title: Accuracy of next-generation sequencing for the identification of clinically relevant variants in cytology smears in lung adenocarcinoma.
abstract: BACKGROUND
  Minimally invasive diagnostic procedures such as needle-core biopsy and fine-needle aspiration provide adequate material for molecular analyses. Advances in precision oncology are trending toward the interrogation of limited amounts of genomic material to guide clinical and therapeutic decisions. The aim of this study was to investigate the minimum cellularity needed on cytologic smears for the identification of clinically relevant variants with next-generation sequencing (NGS).
  
  
  METHODS
  Thirty cases of cytologically diagnosed, resection-proven primary lung adenocarcinoma were identified. Nineteen of the 30 cases were known to harbor actionable variants. One Diff-Quik (DQ)-stained slide and 1 Papanicolaou (Pap)-stained slide were selected from each case. Cases were categorized as containing fewer than 100 tumor cells, 100 to 500 tumor cells, or more than 500 tumor cells. NGS was performed on the Ion Torrent platform.
  
  
  RESULTS
  NGS was successfully performed on all cell blocks and on 90% of the smears. Paired DQ and Pap smears showed similar cellularity, and cases that differed in cellularity were within 1 category of each other. The cases with more than 100 tumor cells had a 93% success rate; this was significantly different from the situation for cases with fewer than 100 tumor cells, which were successfully sequenced only 67% of the time. Overall, NGS was able to provide clinically relevant information for 83% of DQ smears and for 90% of Pap smears tested.
  
  
  CONCLUSIONS
  The data show a significantly higher likelihood of successful NGS with cytologic smears with more than 100 tumor cells. There was a trend for a higher NGS success rate with Pap smears versus DQ smears. Cancer Cytopathol 2017;125:398-406. © 2017 American Cancer Society.
authors.affiliation: Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York.
authors.forename: Jordan E
authors.initials: JE
authors.lastname: Baum
authors.affiliation: Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York.
authors.forename: Pan
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York.
authors.forename: Rana S
authors.initials: RS
authors.lastname: Hoda
authors.affiliation: Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York.
authors.forename: Brian
authors.initials: B
authors.lastname: Geraghty
authors.affiliation: Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York.
authors.forename: Hanna
authors.initials: H
authors.lastname: Rennert
authors.affiliation: Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York.
authors.forename: Navneet
authors.initials: N
authors.lastname: Narula
authors.affiliation: Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York.
authors.forename: Helen D
authors.identifier: http://orcid.org/0000-0003-4548-1904
authors.initials: HD
authors.lastname: Fernandes
mesh_terms: D000091162:AMP-Activated Protein Kinase Kinases; D000230:Adenocarcinoma / Q000235:genetics* / Q000473:pathology; D000077192:Adenocarcinoma of Lung; D025601:Adenomatous Polyposis Coli Protein / Q000235:genetics; D000368:Aged; D000369:Aged, 80 and over; D001399:Azure Stains; D044963:Biopsy, Fine-Needle; D019941:Cyclin-Dependent Kinase Inhibitor p16; D050763:Cyclin-Dependent Kinase Inhibitor p18 / Q000235:genetics; D003584:Cytological Techniques; D066246:ErbB Receptors / Q000235:genetics; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology; D008297:Male; D008751:Methylene Blue; D008875:Middle Aged; D009367:Neoplasm Staging; D065006:Papanicolaou Test; D017346:Protein Serine-Threonine Kinases / Q000235:genetics; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D016283:Proto-Oncogene Proteins p21(ras) / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D016159:Tumor Suppressor Protein p53 / Q000235:genetics; D014966:Xanthenes; D051176:beta Catenin / Q000235:genetics
chemical_list: C555337:APC protein, human; D025601:Adenomatous Polyposis Coli Protein; D001399:Azure Stains; C000614131:CDKN2A protein, human; C495270:CTNNB1 protein, human; D019941:Cyclin-Dependent Kinase Inhibitor p16; D050763:Cyclin-Dependent Kinase Inhibitor p18; C067461:Diff Quik; C117307:KRAS protein, human; C495901:TP53 protein, human; D016159:Tumor Suppressor Protein p53; D014966:Xanthenes; D051176:beta Catenin; C512478:EGFR protein, human; D066246:ErbB Receptors; C482119:BRAF protein, human; D017346:Protein Serine-Threonine Kinases; D048493:Proto-Oncogene Proteins B-raf; C109790:STK11 protein, human; D000091162:AMP-Activated Protein Kinase Kinases; D016283:Proto-Oncogene Proteins p21(ras); D008751:Methylene Blue
keywords: cytologic smears; fine-needle aspiration; lung adenocarcinoma; molecular; next-generation sequencing