Adaptive immune receptor repertoire (AIRR) community guide to TR and IG gene annotation
Loading...
Authors
Marquez, Susanna
Busse, Christian
Lees, William
Ohlin, Mats
Rosenfeld, Aaron
Stervbo, Ulrik
Watson, Corey
Schramm, Chaim
Author (Corporation)
Publication date
28.05.2022
Typ of student thesis
Course of study
Type
04A - Book part
Editors
Langerak, Anton W.
Editor (Corporation)
Supervisor
Parent work
Immunogenetics Methods and Protocols
Special issue
DOI of the original publication
Link
Series
Methods in Molecular Biology
Series number
2453
Volume
Issue / Number
Pages / Duration
279-296
Patent number
Publisher / Publishing institution
Springer
Place of publication / Event location
New York
Edition
Version
Programming language
Assignee
Practice partner / Client
Abstract
High-throughput sequencing of adaptive immune receptor repertoires (AIRR, i.e., IG and TR) has revolutionized the ability to carry out large-scale experiments to study the adaptive immune response. Since the method was first introduced in 2009, AIRR sequencing (AIRR-Seq) has been applied to survey the immune state of individuals, identify antigen-specific or immune-state-associated signatures of immune responses, study the development of the antibody immune response, and guide the development of vaccines and antibody therapies. Recent advancements in the technology include sequencing at the single-cell level and in parallel with gene expression, which allows the introduction of multi-omics approaches to understand in detail the adaptive immune response. Analyzing AIRR-seq data can prove challenging even with high-quality sequencing, in part due to the many steps involved and the need to parameterize each step. In this chapter, we outline key factors to consider when preprocessing raw AIRR-Seq data and annotating the genetic origins of the rearranged receptors. We also highlight a number of common difficulties with common AIRR-seq data processing and provide strategies to address them.
Keywords
AIRR-Seq, B-cell receptor, Germline database, Gene annotation, Preprocessing, Single-cell sequencing, T-cell receptor
Subject (DDC)
Event
Exhibition start date
Exhibition end date
Conference start date
Conference end date
Date of the last check
ISBN
978-1-0716-2115-8
ISSN
Language
English
Created during FHNW affiliation
Yes
Strategic action fields FHNW
Publication status
Published
Review
Peer review of the complete publication
Open access category
Gold
License
Citation
Babrak, L., Marquez, S., Busse, C., Lees, W., Miho, E., Ohlin, M., Rosenfeld, A., Stervbo, U., Watson, C., & Schramm, C. (2022). Adaptive immune receptor repertoire (AIRR) community guide to TR and IG gene annotation. In A. W. Langerak & Department of Immunology Erasmus MC Rotterdam (Eds.), Immunogenetics Methods and Protocols (pp. 279–296). Springer. https://doi.org/10.1007/978-1-0716-2115-8_16