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Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation

Babrak, Lmar ; Marquez, Susanna ; Busse, Christian E. ; Lees, William D. ; Miho, Enkelejda ; Ohlin, Mats LU orcid ; Rosenfeld, Aaron M. ; Stervbo, Ulrik ; Watson, Corey T. and Schramm, Chaim A. (2022) In Methods in Molecular Biology 2453. p.279-296
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... (More)

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.

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author
; ; ; ; ; ; ; ; and
author collaboration
organization
publishing date
type
Chapter in Book/Report/Conference proceeding
publication status
published
subject
keywords
AIRR-Seq, B-cell receptor, Gene annotation, Germline database, Preprocessing, Single-cell sequencing, T-cell receptor
host publication
Immunogenetics : Methods and Protocols - Methods and Protocols
series title
Methods in Molecular Biology
editor
Langerak, Anton W.
volume
2453
pages
18 pages
publisher
Humana Press
external identifiers
  • pmid:35622332
  • scopus:85131108542
ISSN
1064-3745
ISBN
978-1-0716-2114-1
978-1-0716-2115-8
DOI
10.1007/978-1-0716-2115-8_16
language
English
LU publication?
yes
id
e5f8b720-f9f3-45af-8570-edacf524cb26
date added to LUP
2022-12-27 14:44:03
date last changed
2024-05-30 21:21:08
@inbook{e5f8b720-f9f3-45af-8570-edacf524cb26,
  abstract     = {{<p>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.</p>}},
  author       = {{Babrak, Lmar and Marquez, Susanna and Busse, Christian E. and Lees, William D. and Miho, Enkelejda and Ohlin, Mats and Rosenfeld, Aaron M. and Stervbo, Ulrik and Watson, Corey T. and Schramm, Chaim A.}},
  booktitle    = {{Immunogenetics : Methods and Protocols}},
  editor       = {{Langerak, Anton W.}},
  isbn         = {{978-1-0716-2114-1}},
  issn         = {{1064-3745}},
  keywords     = {{AIRR-Seq; B-cell receptor; Gene annotation; Germline database; Preprocessing; Single-cell sequencing; T-cell receptor}},
  language     = {{eng}},
  pages        = {{279--296}},
  publisher    = {{Humana Press}},
  series       = {{Methods in Molecular Biology}},
  title        = {{Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation}},
  url          = {{http://dx.doi.org/10.1007/978-1-0716-2115-8_16}},
  doi          = {{10.1007/978-1-0716-2115-8_16}},
  volume       = {{2453}},
  year         = {{2022}},
}