Test feasibility of next-generation sequencing assays in clinical mutation detection of small biopsy and fine needle aspiration specimens

Gang Zheng, Harrison Tsai, Li Hui Tseng, Peter B Illei, Christopher Gocke, James Eshleman, George Netto, Ming-Tseh Lin

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)696-702
Number of pages7
JournalAmerican Journal of Clinical Pathology
Volume145
Issue number5
DOIs
StatePublished - May 1 2016

Fingerprint

Fine Needle Biopsy
Mutation
INDEL Mutation
Bone and Bones
Neoplasms
Paraffin
Formaldehyde
Colorectal Neoplasms
Melanoma
Lung Neoplasms
Nucleotides
Biopsy

Keywords

  • Biopsy
  • Fine needle aspiration
  • Mutation detection
  • Next-generation sequencing
  • Quality assessment

ASJC Scopus subject areas

  • Medicine(all)

Cite this

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title = "Test feasibility of next-generation sequencing assays in clinical mutation detection of small biopsy and fine needle aspiration specimens",
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.",
keywords = "Biopsy, Fine needle aspiration, Mutation detection, Next-generation sequencing, Quality assessment",
author = "Gang Zheng and Harrison Tsai and Tseng, {Li Hui} and Illei, {Peter B} and Christopher Gocke and James Eshleman and George Netto and Ming-Tseh Lin",
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T1 - Test feasibility of next-generation sequencing assays in clinical mutation detection of small biopsy and fine needle aspiration specimens

AU - Zheng, Gang

AU - Tsai, Harrison

AU - Tseng, Li Hui

AU - Illei, Peter B

AU - Gocke, Christopher

AU - Eshleman, James

AU - Netto, George

AU - Lin, Ming-Tseh

PY - 2016/5/1

Y1 - 2016/5/1

N2 - 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.

AB - 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.

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