title: Multiplexed gene expression and fusion transcript analysis to detect ALK fusions in lung cancer.
abstract: Anaplastic lymphoma kinase gene (ALK) fusions have been identified in approximately 5% of non-small-cell lung carcinomas (NSCLCs) and define a distinct subpopulation of patients with lung cancer who are highly responsive to ALK kinase inhibitors, such as crizotinib. Because of this profound therapeutic implication, the latest National Comprehensive Cancer Network Clinical Practice Guidelines in Oncology recommend upfront ALK screening for all patients with NSCLC. The Food and Drug Administration-approved companion diagnostic test (ie, fluorescence in situ hybridization) for identification of ALK-positive patients, however, is complex and has considerable limitations in terms of cost and throughput, making it difficult to screen many patients. To explore alternative screening modalities for detecting ALK fusions, we designed a combination of two transcript-based assays to detect for presence or absence of ALK fusions using NanoString's nCounter technology. By using this combined gene expression and ALK fusion detection strategy, we developed a multiplexed assay with a quantitative scoring modality that is highly sensitive, reproducible, and capable of detecting low-abundant ALK fusion transcripts, even in samples with a low tumor cell content. In 66 archival NSCLC samples, our results were highly concordant to prior results obtained by fluorescence in situ hybridization and IHC. Our assay offers a cost-effective, easy-to-perform, high-throughput, and FFPE-compatible screening alternative for detection of ALK fusions.
authors.affiliation: Pfizer Oncology, San Diego, California 92121, USA.
authors.forename: Maruja E
authors.initials: ME
authors.lastname: Lira
authors.forename: Tae Min
authors.initials: TM
authors.lastname: Kim
authors.forename: Donghui
authors.initials: D
authors.lastname: Huang
authors.forename: Shibing
authors.initials: S
authors.lastname: Deng
authors.forename: Youngil
authors.initials: Y
authors.lastname: Koh
authors.forename: Bogun
authors.initials: B
authors.lastname: Jang
authors.forename: Heounjeong
authors.initials: H
authors.lastname: Go
authors.forename: Se-Hoon
authors.initials: SH
authors.lastname: Lee
authors.forename: Doo Hyun
authors.initials: DH
authors.lastname: Chung
authors.forename: Woo Ho
authors.initials: WH
authors.lastname: Kim
authors.forename: Eric F P M
authors.initials: EF
authors.lastname: Schoenmakers
authors.forename: Yoon-La
authors.initials: YL
authors.lastname: Choi
authors.forename: Keunchil
authors.initials: K
authors.lastname: Park
authors.forename: Jin Seok
authors.initials: JS
authors.lastname: Ahn
authors.forename: Jong-Mu
authors.initials: JM
authors.lastname: Sun
authors.forename: Myung-Ju
authors.initials: MJ
authors.lastname: Ahn
authors.forename: Dong-Wan
authors.initials: DW
authors.lastname: Kim
authors.forename: Mao
authors.initials: M
authors.lastname: Mao
mesh_terms: D000077548:Anaplastic Lymphoma Kinase; D001483:Base Sequence; D002289:Carcinoma, Non-Small-Cell Lung / Q000175:diagnosis / Q000235:genetics*; D015870:Gene Expression; D006801:Humans; D007150:Immunohistochemistry; D017404:In Situ Hybridization, Fluorescence; D008175:Lung Neoplasms / Q000175:diagnosis / Q000235:genetics*; D008969:Molecular Sequence Data; D050596:Oncogene Fusion; D015514:Oncogene Proteins, Fusion / Q000235:genetics / Q000302:isolation & purification; D016133:Polymerase Chain Reaction; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics*; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D015514:Oncogene Proteins, Fusion; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; D020794:Receptor Protein-Tyrosine Kinases