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

被引：31

作者：

Aouinti, Safa ^{[1
,2
,3
]}

Malouche, Dhafer ^{[2
,3
]}

Giudicelli, Veronique ^{[1
]}

Kossida, Sofia ^{[1
]}

Lefranc, Marie-Paule ^{[1
]}

机构：

[1] Univ Montpellier, Inst Genet Humaine IGH, LIGM,Int ImMunoGeneT Informat Syst, IMGT,UPR CNRS 1142, F-34059 Montpellier 5, France

[2] Univ Carthage, Higher Sch Stat & Informat Anal, Tunis, Tunisia

[3] Univ Tunis El Manar, Natl Sch Engn Tunis, Informat Technol & Commun Dept, Lab U2S, Tunis, Tunisia

来源：

PLOS ONE | 2015年 / 10卷 / 11期

关键词：

FALSE DISCOVERY RATE; V-J; MULTIPLE; CONFIDENCE; BONFERRONI; ONTOLOGY;

D O I：

10.1371/journal.pone.0142353

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 receptors, the immunoglobulins (IG) or antibodies and the T cell receptors (TR) (up to 2.10(12) different IG and TR per individual). IMGT, the international ImMunoGeneTics information system (http://www.imgt.org), was created in 1989 by Marie-Paule Lefranc (Montpellier University 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 immunoprofiles 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

引用

页数：22

共 41 条

[11] RAPID PRODUCTION OF FULL-LENGTH CDNAS FROM RARE TRANSCRIPTS - AMPLIFICATION USING A SINGLE GENE-SPECIFIC OLIGONUCLEOTIDE PRIMER [J].