title: Shifted termination assay (STA) fragment analysis to detect BRAF V600 mutations in papillary thyroid carcinomas.
abstract: BACKGROUND
  BRAF mutation is an important diagnostic and prognostic marker in patients with papillary thyroid carcinoma (PTC). To be applicable in clinical laboratories with limited equipment, diverse testing methods are required to detect BRAF mutation.
  
  
  METHODS
  A shifted termination assay (STA) fragment analysis was used to detect common V600 BRAF mutations in 159 PTCs with DNAs extracted from formalin-fixed paraffin-embedded tumor tissue. The results of STA fragment analysis were compared to those of direct sequencing. Serial dilutions of BRAF mutant cell line (SNU-790) were used to calculate limit of detection (LOD).
  
  
  RESULTS
  BRAF mutations were detected in 119 (74.8%) PTCs by STA fragment analysis. In direct sequencing, BRAF mutations were observed in 118 (74.2%) cases. The results of STA fragment analysis had high correlation with those of direct sequencing (p < 0.00001, κ = 0.98). The LOD of STA fragment analysis and direct sequencing was 6% and 12.5%, respectively. In PTCs with pT3/T4 stages, BRAF mutation was observed in 83.8% of cases. In pT1/T2 carcinomas, BRAF mutation was detected in 65.9% and this difference was statistically significant (p = 0.007). Moreover, BRAF mutation was more frequent in PTCs with extrathyroidal invasion than tumors without extrathyroidal invasion (84.7% versus 62.2%, p = 0.001). To prepare and run the reactions, direct sequencing required 450 minutes while STA fragment analysis needed 290 minutes.
  
  
  CONCLUSIONS
  STA fragment analysis is a simple and sensitive method to detect BRAF V600 mutations in formalin-fixed paraffin-embedded clinical samples.
  The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5684057089135749.
authors.forename: So Young
authors.initials: SY
authors.lastname: Kang
authors.forename: Soomin
authors.initials: S
authors.lastname: Ahn
authors.forename: Sun-Mi
authors.initials: SM
authors.lastname: Lee
authors.forename: Ji Yun
authors.initials: JY
authors.lastname: Jeong
authors.forename: Ji-Youn
authors.initials: JY
authors.lastname: Sung
authors.forename: Young Lyun
authors.initials: YL
authors.lastname: Oh
authors.forename: Kyoung-Mee
authors.initials: KM
authors.lastname: Kim
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D002277:Carcinoma / Q000201:enzymology / Q000235:genetics* / Q000473:pathology; D002291:Carcinoma, Papillary; D002460:Cell Line; D004252:DNA Mutational Analysis / Q000379:methods*; D005260:Female; D005404:Fixatives; D005557:Formaldehyde; D020022:Genetic Predisposition to Disease; D006801:Humans; D057230:Limit of Detection; D008297:Male; D008875:Middle Aged; D009154:Mutation; D016612:Paraffin Embedding; D010641:Phenotype; D011237:Predictive Value of Tests; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics*; D000077273:Thyroid Cancer, Papillary; D013964:Thyroid Neoplasms / Q000201:enzymology / Q000235:genetics* / Q000473:pathology; D016707:Tissue Fixation / Q000379:methods; D055815:Young Adult
chemical_list: D005404:Fixatives; D005557:Formaldehyde; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf