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IMGT standardization for statistical analyses of T cell receptor junctions: the TRAV-TRAJ example

Kevin Bleakley, Véronique Giudicelli, Yan Wu, Marie-Paule Lefranc, Gérard Biau
2006 In Silico Biology  
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  ...  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  ...  We are grateful to Xavier Brochet for his contribution to the improvement of the IMGT/V-QUEST software. We thank Gérard Lefranc for fruitful discussion and the IMGT team for its constant  ... 
pmid:17518765 fatcat:p4hdldbd3bbvdoehszed57rfve

Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools

Kevin Bleakley, Marie-Paule Lefranc, Gérard Biau
2008 BMC Bioinformatics  
This hypothesis was not rejected at standard confidence levels for three of the four trimming processes: TRAV, TRAJ and TRGV.  ...  Nucleotides are trimmed from the ends of variable (V), diversity (D) and joining (J) genes during immunoglobulin (IG) and T cell receptor (TR) rearrangements in B cells and T cells of the immune system  ...  We thank Gérard Lefranc for fruitful discussion and the IMGT ® team for its constant motivation and expertise.  ... 
doi:10.1186/1471-2105-9-408 pmid:18831754 pmcid:PMC2576266 fatcat:cblqhyyp6vh6jhnr7rjlyvnwsy

Topology and expressed repertoire of the Felis catus T cell receptor loci

Araya Radtanakatikanon, Stefan M. Keller, Nikos Darzentas, Peter F. Moore, Géraldine Folch, Viviane Nguefack Ngoune, Marie-Paule Lefranc, William Vernau
2020 BMC Genomics  
The objectives of this study were to annotate the feline T cell receptor (TR) loci and to characterize the expressed repertoire in lymphoid organs of normal cats using high-throughput sequencing.  ...  TRDC, and the TRA locus contains 127 genes: 62 TRAV, 64 TRAJ, 1 TRAC.  ...  Acknowledgements We are grateful to the IMGT team for maintaining the IMGT databases and tools, and for helpful discussion about IMGT nomenclature of Felis catus TR genes and alleles.  ... 
doi:10.1186/s12864-019-6431-5 pmid:31906850 pmcid:PMC6945721 fatcat:6vwqfvrtkjbo7fvmg6tmotenje

High‐throughput sequencing of T‐cell receptor alpha chain clonal rearrangements at the DNA level in lymphoid malignancies

Alexander Komkov, Anna Miroshnichenkova, Gaiaz Nugmanov, Alexander Popov, Mikhail Pogorelyy, Eva Zapletalova, Hana Jelinkova, Sarka Pospisilova, Yuri Lebedev, Dmitriy Chudakov, Yulia Olshanskaya, Karla Plevova (+2 others)
2019 British Journal of Haematology  
Rearrangements of T- and B-cell receptor (TCR and BCR) genes are useful markers for clonality assessment as well as for minimal residual disease (MRD) monitoring during the treatment of haematological  ...  Here we propose the first high-throughput sequencing based method for the identification of clonal TRA gene rearrangements at the DNA level.  ...  This approach has been adopted for all immune receptor genes except for one -T cell receptor alpha (TRA) locus.  ... 
doi:10.1111/bjh.16230 pmid:31587259 fatcat:kfvztv4s2jhrroruyzkvkbuvbm

Comparative analysis of CDR3 regions in paired human αβ CD8 T cells

Kun Yu, Ji Shi, Dan Lu, Qiong Yang
2019 FEBS Open Bio  
The majority of human CD8 cytotoxic T lymphocytes express αβ T-cell receptors that recognize peptide-MHC class I complexes.  ...  Here, we have provided detailed information on CDR3 in paired TCRs expressed on human CD8+ T cells and established the basis of a reference set for αβ TCR repertoires in healthy humans.  ...  Acknowledgement The study was supported by Health Commission of Zhejiang Province (Grant No. 2017KY019).  ... 
doi:10.1002/2211-5463.12690 pmid:31237075 pmcid:PMC6668380 fatcat:blkxxt4nqzcpbgtwvqu5zcnl4q

RNA sequencing identifies clonal structure of T-cell repertoires in patients with adult T-cell leukemia/lymphoma

Amir Farmanbar, Robert Kneller, Sanaz Firouzi
2019 npj Genomic Medicine  
The diversity of T-cell receptor (TCR) repertoires, as generated by somatic DNA rearrangements, is central to immune system function.  ...  Here we examined the diversity of TCR clonality and its association with pathogenesis and prognosis in adult T-cell leukemia/lymphoma (ATL), a malignancy caused by infection with human T-cell leukemia  ...  INTRODUCTION The T-cell receptor (TCR), which is generated through random rearrangement of genomic V(D)J-variable(diversity)joining-segments, is the mediator of specific antigen recognition by T lymphocytes  ... 
doi:10.1038/s41525-019-0084-9 pmid:31069115 pmcid:PMC6502857 fatcat:qb7es33awjhutdokkmasqlvxd4

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  
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  ...  Turner from the Department of Microbiology and Immunology, The University of Melbourne, for helpful discussions and reading of the manuscript; V.  ... 
doi:10.1038/ncomms3333 pmid:23995877 pmcid:PMC3778833 fatcat:fea4thloe5ap3ld5ajhnpoyf7a

CTLA-4 controls the thymic development of both conventional and regulatory T cells through modulation of the TCR repertoire

J. Verhagen, R. Genolet, G. J. Britton, B. J. Stevenson, C. A. Sabatos-Peyton, J. Dyson, I. F. Luescher, D. C. Wraith
2012 Proceedings of the National Academy of Sciences of the United States of America  
To address this topic, we investigated the thymic development of T cells in the presence and absence of CTLA-4 in a T-cell receptor (TCR) transgenic mouse model specific for the myelin basic protein peptide  ...  Tolerance to self-antigens is achieved through thymic deletion of highly autoreactive conventional T (Tconv) cells and generation of FoxP3 + regulatory T (Treg) cells.  ...  For these two TRAV families, millions of sequences were analyzed to define their T-cell receptor α junctional (TRAJ) gene segment use and complementarity determining region 3 (CDR3) compositions.  ... 
doi:10.1073/pnas.1208573110 pmid:23267099 pmcid:PMC3549118 fatcat:hoed4agzqjdffbdmwnhq5mmxki

DNA Vaccination by Electroporation Amplifies Broadly Cross-Restricted Public TCR Clonotypes Shared with HIV Controllers

Madhura Mukhopadhyay, Moran Galperin, Mandar Patgaonkar, Sandhya Vasan, David D. Ho, Alexandre Nouël, Mathieu Claireaux, Daniela Benati, Olivier Lambotte, Yaoxing Huang, Lisa A. Chakrabarti
2017 Journal of Immunology  
Heather and Serghei Mangul for the sharing of TCR clonotype datasets, Pierre Charneau for the gift of plasmids, Mirjam Heemskerk and Bernard Maillère for the gift of cell lines, Anaïs Perilhou for help  ...  with regulatory matters, and the teams of the Center of Human Immunology and of the Flow Cytometry Platform of the Pasteur Institute for help with cell sorting and flow cytometry.  ...  The distribution of TRAV, TRAJ, TRBV, TRBJ, and TRBD genes in the sequence set was computed with the statistics module of IMGT/HighV-QUEST.  ... 
doi:10.4049/jimmunol.1700953 pmid:28993513 fatcat:kzl23v3murd6vj7pj46uuk7sly

Major TCR Repertoire Perturbation by Immunodominant HLA-B*44:03-Restricted CMV-Specific T Cells

Meriem Attaf, Amna Malik, Mai C. Severinsen, Julia Roider, Paul Ogongo, Søren Buus, Thumbi Ndung'u, Alasdair Leslie, Henrik N. Kløverpris, Philippa C. Matthews, Andrew K. Sewell, Philip Goulder
2018 Frontiers in Immunology  
The composition of the T cell receptor (TCR) repertoire underlying this response remains poorly characterised, especially within African populations in which CMV is endemic from infancy.  ...  which in some subjects represents >10% of the circulating CD8+ T cells.  ...  Even by the standards of CMV-specific CD8+ T cell responses, which are renowned to be very large, this is an exceptional example.  ... 
doi:10.3389/fimmu.2018.02539 fatcat:4qfa27yufzeyrhntknsm2k6r3y

Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study

Monika Brüggemann, on behalf of the EuroClonality-NGS working group, Michaela Kotrová, Henrik Knecht, Jack Bartram, Myriam Boudjogrha, Vojtech Bystry, Grazia Fazio, Eva Froňková, Mathieu Giraud, Andrea Grioni, Jeremy Hancock (+26 others)
2019 Leukemia  
Amplicon-based next-generation sequencing (NGS) of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements for clonality assessment, marker identification and quantification of minimal residual  ...  These validated and reproducible quality-controlled EuroClonality-NGS assays can be used for standardized NGS-based identification of IG/TR markers in lymphoid malignancies.  ...  Compliance with ethical standards Conflict of interest The EuroClonality-NGS Working Group is an independent scientific subdivision of EuroClonality that aims at innovation, standardization and education  ... 
doi:10.1038/s41375-019-0496-7 pmid:31243313 pmcid:PMC6756028 fatcat:mn6imbnh6bfdhdwxapqvrme2ty

Paired TCRαβ analysis of virus-specific CD8+ T cells exposes diversity in a previously defined 'narrow' repertoire

Tania Cukalac, Wan-Ting Kan, Pradyot Dash, Jing Guan, Kylie M Quinn, Stephanie Gras, Paul G Thomas, Nicole L La Gruta
2015 Immunology and Cell Biology  
T cell receptor (TCR) usage plays an important role in determining the outcome of CD8+ cytotoxic T lymphocyte (CTL) responses to viruses and other pathogens.  ...  These data have implications for established correlations between the nature of the TCR repertoire and response outcomes after infection, and suggest that analysis of a subset of cells or a single TCR  ...  Acknowledgments The authors wish to thank Prof. Stephen J. Turner for critical review of the manuscript.  ... 
doi:10.1038/icb.2015.44 pmid:25804828 pmcid:PMC4618100 fatcat:4zakkqgvvvbldhj72nbpggilzy

Meta-analysis of RNA sequencing datasets reveals an association between TRAJ23, psoriasis, and IL-17A

Alexander A. Merleev, Alina I. Marusina, Chelsea Ma, James T. Elder, Lam C. Tsoi, Siba P. Raychauduri, Stephan Weidinger, Elizabeth A. Wang, Iannis E. Adamopoulos, Guillaume Luxardi, Johann E. Gudjonsson, Michiko Shimoda (+1 others)
2018 JCI Insight  
Numerous studies of relatively few patients have linked T cell receptor (TCR) genes to psoriasis but have yielded dramatically conflicting results.  ...  These results have implications for the development of targeted therapies for psoriasis and other autoimmune diseases.  ...  Acknowledgments EM is supported by an early career from the Burroughs Wellcome Fund. This project was supported by NIH 1DP2OD008752 and by P30CA093373.  ... 
doi:10.1172/jci.insight.120682 pmid:29997305 fatcat:t7w2oieoebdtnlwinw352hgr7a

CTL Recognition of a Bulged Viral Peptide Involves Biased TCR Selection

J. J. Miles, D. Elhassen, N. A. Borg, S. L. Silins, F. E. Tynan, J. M. Burrows, A. W. Purcell, L. Kjer-Nielsen, J. Rossjohn, S. R. Burrows, J. McCluskey
2005 Journal of Immunology  
Acknowledgments We thank the BioCars staff for assistance in data collection at the Advanced Photon Source, Chicago. Disclosures The authors have no financial conflict of interest.  ...  I CDR3 sequences of HLA-B*3501-restricted, EPLP-specific CTL clones a The first two letters designate the donor origin of the CTL clone. b The designations TRBV, TRBJ, TRAV, and TRAJ follow the IMGT TCR  ...  For instance, in the donor DY, the majority of EPLP-reactive T cells used TRBV19 with the CDR3 motif of TRBV10 T cells.  ... 
doi:10.4049/jimmunol.175.6.3826 pmid:16148129 fatcat:nyl72t3j6rc7jp4znayw7meynq

High Resolution Structures of Highly Bulged Viral Epitopes Bound to Major Histocompatibility Complex Class I

Fleur E. Tynan, Natalie A. Borg, John J. Miles, Travis Beddoe, Diah El-Hassen, Sharon L. Silins, Wendy J. M. van Zuylen, Anthony W. Purcell, Lars Kjer-Nielsen, James McCluskey, Scott R. Burrows, Jamie Rossjohn
2005 Journal of Biological Chemistry  
The rigid, centrally-bulged epitope generates a biased T-cell response. Only the N-terminal face of the peptide bulge is critical for recognition by the dominant clonotype, SB27.  ...  The broad antigen binding cleft of HLA-B*3508 represents a critical feature for engagement of the public TcR, as the narrower binding cleft of HLA-B*3501 LPEPLPQGQLTAY , which differs from HLA-B*3508 by  ...  Lesk for useful discussions, and W. Macdonald, L. Ely and H. Reid for critical reading of the manuscript.  ... 
doi:10.1074/jbc.m503060200 pmid:15849183 fatcat:jprcbi25irctvjwcosf7mshrq4
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