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Supervisor's Foreword; Preface; Parts of this thesis have been published in the following journal articles:DeKosky, B.J., Ippolito, G.C., Deschner, R.P., Lavinder, J.J., Wine, Y., Rawlings, B.M., Varadarajan, N., Giesecke, C., Dorner, T., Andrews, S.F., Wilson, P.C., Hunicke-Smith, S.P., Willson, C.G., Ellington, A.D. & Georgiou, G. High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire. Nature Biotechnology 31, 166-169 (2013). DeKosky, B.J., Kojima, T., Rodin, A., Charab, W., ; Acknowledgements; Contents; Abbreviations; List of Figures.

3 In-Depth Determination and Analysis of the Human Paired Heavy and Light Chain Antibody Repertoire3.1 Introduction; 3.2 Results; 3.2.1 Device Construction; 3.2.2 Single B Cell VH:VL Pairing: Throughput and Pairing Accuracy; 3.2.3 Promiscuous and Public VL Junctions; 3.2.4 Quantifying Allelic Inclusion in Human Memory B Cells; 3.2.5 Antibodies with Gene Signatures of Known Anti-Viral BNAbs; 3.3 Discussion; 3.4 Methods; References; 4 Paired VH:VL Analysis of Naïve B Cell Repertoires and Comparison to Antigen-Experienced B Cell Repertoires in Healthy Human Donors; 4.1 Introduction; 4.2 Results.

4.2.1 VH:VL Gene Usage Across B Cell Subsets4.2.2 CDR3 Length Analysis; 4.2.3 CDR3 Charge; 4.2.4 CDR3 Hydrophobicity; 4.2.5 Public Heavy and Light Chain Sequences; 4.3 Discussion; 4.4 Methods; 4.4.1 Ethics Statement; 4.4.2 Cell Isolation and VH:VL Pairing; 4.4.3 Bioinformatic Analysis; 4.4.4 Statistical Analysis; References; 5 Conclusions and Future Perspectives; References; Appendix A: Chapter 2 Supplementary Information; Appendix A: Chapter 2 Supplementary Information; Appendix B: Chapter 3 Supplementary Information; Appendix C: Chapter 4 Supplementary Information; Index.

List of Tables1 Background; 1.1 Antibodies and Antibody Repertoire Development; 1.2 Adaptive Immune Responses Lead to B-Cell Activation and Antibody Secretion; 1.3 High Throughput Antibody Sequencing; 1.4 Next Generation Antibody Sequencing Data Analysis; 1.5 Monoclonal Antibody Discovery Technologies; 1.6 Single-Cell Sequencing Techniques; 1.7 Synopsis; References; 2 High-Throughput Sequencing of the Paired Human Immunoglobulin Heavy and Light Chain Repertoire; 2.1 Rationale and Supporting Information; 2.2 Methodology; 2.3 Results; 2.4 Discussion; 2.5 Methods; References.

This thesis outlines the development of the very first technology for high-throughput analysis of paired heavy and light-chain antibody sequences, opening the door for the discovery of new antibodies and the investigation of adaptive immune responses to vaccines and diseases. By designing two new technologies for sequencing multiple mRNA transcripts from up to 10 million isolated, single cells, the author directly addresses the limitations to provide information on the identity of immune receptor pairs encoded by individual B or T lymphocytes. Previous methods for high-throughput immune repertoire sequencing have been unable to provide such information. The techniques developed in this thesis have enabled comprehensive investigation of human B-cell repertoires and have been applied for the rapid discovery of new human antibodies, to gain new insights into the development of human antibody repertoires, and for analysis of human immune responses to vaccination and disease.

Online resource; title from PDF title page (EBSCO, viewed June 9, 2017).