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

doi:10.18632/oncotarget.13741

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.

Highlights

Targeted molecular therapies are currently recommended as standard first-line treatments for patients with non-small-cell lung cancer (NSCLC) who harbor driver gene alterations
By using the results of tissue anaplastic lymphoma kinase (ALK) detection as the ‘gold standard’, we found that the sensitivity of capture-based next-generation sequencing (NGS) for all 39 patients studied was more than 50%, but that sensitivity varied in patients with different clinical stages
When patients who received crizotinib were divided into 2 groups according to the NGS results, we did not observe any significant differences in Progression-free survival (PFS) between NGS-positive and NGS-negative groups

Summary

Introduction

Targeted molecular therapies are currently recommended as standard first-line treatments for patients with non-small-cell lung cancer (NSCLC) who harbor driver gene alterations. For ALK detection, the Ventana ALK(D5F3) immunohistochemistry (IHC) test and fluorescence in situ hybridization (FISH) are commonly used in current clinical practice. These two methods have been shown to provide concordant results for ALK detection [7, 8]. The quality and quantity of the available tumor biopsy or cytology material is not always adequate to perform these essential molecular tests since most patients with NSCLC are initially diagnosed with www.impactjournals.com/oncotarget advanced disease [9]. Serial biopsies are invasive examinations and may be technically difficult (eg, for tumor-containing blood vessels or where necrosis exists) and could involve serious risks for patients, especially those with a poor performance status [11]

Methods

Results

Conclusion