Alloreactivity following stem cell transplantation (SCT) is difficult to predict in patients undergoing transplantation from HLA matched donors. In this study we performed whole exome sequencing of SCT donor-recipient pairs (DRP). This allowed determination of entire library of alloreactive peptide sequences which would bind HLA class I molecules in each DRP. Utilizing the HLA binding affinity (IC50) and tissue expression levels of the parent proteins, an aggregate donor T cell response to the recipient alloreactive peptides was calculated using a vector-operator dynamical system model. Marked variability in the simulated CD8+ T cell responses was observed in all the donor recipient pairs.