immunerepertoire

Immunerepertoire refers to the complete set of antigen receptor sequences in an individual’s adaptive immune system. It comprises the B cell receptor (BCR) repertoire, which gives rise to antibodies, and the T cell receptor (TCR) repertoire, which recognizes peptide antigens presented by MHC molecules. Together, these repertoires reflect the diversity of antigen specificities available to the immune system and its history of antigen exposure.

Repertoire diversity arises through genetic mechanisms such as V(D)J recombination, junctional diversification, and, for B cells, somatic hypermutation and class switch recombination. Naive repertoires contain diverse receptor sequences before antigen exposure; upon infection or vaccination, clonal expansion of specific receptors shapes the adaptive response and memory is established. Repertoires can vary across tissues and over time, with aging and disease leading to skewing or reduced diversity.

Repertoire analysis typically uses high-throughput sequencing of receptor genes (repertoire sequencing or AIRR-seq). Key metrics include richness and diversity indices (e.g., Shannon, Simpson), clonality, and the degree of clonal expansion or contraction. Public clonotypes, convergent evolution, and lineage relationships are also studied. Data are curated and shared through standardized AIRR data formats to enable cross-study comparison.

Clinical and research applications include monitoring vaccine responses, infectious diseases, cancer immunotherapy, autoimmunity, and transplantation. Challenges include sampling bias, technological biases, and the need for standardized analysis pipelines. Ongoing efforts by the AIRR Community aim to harmonize data formats and reporting to improve reproducibility and interpretation.