  Stem cell transplants may be considered as dynamical systems to allow
sequence differences across the exomes of the transplant donors and recipients
to be used to simulate an alloreactive T cell response. Whole exome sequencing
was performed on HLA matched stem cell transplant donor-recipient pairs, and
the nucleotide sequence differences translated to peptides. The binding
affinity of the peptides to the relevant HLA in each pair was determined. The
resulting array of peptide-HLA binding affinity values in each patient was used
to simulate an alloreactive donor derived T cell repertoire. This simulated T
cell repertoire reproduces a number of features of clinically observed T cell
repertoire. The simulated, alloreactive T cell repertoire was markedly
different in HLA matched stem cell transplant donors and recipients and
demonstrates a possible correlation with survival.
