ArticleBMC cancer2018
Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral squamous cell carcinoma.
Article in BMC cancer, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 26 citations in OpenAlex.
- Exploring the Impact of Multiple Gene Mutations on Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor Response in Asian Nonsmall Cell Lung Cancer Patients.ACS pharmacology & translational science · 2026Review
- Genetics and Molecular Mechanisms in Oral Squamous Cell Carcinoma: A Narrative Review.Medicina (Kaunas, Lithuania) · 2026Review
- AI-Driven Variant Annotation for Precision Oncology in Breast Cancer.Clinical and translational science · 2025Article
- Biomarkers for Oral Squamous Cell Carcinoma (miR-24, miR-200, and miR-34): Screening and Detection MicroRNA.Asian Pacific journal of cancer prevention : APJCP · 2024Article
- Enhancing oral squamous cell carcinoma prediction: the prognostic power of the worst pattern of invasion and the limited impact of molecular resection margins.Frontiers in oncology · 2023Article
- Corrected Allele Frequency of BRCA1/2 Mutations Is an Independent Prognostic Factor for Treatment Response to PARP-Inhibitors in Ovarian Cancer Patients.Journal of personalized medicine · 2022Article
- Proliferation and Apoptosis Pathways and Factors in Oral Squamous Cell Carcinoma.International journal of molecular sciences · 2022Review
- Genomic Landscape of Head and Neck Squamous Cell Carcinoma Across Different Anatomic Sites in Chinese Population.Frontiers in genetics · 2021Article
- The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers.Life (Basel, Switzerland) · 2020Review
- Study of Caspase 8 mutation in oral cancer and adjacent precancer tissues and implication in progression.PloS one · 2020Article
- The RNA degradation pathway is involved in PPARα-modulated anti-oral tumorigenesis.BioMedicine · 2019Article
- Genomic and human papillomavirus profiling of an oral cancer cohort identifies TP53 as a predictor of overall survival.Cancers of the head & neck · 2019Article
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundWith the development of sequencing technologies, there may be some disputes on sequencing analysis. The aim of this study was to investigate different allele frequency thresholds of mutations in targeted genes on prognostic analyses using a panel of cancer associated gene exons (CAGE) in oral squamous cell carcinoma (OSCC).
methodsForty-six patients were included in this study. Twelve genes were sequenced and analyzed using next-generation sequencing from formalin-fixed paraffin-embedded tissues. Allele frequency thresholds of 10, 5, and 3% were used for prognostic analyses.
resultsWith a mean sequence depth of 3199-fold, 99% of CAGE were represented by at least 10 reads. Ninety-four non-synonymous (missense [70.2%], nonsense [11.7%], splice site [10.6%], and insertion/deletion [7.5%]) mutations were detected in 40 OSCC patients with an allele frequency threshold of 10%. TP53 (78.3%), NOTCH1 (30.4%), CASP8 (13.0%), CDKN2A (10.9%), and CDH1 (6.5%) were the most frequently mutated genes. Using allele frequency thresholds of 10, 5, and 3%, there were no significant differences in clinical outcomes between patients with non-synonymous mutations and wild type genotypes.
conclusionsTP53, NOTCH1, CASP8, CDKN2A, and CDH1 are the most frequently mutated genes in OSCC patients. The allele frequency threshold used in this study does not affect the results of clinical outcome analysis.
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