Table 4.
SLACa Predicted Sites of Lymphoid-Specific Negative Selection
| Codon (NL4-3 residue #) | Patient | p Valueb | Codon description |
|---|---|---|---|
| 10 (10) | UK6 | 0.0257 | NH2-terminal T cell epitope |
| 14 (14) | MACS2 | 0.0167 | NH2-terminal T cell epitopes |
| 67 (62) | MACS2 | 0.0041 | MHC-I downmodulation |
| 68 (63) | MACS1 | 0.0904 | MHC-I downmodulation |
| 69 (insertion at 63) | MACS3 | 0.0709 | MHC-I downmodulation |
a
Single Likelihood Ancestor Counting (HyPhy software package) was used to reconstruct ancestral sequences at each node of a lymphoid-only phylogenetic tree. Substitutions are calculated at each branch and terminal node. Wherever a variation occurs, the dS and dN were calculated.
b
p Values are based on a two-tailed binomial distribution that measures how likely the observed proportion of synonymous substitutions differs from the expected value derived from a global dN/dS ratio fitted to reconstructed ancestral states at each node of patient-specific maximum likelihood phylogentic trees.