Table 1.
Immune genes with P values suggestive of association
| SNP | Gene | OPC P value | OR | CI | Rank | HPV+ P value | Larynx P value | Comments |
|---|---|---|---|---|---|---|---|---|
| rs9922120 | CBFA2T3 | 8.10E–07 | 1.646 | 1.35–2.01 | 6 | 4.52E–03 | 1.16E–02 | Candidate breast cancer tumor suppressor (44) |
| Associated with AML (45) | ||||||||
| rs4240847 | MAPKAPK2 | 3.39E–05 | 1.518 | 1.25–1.85 | 24 | 6.75E–04 | 3.21E–01 | Required for Flu A infection/propagation (46) |
| Activated by inflammatory cytokines (46) | ||||||||
| Major Stabilizer of p38 signaling (47) | ||||||||
| rs895437 | ZAP70 | 6.64E–05 | 1.653 | 1.29–2.12 | 40 | 6.90E–03 | 7.25E–01 | Mutations cause selective T-cell defect (48) |
| Used as a prognostic marker for CLL in B cells (49) | ||||||||
| Mutations results in immune deficiency (50) | ||||||||
| rs3107638 | CRTAM | 8.75E–05 | 1.551 | 1.25–1.93 | 51 | 5.15E–04 | 2.87E–01 | KO mice have reduced viral immunity (51) |
| NK activation and tumor surveillance (52) | ||||||||
| Associated with cervical cancer (37) | ||||||||
| rs1780365 | PBX1 | 2.09E–04 | 0.711 | 0.59–0.85 | 113 | 8.28E–04 | 6.81E–01 | Associated with esophageal SCCA (53) |
| Induces apoptosis (54) | ||||||||
| Retards ovarian tumor growth (55) | ||||||||
| rs2869433 | MAPK10 | 2.80E–04 | 0.708 | 0.59–0.85 | 134 | 4.66E–02 | 9.66E–01 | Activated by pro-inflammatory cytokines (56) |
| Associated with cancer and inflammation (57) | ||||||||
| rs6778945 | CD80 | 3.75E–04 | 0.590 | 0.44–0.79 | 171 | 5.85E–03 | 8.01E–01 | Necessary for T-cell activation and survival (58) |
| Associated with cancer including cervical cancer (38) | ||||||||
| rs3024498 | IL10 | 3.95E–04 | 1.421 | 1.17–1.73 | 181 | 6.75E–04 | 3.03E–01 | Involved in immunoregulation and inflammation (59) |
| Released during immune response to viral infection (60) | ||||||||
| Associated with cervical cancer [PMID: 18341210] | ||||||||
| rs10167561 | SOCS5 | 4.23E–04 | 0.710 | 0.59–0.86 | 192 | 2.00E–02 | 3.32E–01 | Involved in regulating T helper cell differentiation (61) |
| Associated with HIV replication (62) | ||||||||
| Suppresses EGFR signaling (63) | ||||||||
| rs2026811 | TGFβR1 | 4.29E–04 | 1.414 | 1.17–1.72 | 196 | 1.85E–03 | 5.23E–01 | Prooncogenic role (64) |
| Advanced carcinomas and tumor invasiveness (65) | ||||||||
| Polymorphism associated with several cancers (65) | ||||||||
| rs11135045 | EBF1 | 6.71E–04 | 1.437 | 1.16–1.77 | 289 | 1.68E–02 | 2.68E–01 | Associated with cervical cancer (40) |
| Associated with HNSCCA (66) | ||||||||
| Associated with breast cancer (67) | ||||||||
| rs11633294 | IGF1R | 7.03E–04 | 0.725 | 0.60–0.87 | 310 | 4.09E–03 | 5.27E–01 | Antiapoptotic (68) |
| Associated with cancer (68) | ||||||||
| rs2667975 | LYN | 7.56E–04 | 0.706 | 0.58–0.86 | 331 | 1.57E–03 | 1.78E–01 | Associated with myeloid progenitor and monocyte tumors (69) |
| Associated with breast cancer (70) | ||||||||
| rs3816375 | ITGAV | 7.75E–04 | 1.335 | 1.13–1.58 | 338 | 4.90E–02 | 3.11E–01 | Associated with HCC (71);In HIV, associated with Kaposi sarcoma lesions (72) |
NOTE: The table lists the top 14 ranked immune genes and their corresponding SNP and includes the SNP identifier (rs#), the official gene symbol, the overall rank in the oropharyngeal cancer GWAS, the genes most significant SNP's P value from the oropharyngeal cancer, HPV+, and laryngeal cancer association analysis and connection of each gene to cancer, progressive viral infection, or both described in existing scientific literature. The top 10 ranked genes are significant at a gene-based threshold (FDR < 0.05).
Abbreviations: CI, confidence interval; LC, laryngeal cancer; OPC, oropharyngeal cancer; OR, odds ratio.