Polymorphism within the T cell receptor beta (TCRB) variable (TRBV) gene is implicated in PID, autoimmune disease and immune-related adverse events (IRAEs) during immunotherapy. Efforts to evaluate TRBV polymorphism by WGS were hampered by the repetitive nature of TCRB locus. We present a novel long-amplicon TCRB repertoire sequencing approach to enable haplotype analysis of the TRB locus from peripheral blood.
Baseline total RNA from peripheral blood leukocytes from 81 Caucasians treated with checkpoint inhibitor for cancer was used for amplification and sequencing of TCRB chains via the Oncomine TCRB-LR assay (spanning complementarity-determining regions 1, 2 and 3) and the Gene Studio S5. VDJ rearrangements were annotated by comparison to the gold-standard IMGT database, then mined to construct TRBV allele profiles for each individual. Principal component analysis (PCA) of variable gene allele profiles and k-means clustering identified TRBV allele haplotypes.
PCA and k-means clustering of TRBV allele profiles revealed presence of 6 major sets of coincident variable gene alleles, which we term haplotype groups. Allele features varied markedly across haplotype groups, with haplotype group 2 members, comprising approximately one third of the cohort, having limited TRBV allelic diversity and few uncommon alleles compared to members of other groups.
We demonstrate a cost-efficient and rapid method for routine analysis of germline-encoded polymorphism within the TRB locus to enable high-resolution studies of genetic variation and its potential link to IRAEs. This technology could potentially be used to analyze the TRBV to aid in studying thymic output defects, and indicate autoimmunity in PID patients.