Interpretable GWAS by linking clinical phenotypes to quantifiable immune repertoire components

Bridging the gap between genotype and phenotype in GWAS studies is challenging. A multitude of genetic variants have been associated with immune-related diseases, including cancer, yet the interpretability of most variants remains low. Here, we investigate the quantitative components in the T cell receptor (TCR) repertoire, the frequency of clusters of TCR sequences predicted to have common antigen specificity, to interpret the genetic associations of diverse human diseases. We first developed a statistical model to predict the TCR components using variants in the TRB and HLA loci. Applying this model to over 300,000 individuals in the UK Biobank data, we identified 2309 associations between TCR abundances and various immune diseases. TCR clusters predicted to be pathogenic for autoimmune diseases were significantly enriched for predicted autoantigen-specificity. Moreover, four TCR clusters were associated with better outcomes in distinct cancers, where conventional GWAS cannot identify any significant locus. Collectively, our results highlight the integral role of adaptive immune responses in explaining the associations between genotype and phenotype. Analyzing the impact of genetic variants on T cell receptor repertoire components reveals the mechanisms behind susceptibility variants in autoimmune diseases and cancers.