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; AIRR Community

doi:10.1007/978-1-0716-2115-8_15

AIRR Community Guide to Planning and Performing AIRR-Seq Experiments

Methods Mol Biol. 2022:2453:261-278. doi: 10.1007/978-1-0716-2115-8_15.

Authors

Affiliations

¹ Center for Regenerative Therapies Dresden, Faculty of Medicine, TU Dresden, Dresden, Germany.
² Takara Bio USA, San Jose, CA, USA.
³ PACT Pharma, Inc., South Francisco, CA, USA.
⁴ INSERM, Immunology-Immunopathology-Immunotherapy (i3), Sorbonne Université, Paris, France.
⁵ Department of Pathology and Laboratory Medicine, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA.
⁶ Vanderbilt Vaccine Center and Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
⁷ Division of Immunology and Children's Research Center, University Children's Hospital Zurich, University of Zurich (UZH), Zurich, Switzerland.
⁸ Center for Translational Medicine, Immunology, and Transplantation, Medical Department, and Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany. [email protected].
⁹ Department of Pathology and Laboratory Medicine, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA. [email protected].

Abstract

The development of high-throughput sequencing of adaptive immune receptor repertoires (AIRR-seq of IG and TR rearrangements) has provided a new frontier for in-depth analysis of the immune system. The last decade has witnessed an explosion in protocols, experimental methodologies, and computational tools. In this chapter, we discuss the major considerations in planning a successful AIRR-seq experiment together with basic strategies for controlling and evaluating the outcome of the experiment. Members of the AIRR Community have authored several chapters in this edition, which cover step-by-step instructions to successfully conduct, analyze, and share an AIRR-seq project.

Keywords: AIRR-seq; Antibody; Immune repertoire; Immunoglobulin; Next-generation sequencing; T-cell receptor; V(D)J recombination.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

High-Throughput Nucleotide Sequencing* / methods
Receptors, Immunologic* / genetics

Substances

Receptors, Immunologic

Grants and funding

UM1 AI144288/AI/NIAID NIH HHS/United States