Genomic and human papillomavirus profiling of an oral cancer cohort identifies TP53 as a predictor of overall survival

Neil Mundi; Stephenie D Prokopec; Farhad Ghasemi; Andrew Warner; Krupal Patel; Danielle MacNeil; Christopher Howlett; William Stecho; Paul Plantinga; Nicole Pinto; Kara M Ruicci; Mohammed Imran Khan; Myung Woul Han; John Yoo; Kevin Fung; Axel Sahovaler; David A Palma; Eric Winquist; Joe S Mymryk; John W Barrett; Paul C Boutros; Anthony C Nichols

doi:10.1186/s41199-019-0045-0

Genomic and human papillomavirus profiling of an oral cancer cohort identifies TP53 as a predictor of overall survival

Cancers Head Neck. 2019 Dec 5:4:5. doi: 10.1186/s41199-019-0045-0. eCollection 2019.

Authors

Neil Mundi^{1

2}, Stephenie D Prokopec³, Farhad Ghasemi¹, Andrew Warner⁴, Krupal Patel¹, Danielle MacNeil^{1

4}, Christopher Howlett⁵, William Stecho⁵, Paul Plantinga⁵, Nicole Pinto^{1

4}, Kara M Ruicci^{1

4}, Mohammed Imran Khan¹, Myung Woul Han⁶, John Yoo^{1

4}, Kevin Fung^{1

4}, Axel Sahovaler¹, David A Palma⁴, Eric Winquist⁴, Joe S Mymryk^{1

4

7}, John W Barrett^{1

4}, Paul C Boutros^#^{3

8

9}, Anthony C Nichols^#^{1

4}

Affiliations

¹ 1Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON Canada.
² 2Victoria Hospital, London Health Science Centre, Room B3-431A, 800 Commissioners Road East, London, ON N6A 5W9 Canada.
³ 3Ontario Institute for Cancer Research, Toronto, ON Canada.
⁴ 4Department of Oncology, Western University, London, ON Canada.
⁵ 5Department of Pathology, Western University, London, ON Canada.
⁶ 6Department of Otolaryngology, College of Medicine, Ulsan University Hospital, University of Ulsan, Ulsan, South Korea.
⁷ 7Department of Microbiology & Immunology, Western University, London, ON Canada.
⁸ 8Department of Medical Biophysics, University of Toronto, Toronto, ON Canada.
⁹ 9Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON Canada.

^# Contributed equally.

Abstract

Background: The genomic landscape of head and neck cancer has been reported through The Cancer Genome Atlas project. We attempt to determine if high-risk human papillomavirus (HPV) or frequently mutated genes are correlated with survival in an oral cancer cohort.

Methods: Patient demographic data along with data from final pathology was collected. Tumor DNA was analyzed using a custom Illumina targeted sequencing panel. Five high-risk HPV types were tested by qPCR. Statistical analyses were used to identify associations between patient outcome and mutational status.

Results: High-risk HPV types were identified in 7% of cases; HPV status was not associated with survival. Mutations were identified in TP53, TERT promoter, & PIK3CA. Mutations in TP53 were significantly associated with poorer overall survival on multi-variate analysis (p = 0.03).

Conclusions: Mutations in TP53 were associated with poor patient survival. Expanding our sample size may identify further predictors of outcome to direct customized cancer care.

Keywords: Genomics; Mutational status; Oral cancer; Survival; tp53.