Multiple sclerosis (MS) is an autoimmune disease characterized, in part, by expanded clones of antigen-experienced B cells that reside in several compartments of the central nervous system (CNS), including the brain and cerebrospinal fluid (CSF). While it is known that B cells in the CSF can exchange with those in peripheral blood, it is not understood whether this immune infiltrate initiates its development in the CNS or in peripheral tissues. We addressed this question through deep sequencing of B cell immunoglobulin repertoires from paired tissue samples from MS patients. Our results demonstrate that the CNS of patients with MS is populated by B cells that gain antigen experience and mature peripherally, in the draining cervical lymph nodes, prior to trafficking across the blood-brain barrier . Analysis of these large-scale data was made possible through the development of several computational tools and methods that we currently make available to the wider scientific community through the Immcantation tool suite (http://immcantation.readthedocs.io). This includes our Repertoire Sequencing Toolkit (pRESTO) , which handles all stages of sequence processing from raw reads up to the task of V(D)J germline segment assignment, including specific support for paired-end reads, single-molecule barcodes and multi-core processing. To facilitate advanced analysis of the resulting B cell repertoire properties, we have also developed methods  for: novel V segment allele detection, subject-specific germline genotype identification, B cell clone assignment, lineage tree construction, somatic mutation profiling and selection analysis. To gain insights into B cell trafficking patterns in MS, lineage trees were constructed and analyzed using a novel methodology to determine enrichment of specific types of founder cells and parent-child relationships. Application of this method showed that founding members of clonal families that spanned the CNS and periphery were significantly more often found in the draining CLNs. These data provide new evidence that B cells in MS patients traffic freely across the blood-brain barrier with the majority of B cell maturation occurring outside of the CNS in the secondary lymphoid tissue. Along with these insights into MS, this presentation will discuss additional applications of B cell immunoglobulin repertoire sequencing and lineage analysis to infection (HIV and West Nile Virus), vaccination (Influenza), autoimmunity (Myasthenia Gravis) and allergic responses.