Open Access Open Badges Research

A gene expression profile test to resolve head & neck squamous versus lung squamous cancers

Anita Lal1*, Rebecca Panos1, Mira Marjanovic1, Michael Walker1, Eloisa Fuentes1, Gregory J Kubicek2, W David Henner1, Ljubomir J Buturovic1 and Meredith Halks-Miller1

Author affiliations

1 Pathwork Diagnostics, 595 Penobscot Dr, Redwood City, CA 94063, USA

2 Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15232, USA

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Citation and License

Diagnostic Pathology 2013, 8:44  doi:10.1186/1746-1596-8-44

Published: 11 March 2013



The differential diagnosis between metastatic head & neck squamous cell carcinomas (HNSCC) and lung squamous cell carcinomas (lung SCC) is often unresolved because the histologic appearance of these two tumor types is similar. We have developed and validated a gene expression profile test (GEP-HN-LS) that distinguishes HNSCC and lung SCC in formalin-fixed, paraffin-embedded (FFPE) specimens using a 2160–gene classification model.


The test was validated in a blinded study using a pre-specified algorithm and microarray data files for 76 metastatic or poorly-differentiated primary tumors with a known HNSCC or lung SCC diagnosis.


The study met the primary Bayesian statistical endpoint for acceptance. Measures of test performance include overall agreement with the known diagnosis of 82.9% (95% CI, 72.5% to 90.6%), an area under the ROC curve (AUC) of 0.91 and a diagnostics odds ratio (DOR) of 23.6. HNSCC (N = 38) gave an agreement with the known diagnosis of 81.6% and lung SCC (N = 38) gave an agreement of 84.2%. Reproducibility in test results between three laboratories had a concordance of 91.7%.


GEP-HN-LS can aid in resolving the important differential diagnosis between HNSCC and lung SCC tumors.

Virtual Slides

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Diagnostic test; Gene expression; Tissue of origin; Lung cancer; Head & neck cancer