Learning predictive signatures of HLA type from T-cell repertoires
Fig 3
Features of the HLA-related sequences.
(A) CDR3 length distribution of A*02:01-associated TCRs, compared to all TCRs. (B) V gene frequency usage comparison between the same two subsets. Some V gene families are preferentially used in A*02:01-related TCRs (TRBV10, TRBV19, TRBV29) while other genes are underrepresented (TRBV15,TRAV24,TRAV21). (C) Whole-repertoire frequencies of two representative differentially used genes, TRBV19 and TRBV15, in A*02:01 positive vs negative individuals show small but statistcally significant difference in those genes. (D) Network analysis of TCRβ chains associated with different A, B and C HLA-alleles (TCRα were excluded since they formed negligible networks). Each node represent an amino acid CDR3 + V gene clonotype. Edges connect clonotypes that have at most on amino acid mismatch but the same length and V gene. Each color represent the specific HLA to which the TCR is responsive. Shadow color correspond to epitopes for which those TCRs are found to be responsive from the VDJdb database [37].