AIRR Community Guide to Planning and Performing AIRR-Seq Experiments.

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.

Bulk Sequencing from mRNA with UMI for Evaluation of B-Cell Isotype and Clonal Evolution: A Method by the AIRR Community.

During the course of an immune response to a virus such as influenza, B cells undergo activation, clonal expansion, isotype switching, and somatic hypermutation (SHM). Members of an antigen-experienced B-cell clone can have different sequence features including SHM in the immunoglobulin heavy-chain V (IGHV) gene and can use the same IGVH gene in combination with different constant regions or isotypes (e.g., IgM, IgG, IgA). To study these features of expanded clones in an immune response by AIRR-seq, we provide a bulk RNA-based sequencing experimental procedure with unique molecular identifiers (UMIs) and the accompanying bioinformatics analytical workflow.