Simultaneous detection of single-nucleotide variant, deletion/insertion, and fusion in lung and thyroid carcinoma using cytology specimen and an RNA-based next-generation sequencing assay

Natalya V Guseva; Omar Jaber; Aaron A Stence; Krishnaveni Sompallae; Amani Bashir; Ramakrishna Sompallae; Aaron D Bossler; Chris S Jensen; Deqin Ma

doi:10.1002/cncy.21963

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Simultaneous detection of single-nucleotide variant, deletion/insertion, and fusion in lung and thyroid carcinoma using cytology specimen and an RNA-based next-generation sequencing assay

Journal article

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Simultaneous detection of single-nucleotide variant, deletion/insertion, and fusion in lung and thyroid carcinoma using cytology specimen and an RNA-based next-generation sequencing assay

Natalya V Guseva, Omar Jaber, Aaron A Stence, Krishnaveni Sompallae, Amani Bashir, Ramakrishna Sompallae, Aaron D Bossler, Chris S Jensen and Deqin Ma

Cancer cytopathology, Vol.126(3), pp.158-169

03/2018

DOI: 10.1002/cncy.21963

PMID: 29364576

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Abstract

Molecular testing for epidermal growth factor receptor (EGFR) mutation and anaplastic lymphoma kinase (ALK) and ROS proto-oncogene 1, receptor tyrosine kinase (ROS1) fusion is routinely performed in patients with stage IV lung adenocarcinoma to assess their eligibility for targeted therapy. Fine-needle aspiration (FNA)-derived material frequently is the only pathologic material available. The identification of genomic aberrations in thyroid nodules from FNA smears may help stratify cancer risk and spare patients from a second surgery. In the current study, the authors tested nucleic acid extracted from the cytology smears of lung and thyroid carcinomas for simultaneous detection of single-nucleotide variant, insertion/deletion, and gene fusion using an RNA-based next-generation sequencing assay. A total of 27 cases (17 lung and 10 thyroid carcinomas, the majority of which had known variants) were tested. Areas of interest were scrapped from stained smears using a scalpel. Total nucleic acid was extracted. Gene fusion and mutational analysis was performed using the Comprehensive Thyroid and Lung FusionPlex Assay. Data were analyzed using the analysis pipeline provided by the vendor. Eleven cases with available formalin-fixed, paraffin-embedded (FFPE) tissue were tested in parallel. Gene fusions were detected in 6 cases; common single-nucleotide variants in EGFR, RAS, and BRAF in 14 cases; and in-frame deletions within EGFR in 3 cases. A concordance rate of 100% was observed between FNA and FFPE tissue. Cytology preparations can be a reliable source for the detection of both DNA and RNA aberrations. The ability to simultaneously detect multiple types of genomic variants is crucial for patients with advanced cancer and maximizes the usefulness of cytology specimens. Cancer Cytopathol 2018;126:158-69. © 2018 American Cancer Society.

Lung Neoplasms - genetics

Sequence Analysis, RNA - methods

Thyroid Neoplasms - genetics

Humans

RNA, Neoplasm - genetics

Gene Fusion

In Situ Hybridization, Fluorescence

Lung Neoplasms - pathology

Polymorphism, Single Nucleotide

Mutation

INDEL Mutation

Thyroid Neoplasms - pathology

Details

Title: Subtitle: Simultaneous detection of single-nucleotide variant, deletion/insertion, and fusion in lung and thyroid carcinoma using cytology specimen and an RNA-based next-generation sequencing assay
Creators: Natalya V Guseva - Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
Omar Jaber - Department of Pathology, King Hussein Cancer Center, Amman, Jordan
Aaron A Stence - Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
Krishnaveni Sompallae - Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
Amani Bashir - Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
Ramakrishna Sompallae - Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
Aaron D Bossler - Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
Chris S Jensen - Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
Deqin Ma - Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
Resource Type: Journal article
Publication Details: Cancer cytopathology, Vol.126(3), pp.158-169
DOI: 10.1002/cncy.21963
PMID: 29364576
NLM abbreviation: Cancer Cytopathol
ISSN: 1934-662X
eISSN: 1934-6638
Publisher: United States
Grant note: P30 CA086862 / NCI NIH HHS
Language: English
Date published: 03/2018
Academic Unit: Pathology; University of Iowa Health Care
Record Identifier: 9984047797702771

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