Table 1.
Mutant frequency of targeted genes in the 46 patients with oral squamous cell carcinoma
| Gene | AFa ≥ 3% | AF ≥5% | AF ≥10% | TCGA HNSCC database | p-valueb (AF ≥ 10%) |
|---|---|---|---|---|---|
| ANXA1 | 1/46 (2.2%) | 1/46 (2.2%) | 1/46 (2.2%) | 1/279 (0.4%) | 0.263 |
| CASP8 | 9/46 (19.6%) | 7/46 (15.2%) | 6/46 (13.0%) | 23/279 (8.2%) | 0.272 |
| CDH1 | 6/46 (13.0%) | 4/46 (8.7%) | 3/46 (6.5%) | 4/279 (1.4%) | 0.062 |
| CDKN2A | 7/46 (15.2%) | 5/46 (10.9%) | 5/46 (10.9%) | 60/279 (21.5%) | 0.095 |
| CTNNB1 | 3/46 (6.5%) | 3/46 (6.5%) | 0/46 (0) | 2/279 (0.7%) | 1.000 |
| EGFR | 2/46 (4.3%) | 2/46 (4.3%) | 1/46 (2.2%) | 9/279 (3.2%) | 1.000 |
| IGFBP3 | 3/46 (6.5%) | 2/46 (4.3%) | 1/46 (2.2%) | 1/279 (0.4%) | 0.263 |
| PTEN | 1/46 (2.2%) | 0/46 (0) | 0/46 (0) | 5/279 (1.8%) | 1.000 |
| TGFB1 | 4/46 (8.7%) | 2/46 (4.3%) | 1/46 (2.2%) | 1/279 (0.4%) | 0.263 |
| TP63 | 4/46 (8.7%) | 1/46 (2.2%) | 0/46 (0) | 5/279 (1.8%) | 1.000 |
| TP53 | 36/46 (78.3%) | 36/46(78.3%) | 36/46 (78.3%) | 202/279 (72.4%) | 0.406 |
| NOTCH1 | 23/46 (50.0%) | 16/46(34.8%) | 14/46 (30.4%) | 51/279 (18.3%) | 0.056 |
aAF: allele frequency
bThe difference between the mutation rates observed in our cohort and those in the TCGA HNSCC database
Note: Mutation frequency provided how often a mutation may be expressed in a particular genetic population. Allele frequency is the relative frequency of an allele of a gene at a particular locus in a population. Non-synonymous mutations were identified in all the 12 genes if the threshold of allele frequency was defined as ≥3%, ≥5% and ≥ 10%. When compared to the mutational patterns reported in The Cancer Genome Atlas (TCGA) head and neck squamous cell carcinoma (HNSCC) database (containing the whole-exome sequencing data from 279 samples), with the threshold of allele frequency of ≥10%, the frequency of mutations detected in our study was similar to TCGA database, with the exception of NOTCH1and CDH1