Immunosequencing reveals diagnostic signatures of pathogen infection and HLA type in the T-cell Receptor Repertoire

Abstract

Abstract We analyzed the T-cell response to CMV by sequencing rearranged TCRs in 528 subjects (240 CMV+ and 288 CMV−). We assessed concordance between ~80 million unique TCRs and CMV serostatus, looking for significant associations. We identified 104 CMV-associated TCRs at FDR ≈ 0.20. Training a binary classifier on these features, we predict CMV serostatus in a cross-validation procedure with a diagnostic odds ratio of 17 on the same cohort. A second independent cohort of 120 subjects with known CMV serostatus yielded a diagnostic odds ratio of 31. Next, we studied the HLA-restriction of each CMV-associated TCR by assessing enrichment of particular HLA types among subjects that carry each CMV-associated TCR. Of 104 CMV-associated TCRs, 41 were HLA-restricted at p ≤ 10−3, and none of these were significantly associated with multiple alleles in any locus. We find concordance between our data and previously-reported CMV-specific TCRs: most previously-reported CMV-specific TCRs are present in our data, however only 5 CMV-associated TCRs have been previously reported. Of these, four were significantly HLA-restricted in these data, and agreed with previous findings. We investigated the association of TCRs with each HLA allele present in the cohort, with significant results for several higher frequency alleles. Cross validation with binary classifier training resulted in high accuracy prediction for these alleles, indicating that HLA type can be inferred from immunosequencing data. We demonstrate the validity of association studies using immunosequencing for detection and HLA-association of public T-cell responses to infection, and report that assessing the presence of associated T-cell responses can serve as a powerful diagnostic classifier.