|
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
