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

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...

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Bibliographic Details
Published in:ISRN oncology 2012, Vol.2012 (2012), p.1-9
Main Authors: Basmaji, John, Dhaliwal, Sandeep, Xu, Wei, Yoo, John, Chan-Seng-Yue, Michelle, Nichols, Anthony C., Szeto, Christopher C. T., Dowthwaite, Samuel A., Todorovic, Biljana, Starmans, Maud H. W., Lambin, Philippe, Palma, David A., Fung, Kevin, Franklin, Jason H., Wehrli, Bret, Kwan, Keith, Koropatnick, James, Mymryk, Joe S., Boutros, Paul C., Barrett, John W.
Format: Article
Language:English
Subjects:
biomarkers
Blood
Cancer
DNA
Exons
Genomes
Head & neck cancer
Head and neck
Head and neck cancer
Health sciences
Human papillomavirus
Infection
Medical research
mucin
Mutation
Oncology
Patients
squamous cell carcinoma
Surgery
Tongue
Tonsil
Tumors
Zinc finger proteins
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Summary: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.
ISSN:2090-5661
2090-567X
2090-567X
DOI:10.5402/2012/809370