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222 results on '"Giudicelli, Véronique"'

2. IMGT-KG: A Knowledge Graph for Immunogenetics

Author

Sanou, Gaoussou, Giudicelli, Véronique, Abdollahi, Nika, Kossida, Sofia, Todorov, Konstantin, Duroux, Patrice, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Sattler, Ulrike, editor, Hogan, Aidan, editor, Keet, Maria, editor, Presutti, Valentina, editor, Almeida, João Paulo A., editor, Takeda, Hideaki, editor, Monnin, Pierre, editor, Pirrò, Giuseppe, editor, and d’Amato, Claudia, editor

Published
2022
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4. IMGT/RobustpMHC: robust training for class-I MHC peptide binding prediction.

Author

Kushwaha, Anjana, Duroux, Patrice, Giudicelli, Véronique, Todorov, Konstantin, and Kossida, Sofia

Subjects
ARTIFICIAL neural networks, MAJOR histocompatibility complex, TRANSFORMER models, DEEP learning, PEPTIDES
Abstract

The accurate prediction of peptide-major histocompatibility complex (MHC) class I binding probabilities is a critical endeavor in immunoinformatics, with broad implications for vaccine development and immunotherapies. While recent deep neural network based approaches have showcased promise in peptide-MHC (pMHC) prediction, they have two shortcomings: (i) they rely on hand-crafted pseudo-sequence extraction, (ii) they do not generalize well to different datasets, which limits the practicality of these approaches. While existing methods rely on a 34 amino acid pseudo-sequence, our findings uncover the involvement of 147 positions in direct interactions between MHC and peptide. We further show that neural architectures can learn the intricacies of pMHC binding using even full sequences. To this end, we present PerceiverpMHC that is able to learn accurate representations on full-sequences by leveraging efficient transformer based architectures. Additionally, we propose IMGT/RobustpMHC that harnesses the potential of unlabeled data in improving the robustness of pMHC binding predictions through a self-supervised learning strategy. We extensively evaluate RobustpMHC on eight different datasets and showcase an overall improvement of over 6% in binding prediction accuracy compared to state-of-the-art approaches. We compile CrystalIMGT, a crystallography-verified dataset presenting a challenge to existing approaches due to significantly different pMHC distributions. Finally, to mitigate this distribution gap, we further develop a transfer learning pipeline. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Deciphering Gorilla gorilla gorilla immunoglobulin loci in multiple genome assemblies and enrichment of IMGT resources.

Author

Debbagh, Chahrazed, Folch, Géraldine, Jabado-Michaloud, Joumana, Giudicelli, Véronique, and Kossida, Sofia

Subjects
IMMUNOGLOBULIN genes, GORILLA (Genus), IMMUNOGLOBULIN analysis, IMMUNOGENETICS, COMPARATIVE genomics
Abstract

Through the analysis of immunoglobulin genes at the IGH, IGK, and IGL loci from four Gorilla gorilla gorilla genome assemblies, IMGT® provides an in-depth overview of these loci and their individual variations in a species closely related to humans. The similarity between gorilla and human IG gene organization allowed the assignment of gorilla IG gene names based on their human counterparts. This study revealed significant findings, including variability in the IGH locus, the presence of known and new copy number variations (CNVs), and the accurate estimation of IGHG genes. The IGK locus displayed remarkable homogeneity and lacked the gene duplication seen in humans, while the IGL locus showed a previously unconfirmed CNV in the J-C cluster. The curated data from these analyses, available on the IMGT website, enhance our understanding of gorilla immunogenetics and provide valuable insights into primate evolution. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Higher-order connections between stereotyped subsets: implications for improved patient classification in CLL

Author

Agathangelidis, Andreas, Chatzidimitriou, Anastasia, Gemenetzi, Katerina, Giudicelli, Veronique, Karypidou, Maria, Plevova, Karla, Davis, Zadie, Yan, Xiao-Jie, Jeromin, Sabine, Schneider, Christof, Pedersen, Lone Bredo, Tschumper, Renee C., Sutton, Lesley-Ann, Baliakas, Panagiotis, Scarfò, Lydia, van Gastel, Ellen J., Armand, Marine, Tausch, Eugen, Biderman, Bella, Baer, Constance, Bagnara, Davide, Navarro, Alba, Langlois de Septenville, Anne, Guido, Valentina, Mitterbauer-Hohendanner, Gerlinde, Dimovski, Aleksandar, Brieghel, Christian, Lawless, Sarah, Meggendorfer, Manja, Brazdilova, Kamila, Ritgen, Matthias, Facco, Monica, Tresoldi, Cristina, Visentin, Andrea, Patriarca, Andrea, Catherwood, Mark, Bonello, Lisa, Sudarikov, Andrey, Vanura, Katrina, Roumelioti, Maria, Skuhrova Francova, Hana, Moysiadis, Theodoros, Veronese, Silvio, Giannopoulos, Krzysztof, Mansouri, Larry, Karan-Djurasevic, Teodora, Sandaltzopoulos, Raphael, Bödör, Csaba, Fais, Franco, Kater, Arnon, Panovska, Irina, Rossi, Davide, Alshemmari, Salem, Panagiotidis, Panagiotis, Costeas, Paul, Espinet, Blanca, Antic, Darko, Foroni, Letizia, Montillo, Marco, Trentin, Livio, Stavroyianni, Niki, Gaidano, Gianluca, Francia di Celle, Paola, Niemann, Carsten, Campo, Elias, Anagnostopoulos, Achilles, Pott, Christiane, Fischer, Kirsten, Hallek, Michael, Oscier, David, Stilgenbauer, Stephan, Haferlach, Claudia, Jelinek, Diane, Chiorazzi, Nicholas, Pospisilova, Sarka, Lefranc, Marie-Paule, Kossida, Sofia, Langerak, Anton W., Belessi, Chrysoula, Davi, Frederic, Rosenquist, Richard, Ghia, Paolo, and Stamatopoulos, Kostas

Published
2021
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9. IMGT/mAb-KG: the knowledge graph for therapeutic monoclonal antibodies.

Author

Sanou, Gaoussou, Manso, Taciana, Todorov, Konstantin, Giudicelli, Véronique, Duroux, Patrice, and Kossida, Sofia

Subjects
KNOWLEDGE graphs, MONOCLONAL antibodies, SEMANTIC Web, GRAFT rejection, DATABASES
Abstract

Introduction: Therapeutic monoclonal antibodies (mAbs) have demonstrated promising outcomes in diverse clinical indications, including but not limited to graft rejection, cancer, and autoimmune diseases lately.Recognizing the crucial need for the scientific community to quickly and easily access dependable information on monoclonal antibodies (mAbs), IMGT®, the international ImMunoGeneTics information system®, provides a unique and invaluable resource: IMGT/mAb-DB, a comprehensive database of therapeutic mAbs, accessible via a user-friendly web interface. However, this approach restricts more sophisticated queries and segregates information from other databases. Methods: To connect IMGT/mAb-DB with the rest of the IMGT databases, we created IMGT/mAb-KG, a knowledge graph for therapeutic monoclonal antibodies connected to IMGT structures and genomics databases. IMGT/ mAb-KG is developed using the most effective methodologies and standards of semantic web and acquires data from IMGT/mAb-DB. Concerning interoperability, IMGT/mAb-KG reuses terms from biomedical resources and is connected to related resources. Results and discussion: In February 2024, IMGT/mAb-KG, encompassing a total of 139,629 triplets, provides access to 1,489 mAbs, approximately 500 targets, and over 500 clinical indications. It offers detailed insights into the mechanisms of action of mAbs, their construction, and their various products and associated studies. Linked to other resources such as Thera-SAbDab (Therapeutic Structural Antibody Database), PharmGKB (a comprehensive resource curating knowledge on the impact of genetic variation on drug response), PubMed, and HGNC (HUGO Gene Nomenclature Committee), IMGT/mAb-KG is an essential resource for mAb development. A user-friendly web interface facilitates the exploration and analyse of the content of IMGT/mAb-KG. [ABSTRACT FROM AUTHOR]

Published
2024
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13. Figure S2B from Chronic Lymphocytic Leukemia with Mutated IGHV4-34 Receptors: Shared and Distinct Immunogenetic Features and Clinical Outcomes

Author

Xochelli, Aliki, primary, Baliakas, Panagiotis, primary, Kavakiotis, Ioannis, primary, Agathangelidis, Andreas, primary, Sutton, Lesley-Ann, primary, Minga, Eva, primary, Ntoufa, Stavroula, primary, Tausch, Eugen, primary, Yan, Xiao-Jie, primary, Shanafelt, Tait, primary, Plevova, Karla, primary, Boudjogra, Myriam, primary, Rossi, Davide, primary, Davis, Zadie, primary, Navarro, Alba, primary, Sandberg, Yorick, primary, Vojdeman, Fie Juhl, primary, Scarfo, Lydia, primary, Stavroyianni, Niki, primary, Sudarikov, Andrey, primary, Veronese, Silvio, primary, Tzenou, Tatiana, primary, Karan-Djurasevic, Teodora, primary, Catherwood, Mark, primary, Kienle, Dirk, primary, Chatzouli, Maria, primary, Facco, Monica, primary, Bahlo, Jasmin, primary, Pott, Christiane, primary, Pedersen, Lone Bredo, primary, Mansouri, Larry, primary, Smedby, Karin E., primary, Chu, Charles C., primary, Giudicelli, Véronique, primary, Lefranc, Marie-Paule, primary, Panagiotidis, Panagiotis, primary, Juliusson, Gunnar, primary, Anagnostopoulos, Achilles, primary, Vlahavas, Ioannis, primary, Antic, Darko, primary, Trentin, Livio, primary, Montillo, Marco, primary, Niemann, Carsten, primary, Döhner, Hartmut, primary, Langerak, Anton W., primary, Pospisilova, Sarka, primary, Hallek, Michael, primary, Campo, Elias, primary, Chiorazzi, Nicholas, primary, Maglaveras, Nikos, primary, Oscier, David, primary, Gaidano, Gianluca, primary, Jelinek, Diane F., primary, Stilgenbauer, Stephan, primary, Chouvarda, Ioanna, primary, Darzentas, Nikos, primary, Belessi, Chrysoula, primary, Davi, Frederic, primary, Hadzidimitriou, Anastasia, primary, Rosenquist, Richard, primary, Ghia, Paolo, primary, and Stamatopoulos, Kostas, primary

Published
2023
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14. Table S1 from Chronic Lymphocytic Leukemia with Mutated IGHV4-34 Receptors: Shared and Distinct Immunogenetic Features and Clinical Outcomes

Author

Xochelli, Aliki, primary, Baliakas, Panagiotis, primary, Kavakiotis, Ioannis, primary, Agathangelidis, Andreas, primary, Sutton, Lesley-Ann, primary, Minga, Eva, primary, Ntoufa, Stavroula, primary, Tausch, Eugen, primary, Yan, Xiao-Jie, primary, Shanafelt, Tait, primary, Plevova, Karla, primary, Boudjogra, Myriam, primary, Rossi, Davide, primary, Davis, Zadie, primary, Navarro, Alba, primary, Sandberg, Yorick, primary, Vojdeman, Fie Juhl, primary, Scarfo, Lydia, primary, Stavroyianni, Niki, primary, Sudarikov, Andrey, primary, Veronese, Silvio, primary, Tzenou, Tatiana, primary, Karan-Djurasevic, Teodora, primary, Catherwood, Mark, primary, Kienle, Dirk, primary, Chatzouli, Maria, primary, Facco, Monica, primary, Bahlo, Jasmin, primary, Pott, Christiane, primary, Pedersen, Lone Bredo, primary, Mansouri, Larry, primary, Smedby, Karin E., primary, Chu, Charles C., primary, Giudicelli, Véronique, primary, Lefranc, Marie-Paule, primary, Panagiotidis, Panagiotis, primary, Juliusson, Gunnar, primary, Anagnostopoulos, Achilles, primary, Vlahavas, Ioannis, primary, Antic, Darko, primary, Trentin, Livio, primary, Montillo, Marco, primary, Niemann, Carsten, primary, Döhner, Hartmut, primary, Langerak, Anton W., primary, Pospisilova, Sarka, primary, Hallek, Michael, primary, Campo, Elias, primary, Chiorazzi, Nicholas, primary, Maglaveras, Nikos, primary, Oscier, David, primary, Gaidano, Gianluca, primary, Jelinek, Diane F., primary, Stilgenbauer, Stephan, primary, Chouvarda, Ioanna, primary, Darzentas, Nikos, primary, Belessi, Chrysoula, primary, Davi, Frederic, primary, Hadzidimitriou, Anastasia, primary, Rosenquist, Richard, primary, Ghia, Paolo, primary, and Stamatopoulos, Kostas, primary

Published
2023
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16. IMGT-ONTOLOGY

Author

Giudicelli, Véronique, Lefranc, Marie-Paule, Dubitzky, Werner, editor, Wolkenhauer, Olaf, editor, Cho, Kwang-Hyun, editor, and Yokota, Hiroki, editor

Published
2013
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18. IMGT-Choreography: Processing of Complex Immunogenetics Knowledge

Author

Chaume, Denys, Giudicelli, Véronique, Combres, Kora, Ginestoux, Chantal, Lefranc, Marie-Paule, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Dough, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Danos, Vincent, editor, and Schachter, Vincent, editor

Published
2005
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19. Immunoglobulin gene sequence analysis in chronic lymphocytic leukemia:the 2022 update of the recommendations by ERIC, the European Research Initiative on CLL

Author

Agathangelidis, Andreas, Chatzidimitriou, Anastasia, Chatzikonstantinou, Thomas, Tresoldi, Cristina, Davis, Zadie, Giudicelli, Véronique, Kossida, Sofia, Belessi, Chrysoula, Rosenquist, Richard, Ghia, Paolo, Langerak, Anton W., Davi, Frédéric, Stamatopoulos, Kostas, Agathangelidis, Andreas, Chatzidimitriou, Anastasia, Chatzikonstantinou, Thomas, Tresoldi, Cristina, Davis, Zadie, Giudicelli, Véronique, Kossida, Sofia, Belessi, Chrysoula, Rosenquist, Richard, Ghia, Paolo, Langerak, Anton W., Davi, Frédéric, and Stamatopoulos, Kostas

Abstract

The somatic hypermutation (SHM) status of the clonotypic immunoglobulin heavy variable (IGHV) gene is a critical biomarker for assessing the prognosis of patients with chronic lymphocytic leukemia (CLL). Importantly, independent studies have documented that IGHV SHM status is also a predictor of responses to therapy, including both chemoimmunotherapy (CIT) and novel, targeted agents. Moreover, immunogenetic analysis in CLL has revealed that different patients may express (quasi)identical, stereotyped B cell receptor immunoglobulin (BcR IG) and are classified into subsets based on this common feature. Patients in certain stereotyped subsets display consistent biology, clinical presentation, and outcome that are distinct from other patients, even with concordant IGHV gene SHM status. All of the above highlights the relevance of immunogenetic analysis in CLL, which is considered a cornerstone for accurate risk stratification and clinical decision making. Recommendations for robust immunogenetic analysis exist thanks to dedicated efforts by ERIC, the European Research Initiative on CLL, covering all test phases, from the pre-analytical and analytical to the post-analytical, pertaining to the analysis, interpretation, and reporting of the findings. That said, these recommendations apply to Sanger sequencing, which is increasingly being superseded by next generation sequencing (NGS), further underscoring the need for an update. Here, we present an overview of the clinical utility of immunogenetics in CLL and update our analytical recommendations with the aim to assist in the refined management of patients with CLL.

Published
2022

20. Immunoglobulin heavy variable (IGHV) genes and alleles: new entities, new names and implications for research and prognostication in chronic lymphocytic leukaemia

Author

Xochelli, Aliki, Agathangelidis, Andreas, Kavakiotis, Ioannis, Minga, Evangelia, Sutton, Lesley Ann, Baliakas, Panagiotis, Chouvarda, Ioanna, Giudicelli, Véronique, Vlahavas, Ioannis, Maglaveras, Nikos, Bonello, Lisa, Trentin, Livio, Tedeschi, Alessandra, Panagiotidis, Panagiotis, Geisler, Christian, Langerak, Anton W., Pospisilova, Sarka, Jelinek, Diane F., Oscier, David, Chiorazzi, Nicholas, Darzentas, Nikos, Davi, Fred, Ghia, Paolo, Rosenquist, Richard, Hadzidimitriou, Anastasia, Belessi, Chrysoula, Lefranc, Marie-Paule, and Stamatopoulos, Kostas

Published
2015
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21. Stereotyped B-cell receptors in one-third of chronic lymphocytic leukemia: a molecular classification with implications for targeted therapies

Author

Agathangelidis, Andreas, Darzentas, Nikos, Hadzidimitriou, Anastasia, Brochet, Xavier, Murray, Fiona, Yan, Xiao-Jie, Davis, Zadie, van Gastel-Mol, Ellen J., Tresoldi, Cristina, Chu, Charles C., Cahill, Nicola, Giudicelli, Veronique, Tichy, Boris, Pedersen, Lone Bredo, Foroni, Letizia, Bonello, Lisa, Janus, Agnieszka, Smedby, Karin, Anagnostopoulos, Achilles, Merle-Beral, Helene, Laoutaris, Nikolaos, Juliusson, Gunnar, di Celle, Paola Francia, Pospisilova, Sarka, Jurlander, Jesper, Geisler, Christian, Tsaftaris, Athanasios, Lefranc, Marie-Paule, Langerak, Anton W., Oscier, David Graham, Chiorazzi, Nicholas, Belessi, Chrysoula, Davi, Frederic, Rosenquist, Richard, Ghia, Paolo, and Stamatopoulos, Kostas

Published
2012
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22. MZ lymphoproliferations: shared and unique characteristics

Author

Xochelli, Aliki, Bikos, Vasilis, Polychronidou, Eleftheria, Galigalidou, Chrysi, Agathangelidis, Andreas, Charlotte, Frédéric, Moschonas, Panagiotis, Davis, Zadie, Colombo, Monica, Roumelioti, Maria, Sutton, Lesley-Ann, Groenen, Patricia, van den Brand, Michiel, Boudjoghra, Myriam, Algara, Patricia, Traverse-Glehen, Alexandra, Ferrer, Ana, Stalika, Evangelia, Karypidou, Maria, Kanellis, George, Kalpadakis, Christina, Mollejo, Manuella, Pangalis, Gerasimos, Vlamos, Panayiotis, Amini, Rose-Marie, Pospisilova, Sarka, Gonzalez, David, Ponzoni, Maurilio, Anagnostopoulos, Achilles, Giudicelli, Véronique, Lefranc, Marie-Paule, Espinet, Blanca, Panagiotidis, Panagiotis, Piris, Miguel Angel, Du, Ming-Qing, Rosenquist, Richard, Papadaki, Theodora, Belessi, Chrysoula, Ferrarini, Manlio, Oscier, David, Tzovaras, Dimitrios, Ghia, Paolo, Davi, Frederic, Hadzidimitriou, Anastasia, Stamatopoulos, Kostas, Apollo - University of Cambridge Repository, Institute of Applied Biosciences, CERTH, Thessaloniki, Greece., Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Information Technologies Institute, CERTH, Thessaloniki, Greece., Department of Informatics, Ionian University, Corfu, Greece, Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy., Service d'anatomie et cytologie pathologiques [CHU Saint-Antoine], Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Service de pathologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Information Technologies Institute, CERTH, Thessaloniki, Greece, Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK., Molecular Pathology, Ospedale Policlinico SanMartino, Genoa, Italy., First Department of Propaedeutic Medicine, University of Athens, Athens, Greece, Uppsala Universitet [Uppsala], Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden, Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands., Université Pierre et Marie Curie - Paris 6 (UPMC), Service d'Hématologie Biologique [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Hospital Virgen de la Salud, Toledo, Spain, Department of Pathology and Hematology, Hospices Civils de Lyon (HCL), Laboratori de Citologia Hematològica i Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain, Centre for Research and Technology Hellas (CERTH), Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece, Hematopathology Department, Evangelismos Hospital, Athens, Greece., Department of Haematology, University of Crete, Heraklion, Greece., Department of Haematology, Athens Medical Center, Athens, Greece, Department of Informatics [Ionian University], Ionian University [Corfu], Department of Informatics, Ionian University, Corfu, Greece., Department of Genetics and Pathology, Uppsala University Hospital, CEITEC-Central European Institute of Technology, MasarykBrno, Czech Republic., Pathology Unit, Unit of Lymphoid Malignancies, San Raffaele H Scientific Institute, Pathology Unit, San Raffaele Scientific Institute, Milan, Italy, Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoris de Citologia Hematológica/Citogenética Molecular. Servei de Patologia, GRETNHE, IMIM-Hospital del Mar, Laboratori de Citologia Hematològica i Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain., Pathology Department, IIS 'Fundacion Jimenez Diaz', Madrid, Spain, Pathology, University of Cambridge [UK] (CAM), Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK, Hematology Department, Nikea General Hospital, Piraeus, Greece, Direzione Scientifica, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria (AOU) San Martino-IST, Genoa, Italy., Informatics & Telematics Institute (ITI), CERTH, Università Vita e Salute, San Raffaele, Milano, Italy, Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institute of Applied Biosciences, Centre for Research and Technology-Hellas, Thessaloniki, Greece, Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden, Xochelli, Aliki, Bikos, Vasili, Polychronidou, Eleftheria, Galigalidou, Chrysi, Agathangelidis, Andrea, Charlotte, Frédéric, Moschonas, Panagioti, Davis, Zadie, Colombo, Monica, Roumelioti, Maria, Sutton, Lesley-Ann, Groenen, Patricia, van den Brand, Michiel, Boudjoghra, Myriam, Algara, Patricia, Traverse-Glehen, Alexandra, Ferrer, Ana, Stalika, Evangelia, Karypidou, Maria, Kanellis, George, Kalpadakis, Christina, Mollejo, Manuella, Pangalis, Gerasimo, Vlamos, Panayioti, Amini, Rose-Marie, Pospisilova, Sarka, Gonzalez, David, Ponzoni, Maurilio, Anagnostopoulos, Achille, Giudicelli, Véronique, Lefranc, Marie-Paule, Espinet, Blanca, Panagiotidis, Panagioti, Piris, Miguel Angel, Du, Ming-Qing, Rosenquist, Richard, Papadaki, Theodora, Belessi, Chrysoula, Ferrarini, Manlio, Oscier, David, Tzovaras, Dimitrio, Ghia, Paolo, Davi, Frederic, Hadzidimitriou, Anastasia, and Stamatopoulos, Kostas

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, Genes, Immunoglobulin, Genes, Immunoglobulin Heavy Chain, Cancer development and immune defence Radboud Institute for Molecular Life Sciences [Radboudumc 2], [SDV]Life Sciences [q-bio], Immunoglobulin Variable Region, Receptors, Antigen, B-Cell, Lymphoma, B-Cell, Marginal Zone, Rare cancers Radboud Institute for Molecular Life Sciences [Radboudumc 9], Complementarity Determining Regions, marginal zone lymphoma, immunoglobulin gene, antigen, ontogeny, Marginal zone lymphoma, Mutation, Tumor Microenvironment, Humans, Gene Rearrangement, B-Lymphocyte
Abstract

Contains fulltext : 203155.pdf (Publisher’s version ) (Closed access) The B cell receptor immunoglobulin (Ig) gene repertoires of marginal zone (MZ) lymphoproliferations were analyzed in order to obtain insight into their ontogenetic relationships. Our cohort included cases with MZ lymphomas (n = 488), i.e. splenic (SMZL), nodal (NMZL) and extranodal (ENMZL), as well as provisional entities (n = 76), according to the WHO classification. The most striking Ig gene repertoire skewing was observed in SMZL. However, restrictions were also identified in all other MZ lymphomas studied, particularly ENMZL, with significantly different Ig gene distributions depending on the primary site of involvement. Cross-entity comparisons of the MZ Ig sequence dataset with a large dataset of Ig sequences (MZ-related or not; n = 65 837) revealed four major clusters of cases sharing homologous ('public') heavy variable complementarity-determining region 3. These clusters included rearrangements from SMZL, ENMZL (gastric, salivary gland, ocular adnexa), chronic lymphocytic leukemia, but also rheumatoid factors and non-malignant splenic MZ cells. In conclusion, different MZ lymphomas display biased immunogenetic signatures indicating distinct antigen exposure histories. The existence of rare public stereotypes raises the intriguing possibility that common, pathogen-triggered, immune-mediated mechanisms may result in diverse B lymphoproliferations due to targeting versatile progenitor B cells and/or operating in particular microenvironments. Copyright (c) 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Published
2019
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23. IMGT® Biocuration and Analysis of the Rhesus Monkey IG Loci

Author

Nguefack Ngoune, Viviane, primary, Bertignac, Morgane, additional, Georga, Maria, additional, Papadaki, Ariadni, additional, Albani, Alexandre, additional, Folch, Géraldine, additional, Jabado-Michaloud, Joumana, additional, Giudicelli, Véronique, additional, Duroux, Patrice, additional, Lefranc, Marie-Paule, additional, and Kossida, Sofia, additional

Published
2022
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24. IMGT® databases, related tools and web resources through three main axes of research and development

Author

Manso, Taciana, primary, Folch, Géraldine, additional, Giudicelli, Véronique, additional, Jabado-Michaloud, Joumana, additional, Kushwaha, Anjana, additional, Nguefack Ngoune, Viviane, additional, Georga, Maria, additional, Papadaki, Ariadni, additional, Debbagh, Chahrazed, additional, Pégorier, Perrine, additional, Bertignac, Morgane, additional, Hadi-Saljoqi, Saida, additional, Chentli, Imène, additional, Cherouali, Karima, additional, Aouinti, Safa, additional, El Hamwi, Amar, additional, Albani, Alexandre, additional, Elazami Elhassani, Merouane, additional, Viart, Benjamin, additional, Goret, Agathe, additional, Tran, Anna, additional, Sanou, Gaoussou, additional, Rollin, Maël, additional, Duroux, Patrice, additional, and Kossida, Sofia, additional

Published
2021
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26. Liste des collaborateurs

Author

Béné, Marie Christine, primary, Drouet, Christian, additional, Fisson, Sylvain, additional, Seillès, Estelle, additional, Béné, Marie Christine, additional, Billaud, Sandrine, additional, Birklé, Stéphane, additional, Chollet-Martin, Sylvie, additional, Contin-Bordes, Cécile, additional, Freyburger, Ludovic, additional, Gubler, Brigitte, additional, Thibault, Gilles, additional, Amé-Thomas, Patricia, additional, Arafah, Karim, additional, Aubry, Jacques, additional, Aymeric, Jean-Luc, additional, Bulet, Philippe, additional, Capron, Claude, additional, Carcelain, Guislaine, additional, Chevailler, Alain, additional, Delfau-Larue, Marie-Hélène, additional, Diaz, Olivier, additional, Dubucquoi, Sylvain, additional, Favier, Bertrand, additional, Frippiat, Jean-Pol, additional, Gougerot-Pocidalo, Marie-Anne, additional, Legrand-Frossi, Christine, additional, Le Mauff, Brigitte, additional, Lemoine, François, additional, Masson, Damien, additional, Moreau, Jeanne, additional, Nicolas, Jean-François, additional, Nüsse, Olivier, additional, Pagès, Franck, additional, Ponard, Denise, additional, Robert, Philippe, additional, Rouzaire, Paul, additional, Schlecht-Louf, Géraldine, additional, Seddiki, Nabila, additional, Sterkers, Ghislaine, additional, Tridon, Arlette, additional, Velge-Roussel, Florence, additional, Vitte, Joana, additional, Bienvenu, Jacques, additional, Dragon-Duret, Marie-Agnès, additional, Labalette, Myriam, additional, Lefranc, Marie-Paule, additional, Muller, Jean-Yves, additional, Alamyar, Eltaf, additional, Boulland, Marie-Laure, additional, Charignon, Delphine, additional, Chiaroni, Jacques, additional, Defendi, Federica, additional, Duroux, Patrice, additional, Ghannam, Arije, additional, Giudicelli, Véronique, additional, Marotel, Charline, additional, Ratié, Vanessa, additional, Sarda, Marie-Nathalie, additional, Sasorith, Souphatta, additional, and Taupin, Jean-Luc, additional

Published
2014
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34. IMGT® Biocuration and Comparative Study of the T Cell Receptor Beta Locus of Veterinary Species Based on Homo sapiens TRB

Author

Pégorier, Perrine, primary, Bertignac, Morgane, additional, Chentli, Imène, additional, Nguefack Ngoune, Viviane, additional, Folch, Géraldine, additional, Jabado-Michaloud, Joumana, additional, Hadi-Saljoqi, Saida, additional, Giudicelli, Véronique, additional, Duroux, Patrice, additional, Lefranc, Marie-Paule, additional, and Kossida, Sofia, additional

Published
2020
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35. IG and TR single chain fragment variable (scFv) sequence analysis: a new advanced functionality of IMGT/V-QUEST and IMGT/HighV-QUEST

Author

Giudicelli, Véronique, Duroux, Patrice, Kossida, Sofia, Lefranc, Marie-Paule, Institut de génétique humaine (IGH), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
lcsh:Immunologic diseases. Allergy, IG, TR, Methodology Article, [SDV]Life Sciences [q-bio], Receptors, Antigen, T-Cell, High-Throughput Nucleotide Sequencing, Immunoglobulins, Adaptive Immunity, IMGT-ONTOLOGY, scFv, adaptive immune repertoire, IMGT, V-DOMAIN, Immunogenetics, Animals, Humans, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], T cell receptor, single chain fragment variable, lcsh:RC581-607, immunoglobulin, Software, Single-Chain Antibodies
Abstract

Background IMGT®, the international ImMunoGeneTics information system® ( http://www.imgt.org ), was created in 1989 in Montpellier, France (CNRS and Montpellier University) to manage the huge and complex diversity of the antigen receptors, and is at the origin of immunoinformatics, a science at the interface between immunogenetics and bioinformatics. Immunoglobulins (IG) or antibodies and T cell receptors (TR) are managed and described in the IMGT® databases and tools at the level of receptor, chain and domain. The analysis of the IG and TR variable (V) domain rearranged nucleotide sequences is performed by IMGT/V-QUEST (online since 1997, 50 sequences per batch) and, for next generation sequencing (NGS), by IMGT/HighV-QUEST, the high throughput version of IMGT/V-QUEST (portal begun in 2010, 500,000 sequences per batch). In vitro combinatorial libraries of engineered antibody single chain Fragment variable (scFv) which mimic the in vivo natural diversity of the immune adaptive responses are extensively screened for the discovery of novel antigen binding specificities. However the analysis of NGS full length scFv (~850 bp) represents a challenge as they contain two V domains connected by a linker and there is no tool for the analysis of two V domains in a single chain. Methods The functionality "Analyis of single chain Fragment variable (scFv)" has been implemented in IMGT/V-QUEST and, for NGS, in IMGT/HighV-QUEST for the analysis of the two V domains of IG and TR scFv. It proceeds in five steps: search for a first closest V-REGION, full characterization of the first V-(D)-J-REGION, then search for a second V-REGION and full characterization of the second V-(D)-J-REGION, and finally linker delimitation. Results For each sequence or NGS read, positions of the 5′V-DOMAIN, linker and 3′V-DOMAIN in the scFv are provided in the ‘V-orientated’ sense. Each V-DOMAIN is fully characterized (gene identification, sequence description, junction analysis, characterization of mutations and amino changes). The functionality is generic and can analyse any IG or TR single chain nucleotide sequence containing two V domains, provided that the corresponding species IMGT reference directory is available. Conclusion The “Analysis of single chain Fragment variable (scFv)” implemented in IMGT/V-QUEST and, for NGS, in IMGT/HighV-QUEST provides the identification and full characterization of the two V domains of full-length scFv (~850 bp) nucleotide sequences from combinatorial libraries. The analysis can also be performed on concatenated paired chains of expressed antigen receptor IG or TR repertoires.

Published
2017
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37. IMGT®, the international ImMunoGeneTics information system®

Author

Lefranc, Marie-Paule, Giudicelli, Véronique, Ginestoux, Chantal, Jabado-Michaloud, Joumana, Folch, Géraldine, Bellahcene, Fatena, Wu, Yan, Gemrot, Elodie, Brochet, Xavier, Lane, Jérôme, Regnier, Laetitia, Ehrenmann, François, Lefranc, Gérard, and Duroux, Patrice

Published
2009

38. IMGT ® Biocuration and Analysis of the Rhesus Monkey IG Loci.

Author

Nguefack Ngoune, Viviane, Bertignac, Morgane, Georga, Maria, Papadaki, Ariadni, Albani, Alexandre, Folch, Géraldine, Jabado-Michaloud, Joumana, Giudicelli, Véronique, Duroux, Patrice, Lefranc, Marie-Paule, and Kossida, Sofia

Subjects
RHESUS monkeys, IMMUNOGLOBULIN genes, IMMUNOGLOBULIN light chains, LOCUS (Genetics), T cell receptors, IMMUNOGLOBULIN heavy chains
Abstract

The adaptive immune system, along with the innate immune system, are the two main biological processes that protect an organism from pathogens. The adaptive immune system is characterized by the specificity and extreme diversity of its antigen receptors. These antigen receptors are the immunoglobulins (IG) or antibodies of the B cells and the T cell receptors (TR) of the T cells. The IG are proteins that have a dual role in immunity: they recognize antigens and trigger elimination mechanisms, to rid the body of foreign cells. The synthesis of the immunoglobulin heavy and light chains requires gene rearrangements at the DNA level in the IGH, IGK, and IGL loci. The rhesus monkey (Macaca mulatta) is one of the most widely used nonhuman primate species in biomedical research. In this manuscript, we provide a thorough analysis of the three IG loci of the Mmul_10 assembly of rhesus monkey, integrating IMGT previously existing data. Detailed characterization of IG genes includes their localization and position in the loci, the determination of the allele functionality, and the description of the regulatory elements of their promoters as well as the sequences of the conventional recombination signals (RS). This complete annotation of the genomic IG loci of Mmul_10 assembly and the highly detailed IG gene characterization could be used as a model, in additional rhesus monkey assemblies, for the analysis of the IG allelic polymorphism and structural variation, which have been described in rhesus monkeys. [ABSTRACT FROM AUTHOR]

Published
2022
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46. Disease‐biased and shared characteristics of the immunoglobulin gene repertoires in marginal zone B cell lymphoproliferations

Author

Xochelli, Aliki, primary, Bikos, Vasilis, additional, Polychronidou, Eleftheria, additional, Galigalidou, Chrysi, additional, Agathangelidis, Andreas, additional, Charlotte, Frédéric, additional, Moschonas, Panagiotis, additional, Davis, Zadie, additional, Colombo, Monica, additional, Roumelioti, Maria, additional, Sutton, Lesley‐Ann, additional, Groenen, Patricia, additional, van den Brand, Michiel, additional, Boudjoghra, Myriam, additional, Algara, Patricia, additional, Traverse‐Glehen, Alexandra, additional, Ferrer, Ana, additional, Stalika, Evangelia, additional, Karypidou, Maria, additional, Kanellis, George, additional, Kalpadakis, Christina, additional, Mollejo, Manuella, additional, Pangalis, Gerasimos, additional, Vlamos, Panayiotis, additional, Amini, Rose‐Marie, additional, Pospisilova, Sarka, additional, Gonzalez, David, additional, Ponzoni, Maurilio, additional, Anagnostopoulos, Achilles, additional, Giudicelli, Véronique, additional, Lefranc, Marie‐Paule, additional, Espinet, Blanca, additional, Panagiotidis, Panagiotis, additional, Piris, Miguel Angel, additional, Du, Ming‐Qing, additional, Rosenquist, Richard, additional, Papadaki, Theodora, additional, Belessi, Chrysoula, additional, Ferrarini, Manlio, additional, Oscier, David, additional, Tzovaras, Dimitrios, additional, Ghia, Paolo, additional, Davi, Frederic, additional, Hadzidimitriou, Anastasia, additional, and Stamatopoulos, Kostas, additional

Published
2019
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47. No improvement in long-term survival over time for chronic lymphocytic leukemia patients in stereotyped subsets #1 and #2 treated with chemo(immuno)therapy

Author

Baliakas, Panagiotis, Mattsson, Mattias, Hadzidimitriou, Anastasia, Minga, Eva, Agathangelidis, Andreas, Sutton, Lesley-ann, Scarfo, Lydia, Davis, Zadie, Yan, Xiao-jie, Plevova, Karla, Sandberg, Yorick, Vojdeman, Fie J., Tzenou, Tatiana, Chu, Charles C., Veronese, Silvio, Mansouri, Larry, Smedby, Karin E, Giudicelli, Véronique, Nguyen-khac, Florence, Panagiotidis, Panagiotis, Juliusson, Gunnar, Anagnostopoulos, Achilles, Lefranc, Marie-paule, Trentin, Livio, Catherwood, Mark, Montillo, Marco, Niemann, Carsten U., Langerak, Anton W., Pospisilova, Sarka, Stavroyianni, Niki, Chiorazzi, Nicholas, Oscier, David, Jelinek, Diane F, Shanafelt, Tait, Darzentas, Nikos, Belessi, Chrysoula, Davi, Frederic, Ghia, Paolo, Rosenquist, Richard, Stamatopoulos, Kostas, Baliakas, Panagiotis, Mattsson, Mattias, Hadzidimitriou, Anastasia, Minga, Eva, Agathangelidis, Andreas, Sutton, Lesley-ann, Scarfo, Lydia, Davis, Zadie, Yan, Xiao-jie, Plevova, Karla, Sandberg, Yorick, Vojdeman, Fie J., Tzenou, Tatiana, Chu, Charles C., Veronese, Silvio, Mansouri, Larry, Smedby, Karin E, Giudicelli, Véronique, Nguyen-khac, Florence, Panagiotidis, Panagiotis, Juliusson, Gunnar, Anagnostopoulos, Achilles, Lefranc, Marie-paule, Trentin, Livio, Catherwood, Mark, Montillo, Marco, Niemann, Carsten U., Langerak, Anton W., Pospisilova, Sarka, Stavroyianni, Niki, Chiorazzi, Nicholas, Oscier, David, Jelinek, Diane F, Shanafelt, Tait, Darzentas, Nikos, Belessi, Chrysoula, Davi, Frederic, Ghia, Paolo, Rosenquist, Richard, and Stamatopoulos, Kostas

Published
2018

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

Author

Hemadou, Audrey, Giudicelli, Véronique, Smith, Melissa Laird, Lefranc, Marie-Paule, Duroux, Patrice, Kossida, Sofia, Heiner, Cheryl, Hepler, N. Lance, Kuijpers, John, Groppi, Alexis, Korlach, Jonas, Mondon, Philippe, Ottones, Florence, Jacobin-Valat, Marie-Josée, Laroche-Traineau, Jeanny, Clofent-Sanchez, Gisèle, Centre de résonance magnétique des systèmes biologiques (CRMSB), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Pacific Biosciences [Menlo Park], Pacific Biosciences of California, Centre de Bioinformatique de Bordeaux (CBIB), CGFB, and Laboratoire Français du Fractionnement et des Biotechnologies (LFB)

Subjects
lcsh:Immunologic diseases. Allergy, Immunology, chemical and pharmacologic phenomena, respiratory system, IMGT/HighV-QUEST, immunoinformatics, Pacific Biosciences sequencing, phage combinatorial library, Methods, next-generation sequencing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], single chain fragment variable, lcsh:RC581-607, human antibody, immunoglobulin, ComputingMilieux_MISCELLANEOUS
Abstract

Phage-display selection of immunoglobulin (IG) or antibody single chain Fragment variable (scFv) from combinatorial libraries is widely used for identifying new antibodies for novel targets. Next-generation sequencing (NGS) has recently emerged as a new method for the high throughput characterization of IG and T cell receptor (TR) immune repertoires both in vivo and in vitro. However, challenges remain for the NGS sequencing of scFv from combinatorial libraries owing to the scFv length (>800 bp) and the presence of two variable domains [variable heavy (VH) and variable light (VL) for IG] associated by a peptide linker in a single chain. Here, we show that single-molecule real-time (SMRT) sequencing with the Pacific Biosciences RS II platform allows for the generation of full-length scFv reads obtained from an in vivo selection of scFv-phages in an animal model of atherosclerosis. We first amplified the DNA of the phagemid inserts from scFv-phages eluted from an aortic section at the third round of the in vivo selection. From this amplified DNA, 450,558 reads were obtained from 15 SMRT cells. Highly accurate circular consensus sequences from these reads were generated, filtered by quality and then analyzed by IMGT/HighV-QUEST with the functionality for scFv. Full-length scFv were identified and characterized in 348,659 reads. Full-length scFv sequencing is an absolute requirement for analyzing the associated VH and VL domains enriched during the in vivo panning rounds. In order to further validate the ability of SMRT sequencing to provide high quality, full-length scFv sequences, we tracked the reads of an scFv-phage clone P3 previously identified by biological assays and Sanger sequencing. Sixty P3 reads showed 100% identity with the full-length scFv of 767 bp, 53 of them covering the whole insert of 977 bp, which encompassed the primer sequences. The remaining seven reads were identical over a shortened length of 939 bp that excludes the vicinity of primers at 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.

Published
2017
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