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Multi-photon Imaging of Tumor Cell Invasion in an Orthotopic Mouse Model of Oral Squamous Cell Carcinoma
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Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral
Jie Ma1, Yong Fu1, Yao-Yao Tu1
1Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, No 639, Zhizaoju Rd, Shanghai, 200011, China.
BMC Cancer
|July 26, 2018
Summary
Investigating allele frequency thresholds for cancer gene mutations in oral squamous cell carcinoma (OSCC) revealed no significant impact on clinical outcome analysis. This finding supports consistent prognostic analysis regardless of the threshold used for targeted gene sequencing.
Area of Science:
- Oncology
- Genetics
- Bioinformatics
Background:
- Sequencing technologies have advanced, leading to potential disputes in mutation analysis.
- Oral squamous cell carcinoma (OSCC) research requires precise prognostic analysis.
- Understanding the impact of allele frequency thresholds is crucial for accurate genetic profiling.
Purpose of the Study:
- To investigate the effect of different allele frequency thresholds on prognostic analyses.
- To evaluate mutations in cancer-associated gene exons (CAGE) in OSCC.
- To determine the optimal allele frequency threshold for mutation detection in OSCC.
Main Methods:
- Next-generation sequencing of twelve genes in 46 OSCC patients.
- Analysis of formalin-fixed paraffin-embedded tissues.
- Application of allele frequency thresholds of 10%, 5%, and 3% for prognostic analysis.
Main Results:
- Ninety-four non-synonymous mutations were detected in 40 OSCC patients at a 10% allele frequency threshold.
- TP53, NOTCH1, CASP8, CDKN2A, and CDH1 were the most frequently mutated genes.
- No significant differences in clinical outcomes were observed across different allele frequency thresholds (10%, 5%, 3%).
Conclusions:
- TP53, NOTCH1, CASP8, CDKN2A, and CDH1 are frequently mutated in OSCC.
- The choice of allele frequency threshold does not influence the clinical outcome analysis in this OSCC cohort.
- Standardized mutation detection methods are essential for reliable prognostic analysis in OSCC.
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