title: Gene profiling of clinical routine biopsies and prediction of survival in non-small cell lung cancer.
abstract: BACKGROUND
  Global gene expression analysis provides a comprehensive molecular characterization of non-small cell lung cancer (NSCLC).
  
  
  OBJECTIVE
  To evaluate the feasibility of integrating expression profiling into routine clinical work-up by including both surgical and minute bronchoscopic biopsies and to develop a robust prognostic gene expression signature.
  
  
  METHODS
  Tissue samples from 41 chemotherapy-naive patients with NSCLC and 15 control patients with inflammatory lung diseases were obtained during routine clinical work-up and gene expression profiles were gained using an oligonucleotide array platform (NovaChip; 34'207 transcripts). Gene expression signatures were analyzed for correlation with histological and clinical parameters and validated on independent published data sets and immunohistochemistry.
  
  
  RESULTS
  Diagnostic signatures for adenocarcinoma and squamous cell carcinoma reached a sensitivity of 80%/80% and a specificity of 83%/94%, respectively, dependent on the proportion of tumor cells. Sixty-seven of the 100 most discriminating genes were validated with independent observations from the literature. A 13-gene metagene refined on four external data sets was built and validated on an independent data set. The metagene was a strong predictor of survival in our data set (hazard ratio = 7.7, 95% CI [2.8-21.2]) and in the independent data set (hazard ratio = 1.6, 95% CI [1.2-2.2]) and in both cases independent of the International Union against Cancer staging. Vascular endothelial growth factor-beta, one of the key prognostic genes, was further validated by immunohistochemistry on 508 independent tumor samples.
  
  
  CONCLUSIONS
  Integration of functional genomics from small bronchoscopic biopsies allows molecular tumor classification and prediction of survival in NSCLC and might become a powerful adjunct for the daily clinical practice.
authors.affiliation: Pneumologie, Kantonsspital St. Gallen, CH-9007 St. Gallen, Switzerland.
authors.forename: Florent
authors.initials: F
authors.lastname: Baty
authors.forename: Michaël
authors.initials: M
authors.lastname: Facompré
authors.forename: Sergio
authors.initials: S
authors.lastname: Kaiser
authors.forename: Martin
authors.initials: M
authors.lastname: Schumacher
authors.forename: Miklos
authors.initials: M
authors.lastname: Pless
authors.forename: Lukas
authors.initials: L
authors.lastname: Bubendorf
authors.forename: Spasenija
authors.initials: S
authors.lastname: Savic
authors.forename: Estelle
authors.initials: E
authors.lastname: Marrer
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Budach
authors.forename: Martin
authors.initials: M
authors.lastname: Buess
authors.forename: Jeanne
authors.initials: J
authors.lastname: Kehren
authors.forename: Michael
authors.initials: M
authors.lastname: Tamm
authors.forename: Martin H
authors.initials: MH
authors.lastname: Brutsche
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001706:Biopsy; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000401:mortality / Q000473:pathology* / Q000601:surgery; D005240:Feasibility Studies; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D053208:Kaplan-Meier Estimate; D008168:Lung / Q000473:pathology*; D008175:Lung Neoplasms / Q000235:genetics* / Q000401:mortality / Q000473:pathology* / Q000601:surgery; D008297:Male; D056186:Metagenomics; D008875:Middle Aged; D009367:Neoplasm Staging; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D011237:Predictive Value of Tests; D011379:Prognosis; D016016:Proportional Hazards Models; D016019:Survival Analysis; D042561:Vascular Endothelial Growth Factor B / Q000235:genetics
chemical_list: C467485:VEGFB protein, human; D042561:Vascular Endothelial Growth Factor B