title: Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing.
abstract: BACKGROUND
  To determine genomic alterations in head and neck squamous cell carcinoma (HNSCC) using formalin-fixed, paraffin-embedded (FFPE) tumors obtained through routine clinical practice, selected cancer-related genes were evaluated and compared with alterations seen in frozen tumors obtained through research studies.
  
  
  METHODS
  DNA samples obtained from 252 FFPE HNSCC were analyzed using next-generation sequencing-based (NGS) clinical assay to determine sequence and copy number variations in 236 cancer-related genes plus 47 introns from 19 genes frequently rearranged in cancer. Human papillomavirus (HPV) status was determined by presence of the HPV DNA sequence in all samples and corroborated with high-risk HPV in situ hybridization (ISH) and p16 immunohistochemical (IHC) staining in a subset of tumors. Sequencing data from 399 frozen tumors in The Cancer Genome Atlas and University of Chicago public datasets were analyzed for comparison.
  
  
  RESULTS
  Among 252 FFPE HNSCC, 84 (33%) were HPV positive and 168 (67%) were HPV negative by sequencing. A subset of 40 tumors with HPV ISH and p16 IHC results showed complete concordance with NGS-derived HPV status. The most common genes with genomic alterations were PIK3CA and PTEN in HPV-positive tumors and TP53 and CDKN2A/B in HPV-negative tumors. In the pathway analysis, the PI3K pathway in HPV-positive tumors and DNA repair-p53 and cell cycle pathways in HPV-negative tumors were frequently altered. The HPV-positive oropharynx and HPV-positive nasal cavity/paranasal sinus carcinoma shared similar mutational profiles.
  
  
  CONCLUSIONS
  The genomic profile of FFPE HNSCC tumors obtained through routine clinical practice is comparable with frozen tumors studied in research setting, demonstrating the feasibility of comprehensive genomic profiling in a clinical setting. However, the clinical significance of these genomic alterations requires further investigation through application of these genomic profiles as integral biomarkers in clinical trials.
authors.affiliation: Department of Oncology; Department of Otolaryngology-Head and Neck Surgery. Electronic address: cchung11@jhmi.edu.
authors.forename: C H
authors.initials: CH
authors.lastname: Chung
authors.affiliation: Department of Biomedical Engineering, Institute for Computational Medicine.
authors.forename: V B
authors.initials: VB
authors.lastname: Guthrie
authors.affiliation: Department of Biomedical Engineering, Institute for Computational Medicine.
authors.forename: D L
authors.initials: DL
authors.lastname: Masica
authors.affiliation: Department of Biomedical Engineering, Institute for Computational Medicine.
authors.forename: C
authors.initials: C
authors.lastname: Tokheim
authors.affiliation: Department of Oncology.
authors.forename: H
authors.initials: H
authors.lastname: Kang
authors.affiliation: Department of Otolaryngology-Head and Neck Surgery.
authors.forename: J
authors.initials: J
authors.lastname: Richmon
authors.affiliation: Department of Otolaryngology-Head and Neck Surgery.
authors.forename: N
authors.initials: N
authors.lastname: Agrawal
authors.affiliation: Department of Oncology; Department of Otolaryngology-Head and Neck Surgery; Department of Milton J. Dance Head and Neck Center, Baltimore.
authors.forename: C
authors.initials: C
authors.lastname: Fakhry
authors.affiliation: Department of Radiation Oncology.
authors.forename: H
authors.initials: H
authors.lastname: Quon
authors.affiliation: Department of Oncology; Department of Otolaryngology-Head and Neck Surgery; Department of Radiology and Radiological Sciences.
authors.forename: R M
authors.initials: RM
authors.lastname: Subramaniam
authors.affiliation: Department of Medicine, University of Chicago, Chicago.
authors.forename: Z
authors.initials: Z
authors.lastname: Zuo
authors.affiliation: Department of Medicine, University of Chicago, Chicago.
authors.forename: T
authors.initials: T
authors.lastname: Seiwert
authors.affiliation: Foundation Medicine, Inc., Cambridge, USA.
authors.forename: Z R
authors.initials: ZR
authors.lastname: Chalmers
authors.affiliation: Foundation Medicine, Inc., Cambridge, USA.
authors.forename: G M
authors.initials: GM
authors.lastname: Frampton
authors.affiliation: Foundation Medicine, Inc., Cambridge, USA.
authors.forename: S M
authors.initials: SM
authors.lastname: Ali
authors.affiliation: Foundation Medicine, Inc., Cambridge, USA.
authors.forename: R
authors.initials: R
authors.lastname: Yelensky
authors.affiliation: Foundation Medicine, Inc., Cambridge, USA.
authors.forename: P J
authors.initials: PJ
authors.lastname: Stephens
authors.affiliation: Foundation Medicine, Inc., Cambridge, USA.
authors.forename: V A
authors.initials: VA
authors.lastname: Miller
authors.affiliation: Department of Oncology; Department of Biomedical Engineering, Institute for Computational Medicine.
authors.forename: R
authors.initials: R
authors.lastname: Karchin
authors.affiliation: Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore.
authors.forename: J A
authors.initials: JA
authors.lastname: Bishop
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000032:analysis / Q000235:genetics*; D002294:Carcinoma, Squamous Cell / Q000737:chemistry / Q000235:genetics* / Q000473:pathology / Q000821:virology; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000032:analysis; D056915:DNA Copy Number Variations; D004279:DNA, Viral / Q000235:genetics; D030541:Databases, Genetic; D005260:Female; D005404:Fixatives; D005557:Formaldehyde; D020869:Gene Expression Profiling / Q000379:methods*; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D006258:Head and Neck Neoplasms / Q000737:chemistry / Q000235:genetics* / Q000473:pathology / Q000821:virology; D059014:High-Throughput Nucleotide Sequencing; D061809:Human Papillomavirus DNA Tests; D006801:Humans; D007150:Immunohistochemistry; D017403:In Situ Hybridization; D008297:Male; D008875:Middle Aged; D009154:Mutation; D027383:Papillomaviridae / Q000235:genetics; D016612:Paraffin Embedding; D010641:Phenotype; D011237:Predictive Value of Tests; D011379:Prognosis; D000077195:Squamous Cell Carcinoma of Head and Neck; D016707:Tissue Fixation
chemical_list: D014408:Biomarkers, Tumor; D019941:Cyclin-Dependent Kinase Inhibitor p16; D004279:DNA, Viral; D005404:Fixatives; D005557:Formaldehyde
keywords: DNA mutation; copy number variation; head and neck squamous cell carcinoma; human papillomavirus