title: Gene Variability Between Perineural-positive and Perineural-negative Squamous Cell Skin Cancers.
abstract: OBJECTIVE
  To identify differentially expressed genes (DEGs) between perineural invasion-positive (PP) and -negative (PN) cutaneous squamous cell cancers (CSCC).
  
  
  METHODS
  Forty CSCC samples with and without perineural invasion were processed for RNA isolation and hybridization to Affymetrix-U219 DNA microarrays. Raw gene expression data were normalized by Robust Multi-array Averaging (RMA) and log2 transformed. Gene expression-based classification models were created and accuracies evaluated using leave-one-out cross-validation.
  
  
  RESULTS
  At a stringent limma p-value (p<0.001), 24 genes were differentially expressed between PP and PN samples. The cross-validated performance of the eight classification models exhibited a mean accuracy of 85-95%. Diagonal linear discriminant was most accurate at 95%, followed by Bayesian compound covariate at 94%. The poorest accuracy (85%) was observed for 1-Nearest neighbor and Support vector machines.
  
  
  CONCLUSIONS
  Gene expression may distinguish between PP and PN CSCC. Understanding these gene patterns may potentiate more timely diagnosis of perineural invasion and guide comprehensive therapies.
authors.affiliation: Department of Otolaryngology, Wake Forest University School of Medicine, Winston Salem, NC, U.S.A. ashleycmays@gmail.com.
authors.forename: Ashley C
authors.initials: AC
authors.lastname: Mays
authors.affiliation: Center for Public Health Genomics, Department of Biostatistical Sciences, Comprehensive Cancer Center of Wake Forest Baptist Health, Winston Salem, NC, U.S.A.
authors.forename: Jeff
authors.initials: J
authors.lastname: Chou
authors.affiliation: Comprehensive Cancer Center of Wake Forest Baptist Health, Winston Salem, NC, U.S.A.
authors.forename: Ann L
authors.initials: AL
authors.lastname: Craddock
authors.affiliation: Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Health, Winston Salem, NC, U.S.A.
authors.forename: Lance
authors.initials: L
authors.lastname: Miller
authors.affiliation: Department of Otolaryngology, Wake Forest University School of Medicine, Winston Salem, NC, U.S.A.
authors.forename: James D
authors.initials: JD
authors.lastname: Browne
mesh_terms: D001499:Bayes Theorem; D014408:Biomarkers, Tumor / Q000096:biosynthesis / Q000235:genetics; D004847:Epithelial Cells / Q000473:pathology; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D009361:Neoplasm Invasiveness / Q000235:genetics / Q000473:pathology; D009363:Neoplasm Proteins / Q000096:biosynthesis* / Q000235:genetics; D018307:Neoplasms, Squamous Cell / Q000150:complications / Q000235:genetics* / Q000473:pathology; D018317:Nerve Sheath Neoplasms / Q000150:complications / Q000235:genetics* / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012878:Skin Neoplasms / Q000150:complications / Q000235:genetics* / Q000473:pathology; D060388:Support Vector Machine
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins
keywords: Squamous cell skin cancer; genetic markers; molecular markers; perineural invasion