Analytical performance of a highly sensitive system to detect gene variants using next-generation sequencing for lung cancer companion diagnostics

Abstract The recent increase in the number of molecular-targeted agents for non-small cell lung carcinoma and the corresponding target genes has led to the demand for the simultaneous testing of multiple genes. Although gene panels that use next-generation sequencing (NGS) are ideal for this purpose, conventional panels require a high tumor content, and biopsy samples often do not meet this requirement. We developed a new NGS panel, called a compact panel, to accommodate biopsy samples without restricting tumor content. The panel was characterized by high sensitivity, with detection limits for mutations of 0.14%, 0.20%, 0.48%, 0.24%, and 0.20% for EGFR exon 19 deletion, L858R, T790M, BRAF V600E, and KRAS G12C, respectively. Mutation detection also had a high quantitative ability, with correlation coefficients ranging from 0.966 to 0.992. The threshold for fusion detection was 1%. The panel exhibited good concordance with the approved tests. Identity rates are as follows: EGFR positive, 100% (95% confidence interval, 95.5-100); EGFR negative, 90.9 (82.2-96.3); BRAF positive, 100 (59.0-100); BRAF negative, 100 (94.9-100); KRAS G12C positive, 100 (92.7-100); KRAS G12C negative, 100 (93.0-100); ALK positive, 96.7 (83.8-99.9); ALK negative, 98.4 (97.2-99.2); ROS1 positive, 100 (66.4-100); ROS1 negative, 99.0 (94.6-100); MET positive, 98.0 (89.0-99.9); MET negative 100 (92.8-100); RET positive, 93.8 (69.8-100); RET negative, 99.8 (94.9-100). The analytical performance showed that the compact panel could handle various types of biopsy samples obtained by routine clinical practice without requiring strict pathological monitoring, as in the case of conventional NGS panels.