Elucidation of the human B cell immune repertoire by high-throughput sequencing and computational simulation
Wu, Gabriel Chi Sun
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The human immune system carefully balances the need to maintain stable responses to familiar stimuli with the need for agile responses to an ever changing array of potential dangers. Classic techniques allow for detailed evaluation of parts of the immune system, while emerging technologies allow for more systems-level analysis of the immune system as a whole. In this dissertation, I use high-throughput techniques and computational analysis to advance our understanding of the human bone marrow B cell repertoire. First, I describe the variation in composition of human bone marrow plasma cells from the same individual over time. I show that the frequency of gene and gene combination usage, assayed by high-throughput sequencing, is temporally stable over 6.5 years. Next, I describe a computational model that simulates the process of high-throughput sequencing of immune cells and identify the major sources of error in these experiments. Specifically, this simulation demonstrates that the typical shape of the experimental distribution of antibodies may be in large part be due to error generated in the experimental process and not a biologically relevant observation. I go on to demonstrate the current limits in understanding the initial distribution of the immune repertoire due to accumulated noise in the experimental process. The work presented here represents the longest longitudinal study to date of high-throughput sequencing techniques used to study the repertoire of human B cells. In addition, the computational model frames the technical challenges of immunological repertoire analysis. This knowledge will provide the basis of future studies to understand the nature of B cells in human bone marrow. It will be relevant for both academic and clinical researchers studying the immune system at basal state as well as at an active defense state. Ultimately, it provides guidance to the community at large with the intent of improving immunology and human health.