Immunoglobulin clonotype and ontogeny inference

The ability of our immune system to recognize ever-evolving threats is critical to survival. Initial recognition of pathogens depends on generating a diverse repertoire of antibodies (a.k.a. immunoglobulins, Igs) through recombination of gene segments, followed by dynamic modifications as activated B cells undergo cycles of division, somatic hypermutation and affinity-dependent selection. This affinity maturation produces expanded memory B cell clones expressing mutated Igs with high-affinity for the pathogen. Recent developments in high-throughput sequencing bring exciting possibilities, allowing for large-scale characterization of Ig repertoires. Analyzing Ig repertoires offers insights into the infection history of individuals, teaches us about fundamental immune processes and reveals dysregulations. Ig repertoire sequencing and analysis (REP-seq) require dedicated experimental protocols and computational pipelines, which are constantly being developed. Here, we describe the most recent experimental approaches for Ig repertoire sequencing, discuss advantages of different methods for library preparation, review the most up to date computational pipelines for processing Ig repertoire sequencing data and clonal assignment, and demonstrate the importance of the field with examples for basic research as well as clinical applications. The ability to measure and compare Ig repertoire characteristics improves our understanding of adaptive immunity and facilitates the identification of disease-specific repertoire properties.