Adaptive immune receptor repertoire (AIRR) community guide to TR and IG gene annotation
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Autor:innen
Marquez, Susanna
Busse, Christian
Lees, William
Ohlin, Mats
Rosenfeld, Aaron
Stervbo, Ulrik
Watson, Corey
Schramm, Chaim
Autor:in (Körperschaft)
Publikationsdatum
28.05.2022
Typ der Arbeit
Studiengang
Typ
04A - Beitrag Sammelband
Herausgeber:innen
Langerak, Anton W.
Herausgeber:in (Körperschaft)
Department of Immunology Erasmus MC Rotterdam
Betreuer:in
Übergeordnetes Werk
Immunogenetics Methods and Protocols
Themenheft
DOI der Originalpublikation
Link
Reihe / Serie
Methods in Molecular Biology;2453
Reihennummer
Jahrgang / Band
Ausgabe / Nummer
Seiten / Dauer
279-296
Patentnummer
Verlag / Herausgebende Institution
Springer
Verlagsort / Veranstaltungsort
New York
Auflage
Version
Programmiersprache
Abtretungsempfänger:in
Praxispartner:in/Auftraggeber:in
Zusammenfassung
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.
Schlagwörter
AIRR-Seq, B-cell receptor, Germline database, Gene annotation, Preprocessing, Single-cell sequencing, T-cell receptor
Fachgebiet (DDC)
500 - Naturwissenschaften
Veranstaltung
Startdatum der Ausstellung
Enddatum der Ausstellung
Startdatum der Konferenz
Enddatum der Konferenz
Datum der letzten Prüfung
ISBN
978-1-0716-2115-8
ISSN
Sprache
Englisch
Während FHNW Zugehörigkeit erstellt
Ja
Publikationsstatus
Veröffentlicht
Begutachtung
Peer-Review der ganzen Publikation
Open Access-Status
Gold
Lizenz
Zitation
BABRAK, Lmar, Susanna MARQUEZ, Christian BUSSE, William LEES, Enkelejda MIHO, Mats OHLIN, Aaron ROSENFELD, Ulrik STERVBO, Corey WATSON und Chaim SCHRAMM, 2022. Adaptive immune receptor repertoire (AIRR) community guide to TR and IG gene annotation. In: Anton W. LANGERAK und Department of Immunology Erasmus MC Rotterdam (Hrsg.), Immunogenetics Methods and Protocols. New York: Springer. S. 279–296. Methods in Molecular Biology;2453. ISBN 978-1-0716-2115-8. Verfügbar unter: https://doi.org/10.26041/fhnw-4704