Background Precision medicine based on driver oncogenes is now developed for non-small cell lung cancer. Recent approval of next-generation sequencing (NGS)-based companion diagnostics has increased the need for the use of high-quality specimens for the diagnosis. Methods From August 2015 to May 2018, 82 patients who were enrolled in a nation-wide genome screening, LC-SCRUM-Japan, from our institution were examined for the success rates of genetic analysis according to sample types. A NGS analysis, Oncomine Comprehensive Assay, was performed using DNA and RNA extracted from lung cancer specimens. Results The success rates of DNA and RNA analyses were 100% (82/82 cases) and 78% (64/82), respectively. Of the 82 samples analyzed, 80 (98%) were tissues and two (2%) were pleural effusions. The success rates of RNA analysis in the 80 tissue samples were 45/60 (73%) in bronchoscopic byopsy, 10/10(100%) in operation, 5/6(83%) in Percutaneous biopsy and 3/4(75%) in others. Of the 60 bronchoscopic samples, the success rates were 72% (18/25) in EBUS-TBNA, 88% (7/8) in EBUS-GS (large diameter), 69% (11/16) in EBUS-GS (small diameter) and 82% (9/11) in direct vision biopsy. In the 82 cases analyzed, a total of 52 actionable gene alterations (18 KRAS mut, 6 EGFR mut, 6 MET amp/fus, 5 RET fus, 5 ALK fus, 4 PIK3CA mut, 2 ERBB2 mut, 2 ROS1 fus, 2 FGFR1 amp, 1 BRAF mut, 1 FGFR3 fus) were detected in 48 cases (59%). Twelve of the 48 (15%) were registered in ongoing clinical trials of targeted drugs. Conclusions All the samples were available for DNA analysis of the NGS. The success rates of RNA analysis were lower in samples obtained from EBUS-TBNA and EBUS-GS (small diameter), suggesting that the success rates depend on the sample size.
