Dataset Information

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

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.

SUBMITTER: Mundi N

PROVIDER: S-EPMC6894507 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Mundi Neil N Prokopec Stephenie D SD Ghasemi Farhad F Warner Andrew A Patel Krupal K MacNeil Danielle D Howlett Christopher C Stecho William W Plantinga Paul P Pinto Nicole N Ruicci Kara M KM Khan Mohammed Imran MI Han Myung Woul MW Yoo John J Fung Kevin K Sahovaler Axel A Palma David A DA Winquist Eric E Mymryk Joe S JS Barrett John W JW Boutros Paul C PC Nichols Anthony C AC

Cancers of the head & neck 20191205

<h4>Background</h4>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.<h4>Methods</h4>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 analy ...[more]

PMID: 31844556

Similar Datasets

Project description:Background Microbial dysbiosis and microbiome-induced inflammation have emerged as important factors in oral squamous cell carcinoma (OSCC) tumorigenesis during the last two decades. However, the “rare biosphere” of the oral microbiome, including fungi, has been sparsely investigated. This study aimed to characterize the salivary mycobiome in a prospective Sudanese cohort of OSCC patients and to explore patterns of diversities associated with overall survival (OS). Materials and Methods Unstimulated saliva samples (n = 72) were collected from patients diagnosed with OSCC (n = 59) and from non-OSCC control volunteers (n = 13). DNA was extracted using a combined enzymatic–mechanical extraction protocol. The salivary mycobiome was assessed using a next-generation sequencing (NGS)-based methodology by amplifying the ITS2 region. The impact of the abundance of different fungal genera on the survival of OSCC patients was analyzed using Kaplan–Meier and Cox regression survival analyses (SPPS). Results Sixteen genera were identified exclusively in the saliva of OSCC patients. Candida, Malassezia, Saccharomyces, Aspergillus, and Cyberlindnera were the most relatively abundant fungal genera in both groups and showed higher abundance in OSCC patients. Kaplan–Meier survival analysis showed higher salivary carriage of the Candida genus significantly associated with poor OS of OSCC patients (Breslow test: p = 0.043). In contrast, the higher salivary carriage of Malassezia showed a significant association with favorable OS in OSCC patients (Breslow test: p = 0.039). The Cox proportional hazards multiple regression model was applied to adjust the salivary carriage of both Candida and Malassezia according to age (p = 0.029) and identified the genus Malassezia as an independent predictor of OS (hazard ratio = 0.383, 95% CI = 0.16–0.93, p = 0.03). Conclusion The fungal compositional patterns in saliva from OSCC patients were different from those of individuals without OSCC. The fungal genus Malassezia was identified as a putative prognostic biomarker and therapeutic target for OSCC.

Dataset Information

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

Background

Methods

Results

Conclusions

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets