Abstract
The adaptive immune responses of humans and of other jawed vertebrate species(gnasthostomata) are characterized by the B and T cells and their specific antigen recep-tors, the immunoglobulins (IG) or antibodies and the T cell receptors (TR) (up to 2.10 12 dif-ferent IG and TR per individual). IMGT, the international ImMunoGeneTics informationsystem (http://www.imgt.org), was created in 1989 by Marie-Paule Lefranc (Montpellier Uni-versity and CNRS) to manage the huge and complex diversity of these antigen receptors.IMGT built on IMGT-ONTOLOGY concepts of identification (keywords), description (labels),classification (gene and allele nomenclature) and numerotation (IMGT unique numbering),is at the origin of immunoinformatics, a science at the interface between immunogeneticsand bioinformatics. IMGT/HighV-QUEST, the first web portal, and so far the only one, forthe next generation sequencing (NGS) analysis of IG and TR, is the paradigm for immunerepertoire standardized outputs and immunoprofiles of the adaptive immune responses. Itprovides the identification of the variable (V), diversity (D) and joining (J) genes and alleles,analysis of the V-(D)-J junction and complementarity determining region 3 (CDR3) and thecharacterization of the ‘IMGT clonotype (AA)’ (AA for amino acid) diversity and expression.IMGT/HighV-QUEST compares outputs of different batches, up to one million nucleotidesequencesfor the statistical module. These high throughput IG and TR repertoire immuno-profiles are of prime importance in vaccination, cancer, infectious diseases, autoimmunityand lymphoproliferative disorders, however their comparative statistical analysis stillremains a challenge. We present a standardized statistical procedure to analyze IMGT/HighV-QUEST outputs for the evaluation of the significance of the IMGT clonotype (AA)diversity differences in proportions, per gene of a given group, between NGS IG and TR repertoire immunoprofiles. The procedure is generic and suitable for evaluating significanceof the IMGT clonotype (AA) diversity and expression per gene, and for any IG and TR immu-noprofiles of any species.