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

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.

Liquid Biopsy in Non-Small Cell Lung Cancer: Highlights and Challenges

“…Mutational analysis of cfDNA at the progression time identified novel ALK point mutations in five out of 20 patients. Notably, the authors also observed a positive correlation between the decrease of ALK acquired mutations in the cfDNA and the radiological response, suggesting that monitoring of resistance ALK mutations can be useful as a response parameter [45]. Similarly, another study demonstrated the efficacy of cfDNA analysis to detect ALK fusions and identify resistance mechanisms by a 70-gene NGS panel (Guardant360 test) [46].…”

“…Besides EGFR mutational status, both ALK rearrangements and point mutations linked to resistance to tyrosine kinase inhibitors were successfully evaluated in plasmatic cfDNA of lung cancer patients [45][46][47][48]. In this context, Bordi et al performed a screening of the cfDNA from 20 ALK positive NSCLC patients treated with crizotinib who suffered progression.…”

Clinical Utility of Cell-Free DNA for the Detection of ALK Fusions and Genomic Mechanisms of ALK Inhibitor Resistance in Non–Small Cell Lung Cancer

“…Small studies, such as a recent report that identified two cfDNA ALK fusions in a cohort of 102 patients show that the detection of these alterations is feasible, albeit more technically challenging than somatic mutation detection, while a longitudinal evaluation of 22 patients was able to detect ALK fusions in 86% at progression. 18,23,25–27 Additionally, although numerous tumor-tissue based studies have demonstrated mechanisms of resistance to ALKi, the use of cfDNA for the evaluation of drug resistance mechanisms in ALK -positive NSCLC has not been published.…”

Possible application of circulating free tumor DNA in non-small cell lung cancer patients

“…Capture-based NGS has been used for the detection of ALK fusions in cfDNA with an overall sensitivity, specificity and accuracy of 54%, 100% and 72%, respectively (42). Very interestingly Bordi and colleagues have shown that KRAS mutations can emerge as a mechanism of resistance to crizotinib in ALK positive NSCLC patients (43).…”