Table 3.

TILs are depleted in EGFR-amplified and homozygous PTEN-deleted tumors

CNA%χ2P value (0, 1+, 2+)χ2P value (0 vs. 1+, 2+ combined)χ2P value (0, 1+ combined vs. 2+)
Amplifications
 EGFR49.30.050.040.06
 CDK414.50.370.220.47
 PDGFRA14.10.610.730.47
 MDM49.90.230.240.64
 MDM29.30.810.821.00
 MET8.80.570.790.48
 CDK67.00.750.650.69
 CCND24.01.001.001.00
 AKT33.21.001.001.00
 MYCN2.61.000.621.00
 PIK3CA2.40.690.601.00
Deletions
 CDKN2A62.00.230.090.48
 CDKN2B61.00.230.090.48
 PTEN10.30.090.030.69
 RB13.60.871.000.57
 CDKN2C3.60.711.000.51
 PARK22.01.001.001.00
 NF11.20.070.100.30

NOTE: χ2 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 less than 5 observations. Effective sample size was 153. Categories were combined to identify associations driven by cases with either complete absence or abundance of lymphocytes.