title: A gene expression profile test to resolve head & neck squamous versus lung squamous cancers.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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%.
  
  
  CONCLUSIONS
  GEP-HN-LS can aid in resolving the important differential diagnosis between HNSCC and lung SCC tumors.
  The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1753227817890930.
authors.affiliation: Pathwork Diagnostics, 595 Penobscot Dr, Redwood City, CA 94063, USA. anita.lal08@gmail.com
authors.forename: Anita
authors.initials: A
authors.lastname: Lal
authors.forename: Rebecca
authors.initials: R
authors.lastname: Panos
authors.forename: Mira
authors.initials: M
authors.lastname: Marjanovic
authors.forename: Michael
authors.initials: M
authors.lastname: Walker
authors.forename: Eloisa
authors.initials: E
authors.lastname: Fuentes
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Kubicek
authors.forename: W David
authors.initials: WD
authors.lastname: Henner
authors.forename: Ljubomir J
authors.initials: LJ
authors.lastname: Buturovic
authors.forename: Meredith
authors.initials: M
authors.lastname: Halks-Miller
mesh_terms: D000328:Adult; D000368:Aged; D000465:Algorithms; D019540:Area Under Curve; D001499:Bayes Theorem; D014408:Biomarkers, Tumor / Q000235:genetics*; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000556:secondary; D003937:Diagnosis, Differential; D005404:Fixatives; D005557:Formaldehyde; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D005820:Genetic Testing / Q000379:methods; D006258:Head and Neck Neoplasms / Q000235:genetics* / Q000473:pathology; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology; D008875:Middle Aged; D016017:Odds Ratio; D020411:Oligonucleotide Array Sequence Analysis; D016612:Paraffin Embedding; D011237:Predictive Value of Tests; D012372:ROC Curve; D015203:Reproducibility of Results; D016707:Tissue Fixation
chemical_list: D014408:Biomarkers, Tumor; D005404:Fixatives; D005557:Formaldehyde