Ultra-deep targeted sequencing of advanced oral squamous cell carcinoma identifies a mutation-based prognostic gene signature

Shu-Jen Chen; Hsuan Liu; Chun-Ta Liao; Po-Jung Huang; Yi Huang; An Hsu; Petrus Tang; Yu-Sun Chang; Hua-Chien Chen; Tzu-Chen Yen

doi:10.18632/oncotarget.3768

Ultra-deep targeted sequencing of advanced oral squamous cell carcinoma identifies a mutation-based prognostic gene signature

Oncotarget. 2015 Jul 20;6(20):18066-80. doi: 10.18632/oncotarget.3768.

Authors

Shu-Jen Chen^{1

2

3}, Hsuan Liu^{2

3}, Chun-Ta Liao⁴, Po-Jung Huang⁵, Yi Huang², An Hsu³, Petrus Tang⁵, Yu-Sun Chang², Hua-Chien Chen^{1

2

3}, Tzu-Chen Yen⁶

Affiliations

¹ Department of Biomedical Sciences, Chang Gung University, Taoyuan, 33302, Taiwan.
² Genomic Core Laboratory, Chang Gung University, Taoyuan, 33302, Taiwan.
³ Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, 33302, Taiwan.
⁴ Department of Otorhinolaryngology, Chang Gung Memorial Hospital, Taoyuan, 33305, Taiwan.
⁵ Bioinformatics Core Laboratory, Chang Gung University, Taoyuan, 33305, Taiwan.
⁶ Department of Nuclear Medicine, Chang Gung Memorial Hospital, Taoyuan, 33305, Taiwan.

Abstract

Background: Patients with advanced oral squamous cell carcinoma (OSCC) have heterogeneous outcomes that limit the implementation of tailored treatment options. Genetic markers for improved prognostic stratification are eagerly awaited.

Methods: Herein, next-generation sequencing (NGS) was performed in 345 formalin-fixed paraffin-embedded (FFPE) samples obtained from advanced OSCC patients. Genetic mutations on the hotspot regions of 45 cancer-related genes were detected using an ultra-deep (>1000×) sequencing approach. Kaplan-Meier plots and Cox regression analyses were used to investigate the associations between the mutation status and disease-free survival (DFS).

Results: We identified 1269 non-synonymous mutations in 276 OSCC samples. TP53, PIK3CA, CDKN2A, HRAS and BRAF were the most frequently mutated genes. Mutations in 14 genes were found to predict DFS. A mutation-based signature affecting ten genes (HRAS, BRAF, FGFR3, SMAD4, KIT, PTEN, NOTCH1, AKT1, CTNNB1, and PTPN11) was devised to predict DFS. Two different resampling methods were used to validate the prognostic value of the identified gene signature. Multivariate analysis demonstrated that presence of a mutated gene signature was an independent predictor of poorer DFS (P = 0.005).

Conclusions: Genetic variants identified by NGS technology in FFPE samples are clinically useful to predict prognosis in advanced OSCC patients.

Keywords: mutation; next-generation sequencing; oral squamous cell carcinoma; prognosis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adult
Aged
Biomarkers, Tumor / genetics*
Carcinoma, Squamous Cell / genetics*
Carcinoma, Squamous Cell / mortality
Carcinoma, Squamous Cell / pathology
Carcinoma, Squamous Cell / therapy
DNA Mutational Analysis*
Disease-Free Survival
Female
Gene Expression Profiling / methods*
Genetic Predisposition to Disease
Head and Neck Neoplasms / genetics*
Head and Neck Neoplasms / mortality
Head and Neck Neoplasms / pathology
Head and Neck Neoplasms / therapy
High-Throughput Nucleotide Sequencing*
Humans
Kaplan-Meier Estimate
Male
Middle Aged
Mouth Neoplasms / genetics*
Mouth Neoplasms / mortality
Mouth Neoplasms / pathology
Mouth Neoplasms / therapy
Multivariate Analysis
Mutation*
Neoplasm Staging
Oligonucleotide Array Sequence Analysis*
Phenotype
Predictive Value of Tests
Proportional Hazards Models
Reproducibility of Results
Retrospective Studies
Risk Factors
Squamous Cell Carcinoma of Head and Neck
Time Factors
Treatment Outcome

Substances

Biomarkers, Tumor