The adaptive immune response selectively expands B and T-cell clones following antigen recognition by the B- or T-cell receptors (BCR and TCR) respectively. BCRs are the membrane-bound form of antibodies and are generated through DNA recombination, with potential to recognise a vast array of pathogens. Currently, little is known about the interplay between B-cell differentiation, BCR somatic hypermutation, class switching, and antigen specificity in health and disease.

Here we describe novel methods to characterise the human adaptive immune response by high-throughput sequencing of B-cell receptor antigen-binding regions and antibody class (isotype), which can be used to quantify multiple aspects of B-cell immune status from single blood samples. Using these methods, we demonstrate for the first time, the relationships between B-cell differentiation, diversification through somatic hypermutation, and changes in function through isotype usages. We provide a comprehensive analysis of how distinct B-cell populations contribute to total peripheral blood, and how these can be used to infer the immune B-cell status of an individual. We demonstrate how B-cell receptor repertoire sequencing can be used to understand B-cell population changes in a range of autoimmune diseases and leukeamia, giving unique insights into B-cell pathology. We further demonstrate the effect of different therapies on B-cell populations, including analysis of B-cell reconstitution after immunosuppression, and the nature of persistent B-cell clones. These methods enable tracking of pathogenic B-cell clones in serial patient samples with unprecedented sensitivity, and allow for phylogenetic reconstruction of the clonal history of these B-cell clones, thus giving insights into the mechanisms of clonal diversification and disease relapse. These findings give a unique perspective into the clonal dynamics and function of B-cells in health and disease, and provides an exciting platform for understanding the impact of different immuno-modulatory treatments.