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

From: Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in 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
  1. aAF: allele frequency
  2. bThe difference between the mutation rates observed in our cohort and those in the TCGA HNSCC database
  3. 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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