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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Published inISRN oncology Vol. 2012; no. 2012; pp. 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 Journal Article
LanguageEnglish
Published Cairo, Egypt Hindawi Puplishing Corporation 2012
International Scholarly Research Network
Hindawi Limited
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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Abstract 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.
AbstractList 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.
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.
Author Franklin, Jason H.
Yoo, John
Koropatnick, James
Szeto, Christopher C. T.
Dowthwaite, Samuel A.
Boutros, Paul C.
Wehrli, Bret
Kwan, Keith
Mymryk, Joe S.
Basmaji, John
Dhaliwal, Sandeep
Palma, David A.
Xu, Wei
Todorovic, Biljana
Starmans, Maud H. W.
Nichols, Anthony C.
Lambin, Philippe
Barrett, John W.
Chan-Seng-Yue, Michelle
Fung, Kevin
AuthorAffiliation 1 Department 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
9 Department of Radiation Oncology (MAASTRO), GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands
10 Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 2M9
7 Department of Biostatistics, University of Toronto, Toronto, ON, Canada M5T 3M7
4 Department of Oncology, Western University, London, ON, Canada N6A 4L6
5 Department of Pathology, Western University, London, ON, Canada N6A 5C1
2 London Regional Cancer Program, London, ON, Canada N6A 4L6
8 Department of Microbiology and Immunology, Western University, London, ON, Canada N6A 5C1
3 Lawson Health Research Institute, London, ON, Canada N6C 2R5
6 Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Cana
AuthorAffiliation_xml – name: 8 Department of Microbiology and Immunology, Western University, London, ON, Canada N6A 5C1
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– name: 1 Department 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
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ContentType Journal Article
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Yoo, John
Koropatnick, James
Wehrli, Bret
Kwan, Keith
Basmaji, John
Dhaliwal, Sandeep
Xu, Wei
Todorovic, Biljana
Nichols, Anthony C
Dowthwaite, Samuel A
Palma, David A
Lambin, Philippe
Szeto, Christopher C. T
Starmans, Maud H. W
Chan-Seng-Yue, Michelle
Fung, Kevin
Franklin, Jason H
Barrett, John W
Boutros, Paul C
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Copyright Copyright © 2012 Anthony C. Nichols et al.
Copyright © 2012 Anthony C. Nichols et al. 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.
Copyright © 2012 Anthony C. Nichols et al. 2012
Copyright_xml – notice: Copyright © 2012 Anthony C. Nichols et al.
– notice: Copyright © 2012 Anthony C. Nichols et al. 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.
– notice: Copyright © 2012 Anthony C. Nichols et al. 2012
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Snippet Background. Next-generation sequencing of cancers has identified important therapeutic targets and biomarkers. The goal of this pilot study was to compare the...
Background . Next-generation sequencing of cancers has identified important therapeutic targets and biomarkers. The goal of this pilot study was to compare the...
Background . Next-generation sequencing of cancers has identified important therapeutic targets and biomarkers. The goal of this pilot study was to compare the...
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SubjectTerms 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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Title A Pilot Study Comparing HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas by Whole Exome Sequencing
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https://dx.doi.org/10.5402/2012/809370
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Volume 2012
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