- About this Journal
- Abstracting and Indexing
- Aims and Scope
- Article Processing Charges
- Articles in Press
- Author Guidelines
- Bibliographic Information
- Citations to this Journal
- Contact Information
- Editorial Board
- Editorial Workflow
- Free eTOC Alerts
- Publication Ethics
- Submit a Manuscript
- Subscription Information
- Table of Contents
Volume 2012 (2012), Article ID 809370, 9 pages
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.
- A. Jemal, M. J. Thun, L. A. G. Ries et al., “Annual report to the nation on the status of cancer, 1975–2005, featuring trends in lung cancer, tobacco use, and tobacco control,” Journal of the National Cancer Institute, vol. 100, no. 23, pp. 1672–1694, 2008.
- L. A. Ries, D. Melbert, M. Krapcho, et al., “SEER Cancer Statistics Review, 1975–2004. Periodical,” National Cancer Institute, Bethesda, Md, USA, 2007.
- A. K. Chaturvedi, E. A. Engels, R. M. Pfeiffer, et al., “Human papillomavirus and rising oropharyngeal cancer incidence in the United States,” Journal of Clinical Oncology, vol. 29, no. 32, pp. 4294–4301, 2011.
- A. Näsman, P. Attner, L. Hammarstedt et al., “Incidence of human papillomavirus (HPV) positive tonsillar carcinoma in Stockholm, Sweden: an epidemic of viral-induced carcinoma?” International Journal of Cancer, vol. 125, no. 2, pp. 362–366, 2009.
- M. L. Gillison, “Human papillomavirus-associated head and neck cancer is a distinct epidemiologic, clinical, and molecular entity,” Seminars in Oncology, vol. 31, no. 6, pp. 744–754, 2004.
- N. Agrawal, M. J. Frederick, C. R. Pickering , et al., “Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1,” Science, vol. 333, no. 6046, pp. 1154–1157, 2011.
- N. Stransky, A. M. Egloff, A. D. Tward, et al., “The mutational landscape of head and neck squamous cell carcinoma,” Science, vol. 333, no. 6046, pp. 1157–1160, 2011.
- A. C. Nichols, W. C. Faquin, W. H. Westra et al., “HPV-16 infection predicts treatment outcome in oropharyngeal squamous cell carcinoma,” Otolaryngology—Head and Neck Surgery, vol. 140, no. 2, pp. 228–234, 2009.
- S. Begum, M. L. Gillison, M. A. Ansari-Lari, K. Shah, and W. H. Westra, “Detection of human papillomavirus in cervical lymph nodes: a highly effective strategy for localizing site of tumor origin,” Clinical Cancer Research, vol. 9, no. 17, pp. 6469–6475, 2003.
- N. Homer, B. Merriman, and S. F. Nelson, “BFAST: an alignment tool for large scale genome resequencing,” PLoS ONE, vol. 4, no. 11, Article ID e7767, 2009.
- A. McKenna, M. Hanna, E. Banks et al., “The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data,” Genome Research, vol. 20, no. 9, pp. 1297–1303, 2010.
- K. Wang, M. Li, and H. Hakonarson, “ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data,” Nucleic Acids Research, vol. 38, no. 16, p. e164, 2010.
- D. J. Hedges, T. Guettouche, S. Yang et al., “Comparison of three targeted enrichment strategies on the SOLiD sequencing platform,” PLoS ONE, vol. 6, no. 4, Article ID e18595, 2011.
- A. L. Reed, J. Califano, P. Cairns et al., “High frequency of p16 (CDKN2/MTS-1/INK4A) inactivation in head and neck squamous cell carcinoma,” Cancer Research, vol. 56, no. 16, pp. 3630–3633, 1996.
- D. W. Kufe, “Mucins in cancer: function, prognosis and therapy,” Nature Reviews Cancer, vol. 9, no. 12, pp. 874–885, 2009.
- S. S. Krishna, I. Majumdar, and N. V. Grishin, “Structural classification of zinc fingers: survey and summary,” Nucleic Acids Research, vol. 31, no. 2, pp. 532–550, 2003.
- M. J. Lace, J. R. Anson, J. P. Klussmann et al., “Human papillomavirus type 16 (HPV-16) genomes integrated in head and neck cancers and in HPV-16-immortalized human keratinocyte clones express chimeric virus-cell mRNAs similar to those found in cervical cancers,” Journal of Virology, vol. 85, no. 4, pp. 1645–1654, 2011.
- H. Feng, M. Shuda, Y. Chang, and P. S. Moore, “Clonal integration of a polyomavirus in human Merkel cell carcinoma,” Science, vol. 319, no. 5866, pp. 1096–1100, 2008.
- A. C. Nichols, J. Yoo, D. A. Palma, et al., “Frequent mutations in TP53 and CDKN2A found by next-generation sequencing of head and neck cancer cell lines,” Archives of Otolaryngology—Head & Neck Surgery, vol. 138, no. 8, pp. 732–739, 2012.