1. A Novel Mass Spectrometry–Based Assay for Diagnosis of EML4-ALK–Positive Non–Small Cell Lung Cancer
- Author
-
Kazuto Nishio, Yoshihiko Fujita, Kazuko Sakai, Hideharu Kimura, Kazuko Matsumoto, Tokuzo Arao, Ken Takezawa, Isamu Okamoto, Tomonori Hirashima, Masayuki Takeda, Kazuhiko Nakagawa, and Hiroyasu Kaneda
- Subjects
Pulmonary and Respiratory Medicine ,Lung Neoplasms ,Oncogene Proteins, Fusion ,EML4-ALK ,Paraffin-embedded tissue ,In situ hybridization ,Biology ,Primer extension ,law.invention ,Fusion gene ,law ,Carcinoma, Non-Small-Cell Lung ,hemic and lymphatic diseases ,Diagnosis ,medicine ,Tumor Cells, Cultured ,Anaplastic lymphoma kinase ,Humans ,Non–small cell lung cancer ,Polymerase chain reaction ,In Situ Hybridization, Fluorescence ,Gene Rearrangement ,Paraffin Embedding ,medicine.diagnostic_test ,Mass spectrometry ,Genetic Variation ,Gene rearrangement ,Prognosis ,Molecular biology ,Subcloning ,Oncology ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Feasibility Studies ,Fluorescence in situ hybridization - Abstract
Introduction: The presence of the transforming fusion gene echinoderm microtubule-associated protein–like 4 (EML4)–anaplastic lymphoma kinase (ALK) in non–small-cell lung cancer (NSCLC) is a predictive marker for the efficacy of anaplastic lymphoma kinase inhibitors. However, the currently available assays for the detection of the different variants of EML4-ALK have limitations. Methods: We developed an assay system for the detection of EML4-ALK variants 1, 2, 3a, 3b, 4, 5a, 5b, 6, or 7 transcripts in total RNA obtained from formalin-fixed, paraffin-embedded (FFPE) specimens of NSCLC tissue. The assay is based on region-specific polymerase chain reaction amplification of EML4-ALK complementary DNA followed by specific single-base primer extension and analysis of the extension products by matrix-assisted laser desorption/ionization–time of flight mass spectrometry. The assay was validated by fluorescence in situ hybridization and the results confirmed by subcloning and sequencing of polymerase chain reaction products. Results: Evaluation of the analytic sensitivity of the assay with serial dilutions of plasmids containing EML4-ALK complementary DNA sequences revealed it to be capable of the reliable detection of one copy of each plasmid per reaction. The assay also detected EML4-ALK variants 1 or 3 in three FFPE samples of surgically resected NSCLC shown to be positive for anaplastic lymphoma kinase rearrangement by fluorescence in situ hybridization. Furthermore, the assay identified variant 1 of EML4-ALK in 3 of 20 FFPE biopsy samples from patients with advanced NSCLC. All positive samples were confirmed by subcloning and sequencing. Conclusions: Our novel assay is highly sensitive and effective for the detection of EML4-ALK in FFPE specimens.
- Published
- 2012
- Full Text
- View/download PDF