Impact of CMV reactivation on CD8 Tem TCR repertoire holes. (A-B) For panels A-B, V, and J genes are represented along the x-y axes, whereas the difference in the V-J–specific proportions of unique clones are represented along the z-axis and labeled “Freq.” TCE and holes analysis was performed as described in “Methods.” Panels A and B depict wireframe 3-dimensional graphs (created using the Lattice graphics package in R) for 2 representative patients (001-008, panel A and 001-005, panel B). Both TCEs and holes in the TCR repertoire are depicted in these graphs, with V-J families in orange depicting TCEs and those in green depicting holes. Those families shown in light gray are already sparse in the VJ^r and thus were not evaluated for holes. (C) Summary analysis showing the mean number of holes in the CD8 Tem from the +CMV (red squares) and −CMV (blue circles) patients using the VJ^r. **P < .01. (D) Summary analysis showing the mean number of holes in the CD8 Tem from the +CMV (red) and −CMV (blue) patients using the VJ^r-transplant. **P < .01. (E) Analysis of the number of holes in −CMV patients that either did not develop GVHD (green squares, left) or did develop GVHD (purple hexagons, right) compared with the VJ^r. P = 1.0. (F) Analysis of the number of holes in +GVHD patients that either did reactivate CMV (red squares) or did not reactivate CMV (blue circles) compared with the VJ^r. *P < .05.