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Table of Contents

1. The Advent of Precision Immunology: Immunogenetics at the Center of Immune Cell Analysis in Health and Disease

Anton W. Langerak

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, Patricia J.T.A. Groenen on behalf of the EuroClonality Consortium

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, Mikael Salson, and Elizabeth Macintyre

4. Immunoglobulin/T-Cell Receptor Gene Rearrangement Analysis Using RNA-Seq

Vincent H.J. van der Velden, Lorenz Bastian, Monika Bruggemann, Alina Hartmann, and Nikos Darzentas

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

6. Quality Control for IG/TR Marker Identification and MRD Analysis

Eva Fronkova, Michael Svaton, and Jan Trka

7. cfDNA-Based NGS IG Analysis in Lymphoma

Christiane Pott, Michaela Kotrova, Nikos Darzentas, Monika Bruggemann, and Mouhamad Khouja on behalf of the EuroClonality-NGS Working Group

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

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

10. Immunoglobulin Gene Mutational Status Assessment by Next Generation Sequencing in Chronic Lymphocytic Leukemia

Anne Langlois de Septenville, Myriam Boudjoghra, Clotilde Bravetti, Marine Armand, Mikael Salson, Mathieu Giraud, and Frederic Davi

11. NGS-Based B-Cell Receptor Repertoire Analysis in the Context of Inborn Errors of Immunity

Pauline A. van Schouwenburg, Mirjam van der Burg, and Hanna IJspeert

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

13. Gene Engineering T-Cells with T-Cell Receptor for Adoptive Therapy

Dian Kortleve, Mandy van Brakel, Rebecca Wijers, Reno Debets, and Dora Hammerl

14. Combined Analysis of Transcriptome and T-Cell Receptor Alpha 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

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 Truck, Ulrik Stervbo, Eline T. Luning Prak on behalf of the AIRR Community

16. Adaptive Immune Receptor Repertoires (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

17. Adaptive Immune Receptor Repertoires (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

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

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

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 Reinhard, Encarnita Mariotti-Ferrandiz, Kevin Mujangi-Ebeka, Kristen Martins-Taylor, and Anne Eugster

21. Quality Control: Chain Pairing Precision and Monitoring of Cross-Sample Contamination: A Method by the AIRR Community

Cheng-Yu Chung, Matias Gutierrez-Gonzalez, Sheila N. Lopez Acevedo, Ahmed S. Fahad, and Brandon J. DeKosky on behalf of the AIRR Community

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

23. Data Sharing and Re-Use: 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

24. IMGT (R) Immunoinformatics Tools for Standardized V-DOMAIN Analysis

Veronique Giudicelli, Patrice Duroux, Mael Rollin, Safa Aouinti, Geraldine Folch, Joumana Jabado Michaloud, Marie-Paule Lefranc, and Sofia Kossida

25. IMGT/3Dstructure-DB: T-Cell Receptor TR Paratope and Peptide/Major Histocompatibility pMH Contact Sites and Epitope

Marie-Paule Lefranc and Gerard Lefranc

26. ARResT/Interrogate Immunoprofiling Platform: Concepts, Workflows, and Insights

Nikos Darzentas

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

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