Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral squamous cell carcinoma

Table 1 Mutant frequency of targeted genes in the 46 patients with oral squamous cell carcinoma

Gene	AF^a ≥ 3%	AF ≥5%	AF ≥10%	TCGA HNSCC database	p-value^b (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

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