Contents

• Preface
• Contributors
• 1. The Advent of Precision Immunology: Immunogenetics at the Center of Immune Cell Analysis in Health and Disease
  Anton W. Langerak.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Immunogenetics in the Hematology-Immunology Domain
  • 3. Immunogenetics Methods
  • 4. (Pre- and Post-)Analytical Aspects of Immunogenetics
  • 5. Immunogenetics at the Basis of Precision Immunology
  • References
• 2. Next-Generation Sequencing-Based Clonality Detection of Immunoglobulin Gene Rearrangements in B-Cell Lymphoma
  Diede A. G. van Bladel, Jessica L. M. van der Last-Kempkes, Blanca Scheijen, and Patricia J. T. A. Groenen; on behalf of the EuroClonality Consortium.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • Acknowledgments
  • References
• 3. One-Step Next-Generation Sequencing of Immunoglobulin and T-Cell Receptor Gene Recombinations for MRD Marker Identification in Acute Lymphoblastic Leukemia
  Patrick Villarese, Chrystelle Abdo, Matthieu Bertrand, Florian Thonier, Mathieu Giraud, Mikaël Salson, and Elizabeth Macintyre.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • References
• 4. Immunoglobulin/T-Cell Receptor Gene Rearrangement Analysis Using RNA-Seq
  Vincent H. J. van der Velden, Lorenz Bastian, Monika Brüggemann, Alina M. Hartmann, and Nikos Darzentas.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • Acknowledgments
  • References
• 5. Minimal Residual Disease Analysis by Monitoring Immunoglobulin and T-Cell Receptor Gene Rearrangements by Quantitative PCR and Droplet Digital PCR
  Irene Della Starza, Cornelia Eckert, Daniela Drandi, and Giovanni Cazzaniga; on behalf of the EuroMRD Consortium.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • References
• 6. Quality Control for IG /TR Marker Identification and MRD Analysis
  Eva Fronkova, Michael Svaton, and Jan Trka.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. IG /TR Marker Identification
  • 3. Interpretation of RQ-PCR MRD Analysis Results
  • 4. Conclusion
  • Acknowledgments
  • References
• 7. cfDNA-Based NGS IG Analysis in Lymphoma
  Christiane Pott, Michaela Kotrova, Nikos Darzentas, Monika Brüggemann, and Mouhamad Khouja; on behalf of the EuroClonality-NGS Working Group.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • Acknowledgments
  • References
• 8. Targeted Locus Amplification as Marker Screening Approach to Detect Immunoglobulin (IG) Translocations in B-Cell Non-Hodgkin Lymphomas
  Elisa Genuardi, Beatrice Alessandria, Aurora Maria Civita, and Simone Ferrero.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • References
• 9. Immunoglobulin/T Cell Receptor Capture Strategy for Comprehensive Immunogenetics
  James Peter Stewart, Jana Gazdova, Shambhavi Srivastava, Julia Revolta, Louise Harewood, Manisha Maurya, Nikos Darzentas, and David Gonzalez.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • Acknowledgments
  • References
• 10. Immunoglobulin Gene Mutational Status Assessment by Next Generation Sequencing in Chronic Lymphocytic Leukemia
  Anne Langlois de Septenville, Myriam Boudjoghra, Clotilde Bravetti, Marine Armand, Mikaël Salson, Mathieu Giraud, and Frederic Davi.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • Acknowledgments
  • References
• 11. NGS-Based B-Cell Receptor Repertoire AnalysisRepertoire analyses in the Context of Inborn Errors of Immunity
  Pauline A. van Schouwenburg, Mirjam van der Burg, and Hanna IJspeert.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • References
• 12. Generic Multiplex Digital PCR for Accurate Quantification of T Cells in Copy Number Stable and Unstable DNA Samples
  Rogier J. Nell, Willem H. Zoutman, Mieke Versluis, and Pieter A. van der Velden.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • References
• 13. Gene Engineering T Cells with T-Cell Receptor for Adoptive Therapy
  Dian Kortleve, Mandy van Brakel, Rebecca Wijers, Reno Debets, and Dora Hammerl.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • References
• 14. Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level
  Nicolle H. R. Litjens, Anton W. Langerak, Zakia Azmani, Xander den Dekker, Michiel G. H. Betjes, Rutger W. W. Brouwer, and Wilfred F. J. van IJcken.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • Acknowledgments
  • References
• 15. AIRR Community Guide to Planning and Performing AIRR-Seq Experiments
  Anne Eugster, Magnolia L. Bostick, Nidhi Gupta, Encarnita Mariotti-Ferrandiz, Gloria Kraus, Wenzhao Meng, Cinque Soto, Johannes Trück, Ulrik Stervbo, and Eline T. Luning Prak; on behalf of the AIRR Community.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Planning the Experiment
  • 3. Interpreting the Results
  • 4. Conclusion
  • Acknowledgments
  • References
• 16. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation
  Lmar Babrak, Susanna Marquez, Christian E. Busse, William D. Lees, Enkelejda Miho, Mats Ohlin, Aaron M. Rosenfeld, Ulrik Stervbo, Corey T. Watson, and Chaim A. Schramm; on behalf of the AIRR Community.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Conclusion
  • Acknowledgments
  • References
• 17. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis
  Susanna Marquez, Lmar Babrak, Victor Greiff, Kenneth B. Hoehn, William D. Lees, Eline T. Luning Prak, Enkelejda Miho, Aaron M. Rosenfeld, Chaim A. Schramm, and Ulrik Stervbo; on behalf of the AIRR Community.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Conclusion
  • Acknowledgments
  • References
• 18. Bulk gDNA Sequencing of Antibody Heavy-Chain Gene Rearrangements for Detection and Analysis of B-Cell Clone Distribution: A Method by the AIRR Community
  Aaron M. Rosenfeld, Wenzhao Meng, Kalisse I. Horne, Elaine C. Chen, Davide Bagnara, Ulrik Stervbo, and Eline T. Luning Prak; on behalf of the AIRR Community.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • Acknowledgments
  • References
• 19. Bulk Sequencing from mRNA with UMI for Evaluation of B-Cell Isotype and Clonal Evolution: A Method by the AIRR Community
  Nidhi Gupta, Susanna Marquez, Cinque Soto, Elaine C. Chen, Magnolia L. Bostick, Ulrik Stervbo, and Andrew Farmer.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • Acknowledgments
  • References
• 20. Single-Cell Analysis and Tracking of Antigen-Specific T Cells: Integrating Paired Chain AIRR-Seq and Transcriptome Sequencing: A Method by the AIRR Community
  Nidhi Gupta, Ida Lindeman, Susanne Reinhardt, Encarnita Mariotti-Ferrandiz, Kevin Mujangi-Ebeka, Kristen Martins-Taylor, and Anne Eugster.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • Acknowledgments
  • References
• 21. Quality Control: Chain Pairing Precision and Monitoring of Cross-Sample Contamination: A Method by the AIRR Community
  Cheng-Yu Chung, Matías Gutiérrez-González, Sheila N. López Acevedo, Ahmed S. Fahad, and Brandon J. DeKosky; on behalf of the AIRR Community.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • Acknowledgments
  • References
• 22. Immune Repertoire Analysis on High-Performance Computing Using VDJServer V1: A Method by the AIRR Community
  Scott Christley, Ulrik Stervbo, and Lindsay G. Cowell; on behalf of the AIRR Community.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • References
• 23. Data Sharing and Reuse: A Method by the AIRR Community
  Brian D. Corrie, Scott Christley, Christian E. Busse, Lindsay G. Cowell, Kira C. M. Neller, Florian Rubelt, and Nicholas Schwab; on behalf of the AIRR Community.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • Acknowledgments
  • References
• 24. IMGT^® Immunoinformatics Tools for Standardized V-DOMAIN Analysis
  Véronique Giudicelli, Patrice Duroux, Maël Rollin, Safa Aouinti, Géraldine Folch, Joumana Jabado-Michaloud, Marie-Paule Lefranc, and Sofia Kossida.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. IMGT Scientific Chart Rules for the Analysis of the V-DOMAIN
  • 3. IMGT/V-QUEST
  • 4. IMGT/HighV-QUEST
  • 5. IMGT/StatClonotype
  • 6. IMGT/DomainGapAlign
  • 7. IMGT/Collier-de-Perles
  • 8. Notes
  • Acknowledgements
  • References
• 25. IMGT/3Dstructure-DB: T-Cell Receptor TR Paratope and Peptide/Major Histocompatibility pMH Contact Sites and Epitope
  Marie-Paule Lefranc and Gérard Lefranc.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. TR and MH Standardized Description in IMGT/3Dstructure-DB
  • 3. IMGT pMH Contact Analysis
  • 4. IMGT/3Dstructure-DB Domain Pair Contacts
  • 5. Availability and Citation
  • 6. Notes
  • Acknowledgements
  • References
• 26. ARResT/Interrogate Immunoprofiling Platform: Concepts, Workflows, and Insights
  Nikos Darzentas.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Materials
  • 3. Methods
  • 4. Notes
  • References
• 27. Purpose-Built Immunoinformatics for BcR IG/TR Repertoire Data Analysis
  Chrysi Galigalidou, Laura Zaragoza-Infante, Anastasia Chatzidimitriou, Kostas Stamatopoulos, Fotis Psomopoulos, and Andreas Agathangelidis.
  Published online: May 28, 2022.
  • 1. Introduction
  • 2. Data Processing
  • 3. Sequence Annotation with IMGT/HighV-QUEST
  • 4. IMGT/HighV-QUEST Meta-Data Analysis with TRIP
  • 5. High-Throughput Data Analysis with TRIP
  • Acknowledgments
  • References