title: IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling.
abstract: T cell repertoire diversity and clonotype follow-up in vaccination, cancer, infectious and immune diseases represent a major challenge owing to the enormous complexity of the data generated. Here we describe a next generation methodology, which combines 5'RACE PCR, 454 sequencing and, for analysis, IMGT, the international ImMunoGeneTics information system (IMGT), IMGT/HighV-QUEST web portal and IMGT-ONTOLOGY concepts. The approach is validated in a human case study of T cell receptor beta (TRB) repertoire, by chronologically tracking the effects of influenza vaccination on conventional and regulatory T cell subpopulations. The IMGT/HighV-QUEST paradigm defines standards for genotype/haplotype analysis and characterization of IMGT clonotypes for clonal diversity and expression and achieves a degree of resolution for next generation sequencing verifiable by the user at the sequence level, while providing a normalized reference immunoprofile for human TRB.
authors.affiliation: Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria 3052, Australia.
authors.forename: Shuo
authors.initials: S
authors.lastname: Li
authors.forename: Marie-Paule
authors.initials: MP
authors.lastname: Lefranc
authors.forename: John J
authors.initials: JJ
authors.lastname: Miles
authors.forename: Eltaf
authors.initials: E
authors.lastname: Alamyar
authors.forename: Véronique
authors.initials: V
authors.lastname: Giudicelli
authors.forename: Patrice
authors.initials: P
authors.lastname: Duroux
authors.forename: J Douglas
authors.initials: JD
authors.lastname: Freeman
authors.forename: Vincent D A
authors.initials: VD
authors.lastname: Corbin
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Scheerlinck
authors.forename: Michael A
authors.initials: MA
authors.lastname: Frohman
authors.forename: Paul U
authors.initials: PU
authors.lastname: Cameron
authors.forename: Magdalena
authors.initials: M
authors.lastname: Plebanski
authors.forename: Bruce
authors.initials: B
authors.lastname: Loveland
authors.forename: Scott R
authors.initials: SR
authors.lastname: Burrows
authors.forename: Anthony T
authors.initials: AT
authors.lastname: Papenfuss
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Gowans
mesh_terms: D000483:Alleles; D002999:Clone Cells; D019295:Computational Biology / Q000379:methods*; D005434:Flow Cytometry; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D007125:Immunogenetics / Q000379:methods*; D020407:Internet; D008297:Male; D008875:Middle Aged; D011948:Receptors, Antigen, T-Cell / Q000235:genetics*; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics
chemical_list: D011948:Receptors, Antigen, T-Cell; D016693:Receptors, Antigen, T-Cell, alpha-beta