Global survey of the immunoglobulin repertoire using next generation sequencing technology

textSpecific and sensitive recognition of foreign agents is a critical attribute of the overall effective immune system required for maintaining host protection against challenge from pathogenic cells. In the humoral arm of the immune system, this recognition attribute is carried out by the cell surface bound immunoglobulin-like receptors (BCR) and its soluble forms i.e. antibodies. Over several million years of evolution, the immune system has adopted several strategies for diversifying the antibody sequence and thus its ability to recognize an astronomical variety of molecules through the combinatorial assembly of a small number of DNA segments or genes. Among these immunoglobulin gene diversification strategies, antibody somatic VDJ recombination and junctional diversity are the fundamental mechanisms in generating a broad range of antibody specificities. Understanding how the genetic diversity of antibodies is affected in health and disease is critical for a wide range of medical applications, from vaccine evaluation to diagnostics and therapeutics discovery. Because of the very large number of distinct antibodies encoded by the more than 100 billion B cells in humans, it is essential to use high throughput next generation sequencing technologies in order to obtain an adequate sampling of the sequences and relative abundance of different antibodies expressed by B cells in clinical samples. The process requires rigorous methods for first, experimentally determining the sequences of antibodies in a sample and for second, informatics tools designed for distilling this information for practical purposes. This dissertation describes a variety of experimental approaches and informatics tools developed for the determination and mining of the antibody repertoire. The information from this work has led to major conclusions regarding the nature of the antibody repertoire in healthy individuals, in volunteers following vaccination, and in HIV-1 patients.Biomedical Engineerin