title: DNA methylation analysis for the diagnosis of thyroid nodules - a pilot study with reference to BRAF(V) (600E) mutation and cytopathology results.
abstract: OBJECTIVE
  Promoter hypermethylation and the BRAF(V) (600E) mutation are both involved in thyroid tumorigenesis. We conducted a pilot study on the diagnosis of thyroid nodules by analysis of promoter hypermethylation status with reference to BRAF(V) (600E) mutation and cytopathology results using formalin-fixed, paraffin-embedded (FFPE) tissues and liquid-based preparation (LBP) thyroid fine needle aspiration (FNA) samples to predict more reliably the possibility of papillary carcinoma.
  
  
  METHODS
  We initially performed MethyLight analysis for 30 genes that are known to be hypermethylated in malignancies using 164 papillary carcinomas and 77 benign tissue samples. Five genes selected from the tissue analysis were subsequently analysed in 75 surgically proven benign and 66 surgically proven papillary carcinoma LBP FNA samples. Samples that showed two or more positive results among the five genes were classified as methylation positive. We also analysed the BRAF(V) (600E) mutation status of the FNA samples.
  
  
  RESULTS
  We identified five genes that were significantly hypermethylated in malignant tissues: PTGS2, HOXA1, TMEFF2, p16 and PTEN. With respect to diagnostic potential, results obtained using the BRAF(V) (600E) mutation test combined with cytological examination were not significantly different from those obtained with cytological examination only. Combining methylation analyses with cytological examination or performing all three tests for diagnoses did not improve significantly the negative predictive values and sensitivity, but a significant decrease in positive predictive value and specificity was observed.
  
  
  CONCLUSIONS
  Further studies are needed on larger samples to assess the potential value of methylation analysis of thyroid FNA.
authors.affiliation: Department of Pathology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, South Korea.
authors.forename: H
authors.initials: H
authors.lastname: Chang
authors.affiliation: Department of Pathology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, South Korea.
authors.forename: B K
authors.initials: BK
authors.lastname: Shin
authors.affiliation: Department of Pathology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, South Korea.
authors.forename: A
authors.initials: A
authors.lastname: Kim
authors.affiliation: Department of Pathology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, South Korea.
authors.forename: H K
authors.initials: HK
authors.lastname: Kim
authors.affiliation: Department of Pathology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, South Korea.
authors.forename: B H
authors.initials: BH
authors.lastname: Kim
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D044963:Biopsy, Fine-Needle; D002291:Carcinoma, Papillary / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology; D019941:Cyclin-Dependent Kinase Inhibitor p16; D051546:Cyclooxygenase 2 / Q000235:genetics; D003581:Cytodiagnosis; D019175:DNA Methylation / Q000235:genetics*; D005260:Female; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D008297:Male; D008565:Membrane Proteins / Q000235:genetics; D008875:Middle Aged; D009154:Mutation; D009363:Neoplasm Proteins / Q000235:genetics; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology; D051059:PTEN Phosphohydrolase / Q000235:genetics; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics*; D013961:Thyroid Gland / Q000473:pathology; D016606:Thyroid Nodule / Q000175:diagnosis / Q000473:pathology; D014157:Transcription Factors / Q000235:genetics; D000099261:Homeobox A1 Protein
chemical_list: D019941:Cyclin-Dependent Kinase Inhibitor p16; D051546:Cyclooxygenase 2; D018398:Homeodomain Proteins; D008565:Membrane Proteins; D009363:Neoplasm Proteins; D051059:PTEN Phosphohydrolase; D048493:Proto-Oncogene Proteins B-raf; D014157:Transcription Factors; D000099261:Homeobox A1 Protein; C000614131:CDKN2A protein, human; C423567:TMEFF2 protein, human; C496540:PTGS2 protein, human; C482119:BRAF protein, human; C494929:PTEN protein, human
keywords: BRAF; liquid-based preparation; methylation; papillary carcinoma; thyroid