title: Multiplatform comparison of molecular oncology tests performed on cytology specimens and formalin-fixed, paraffin-embedded tissue.
abstract: BACKGROUND
  Molecular oncology testing is important for patient management, and requests for the molecular analysis of cytology specimens are increasingly being made. Formalin-fixed, paraffin-embedded (FFPE) cell blocks of such specimens have been routinely used for molecular diagnosis. However, the inability to assess cellularity before cell block preparation is a pitfall of their use. In this study, various cytologic preparations were tested with several molecular test platforms, and the results were compared with paired FFPE tissue.
  
  
  METHODS
  Seventy-seven cytology cases, including fine-needle aspiration smears, touch preparations, and SurePath thin-layer preparations, were selected from the archives. Areas of interest were removed from the slide with a matrix capture solution. DNA extracted from the cells was evaluated by mutation analysis for BRAF, epidermal growth factor receptor (EGFR), RAS, and a 50-gene panel with various testing platforms (single-nucleotide primer extension assay, Sanger sequencing, and next-generation sequencing). Thirty-eight tumors with available FFPE tissue were tested in parallel.
  
  
  RESULTS
  The average DNA concentration was 299 ng/µL for the cytology specimens and 171 ng/µg for the paired FFPE tissue. Point mutations and large deletions were detected in BRAF, KRAS, NRAS, HRAS, and EGFR genes. In comparison with FFPE tissue, 5- to 8-fold less input DNA was needed when cytology preparations were used. The concordance between cytology specimens and FFPE tissue was 100%.
  
  
  CONCLUSIONS
  Cytologic preparations were found to be a reliable source for molecular oncology testing. DNA derived from cytology specimens performed well on multiple platforms, and 100% concordance was observed between cytology specimens and FFPE tissue.
authors.affiliation: Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Gailey
authors.forename: Aaron A
authors.initials: AA
authors.lastname: Stence
authors.forename: Chris S
authors.initials: CS
authors.lastname: Jensen
authors.forename: Deqin
authors.initials: D
authors.lastname: Ma
mesh_terms: D003581:Cytodiagnosis; D066246:ErbB Receptors / Q000235:genetics; D020558:GTP Phosphohydrolases / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008565:Membrane Proteins / Q000235:genetics; D053842:Microsatellite Instability; D009154:Mutation; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics* / Q000473:pathology; D016612:Paraffin Embedding; D011518:Proto-Oncogene Proteins / Q000235:genetics; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D016283:Proto-Oncogene Proteins p21(ras); D018631:ras Proteins / Q000235:genetics
chemical_list: C117307:KRAS protein, human; D008565:Membrane Proteins; D011518:Proto-Oncogene Proteins; D066246:ErbB Receptors; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf; D020558:GTP Phosphohydrolases; C579846:NRAS protein, human; D016283:Proto-Oncogene Proteins p21(ras); D018631:ras Proteins
keywords: DNA extraction; Sanger sequencing; fine-needle aspirate; molecular oncology test; next-generation sequencing; single-nucleotide primer extension assay