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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
Author(s) -
Guseva Natalya V.,
Jaber Omar,
Stence Aaron A.,
Sompallae Krishnaveni,
Bashir Amani,
Sompallae Ramakrishna,
Bossler Aaron D.,
Jensen Chris S.,
Ma Deqin
Publication year - 2018
Publication title -
cancer cytopathology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.29
H-Index - 57
eISSN - 1934-6638
pISSN - 1934-662X
DOI - 10.1002/cncy.21963
Subject(s) - ros1 , anaplastic lymphoma kinase , medicine , lung cancer , thyroid nodules , thyroid carcinoma , adenocarcinoma , pathology , epidermal growth factor receptor , fine needle aspiration , fusion gene , cancer research , thyroid , kras , carcinoma , cancer , biology , gene , biopsy , genetics , colorectal cancer , malignant pleural effusion
BACKGROUND 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. METHODS 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. RESULTS 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. CONCLUSIONS 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 .