Oncotarget

Research Papers:

Use of capture-based next-generation sequencing to detect ALK fusion in plasma cell-free DNA of patients with non-small-cell lung cancer

Shaohua Cui, Wei Zhang, Liwen Xiong, Feng Pan, Yanjie Niu, Tianqing Chu, Huimin Wang, Yizhuo Zhao and Liyan Jiang _

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Oncotarget. 2017; 8:2771-2780. https://doi.org/10.18632/oncotarget.13741

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Abstract

Shaohua Cui1,*, Wei Zhang1,*, Liwen Xiong1, Feng Pan1, Yanjie Niu1, Tianqing Chu1, Huimin Wang1, Yizhuo Zhao1, Liyan Jiang1

1Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China

*These authors contributed equally to this work

Correspondence to:

Liyan Jiang, email: [email protected]

Yizhuo Zhao, email: [email protected]

Keywords: liquid biopsy, anaplastic lymphoma kinase (ALK), capture-based next-generation sequencing, cell-free DNA (cfDNA), non-small-cell lung cancer (NSCLC)

Received: September 23, 2016     Accepted: November 23, 2016     Published: December 01, 2016

ABSTRACT

Capture-based next-generation sequencing (NGS) is a potentially useful diagnostic method to measure tumor tissue DNA in blood as it can identify concordant mutations between cell-free DNA (cfDNA) and primary tumor DNA in lung cancer patients. In this study, the sensitivity, specificity and accuracy of capture-based NGS for detecting ALK fusion in plasma cfDNA was assessed. 24 patients with tissue ALK-positivity and 15 who did not harbor ALK fusion were enrolled. 13 ALK-positive samples were identified by capture-based NGS among the 24 samples with tissue ALK-positivity. In addition to EML4-ALK, 2 rare fusion types (FAM179A-ALK and COL25A1-ALK) were also identified. The overall sensitivity, specificity and accuracy for all cases were 54.2%, 100% and 71.8%, respectively. For patients without distant metastasis (M0-M1a) and patients with distant metastasis (M1b), the sensitivities were 28.6% and 64.7%, respectively. In the 15 patients who received crizotinib, the estimated median PFS was 9.93 months. Thus, captured-based NGS has acceptable sensitivity and excellent specificity for the detection of ALK fusion in plasma cfDNA, especially for patients with distant metastasis. This non-invasive method is clinically feasible for detecting ALK fusion in patients with advanced-stage NSCLC who cannot undergo traumatic examinations or have insufficient tissue samples for molecular tests.


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