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ISRN Oncology
Volume 2012 (2012), Article ID 809370, 9 pages
Research Article

A Pilot Study Comparing HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas by Whole Exome Sequencing

1Department of Otolaryngology-Head and Neck Surgery, Western University, Victoria Hospital, London Health Science Centre, Room B3-431A, 800 Commissioners Road East, London, ON, Canada N6A 5W9
2London Regional Cancer Program, London, ON, Canada N6A 4L6
3Lawson Health Research Institute, London, ON, Canada N6C 2R5
4Department of Oncology, Western University, London, ON, Canada N6A 4L6
5Department of Pathology, Western University, London, ON, Canada N6A 5C1
6Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada M5G 0A3
7Department of Biostatistics, University of Toronto, Toronto, ON, Canada M5T 3M7
8Department of Microbiology and Immunology, Western University, London, ON, Canada N6A 5C1
9Department of Radiation Oncology (MAASTRO), GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands
10Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 2M9

Received 31 October 2012; Accepted 22 November 2012

Academic Editors: R.-J. Bensadoun and H.-W. Lo

Copyright © 2012 Anthony C. Nichols et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Background. Next-generation sequencing of cancers has identified important therapeutic targets and biomarkers. The goal of this pilot study was to compare the genetic changes in a human papillomavirus- (HPV-)positive and an HPV-negative head and neck tumor. Methods. DNA was extracted from the blood and primary tumor of a patient with an HPV-positive tonsillar cancer and those of a patient with an HPV-negative oral tongue tumor. Exome enrichment was performed using the Agilent SureSelect All Exon Kit, followed by sequencing on the ABI SOLiD platform. Results. Exome sequencing revealed slightly more mutations in the HPV-negative tumor (73) in contrast to the HPV-positive tumor (58). Multiple mutations were noted in zinc finger genes (ZNF3, 10, 229, 470, 543, 616, 664, 638, 716, and 799) and mucin genes (MUC4, 6, 12, and 16). Mutations were noted in MUC12 in both tumors. Conclusions. HPV-positive HNSCC is distinct from HPV-negative disease in terms of evidence of viral infection, p16 status, and frequency of mutations. Next-generation sequencing has the potential to identify novel therapeutic targets and biomarkers in HNSCC.