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Standardized Sequence and Structure Analysis of Antibody Using IMGT® [chapter]

François Ehrenmann, Patrice Duroux, Véronique Giudicelli, Marie-Paule Lefranc
2010 Antibody Engineering  
The accuracy and the consistency of the IMGT 1 data are based on IMGT-ONTOLOGY, the first ontology for immunogenetics and immunoinformatics (Giudicelli and Lefranc 1999; Lefranc et al. 2004; Duroux et  ...  immunogenetics data, the IMGT Scientific chart rules (http://www.imgt.org/textes/IMGTScientificChart/) have been implemented, based on IMGT-ONTOLOGY (Giudicelli and Lefranc 1999; Lefranc et al. 2004; Duroux  ... 
doi:10.1007/978-3-642-01147-4_2 fatcat:2l3ri26k2nbhbd7fuiwtgyesx4

Immunogenetic sequence annotation based on IMGT-ONTOLOGY

Joumana Jabado-Michaloud, Marie-Paule Lefranc, Géraldine Folch, Fatena Bellahcene, François Ehrenmann, Patrice Duroux, Véronique Giudicelli
2009 Nature Precedings  
in vitro cDNA) mRNA (or in vitro cDNA) ).[2]Duroux, P. et al., Biochimie, 90, 570-583 (2008).[3] Giudicelli, V. and Lefranc, M.-P.  ...  ,Bioinformatics, 15, 1047Bioinformatics, 15, -1054Bioinformatics, 15, (1999.[4]Duroux, P. et al., Biochimie, 90, 570-583 (2008).  ... 
doi:10.1038/npre.2009.3165.1 fatcat:4dtmiolo45hsvhy5lwwdecgbyi

IMGT-Kaleidoscope, the formal IMGT-ONTOLOGY paradigm

Patrice Duroux, Quentin Kaas, Xavier Brochet, Jérôme Lane, Chantal Ginestoux, Marie-Paule Lefranc, Véronique Giudicelli
2008 Biochimie  
Duroux et al. / Biochimie 90 (2008) 570e583  ... 
doi:10.1016/j.biochi.2007.09.003 pmid:17949886 fatcat:epwhbxlop5fgddmsv2zaunirle

Predicting L-PART1 exon using deep learning

Merouane Elazami Elhassani, Loic Maisonnasse, Antoine Olgiati, Jérôme REY, Veronique Giudicelli, Patrice Duroux, Sofia Kossida
2021 EMBnet journal  
Identifying and annotating Immunoglobulins (IG), T cell receptors (TR) genes of jawed vertebrate species effectively and precisely is still an arduous task, essentially due to the continuous avalanche of large genomic sequences produced by NGS technologies. In this study, to predict the L-PART1 exon (the first exon of IG and TR variable V-GENE), different Deep Neural Network-based models (DNN, CNN, RNN, CNN-RNN) were trained in a supervised manner, which automatically learn features from
more » ... ed IG and TR genes. Those models will then be used to predict the L-PART1 exon within newly given sequences. Correct detection of this component would dramatically increase the chances to find the subsequent components constituting the V-GENE of the IG and TR. Sequence data were extracted from IMGT/ LIGM-DB, the IMGT® (Lefranc et al., 2015) nucleotides database: around 2756 L-PART1 of 354 species tagged as positive samples, negative samples were generated with different noise strategies. The final training datasets were formed by shuffling a portion of positive and negative samples. The majority of the trained models showed promising results. However, further studies are needed to investigate the possibility of predicting and locating all the components within the V-GENE of IG and TR.
doi:10.14806/ej.26.a.957 fatcat:ewmjh5rf2va6jnnd3wf33sa7da

IMGT/GENE-DB: genomic reference sequences for human and mouse IG and TR genes and alleles

Fatena Bellahcene, Marie-Paule Lefranc, Géraldine Folch, Joumana Jabado-Michaloud, Chantal Ginestoux, Patrice Duroux, Véronique Giudicelli
2009 Nature Precedings  
http://www.imgt.org IMGT/GENE-DB: genomic reference sequences for human and mouse IG and TR genes and allelesFatena Bellahcene, Géraldine Folch, Joumana Jabado-Michaloud, Chantal Ginestoux, Patrice Duroux  ... 
doi:10.1038/npre.2009.3158.1 fatcat:wtm3zo33krcnpm2rgdlygz2soa

IMGT® Biocuration and Comparative Analysis of Bos taurus and Ovis aries TRA/TRD Loci

Perrine Pégorier, Morgane Bertignac, Viviane Nguefack Ngoune, Géraldine Folch, Joumana Jabado-Michaloud, Véronique Giudicelli, Patrice Duroux, Marie-Paule Lefranc, Sofia Kossida
2020 Genes  
The adaptive immune response provides the vertebrate immune system with the ability to recognize and remember specific pathogens to generate immunity, and mount stronger attacks each time the pathogen is encountered. T cell receptors are the antigen receptors of the adaptive immune response expressed by T cells, which specifically recognize processed antigens, presented as peptides by the highly polymorphic major histocompatibility (MH) proteins. T cell receptors (TR) are divided into two
more » ... , αβ and γδ, which express distinct TR containing either α and β, or γ and δ chains, respectively. The TRα locus (TRA) and TRδ locus (TRD) of bovine (Bos taurus) and the sheep (Ovis aries) have recently been described and annotated by IMGT® biocurators. The aim of the present study is to present the results of the biocuration and to compare the genes of the TRA/TRD loci among these ruminant species based on the Homo sapiens repertoire. The comparative analysis shows similarities but also differences, including the fact that these two species have a TRA/TRD locus about three times larger than that of humans and therefore have many more genes which may demonstrate duplications and/or deletions during evolution.
doi:10.3390/genes12010030 pmid:33379283 pmcid:PMC7824213 fatcat:itbwg2shx5fmfhche6il3cuo34

IG and TR single chain fragment variable (scFv) sequence analysis: a new advanced functionality of IMGT/V-QUEST and IMGT/HighV-QUEST

Véronique Giudicelli, Patrice Duroux, Sofia Kossida, Marie-Paule Lefranc
2017 BMC Immunology  
Giudicelli, P Duroux, S Kossida, M.P. Lefranc To cite this version: V. Giudicelli, P Duroux, S Kossida, M.P. Lefranc.  ... 
doi:10.1186/s12865-017-0218-8 pmid:28651553 pmcid:PMC5485737 fatcat:vlkvfytryzh4ricc22dsukuxqe

IMGT®, the international ImMunoGeneTics information system® 25 years on

Marie-Paule Lefranc, Véronique Giudicelli, Patrice Duroux, Joumana Jabado-Michaloud, Géraldine Folch, Safa Aouinti, Emilie Carillon, Hugo Duvergey, Amélie Houles, Typhaine Paysan-Lafosse, Saida Hadi-Saljoqi, Souphatta Sasorith (+2 others)
2014 Nucleic Acids Research  
IMGT R , the international ImMunoGeneTics information system R (http://www.imgt.org) is the global reference in immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), IMGT R marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT R is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) and proteins of the IgSF
more » ... nd MhSF superfamilies. IMGT R is built on the IMGT-ONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and 3D structures. The concepts include the IMGT R standardized keywords (identification), IMGT R standardized labels (description), IMGT R standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGT R comprises 7 databases, 17 online tools and 15 000 pages of web resources, and provides a high-quality and integrated system for analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses, including NGS high-throughput data. Tools and databases are used in basic, veterinary and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. The IMGT/mAb-DB interface was developed for therapeutic antibodies and fusion proteins for immunologi-cal applications (FPIA). IMGT R is freely available at http://www.imgt.org.
doi:10.1093/nar/gku1056 pmid:25378316 pmcid:PMC4383898 fatcat:q5x3oufdlvggrjrpwoqge7tehq

From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT® standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences

Jérôme Lane, Patrice Duroux, Marie-Paule Lefranc
2010 BMC Bioinformatics  
The antigen receptors, immunoglobulins (IG) and T cell receptors (TR), are specific molecular components of the adaptive immune response of vertebrates. Their genes are organized in the genome in several loci (7 in humans) that comprise different gene types: variable (V), diversity (D), joining (J) and constant (C) genes. Synthesis of the IG and TR proteins requires rearrangements of V and J, or V, D and J genes at the DNA level, followed by the splicing at the RNA level of the rearranged V-J
more » ... d V-D-J genes to C genes. Owing to the particularities of IG and TR gene structures related to these molecular mechanisms, conventional bioinformatic software and tools are not adapted to the identification and description of IG and TR genes in large genomic sequences. In order to answer that need, IMGT ® , the international ImMunoGeneTics information system ® , has developed IMGT/LIGMotif, a tool for IG and TR gene annotation. This tool is based on standardized rules defined in IMGT-ONTOLOGY, the first ontology in immunogenetics and immunoinformatics. Results: IMGT/LIGMotif currently annotates human and mouse IG and TR loci in large genomic sequences. The annotation includes gene identification and orientation on DNA strand, description of the V, D and J genes by assigning IMGT ® labels, gene functionality, and finally, gene delimitation and cluster assembly. IMGT/LIGMotif analyses sequences up to 2.5 megabase pairs and can analyse them in batch files. Conclusions: IMGT/LIGMotif is currently used by the IMGT ® biocurators to annotate, in a first step, IG and TR genomic sequences of human and mouse in new haplotypes and those of closely related species, nonhuman primates and rat, respectively. In a next step, and following enrichment of its reference databases, IMGT/LIGMotif will be used to annotate IG and TR of more distantly related vertebrate species. IMGT/LIGMotif is available at http://www.imgt.org/ ligmotif/.
doi:10.1186/1471-2105-11-223 pmid:20433708 pmcid:PMC2880031 fatcat:jbgpybbl55bd3gf7zl7iw6niba

IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST

Safa Aouinti, Véronique Giudicelli, Patrice Duroux, Dhafer Malouche, Sofia Kossida, Marie-Paule Lefranc
2016 Frontiers in Immunology  
IMGt/statClonotype for Pairwise evaluation and Visualization of NGs IG and tR IMGt Clonotype (AA) diversity or expression from IMGt/highV-QUest Safa Aouinti 1,2 *, Véronique Giudicelli 1 , Patrice Duroux  ... 
doi:10.3389/fimmu.2016.00339 pmid:27667992 pmcid:PMC5016520 fatcat:v2atymel2fbf3dhxt5f2rmuoaa

IMGT® Biocuration and Comparative Study of the T Cell Receptor Beta Locus of Veterinary Species Based on Homo sapiens TRB

Perrine Pégorier, Morgane Bertignac, Imène Chentli, Viviane Nguefack Ngoune, Géraldine Folch, Joumana Jabado-Michaloud, Saida Hadi-Saljoqi, Véronique Giudicelli, Patrice Duroux, Marie-Paule Lefranc, Sofia Kossida
2020 Frontiers in Immunology  
IMGT®, the international ImMunoGeneTics information system® is the global reference in immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT® is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH), and proteins of the IgSF and MhSF superfamilies. T
more » ... ell receptors are divided into two groups, αβ and γδ TR, which express distinct TR containing either α and β, or γ and δ chains, respectively. The TRβ locus (TRB) was recently described and annotated by IMGT® biocurators for several veterinary species, i.e., cat (Felis catus), dog (Canis lupus familiaris), ferret (Mustela putorius furo), pig (Sus scrofa), rabbit (Oryctolagus cuniculus), rhesus monkey (Macaca mulatta), and sheep (Ovis aries). The aim of the present study is to compare the genes of the TRB locus among these different veterinary species based on Homo sapiens. The results reveal that there are similarities but also differences including the number of genes by subgroup which may demonstrate duplications and/or deletions during evolution.
doi:10.3389/fimmu.2020.00821 pmid:32431713 pmcid:PMC7216736 fatcat:fbdkh2pntrc5nfdtxvczslogwq

IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling

Shuo Li, Marie-Paule Lefranc, John J. Miles, Eltaf Alamyar, Véronique Giudicelli, Patrice Duroux, J. Douglas Freeman, Vincent D. A. Corbin, Jean-Pierre Scheerlinck, Michael A. Frohman, Paul U. Cameron, Magdalena Plebanski (+4 others)
2013 Nature Communications  
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 0 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
more » ... ) 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.
doi:10.1038/ncomms3333 pmid:23995877 pmcid:PMC3778833 fatcat:fea4thloe5ap3ld5ajhnpoyf7a

Coupling of Single Molecule, Long Read Sequencing with IMGT/HighV-QUEST Analysis Expedites Identification of SIV gp140-Specific Antibodies from scFv Phage Display Libraries

Seung Yub Han, Alesia Antoine, David Howard, Bryant Chang, Woo Sung Chang, Matthew Slein, Gintaras Deikus, Sofia Kossida, Patrice Duroux, Marie-Paule Lefranc, Robert P. Sebra, Melissa L. Smith (+1 others)
2018 Frontiers in Immunology  
The simian immunodeficiency virus (SIV)/macaque model of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome pathogenesis is critical for furthering our understanding of the role of antibody responses in the prevention of HIV infection, and will only increase in importance as macaque immunoglobulin (IG) gene databases are expanded. We have previously reported the construction of a phage display library from a SIV-infected rhesus macaque (Macaca mulatta) using oligonucleotide
more » ... imers based on human IG gene sequences. Our previous screening relied on Sanger sequencing, which was inefficient and generated only a few dozen sequences. Here, we re-analyzed this library using single molecule, real-time (SMRT) sequencing on the Pacific Biosciences (PacBio) platform to generate thousands of highly accurate circular consensus sequencing (CCS) reads corresponding to full length single chain fragment variable. CCS data were then analyzed through the international ImMunoGeneTics information system ® (IMGT ® )/HighV-QUEST (www.imgt.org) to identify variable genes and perform statistical analyses. Overall the library was very diverse, with 2,569 different IMGT clonotypes called for the 5,238 IGHV sequences assigned to an IMGT clonotype. Within the library, SIV-specific antibodies represented a relatively limited number of clones, with only 135 different IMGT clonotypes called from 4,594 IGHV-assigned sequences. Our data did confirm that the IGHV4 and IGHV3 gene usage was the most abundant within the rhesus antibodies screened, and that these genes were even more enriched among SIV gp140-specific antibodies. Although a broad range of VH CDR3 amino acid (AA) lengths was observed in the unpanned library, the vast majority of SIV gp140-specific antibodies demonstrated a more uniform VH CDR3 length (20 AA). This uniformity was far less apparent when VH CDR3 were classified according to their clonotype (range: 9-25 AA), which we believe is more relevant for specific antibody identification. Only 174 IGKV and 588 IGLV clonotypes were identified within the VL sequences associated with SIV gp140-specific VH. Together, these data strongly suggest that the combination of 2 Han et al. PacBio-IMGT/HighV-QUEST-Based Characterization of SIV-Specific Antibodies
doi:10.3389/fimmu.2018.00329 pmid:29545792 pmcid:PMC5837965 fatcat:b7vj77te3rdexfi3m6lfqbexja

Pacific Biosciences Sequencing and IMGT/HighV-QUEST Analysis of Full-Length Single Chain Fragment Variable from an In Vivo Selected Phage-Display Combinatorial Library

Audrey Hemadou, Véronique Giudicelli, Melissa Laird Smith, Marie-Paule Lefranc, Patrice Duroux, Sofia Kossida, Cheryl Heiner, N. Lance Hepler, John Kuijpers, Alexis Groppi, Jonas Korlach, Philippe Mondon (+4 others)
2017 Frontiers in Immunology  
Hemadou et al. PacBio scFv Sequencing and IMGT/HighV-QUEST Analysis Frontiers in Immunology | www.frontiersin.org December 2017 | Volume 8 | Article 1796 both ends. Interestingly these reads were obtained from each of the 15 SMRT cells. Thus, the SMRT sequencing method and the IMGT/HighV-QUEST functionality for scFv provides a straightforward protocol for characterization of full-length scFv from combinatorial phage libraries.
doi:10.3389/fimmu.2017.01796 pmid:29326697 pmcid:PMC5742356 fatcat:o6inxnowovdgvdros3li7zjncy

Biomarkers in Rheumatoid Arthritis

Vincent Goëb, Patrice Fardellone, Jean Sibilia, Frédérique Ponchel
2014 Mediators of Inflammation  
Vincent Goëb Patrice Fardellone Jean Sibilia Frédérique Ponchel  ...  Duroux-Richard et al. will thus explain how circulating Mediators of Inflammation micro-RNA, and notably miRNA-125b, are potential valuable biomarkers in RA in "Circulating miRNA-125b is a potential biomarker  ... 
doi:10.1155/2014/379310 pmid:25061261 pmcid:PMC4100293 fatcat:j2ngzylyffgfxpah2vsgmwqmfm
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