Table 3.
TILs are depleted in EGFR-amplified and homozygous PTEN-deleted tumors
| CNA | (%) | Chi square p-value (0, 1+, 2+) |
Chi square p-value (0 vs 1+, 2+ combined) |
Chi square p-value (0, 1+ combined vs 2+) |
|---|---|---|---|---|
| Amplifications | ||||
| EGFR | 49.3 | 0.05 | 0.04 | 0.06 |
| CDK4 | 14.5 | 0.37 | 0.22 | 0.47 |
| PDGFRA | 14.1 | 0.61 | 0.73 | 0.47 |
| MDM4 | 9.9 | 0.23 | 0.24 | 0.64 |
| MDM2 | 9.3 | 0.81 | 0.82 | 1.00 |
| MET | 8.8 | 0.57 | 0.79 | 0.48 |
| CDK6 | 7.0 | 0.75 | 0.65 | 0.69 |
| CCND2 | 4.0 | 1.00 | 1.00 | 1.00 |
| AKT3 | 3.2 | 1.00 | 1.00 | 1.00 |
| MYCN | 2.6 | 1.00 | 0.62 | 1.00 |
| PIK3CA | 2.4 | 0.69 | 0.60 | 1.00 |
| Deletions | ||||
| CDKN2A | 62.0 | 0.23 | 0.09 | 0.48 |
| CDKN2B | 61.0 | 0.23 | 0.09 | 0.48 |
| PTEN | 10.3 | 0.09 | 0.03 | 0.69 |
| RB1 | 3.6 | 0.87 | 1.00 | 0.57 |
| CDKN2C | 3.6 | 0.71 | 1.00 | 0.51 |
| PARK2 | 2.0 | 1.00 | 1.00 | 1.00 |
| NF1 | 1.2 | 0.07 | 0.10 | 0.30 |
Chi-square test was used to examine associations between lymphocytes (0, 1+, 2+) and CNAs
Fisher’s exact test was used when 25% of the cells had <5 observations
Effective Sample Size 153
Categories were combined to identify associations driven by cases with either complete absence or abundance of lymphocytes