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Background  Next‐generation sequencing has mostly been used for genotyping cell‐free DNA (cfDNA) in plasma. However, this assay has several clinical limitations. We evaluated the clinical utility of a novel polymerase chain reaction–free nanowire (NW)‐based plasma cfDNA assay for detecting  ALK  fusion and mutations.    Patients, Materials, and Methods  We consecutively enrolled 99 patients with advanced non‐small cell lung cancer undergoing a fluorescence in situ hybridization (FISH) test for  ALK  fusion;  ALK‐ positive ( n  = 36). The NW‐based assay was performed using 50–100 μL of plasma collected at pretreatment and every 8 weeks during ALK inhibitor treatment.    Results  There was high concordance between the NW‐based assay and the FISH test for identification of  ALK  fusion (94.9% with a kappa coefficient value of 0.892, 95% confidence interval [CI], 0.799–0.984). There was no difference in the response rate to the first anaplastic lymphoma kinase inhibitor between the  ALK ‐positive patients identified by the NW‐based assay and by the FISH test (73.5% vs. 72.2%,  p  = .931). In the  ALK  variant analysis, variants 1 and 3 subgroups were detected in 27 (75.0%) and 8 (22.2%) patients, respectively. Among 24 patients treated with crizotinib, variant 3 subgroup was associated with worse median overall survival than variant 1 subgroup (36.5 months; 95% CI, 0.09–87.6 vs. 19.8 months; 95% CI, 9.9–not reached,  p  = .004]. A serial assessment identified that  ALK  L1196M resistance mutation emerged before radiologic progression during crizotinib treatment.    Conclusion  The newly developed simple NW‐based cfDNA assay may be clinically applicable for rapid diagnosis of  ALK  fusion with its variant forms and early detection of resistance.    Implications for Practice  The authors developed a novel one‐step polymerase chain reaction–free nanowire (NW)‐based plasma cell‐free DNA (cfDNA) assay. This study evaluated the clinical utility of this novel method for the diagnosis of  EML4‐ALK  fusion in advanced non‐small cell lung cancer (NSCLC). The NW‐based assay and FISH test showed high concordance rate in 99 patients with advanced NSCLC. Serial cfDNA assessment demonstrated this method provided early detection of resistance before radiologic progression during crizotinib treatment. Taken together, plasma cfDNA genotyping by the NW‐based cfDNA assay may be useful for the rapid diagnosis of  ALK  fusion, classifying variants, and early detection of resistance.

the oncologist

One‐Step  Polymerase Chain Reaction‐Free  Nanowire‐Based  Plasma  Cell‐Free DNA  Assay to Detect   EML4 ‐ ALK   Fusion and to Monitor Resistance in Lung Cancer