IMGT/HighV-QUEST Statistical Significance of IMGT Clonotype (AA) Diversity per Gene for Standardized Comparisons of Next Generation Sequencing Immunoprofiles of Immunoglobulins and T Cell Receptors

Safa Aouinti (1, 2) , Dhafer Malouche (3) , Véronique Giudicelli (1) , Sofia Kossida (1) , Marie-Paule Lefranc (1)

1 IGH - Institut de génétique humaine
2 UCAR - Université de Carthage (Tunisie)
3 ENIT - Ecole Nationale d'Ingénieurs de Tunis

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 information system (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 immunogenetics and bioinformatics. IMGT/HighV-QUEST, the first web portal, and so far the only one, for the next generation sequencing (NGS) analysis of IG and TR, is the paradigm for immune repertoire standardized outputs and immunoprofiles of the adaptive immune responses. It provides 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 the characterization of the ‘IMGT clonotype (AA)’ (AA for amino acid) diversity and expression. IMGT/HighV-QUEST compares outputs of different batches, up to one million nucleotide sequencesfor the statistical module. These high throughput IG and TR repertoire immuno- profiles are of prime importance in vaccination, cancer, infectious diseases, autoimmunity and lymphoproliferative disorders, however their comparative statistical analysis still remains 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 significance of the IMGT clonotype (AA) diversity and expression per gene, and for any IG and TR immu- noprofiles of any species.

Domaines: Bio-informatique [q-bio.QM]; Génétique

Safa Aouinti, Dhafer Malouche, Véronique Giudicelli, Sofia Kossida, Marie-Paule Lefranc. IMGT/HighV-QUEST Statistical Significance of IMGT Clonotype (AA) Diversity per Gene for Standardized Comparisons of Next Generation Sequencing Immunoprofiles of Immunoglobulins and T Cell Receptors. PLoS ONE, 2015, 10 (11), pp.e142353. ⟨10.1371/journal.pone.0142353⟩. ⟨hal-01228428⟩