High-throughput pairing of antigen receptor chains
department or school: Science, Faculty of
data provider: DSpace
degree campus: UBCV
creator: Mewis, Georgia
issued: 2015-10-24T07:59:00
issued: 2015
related degree: Master of Science - MSc
degree grantor: University of British Columbia
description: The specificity of antigen recognition by a T cell or B cell is determined by its unique T cell receptor (TCR) or B cell receptor (BCR), each consisting of two, paired polypeptide chains (alpha and beta, or heavy and light, respectively). An immense diversity of receptors is created during T cell and B cell development through a process of gene recombination. Previously, this diversity has been studied by extracting RNA from large numbers of cells, amplifying the alpha and beta chain (or heavy and light chain) transcripts, and then deep sequencing. However, through this process, information on correct chain pairing is lost. In this thesis, I present a high-throughput approach for maintaining paired-chain information in next-generation sequencing libraries. Briefly, a bulk cell population is divided into a number of sub-populations, and TCR or BCR transcripts are independently amplified; chains are considered paired if they co-occur in more sub-populations than expected by random chance. Fundamental to this approach is a reliable, sensitive library preparation chemistry in which a sub-population specific index can be incorporated. Such a chemistry was validated on primary human CD8⁺ T cells. This approach for antigen receptor chain pairing will enable in-depth studies of immune dynamics, tracking of disease progression, and personalized immunotherapeutics.
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/55115
note: HIGH-THROUGHPUT PAIRING OF ANTIGEN RECEPTOR CHAINS by Georgia Mewis BASc., University of Waterloo, 2012 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Genome Science and Technology) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) October, 2015 © Georgia Mewis, 2015 ii Abstract The specificity of antigen recognition by a T cell or B cell is determined by its unique T cell receptor (TCR) or B cell receptor (BCR), each consisting of two, paired polypeptide chains (alpha and beta, or heavy and light, respectively). An immense diversity of receptors is created during T cell and B cell development through a process of gene recombination. Previously, this diversity has been studied by extracting RNA from large numbers of cells, amplifying the alpha and beta chain (or heavy and light chain) transcripts, and then deep sequencing. However, through this process, information on correct chain pairing is lost. In this thesis, I present a high-throughput approach for maintaining paired-chain information in next-generation sequencing libraries. Briefly, a bulk cell population is divided into a number of sub-populations, and TCR or BCR transcripts are independently amplified; chains are considered paired if they co-occur in more sub-populations than expected by random chance. Fundamental to this approach is a reliable, sensitive library preparation chemistry in which a sub-population specific index can be incorporated. Such a chemistry was validated on primary human CD8+ T cells. This approach for antigen receptor chain pairing will enable in-depth studies of immune dynamics, tracking of disease progression, and personalized immunotherapeutics. iii Preface This dissertation does not contain any previously published material. All work was performed by the author, Georgia Mewis, apart from the following contributions: Kathleen Lisaingo assisted with PBMC isolation, Marketa Ricicova p…
has type: Thesis/Dissertation
date issued: 2015-11
is shown at: 10.14288/1.0166805
language: eng
degree discipline: Genome Science and Technology
provider: Vancouver : University of British Columbia Library
publisher: University of British Columbia
rights: Attribution-NonCommercial-NoDerivs 2.5 Canada
rights URI: http://creativecommons.org/licenses/by-nc-nd/2.5/ca/
scholar level: Graduate
type: Text
identifier URI: http://hdl.handle.net/2429/55115