Test feasibility of next-generation sequencing assays in clinical mutation detection of small biopsy and fine needle aspiration specimens
Journal
American Journal of Clinical Pathology
Journal Volume
145
Journal Issue
5
Pages
696-702
Date Issued
2016
Author(s)
Abstract
Objectives: 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. Thirtyeight 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. ? American Society for Clinical Pathology, 2016. All rights reserved.
Subjects
Biopsy; Fine needle aspiration; Mutation detection; Next-generation sequencing; Quality assessment
SDGs
Other Subjects
B Raf kinase; epidermal growth factor receptor 2; K ras protein; n ras protein; PIK3CA protein; protein; protein kinase B; stem cell factor; unclassified drug; vasculotropin receptor; Article; bone metastasis; clinical laboratory; colorectal cancer; controlled study; core biopsy; endoscopic biopsy; fine needle aspiration biopsy; gastrointestinal stromal tumor; gene mutation; human; human tissue; indel mutation; intermethod comparison; lung cancer; melanoma; mutational analysis; next generation sequencing; priority journal; punch biopsy; retrospective study; shave biopsy; single nucleotide polymorphism; small biopsy; tumor biopsy; biopsy; dna mutational analysis; feasibility study; fine needle aspiration biopsy; genetics; high throughput sequencing; neoplasm; procedures; Biopsy; Biopsy, Fine-Needle; DNA Mutational Analysis; Feasibility Studies; High-Throughput Nucleotide Sequencing; Humans; Neoplasms; Retrospective Studies
Publisher
American Society of Clinical Pathologists
Type
journal article