Table 1.
Summary of genomics in head and neck neoplasms.
| Studied marker | Type of tumor | No. of patients | Sample type | Expression | Test accuracy indices | References | ||
|---|---|---|---|---|---|---|---|---|
| Sens. | Spec. | Accuracy | ||||||
| (PROMOTER) HYPERMETHYLATION | ||||||||
| Promoter hypermethylation panel (HOXA9 and NID2) | OSCC | 179 | Tissue biopsy, salivary rinses | ↓ | Tissue | (3) | ||
| 94% | 75% | – | ||||||
| Saliva | ||||||||
| 75% | 53% | – | ||||||
| Methylation of cg01009664 of the thyrotropin-releasing hormone (TRH) gene | OSCC and OPSCC | 89 | Oral rinse and swab | ↓ | Swab | (11) | ||
| 91.30% | 84.85% | – | ||||||
| Rinse | ||||||||
| 86.15% | 89.66% | – | ||||||
| Promoter hypermethylation panel (PTEN and p16) | OSCC | 50 | Tissue biopsy | ↓ | – | (12) | ||
| EBV DNA load + hypermethylation panel (RASSF1A, WIF1, DAPK1, and RARβ2) | NPC | 252 | Tissue biopsy, NP brushing, cell-free plasma | ↓/↑ | EBV DNA positive and hypermethylation panel in cell-free plasma | (13) | ||
| – | 88% | – | ||||||
| Hypermethylation panel in NPC biopsies and NP brushings | ||||||||
| 95.8% | 67.4% | – | ||||||
| EBV RELATED MARKERS | ||||||||
| IgA VCA + EBV DNA load | NPC | 139 | Blood sample | ↑ | 99% | 96–98% | – | (14) |
| miRNA | ||||||||
| Combination of miR-196a and miR-196b | Oral cancer | 90 | Blood sample | ↑ | 88% | 93% | – | (15) |
| Three-plasma miRNA panel (miR-222-3p, miR-150-5p, and miR-423-5p) | OL, OSCC | 250 | Blood sample | ↑ | – | (16) | ||
| miR-331-3p, miR-603, miR-1303, miR-660-5p, and miR-212-3p individually | LSCC | 20 | Blood sample | ↑ | – | (7) | ||
| Combination of hsa-miR-657 and hsa-miR-1287 | Larynx carcinoma | 39 | Tissue biopsy | ↓/↑ | 86.21% | 100% | – | (15) |
| miR-155 | LSCC | 280 | Tissue biopsy, blood sample | ↑ | 58.4% | 69.5% | – | (17) |
| INTERFERONS | ||||||||
| Interferon inducible transmembrane protein 1 (IFITM1) | OSCC | 38 | Tissue biopsy | ↑ | – | (18) | ||
| ISG15 | OSCC | 30 | Tissue biopsy | ↑ | – | (19) | ||
| ANTIGENS | ||||||||
| Melanoma associated antigens-A (MAGE-A) | OSCC | 70 | Brush biopsy | ↑ | – | (20) | ||
| UPREGULATED GENES | ||||||||
| ADAM15, CDC7, IL12RB2, and TNFRSF8 | OSCC | 33 | Tissue biopsy | ↑ | ADAM15 | (21) | ||
| 52.9% | 82.4% | – | ||||||
| CDC7 | ||||||||
| 52.9% | 82.4 | – | ||||||
| IL12RB2 | ||||||||
| 35.5% | 94.1% | – | ||||||
| TNFRSF8 | ||||||||
| 35.5% | 88.2% | – | ||||||
| HPV RELATED MARKERS | ||||||||
| HPV-16 E6 antibodies | OPC (HPV driven (n = 5) and non-HPV driven [n = 4)] | 9 | Blood sample | Seropositive | HPV-driven OPC | (22) | ||
| 100% (95% CI = 48–100%) |
– | – | ||||||
| Non-HPV driven OPC | ||||||||
| – | 100% (95% CI = 40–100%) |
– | ||||||
| HPV-16 E6 antibodies | OPSCC (HPV driven) | 63 | Blood sample | Seropositive | 96% (95%CI = 88–98%) |
98 (95% CI = 90–100%) | 97% (95% CI = 92–99%) | (23) |
| HPV-16 E6 antibodies | HNSCC (excluding OPC) | 3 | Blood sample | Seropositive | 50% (95% CI = 19–81%) | 100% (95% CI = 96–100%) | 97% (95% CI = 91–99%) | (23) |
| HPV-16 E7 | HNSCC (HPV driven) | 30 | Blood sample | Seropositive | – | – | – | (24) |
| Saliva sample | – | – | – | |||||
| OTHERS | ||||||||
| 5-hydroxylmethylcytosine (5-hmC) | OSCC | 23 | Tissue biopsy | ↓ | – | (25) | ||
| Total cfDNA | HNSCC, especially OPSCC | 27 | Blood sample | ↑ | – | (26) | ||
EBV, Epstein-Barr virus; HNSCC, head and neck squamous cell carcinoma; HPV, human papillomavirus; LSCC, laryngeal squamous cell carcinoma; miRNA, microRNA; NPC, nasopharyngeal carcinoma; OL, oral leukoplakia; OPC, oropharyngeal carcinoma; OPSCC, oropharyngeal squamous cell carcinoma; OSCC, oral squamous cell carcinoma.