title: Test Feasibility of Next-Generation Sequencing Assays in Clinical Mutation Detection of Small Biopsy and Fine Needle Aspiration Specimens.
abstract: OBJECTIVE
  To evaluate preanalytic factors contributing to failure of next-generation sequencing (NGS) assays.
  
  
  METHODS
  AmpliSeq Cancer Hotspot Panel was conducted in 1,121 of 1,152 formalin-fixed paraffin-embedded tissues submitted to a clinical laboratory, including 493 small biopsy or fine needle aspiration (FNA) specimens (44%) and 25 metastatic bone specimens (2.2%).
  
  
  RESULTS
  Single nucleotide mutations and/or insertion/deletion mutations were detected in 702 specimens. Thirty-eight specimens (3.4%) were reported as "no results" due to NGS assay failure. Higher failure rates were observed in specimens submitted for lung cancer panel and melanoma panel (3.1% and 3.7% vs 1.0% colorectal cancer panel), metastatic bone specimens (36% vs 2.6% nonbone specimens), referred specimens (5.0% vs 1.8% in-house specimens), and small biopsy and FNA specimens (5.8% and 3.1% vs 0.7% resection/excision specimens). Test feasibility was higher in in-house specimens than referred specimens (99.1% vs 96.9% in resection specimens, 94.4% vs 87.3% in small biopsy specimens, and 94.3% vs 58.8% in FNA specimens).
  
  
  CONCLUSIONS
  NGS assays demonstrated clinical utility in solid tumor specimens, including those taken by biopsy or FNA. Preanalytic factors identified by this study that may contribute to NGS assay failure highlight the need for pathologists to revisit tissue processing protocols in order to better optimize cancer mutational profiling.
authors.affiliation: From the Departments of Pathology and.
authors.forename: Gang
authors.initials: G
authors.lastname: Zheng
authors.affiliation: From the Departments of Pathology and.
authors.forename: Harrison
authors.initials: H
authors.lastname: Tsai
authors.affiliation: From the Departments of Pathology and Department of Medical Genetics, National Taiwan University Hospital, Taipei.
authors.forename: Li-Hui
authors.initials: LH
authors.lastname: Tseng
authors.affiliation: From the Departments of Pathology and.
authors.forename: Peter
authors.initials: P
authors.lastname: Illei
authors.affiliation: From the Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Gocke
authors.affiliation: From the Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD.
authors.forename: James R
authors.initials: JR
authors.lastname: Eshleman
authors.affiliation: From the Departments of Pathology and.
authors.forename: George
authors.initials: G
authors.lastname: Netto
authors.affiliation: From the Departments of Pathology and mlin36@jhmi.edu.
authors.forename: Ming-Tseh
authors.initials: MT
authors.lastname: Lin
mesh_terms: D001706:Biopsy; D044963:Biopsy, Fine-Needle; D004252:DNA Mutational Analysis / Q000379:methods*; D005240:Feasibility Studies; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D012189:Retrospective Studies
keywords: Biopsy; Fine needle aspiration; Mutation detection; Next-generation sequencing; Quality assessment