title: Ultra-deep targeted sequencing of advanced oral squamous cell carcinoma identifies a mutation-based prognostic gene signature.
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.
authors.affiliation: Department of Biomedical Sciences, Chang Gung University, Taoyuan, 33302, Taiwan.|Genomic Core Laboratory, Chang Gung University, Taoyuan, 33302, Taiwan.|Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, 33302, Taiwan.
authors.forename: Shu-Jen
authors.initials: SJ
authors.lastname: Chen
authors.affiliation: Genomic Core Laboratory, Chang Gung University, Taoyuan, 33302, Taiwan.|Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, 33302, Taiwan.
authors.forename: Hsuan
authors.initials: H
authors.lastname: Liu
authors.affiliation: Department of Otorhinolaryngology, Chang Gung Memorial Hospital, Taoyuan, 33305, Taiwan.
authors.forename: Chun-Ta
authors.initials: CT
authors.lastname: Liao
authors.affiliation: Bioinformatics Core Laboratory, Chang Gung University, Taoyuan, 33305, Taiwan.
authors.forename: Po-Jung
authors.initials: PJ
authors.lastname: Huang
authors.affiliation: Genomic Core Laboratory, Chang Gung University, Taoyuan, 33302, Taiwan.
authors.forename: Yi
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, 33302, Taiwan.
authors.forename: An
authors.initials: A
authors.lastname: Hsu
authors.affiliation: Bioinformatics Core Laboratory, Chang Gung University, Taoyuan, 33305, Taiwan.
authors.forename: Petrus
authors.initials: P
authors.lastname: Tang
authors.affiliation: Genomic Core Laboratory, Chang Gung University, Taoyuan, 33302, Taiwan.
authors.forename: Yu-Sun
authors.initials: YS
authors.lastname: Chang
authors.affiliation: Department of Biomedical Sciences, Chang Gung University, Taoyuan, 33302, Taiwan.|Genomic Core Laboratory, Chang Gung University, Taoyuan, 33302, Taiwan.|Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, 33302, Taiwan.
authors.forename: Hua-Chien
authors.initials: HC
authors.lastname: Chen
authors.affiliation: Department of Nuclear Medicine, Chang Gung Memorial Hospital, Taoyuan, 33305, Taiwan.
authors.forename: Tzu-Chen
authors.initials: TC
authors.lastname: Yen
mesh_terms: D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics*; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000401:mortality / Q000473:pathology / Q000628:therapy; D004252:DNA Mutational Analysis; D018572:Disease-Free Survival; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D020022:Genetic Predisposition to Disease; D006258:Head and Neck Neoplasms / Q000235:genetics* / Q000401:mortality / Q000473:pathology / Q000628:therapy; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D053208:Kaplan-Meier Estimate; D008297:Male; D008875:Middle Aged; D009062:Mouth Neoplasms / Q000235:genetics* / Q000401:mortality / Q000473:pathology / Q000628:therapy; D015999:Multivariate Analysis; D009154:Mutation; D009367:Neoplasm Staging; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D011237:Predictive Value of Tests; D016016:Proportional Hazards Models; D015203:Reproducibility of Results; D012189:Retrospective Studies; D012307:Risk Factors; D000077195:Squamous Cell Carcinoma of Head and Neck; D013997:Time Factors; D016896:Treatment Outcome
chemical_list: D014408:Biomarkers, Tumor
keywords: mutation; next-generation sequencing; oral squamous cell carcinoma; prognosis