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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
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
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
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