title: IMGT standardization for statistical analyses of T cell receptor junctions: the TRAV-TRAJ example.
abstract: The diversity of immunoglobulin (IG) and T cell receptor (TR) chains depends on several mechanisms: combinatorial diversity, which is a consequence of the number of V, D and J genes and the N-REGION diversity, which creates an extensive and clonal somatic diversity at the V-J and V-D-J junctions. For the IG, the diversity is further increased by somatic hypermutations. The number of different junctions per chain and per individual is estimated to be 10(12). We have chosen the human TRAV-TRAJ junctions as an example in order to characterize the required criteria for a standardized analysis of the IG and TR V-J and V-D-J junctions, based on the IMGT-ONTOLOGY concepts, and to serve as a first IMGT junction reference set (IMGT, http://imgt.cines.fr). We performed a thorough statistical analysis of 212 human rearranged TRAV-TRAJ sequences, which were aligned and analysed by the integrated IMGT/V-QUEST software, which includes IMGT/JunctionAnalysis, then manually expert-verified. Furthermore, we compared these 212 sequences with 37 other human TRAV-TRAJ junction sequences for which some particularities (potential sequence polymorphisms, sequencing errors, etc.) did not allow IMGT/JunctionAnalysis to provide the correct biological results, according to expert verification. Using statistical learning, we constructed an automatic warning system to predict if new, automatically analysed TRAV-TRAJ sequences should be manually re-checked. We estimated the robustness of this automatic warning system.
authors.affiliation: Institut de Mathématiques et de Modélisation de Montpellier, UMR CNRS 5149, Equipe de Probabilités et Statistique, Université Montpellier II, Montpellier, France. bleakley@math.univ-montp2.fr
authors.forename: Kevin
authors.initials: K
authors.lastname: Bleakley
authors.forename: Véronique
authors.initials: V
authors.lastname: Giudicelli
authors.forename: Yan
authors.initials: Y
authors.lastname: Wu
authors.forename: Marie-Paule
authors.initials: MP
authors.lastname: Lefranc
authors.forename: Gérard
authors.initials: G
authors.lastname: Biau
mesh_terms: D001185:Artificial Intelligence; D022801:Complementarity Determining Regions / Q000235:genetics; D019295:Computational Biology / Q000592:standards*; D015329:Gene Rearrangement, T-Lymphocyte; D023281:Genomics / Q000706:statistics & numerical data; D006801:Humans; D008957:Models, Genetic; D011948:Receptors, Antigen, T-Cell / Q000235:genetics*; D012984:Software
chemical_list: D022801:Complementarity Determining Regions; D011948:Receptors, Antigen, T-Cell