Table 4.
Comparison of biomarker frequencies (immunohistochemical, in situ hybridization, and next‐generation sequencing) in human papillomavirus–positive and negative head and neck squamous cell carcinoma subgroups.
| HPV+ | HPV‐ | Statistical analysis | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Biomarker | HPV+ no. tested | HPV+ no. altered | HPV+, % | HPV− no. tested | HPV− no. altered | HPV−, % | p values | Bonferroni corrected significance | Bonferroni corrected p value |
| AR | 38 | 1 | 2.632 | 45 | 2 | 4.444 | 1 | Not significant | 1 |
| BCRP | 2 | 1 | 50.000 | 4 | 0 | 0.000 | .3333 | Not significant | 1 |
| cKIT | 24 | 0 | 0.000 | 42 | 1 | 2.381 | 1 | Not significant | 1 |
| cMET | 16 | 3 | 18.750 | 10 | 2 | 20.000 | 1 | Not significant | 1 |
| COX2 | 1 | 1 | 100.000 | 4 | 0 | 0.000 | .2 | Not significant | 1 |
| EGFR | 7 | 7 | 100.000 | 6 | 6 | 100.000 | 1 | Not significant | 1 |
| ER | 38 | 5 | 13.158 | 46 | 1 | 2.174 | .0866 | Not significant | 1 |
| ERCC1* | 26 | 14 | 53.846 | 41 | 17 | 41.463 | .4511 | Not significant | 1 |
| HER2 | 39 | 2 | 5.128 | 47 | 0 | 0.000 | .2027 | Not significant | 1 |
| MGMT* | 39 | 13 | 33.333 | 49 | 27 | 55.102 | .0534 | Not significant | 1 |
| MRP1 | 24 | 20 | 83.333 | 42 | 39 | 92.857 | .246 | Not significant | 1 |
| PD1 | 21 | 14 | 66.667 | 20 | 5 | 25.000 | .0122 | Not significant | 1 |
| PDL1 | 21 | 4 | 19.048 | 21 | 8 | 38.000 | .3058 | Not significant | 1 |
| PDGFRA | 2 | 0 | 0.000 | 4 | 0 | 0.000 | 1 | Not significant | 1 |
| PGP | 39 | 0 | 0.000 | 47 | 1 | 2.128 | 1 | Not significant | 1 |
| PR | 38 | 1 | 2.632 | 46 | 6 | 13.043 | .1212 | Not significant | 1 |
| PTEN* | 39 | 23 | 58.974 | 49 | 34 | 69.388 | .2661 | Not significant | 1 |
| RRM1* | 39 | 19 | 48.718 | 48 | 29 | 60.417 | .2887 | Not significant | 1 |
| SPARC(m) | 38 | 13 | 34.211 | 48 | 10 | 20.833 | .2208 | Not significant | 1 |
| TLE3 | 17 | 10 | 58.824 | 11 | 7 | 63.636 | 1 | Not significant | 1 |
| TOP2A | 38 | 35 | 92.105 | 49 | 39 | 79.592 | .1352 | Not significant | 1 |
| TOPO1 | 39 | 19 | 48.718 | 47 | 17 | 36.170 | .277 | Not significant | 1 |
| TS* | 39 | 23 | 58.974 | 47 | 31 | 65.957 | .6544 | Not significant | 1 |
| TUBB3* | 15 | 11 | 73.333 | 6 | 4 | 66.667 | 1 | Not significant | 1 |
| cMET ISH | 15 | 0 | 0.000 | 11 | 0 | 0.000 | 1 | Not significant | 1 |
| EGFR ISH | 16 | 0 | 0.000 | 33 | 9 | 27.273 | .0208 | Not significant | 1 |
| HER2 ISH | 19 | 0 | 0.000 | 14 | 1 | 7.143 | .4242 | Not significant | 1 |
| PIK3CA ISH | 1 | 0 | 0.000 | 2 | 1 | 50.000 | 1 | Not significant | 1 |
| TOP2A ISH | 2 | 0 | 0.000 | 3 | 1 | 33.333 | 1 | Not significant | 1 |
| ABL | 36 | 0 | 0.000 | 47 | 0 | 0.000 | .41860465 | Not significant | 1 |
| AKT | 36 | 0 | 0.000 | 47 | 0 | 0.000 | .42261427 | Not significant | 1 |
| ALK | 37 | 0 | 0.000 | 47 | 0 | 0.000 | .42680615 | Not significant | 1 |
| APC | 36 | 3 | 8.333 | 47 | 4 | 8.511 | .5556178 | Not significant | 1 |
| ATM | 36 | 0 | 0.000 | 46 | 1 | 2.174 | .4254446 | Not significant | 1 |
| BRAF | 36 | 0 | 0.000 | 47 | 1 | 2.128 | 1 | Not significant | 1 |
| BRCA1 | 3 | 0 | 0.000 | 2 | 0 | 0.000 | 1 | Not significant | 1 |
| BRCA2 | 3 | 1 | 33.333 | 2 | 1 | 50.000 | 1 | Not significant | 1 |
| CDH1 | 37 | 0 | 0.000 | 47 | 1 | 2.128 | 1 | Not significant | 1 |
| cKIT | 36 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| cMET | 36 | 3 | 8.333 | 47 | 0 | 0.000 | .0777 | Not significant | 1 |
| CSF1R | 37 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| CTNNB1 | 37 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| EGFR | 37 | 0 | 0.000 | 47 | 1 | 2.128 | 1 | Not significant | 1 |
| ERBB4 | 36 | 0 | 0.000 | 47 | 1 | 2.128 | 1 | Not significant | 1 |
| FBXW7 | 36 | 3 | 8.333 | 47 | 1 | 2.128 | .3117 | Not significant | 1 |
| FGFR1 | 37 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| FGFR2 | 37 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| FLT3 | 37 | 0 | 0.000 | 47 | 1 | 2.128 | 1 | Not significant | 1 |
| GNA11 | 36 | 0 | 0.000 | 45 | 0 | 0.000 | 1 | Not significant | 1 |
| GNAQ | 29 | 0 | 0.000 | 45 | 0 | 0.000 | 1 | Not significant | 1 |
| GNAS | 37 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| HER2 | 37 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| HNF1A | 33 | 1 | 3.030 | 47 | 0 | 0.000 | .4125 | Not significant | 1 |
| HRAS | 33 | 0 | 0.000 | 45 | 1 | 2.222 | 1 | Not significant | 1 |
| IDH1 | 37 | 0 | 0.000 | 47 | 1 | 2.128 | 1 | Not significant | 1 |
| JAK2 | 37 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| JAK3 | 37 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| KDR | 36 | 1 | 2.778 | 47 | 2 | 4.255 | 1 | Not significant | 1 |
| KRAS | 36 | 2 | 5.556 | 47 | 0 | 0.000 | .1851 | Not significant | 1 |
| MLH1 | 36 | 0 | 0.000 | 45 | 0 | 0.000 | 1 | Not significant | 1 |
| MPL | 37 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| NOTCH1 | 36 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| NPM1 | 36 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| NRAS | 37 | 1 | 2.703 | 47 | 0 | 0.000 | .4405 | Not significant | 1 |
| PDGFRA | 36 | 1 | 2.778 | 47 | 3 | 6.383 | .6294 | Not significant | 1 |
| PIK3CA | 36 | 3 | 8.333 | 46 | 1 | 2.174 | .3148 | Not significant | 1 |
| PTEN | 36 | 3 | 8.333 | 46 | 1 | 2.174 | .3148 | Not significant | 1 |
| PTPN11 | 37 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| RB | 36 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| RET | 37 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| SMAD4 | 36 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| SMARCB1 | 37 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| SMO | 32 | 0 | 0.000 | 46 | 0 | 0.000 | 1 | Not significant | 1 |
| STK11 | 35 | 0 | 0.000 | 47 | 0 | 0.000 | 1 | Not significant | 1 |
| TP53 | 37 | 0 | 0.000 | 47 | 27 | 57.447 | 1.16E‐06 | Significant | 8.83E‐05 |
| VHL | 35 | 0 | 0.000 | 45 | 0 | 0.000 | 1 | Not significant | 1 |
Abbreviations: HPV+, human papillomavirus–positive; HPV‐, human papillomavirus–negative.
The p values in bold indicate statistical significance before correction for multiple comparisons.