title: Using "residual" FNA rinse and body fluid specimens for next-generation sequencing: An institutional experience.
abstract: BACKGROUND
  Tissue specimens are typically considered optimal for molecular testing; however, in the current era of personalized medicine, cytopathology specimens are increasingly recognized as potential sources for molecular testing. This is often accomplished by using cell block specimens and/or fine-needle aspiration (FNA) smear preparations. In this study, the authors investigated the feasibility, performance, and quality of "residual" FNA rinse and body effusion fluids used for next-generation sequencing (NGS).
  
  
  METHODS
  Sequence data were generated from 17 malignancies in 16 patients from 13 FNA (10 lymph nodes, 1 lung, and 2 bone lesions) and 4 effusion (3 pleural and 1 pericardial) specimens. Malignancies included carcinomas (lung, breast, ovarian, and unknown primary), melanoma, and myeloma. Paired NGS testing was performed in 7 patients who had surgical biopsy or cell block specimens available. Routinely processed residual FNA rinse material and body fluids were used for DNA extraction and NGS (targeted gene panel).
  
  
  RESULTS
  NGS was successfully performed on all 17 specimens. A significant amount of DNA was obtained from the residual FNA rinse (176.3 ng/μL) compared with the paired cell block slides (10.6 ng/μL). Two of the 10 lung adenocarcinomas (20%) demonstrated epidermal growth factor receptor (EGFR) mutations, including 1 leucine-to-arginine substitution at codon 858 (L858R) in exon 21 and 1 codon 2235_2249 deletion (resulting in an in-frame deletion of 5 amino acids from position 746 to 750 [glutamic acid, leucine, arginine, glutamic acid, and alanine]; E746_A750del) in exon 19. Three KRAS [Kirsten rat sarcoma viral oncogene homolog] mutations, 1 BRAF (v-Raf murine sarcoma viral oncogene homolog B1) mutation, and 1 NRAS (neuroblastoma RAS viral oncogene homolog) mutation were identified in the remaining lung adenocarcinomas. Patients who underwent paired testing demonstrated 100% concordant mutations.
  
  
  CONCLUSIONS
  Targeted NGS can be performed on residual FNA rinse and body fluid specimens. This approach is particularly important when a paucicellular cell block or biopsy specimen is encountered. Cancer Cytopathol 2016;124:324-29. © 2015 American Cancer Society.
authors.affiliation: Department of Pathology and Laboratory Medicine, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania.
authors.forename: Shuanzeng
authors.initials: S
authors.lastname: Wei
authors.affiliation: Department of Pathology and Laboratory Medicine, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania.
authors.forename: David
authors.initials: D
authors.lastname: Lieberman
authors.affiliation: Department of Pathology and Laboratory Medicine, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania.
authors.forename: Jennifer J D
authors.initials: JJ
authors.lastname: Morrissette
authors.affiliation: Department of Pathology and Laboratory Medicine, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania.
authors.forename: Zubair W
authors.initials: ZW
authors.lastname: Baloch
authors.affiliation: Department of Pathology and Laboratory Medicine, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania.
authors.forename: David B
authors.initials: DB
authors.lastname: Roth
authors.affiliation: Department of Pathology and Laboratory Medicine, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania.
authors.forename: Cindy
authors.initials: C
authors.lastname: McGrath
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D044963:Biopsy, Fine-Needle / Q000379:methods*; D001826:Body Fluids / Q000737:chemistry / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009154:Mutation / Q000235:genetics; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor
keywords: cytopathology; fine-needle aspiration (FNA); next-generation sequencing (NGS); personalized medicine