title: Identification of human papillomavirus status specific biomarker in head and neck cancer.
abstract: BACKGROUND
  In an attempt to improve the prognosis of patients with head and neck cancer, it could be necessary to identify biomarkers in homogeneous subgroups of patients with head and neck cancer.
  
  
  METHODS
  We explored the necessity of human papillomavirus (HPV) status-specific biomarkers in patients with head and neck cancer and identified an HPV status-specific gene set. The identified gene set was validated with the external microarray datasets. For this purpose, we used 4 microarray datasets obtained from a public database. One dataset was used for identifying the HPV status specific gene set, and the other datasets were used for validation.
  
  
  RESULTS
  The identified gene set for distinguishing head and neck cancer from head and neck normal, did not accurately discriminate the HPV specific patients with head and neck cancer from the head and neck normal group. Also, it was demonstrated that some HPV-positive (HPV+) head and neck cancer-specific genes may not be significant in HPV-negative (HPV-) head and neck cancer patients. The identified HPV specific gene sets showed good performance in validation datasets. The HPV+ head and neck cancer-specific gene set included various metabolism-related pathways, and the HPV- head and neck cancer-specific gene set included several pathways; fibroblast, collagen degradation, actin-binding, and actin cytoskeleton.
  
  
  CONCLUSIONS
  The identification of HPV status-specific significant gene set was necessary. It is expected that HPV status-specific biomarkers can be helpful in deciding therapeutic methods for patients with head and neck cancer, after biological validation and large prospective trials.
authors.affiliation: Oral Cancer Research Institute, College of Dentistry, Yonsei University, Seoul.
authors.forename: Ki-Yeol
authors.initials: KY
authors.lastname: Kim
authors.affiliation: Department of Pathology, Yanbian University Medical College, Yanji City, Jilin Province, China.
authors.forename: Xianglan
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Oral Cancer Research Institute, College of Dentistry, Yonsei University, Seoul.|Department of Oral and Maxillofacial Surgery, College of Dentistry, Yonsei University, Seoul.
authors.forename: In-Ho
authors.initials: IH
authors.lastname: Cha
mesh_terms: D000328:Adult; D000368:Aged; D002294:Carcinoma, Squamous Cell / Q000235:genetics / Q000503:physiopathology / Q000821:virology*; D004279:DNA, Viral / Q000235:genetics*; D016208:Databases, Factual; D005260:Female; D020869:Gene Expression Profiling; D015967:Gene Expression Regulation, Viral; D006258:Head and Neck Neoplasms / Q000235:genetics / Q000503:physiopathology / Q000821:virology*; D006801:Humans; D008297:Male; D046228:Microarray Analysis; D008875:Middle Aged; D027383:Papillomaviridae / Q000235:genetics* / Q000302:isolation & purification; D030361:Papillomavirus Infections / Q000175:diagnosis / Q000235:genetics*; D011379:Prognosis; D015203:Reproducibility of Results; D018570:Risk Assessment; D012494:Sampling Studies; D012680:Sensitivity and Specificity; D018709:Statistics, Nonparametric
chemical_list: D004279:DNA, Viral
keywords: head and neck cancer; human papillomavirus; human papillomavirus (HPV) status-specific gene set; microarray data; prognosis