title: Does addition of BRAF V600E mutation testing modify sensitivity or specificity of the Afirma Gene Expression Classifier in cytologically indeterminate thyroid nodules?
abstract: OBJECTIVE
  The purpose of this study was to determine the frequency of BRAF mutation in cytologically indeterminate thyroid nodules and to investigate whether adding the BRAF test improves diagnostic accuracy of the Afirma Gene Expression Classifier (GEC).
  
  
  METHODS
  BRAF V600E mutational status was determined for DNA extracted from cytologically benign (n = 40), indeterminate (n = 208), and malignant (n = 48) fine-needle aspiration specimens previously categorized by GEC as molecularly Benign or Suspicious. Analytical performance of the BRAF assay was assessed to establish reproducibility and limits of detection. Molecular testing results were correlated with blinded expert histopathological diagnoses.
  
  
  RESULTS
  The BRAF assay detected mutations reproducibly to 2.5% mutant allele frequency. The prevalence of BRAF mutations in cytologically benign specimens was 2 of 40 (5.0%, 95% confidence interval [CI], 0-16) and in cytologically malignant specimens was 36 of 48 (75.0%, 95% CI, 60-86). In the cytologically indeterminate category, 10.1% of specimens were BRAF+: 2 of 95 were subcategorized as atypia of undetermined significance or follicular lesion of undetermined significance (2.1%, 95% CI, 0-7); 1 of 70 as follicular neoplasm or suspicious for follicular neoplasm (1.4%, 95% CI, 0-9); and 18 of 43 as suspicious for malignancy (41.9%, 95% CI, 27-58). All BRAF+ specimens were classified as Suspicious by the GEC.
  
  
  CONCLUSIONS
  BRAF mutations are uncommon in nodules with atypia of undetermined significance or follicular lesion of undetermined significance or follicular neoplasm or suspicious for follicular neoplasm cytology. Most cytologically indeterminate nodules that proved to be malignant were also BRAF-, and all nodules that were false-negative by GEC were also BRAF-. Similarly, all BRAF+ specimens were also GEC Suspicious. Neither GEC test sensitivity nor specificity was improved by addition of BRAF mutation testing.
authors.affiliation: Veracyte, Inc, South San Francisco, CA 94080, USA.
authors.forename: Richard T
authors.initials: RT
authors.lastname: Kloos
authors.forename: Jessica D
authors.initials: JD
authors.lastname: Reynolds
authors.forename: P Sean
authors.initials: PS
authors.lastname: Walsh
authors.forename: Jonathan I
authors.initials: JI
authors.lastname: Wilde
authors.forename: Edward Y
authors.initials: EY
authors.lastname: Tom
authors.forename: Moraima
authors.initials: M
authors.lastname: Pagan
authors.forename: Catalin
authors.initials: C
authors.lastname: Barbacioru
authors.forename: Darya I
authors.initials: DI
authors.lastname: Chudova
authors.forename: Mei
authors.initials: M
authors.lastname: Wong
authors.forename: Lyssa
authors.initials: L
authors.lastname: Friedman
authors.forename: Virginia A
authors.initials: VA
authors.lastname: LiVolsi
authors.forename: Juan
authors.initials: J
authors.lastname: Rosai
authors.forename: Richard B
authors.initials: RB
authors.lastname: Lanman
authors.forename: Giulia C
authors.initials: GC
authors.lastname: Kennedy
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics / Q000502:physiology; D044963:Biopsy, Fine-Needle; D003584:Cytological Techniques; D004252:DNA Mutational Analysis; D003937:Diagnosis, Differential; D020869:Gene Expression Profiling / Q000145:classification; D005820:Genetic Testing / Q000379:methods*; D018698:Glutamic Acid / Q000235:genetics; D019073:HT29 Cells; D006801:Humans; D020125:Mutation, Missense / Q000502:physiology*; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics* / Q000502:physiology; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016606:Thyroid Nodule / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology; D014633:Valine / Q000235:genetics
chemical_list: D018698:Glutamic Acid; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf; D014633:Valine