Clinical mutational profiling of bone metastases of lung and colon carcinoma and malignant melanoma using next-generation sequencing

Research output: Contribution to journalArticle

Abstract

BACKGROUND: Bone is a common metastatic site for solid tumors and is often the only source for molecular testing. Current routine decalcification protocols for the processing of bone specimens damage nucleic acids, leading to a high failure rate. METHODS: In this retrospective quality-assessment analysis, preanalytic factors that contributed to the failure of mutational profiling in metastatic bone specimens were evaluated using a next-generation sequencing assay. RESULTS: Mutational profiling was conducted in 33 formalin-fixed, paraffin-embedded bone lesions that were submitted to a clinical laboratory. Adequate depth of coverage was obtained in 21 specimens, of which, 16 had mutations detected. “No results” were reported in 12 specimens because the NGS assay failed. There was a significantly higher failure rate in bone specimens compared with nonbone specimens (36% vs 2.3%, respectively). Although nonbone specimens had a higher failure rate in biopsy/fine-needle aspiration (FNA) specimens, in-house bone biopsy/FNA specimens with or without short-duration surface decalcification had a lower failure rate than resected bone specimens (11% vs 60%, respectively). The high failure rate in resected metastatic bone specimens was associated with regular decalcification but not with low DNA input. CONCLUSIONS: Next-generation sequencing assays demonstrated clinical utility in metastatic bone specimens. FNA (smear and cell block) and core-biopsy specimens provided adequate resources of nucleic acids for molecular profiling of metastatic bone lesions. The current findings suggest the need for developing specific tissue procurement and processing protocols for bone metastases and greater use of small biopsy and FNA specimens. Cancer Cytopathol 2016;124:744–53.

Original languageEnglish (US)
Pages (from-to)744-753
Number of pages10
JournalCancer cytopathology
Volume124
Issue number10
DOIs
StatePublished - Oct 1 2016

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Melanoma
Colon
Neoplasm Metastasis
Carcinoma
Bone and Bones
Lung
Fine Needle Biopsy
Nucleic Acids
Tissue and Organ Procurement
Paraffin
Formaldehyde
Statistical Factor Analysis
Neoplasms
Biopsy
Mutation
DNA

Keywords

  • bone metastasis
  • core biopsy
  • decalcification
  • fine-needle aspiration
  • mutation detection
  • next-generation sequencing

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

@article{84aaa9cfdd9947b7ad5f6770ee11c37a,
title = "Clinical mutational profiling of bone metastases of lung and colon carcinoma and malignant melanoma using next-generation sequencing",
abstract = "BACKGROUND: Bone is a common metastatic site for solid tumors and is often the only source for molecular testing. Current routine decalcification protocols for the processing of bone specimens damage nucleic acids, leading to a high failure rate. METHODS: In this retrospective quality-assessment analysis, preanalytic factors that contributed to the failure of mutational profiling in metastatic bone specimens were evaluated using a next-generation sequencing assay. RESULTS: Mutational profiling was conducted in 33 formalin-fixed, paraffin-embedded bone lesions that were submitted to a clinical laboratory. Adequate depth of coverage was obtained in 21 specimens, of which, 16 had mutations detected. “No results” were reported in 12 specimens because the NGS assay failed. There was a significantly higher failure rate in bone specimens compared with nonbone specimens (36{\%} vs 2.3{\%}, respectively). Although nonbone specimens had a higher failure rate in biopsy/fine-needle aspiration (FNA) specimens, in-house bone biopsy/FNA specimens with or without short-duration surface decalcification had a lower failure rate than resected bone specimens (11{\%} vs 60{\%}, respectively). The high failure rate in resected metastatic bone specimens was associated with regular decalcification but not with low DNA input. CONCLUSIONS: Next-generation sequencing assays demonstrated clinical utility in metastatic bone specimens. FNA (smear and cell block) and core-biopsy specimens provided adequate resources of nucleic acids for molecular profiling of metastatic bone lesions. The current findings suggest the need for developing specific tissue procurement and processing protocols for bone metastases and greater use of small biopsy and FNA specimens. Cancer Cytopathol 2016;124:744–53.",
keywords = "bone metastasis, core biopsy, decalcification, fine-needle aspiration, mutation detection, next-generation sequencing",
author = "Gang Zheng and Ming-Tseh Lin and Parvez Lokhandwala and Katie Beierl and Netto, {George J.} and Christopher Gocke and James Eshleman and McCarthy, {Edward F} and Illei, {Peter B}",
year = "2016",
month = "10",
day = "1",
doi = "10.1002/cncy.21743",
language = "English (US)",
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pages = "744--753",
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TY - JOUR

T1 - Clinical mutational profiling of bone metastases of lung and colon carcinoma and malignant melanoma using next-generation sequencing

AU - Zheng, Gang

AU - Lin, Ming-Tseh

AU - Lokhandwala, Parvez

AU - Beierl, Katie

AU - Netto, George J.

AU - Gocke, Christopher

AU - Eshleman, James

AU - McCarthy, Edward F

AU - Illei, Peter B

PY - 2016/10/1

Y1 - 2016/10/1

N2 - BACKGROUND: Bone is a common metastatic site for solid tumors and is often the only source for molecular testing. Current routine decalcification protocols for the processing of bone specimens damage nucleic acids, leading to a high failure rate. METHODS: In this retrospective quality-assessment analysis, preanalytic factors that contributed to the failure of mutational profiling in metastatic bone specimens were evaluated using a next-generation sequencing assay. RESULTS: Mutational profiling was conducted in 33 formalin-fixed, paraffin-embedded bone lesions that were submitted to a clinical laboratory. Adequate depth of coverage was obtained in 21 specimens, of which, 16 had mutations detected. “No results” were reported in 12 specimens because the NGS assay failed. There was a significantly higher failure rate in bone specimens compared with nonbone specimens (36% vs 2.3%, respectively). Although nonbone specimens had a higher failure rate in biopsy/fine-needle aspiration (FNA) specimens, in-house bone biopsy/FNA specimens with or without short-duration surface decalcification had a lower failure rate than resected bone specimens (11% vs 60%, respectively). The high failure rate in resected metastatic bone specimens was associated with regular decalcification but not with low DNA input. CONCLUSIONS: Next-generation sequencing assays demonstrated clinical utility in metastatic bone specimens. FNA (smear and cell block) and core-biopsy specimens provided adequate resources of nucleic acids for molecular profiling of metastatic bone lesions. The current findings suggest the need for developing specific tissue procurement and processing protocols for bone metastases and greater use of small biopsy and FNA specimens. Cancer Cytopathol 2016;124:744–53.

AB - BACKGROUND: Bone is a common metastatic site for solid tumors and is often the only source for molecular testing. Current routine decalcification protocols for the processing of bone specimens damage nucleic acids, leading to a high failure rate. METHODS: In this retrospective quality-assessment analysis, preanalytic factors that contributed to the failure of mutational profiling in metastatic bone specimens were evaluated using a next-generation sequencing assay. RESULTS: Mutational profiling was conducted in 33 formalin-fixed, paraffin-embedded bone lesions that were submitted to a clinical laboratory. Adequate depth of coverage was obtained in 21 specimens, of which, 16 had mutations detected. “No results” were reported in 12 specimens because the NGS assay failed. There was a significantly higher failure rate in bone specimens compared with nonbone specimens (36% vs 2.3%, respectively). Although nonbone specimens had a higher failure rate in biopsy/fine-needle aspiration (FNA) specimens, in-house bone biopsy/FNA specimens with or without short-duration surface decalcification had a lower failure rate than resected bone specimens (11% vs 60%, respectively). The high failure rate in resected metastatic bone specimens was associated with regular decalcification but not with low DNA input. CONCLUSIONS: Next-generation sequencing assays demonstrated clinical utility in metastatic bone specimens. FNA (smear and cell block) and core-biopsy specimens provided adequate resources of nucleic acids for molecular profiling of metastatic bone lesions. The current findings suggest the need for developing specific tissue procurement and processing protocols for bone metastases and greater use of small biopsy and FNA specimens. Cancer Cytopathol 2016;124:744–53.

KW - bone metastasis

KW - core biopsy

KW - decalcification

KW - fine-needle aspiration

KW - mutation detection

KW - next-generation sequencing

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DO - 10.1002/cncy.21743

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