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

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.

NATURVETENSKAP Biologi Bioinformatik och systembiologi hsv//swe
NATURAL SCIENCES Biological Sciences Bioinformatics and Systems Biology hsv//eng
AIRR-Seq
B-cell receptor
Gene annotation
Germline database
Preprocessing
Single-cell sequencing
T-cell receptor

Marquez, SusannaYale University (författare)
Busse, Christian E.German Cancer Research Centre (författare)
Lees, William D.Birkbeck, University of London (författare)
Miho, EnkelejdaSwiss Institute for Bioinformatics (SIB) (författare)
Ohlin, MatsLund University,Lunds universitet,Institutionen för immunteknologi,Institutioner vid LTH,Lunds Tekniska Högskola,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Department of Immunotechnology,Departments at LTH,Faculty of Engineering, LTH,LUCC: Lund University Cancer Centre,Other Strong Research Environments(Swepub:lu)immt-moh (författare)
Rosenfeld, Aaron M.University of Pennsylvania (författare)
Stervbo, Ulrik (författare)
Watson, Corey T.University of Louisville Health Sciences Center (författare)
Schramm, Chaim A.National Institute of Allergy and Infectious Diseases (författare)
Langerak, Anton W. (redaktör/utgivare)
Yale UniversityGerman Cancer Research Centre (creator_code:org_t)
on behalf of the AIRR Community

Ingår i:Immunogenetics : Methods and Protocols - Methods and ProtocolsNew York, NY : Springer US2453, s. 279-2961064-374597810716211419781071621158

Av författaren/redakt...: Babrak, Lmar; Marquez, Susanna; Busse, Christian ...; Lees, William D.; Miho, Enkelejda; Ohlin, Mats; visa fler...; Rosenfeld, Aaron ...; Stervbo, Ulrik; Watson, Corey T.; Schramm, Chaim A ...; Langerak, Anton ...; visa färre...

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