title: DNA hypermethylation analysis in sputum for the diagnosis of lung cancer: training validation set approach.
abstract: BACKGROUND
  Lung cancer has the highest mortality of all cancers. The aim of this study was to examine DNA hypermethylation in sputum and validate its diagnostic accuracy for lung cancer.
  
  
  METHODS
  DNA hypermethylation of RASSF1A, APC, cytoglobin, 3OST2, PRDM14, FAM19A4 and PHACTR3 was analysed in sputum samples from symptomatic lung cancer patients and controls (learning set: 73 cases, 86 controls; validation set: 159 cases, 154 controls) by quantitative methylation-specific PCR. Three statistical models were used: (i) cutoff based on Youden's J index, (ii) cutoff based on fixed specificity per marker of 96% and (iii) risk classification of post-test probabilities.
  
  
  RESULTS
  In the learning set, approach (i) showed that RASSF1A was best able to distinguish cases from controls (sensitivity 42.5%, specificity 96.5%). RASSF1A, 3OST2 and PRDM14 combined demonstrated a sensitivity of 82.2% with a specificity of 66.3%. Approach (ii) yielded a combination rule of RASSF1A, 3OST2 and PHACTR3 (sensitivity 67.1%, specificity 89.5%). The risk model (approach iii) distributed the cases over all risk categories. All methods displayed similar and consistent results in the validation set.
  
  
  CONCLUSIONS
  Our findings underscore the impact of DNA methylation markers in symptomatic lung cancer diagnosis. RASSF1A is validated as diagnostic marker in lung cancer.
authors.affiliation: Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands.
authors.forename: A J
authors.initials: AJ
authors.lastname: Hubers
authors.affiliation: Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands.
authors.forename: D A M
authors.initials: DA
authors.lastname: Heideman
authors.affiliation: Department of Thoracic Oncology, NKI-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
authors.forename: S A
authors.initials: SA
authors.lastname: Burgers
authors.affiliation: Department of Pulmonary Diseases, Sint Antonius Hospital, Nieuwegein, The Netherlands.
authors.forename: G J M
authors.initials: GJ
authors.lastname: Herder
authors.affiliation: Department of Pulmonary Diseases, Academic Medical Center, Amsterdam, The Netherlands.
authors.forename: P J
authors.initials: PJ
authors.lastname: Sterk
authors.affiliation: Department of Pulmonary Diseases, Academic Medical Center, Amsterdam, The Netherlands.
authors.forename: R J
authors.initials: RJ
authors.lastname: Rhodius
authors.affiliation: Department of Pulmonary Diseases, Sint Lucas Andreas Hospital, Amsterdam, The Netherlands.
authors.forename: H J
authors.initials: HJ
authors.lastname: Smit
authors.affiliation: Department of Pulmonary Diseases, Spaarne Hospital, Hoofddorp, The Netherlands.
authors.forename: F
authors.initials: F
authors.lastname: Krouwels
authors.affiliation: Department of Pulmonary Diseases, Medisch Centrum Alkmaar, Alkmaar, The Netherlands.
authors.forename: A
authors.initials: A
authors.lastname: Welling
authors.affiliation: Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands.
authors.forename: B I
authors.initials: BI
authors.lastname: Witte
authors.affiliation: Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands.
authors.forename: S
authors.initials: S
authors.lastname: Duin
authors.affiliation: Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands.
authors.forename: R
authors.initials: R
authors.lastname: Koning
authors.affiliation: Department of Nuclear Medicine, VU University Medical Center, Amsterdam, The Netherlands.
authors.forename: E F I
authors.initials: EF
authors.lastname: Comans
authors.affiliation: Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands.
authors.forename: R D M
authors.initials: RD
authors.lastname: Steenbergen
authors.affiliation: Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands.
authors.forename: P E
authors.initials: PE
authors.lastname: Postmus
authors.affiliation: Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands.
authors.forename: G A
authors.initials: GA
authors.lastname: Meijer
authors.affiliation: Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands.
authors.forename: P J F
authors.initials: PJ
authors.lastname: Snijders
authors.affiliation: Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands.
authors.forename: E F
authors.initials: EF
authors.lastname: Smit
authors.affiliation: Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands.
authors.forename: E
authors.initials: E
authors.lastname: Thunnissen
mesh_terms: D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics; D016022:Case-Control Studies; D019175:DNA Methylation; D005260:Female; D006801:Humans; D008175:Lung Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013183:Sputum / Q000737:chemistry
chemical_list: D014408:Biomarkers, Tumor