventional approach involves T cell cloning by limiting dilution, identification of reactive T cell clones, and subsequent isolation and sequencing of TCR cDNA. 17 This approach is time consuming and technically challenging, with a high failure rate. These challenges can be summarized in the following four points.…”

ERIC recommendations on IGHV gene mutational status analysis in chronic lymphocytic leukemia

“…Alignment: Among the immunoglobulin databases available on line international immunogenetics information (IMGT) (http://imgt.cines.fr), V-Base (http://vbase.mrc-cpe.cam.ac.uk/) and GenBank (http://www.ncbi.nlm.nih.gov/igblast/), IMGT/ GENE-DB 19,20 is the most comprehensive and more regularly updated database in terms of immunoglobulin gene polymorphisms/alleles. This is an essential point to reach a correct calculation of the percentage of IGHV gene identity compared to the closest IGHV germline gene.…”

“…21,22 More recently, the IMGT/V-QUEST tool has been improved so it also provides automatically the calculation of the percentage of IGHV identity to germline, the number and description of mutations per FR-IMGT and CDR-IMGT, and the identification and localization of the hot spots in the germline. 20 One has also to keep in mind that nucleotide insertions/duplications or deletions in IGH genes may occur in up to 3% of CLL sequences. 23 This does not allow a proper alignment using both V-QUEST and DNA plot, hampering a correct analysis.…”