Dataset Information

A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation.

ABSTRACT: To identify a prognostic gene signature for patients with human papilloma virus (HPV)-negative oral squamous cell carcinomas (OSCC).Two gene expression datasets were used: a training dataset from the Fred Hutchinson Cancer Research Center (FHCRC, Seattle, WA; n = 97) and a validation dataset from the MD Anderson Cancer Center (MDACC, Houston, TX; n = 71). We applied L1/L2-penalized Cox regression models to the FHCRC data on the 131-gene signature previously identified to be prognostic in patients with OSCCs to identify a prognostic model specific for patients with high-risk HPV-negative OSCCs. The models were tested with the MDACC dataset using a receiver operating characteristic (ROC) analysis.A 13-gene model was identified as the best predictor of HPV-negative OSCC-specific survival in the training dataset. The risk score for each patient in the validation dataset was calculated from this model and dichotomized at the median. The estimated 2-year mortality (± SE) of patients with high-risk scores was 47.1% (± 9.24%) compared with 6.35% (± 4.42) for patients with low-risk scores. ROC analyses showed that the areas under the curve for the age, gender, and treatment modality-adjusted models with risk score [0.78; 95% confidence interval (CI), 0.74-0.86] and risk score plus tumor stage (0.79; 95% CI, 0.75-0.87) were substantially higher than for the model with tumor stage (0.54; 95% CI, 0.48-0.62).We identified and validated a 13-gene signature that is considerably better than tumor stage in predicting survival of patients with HPV-negative OSCCs. Further evaluation of this gene signature as a prognostic marker in other populations of patients with HPV-negative OSCC is warranted.

SUBMITTER: Lohavanichbutr P

PROVIDER: S-EPMC3593802 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature

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A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation.

Lohavanichbutr Pawadee P Méndez Eduardo E Holsinger F Christopher FC Rue Tessa C TC Zhang Yuzheng Y Houck John J Upton Melissa P MP Futran Neal N Schwartz Stephen M SM Wang Pei P Chen Chu C

Clinical cancer research : an official journal of the American Association for Cancer Research 20130114 5

<h4>Purpose</h4>To identify a prognostic gene signature for patients with human papilloma virus (HPV)-negative oral squamous cell carcinomas (OSCC).<h4>Experimental design</h4>Two gene expression datasets were used: a training dataset from the Fred Hutchinson Cancer Research Center (FHCRC, Seattle, WA; n = 97) and a validation dataset from the MD Anderson Cancer Center (MDACC, Houston, TX; n = 71). We applied L1/L2-penalized Cox regression models to the FHCRC data on the 131-gene signature previ ...[more]

PMID: 23319825

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Dataset Information

A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation.

Publications

A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation.

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