Immunogenetics: Methods and Protocols

ISBN-13: 9781071621141 / Angielski / Twarda / 2022

Langerak, Anton W.

Opis

This open access book explores techniques for working in the field of immunogenetics, i.e. fundamental and translational research into the adaptive immune receptor repertoire. Many chapters are dedicated to lab protocols, bioinformatics, and immunoinformatics analysis of high-resolution immunome analysis, exemplified by numerous applications. Additionally, the newest technological variations on these protocols are discussed, including non-amplicon, single-cell, and cell-free strategies. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Immunogenetics: Methods and Protocols covers a broad spectrum of methodologies for applications in research and clinical diagnostics to illustrate the impact that immunogenetics has achieved and will further expand in all fields of medicine, from infection and (auto)immunity, to vaccination, to lymphoid malignancy and tumor immunity.

Spis treści

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, Mikaël Salson, and Elizabeth Macintyre

 

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

            Vincent H.J. van der Velden, Lorenz Bastian, Monika Brüggemann, 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 Brüggemann, 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, Mikaël 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 Trück, 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 Gutiérrez-González, Sheila N. López 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® 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

 

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

            Marie-Paule Lefranc and Gérard 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