Abstract 819: Comparison of DNA+RNA-NGS and DNA-NGS for detecting targetable driver gene alterations in Chinese patients with advanced NSCLC
Authors: Guohao Xia, Ping Liu, Lin Shi, Gao Ning, Ding Zhang
Journal: Cancer Research (2025)

Abstract Background: Patients with advanced non-small cell lung cancer (NSCLC) require genetic testing to enable precision treatment. The conventional method for genetic testing is next-generation sequencing (NGS) using DNA templates (DNA-NGS). However, multiple studies have shown that DNA-NGS often fails to detect fusion mutations, while RNA-based NGS demonstrates superior detection rates for these alterations. This study evaluates the rate of targetable driver gene alterations (AGAs) in NSCLC patients using DNA+RNA-NGS compared to DNA-NGS in real-world settings, providing reliable evidence to support clinical practice. Methods: This study included 143 Chinese patients with advanced untreated NSCLC from November 2022 to October 2024. Eighty patients underwent DNA-NGS testing, and 63 underwent DNA+RNA-NGS testing. In DNA+RNA-NGS, DNA and RNA were extracted from the same tissue specimens. RNA was reverse transcribed into complementary DNA (cDNA) and combined with DNA. Detection was performed in a single workflow, using DNA for single nucleotide variant (SNV) and insertion/deletion (indel) detection, while RNA was utilized for rearrangement detection. Results: In the DNA+RNA-NGS cohort, the median age was 68 years (63.5% male), while in the DNA-NGS cohort, it was 64 years (67.5% male). The detection rate of AGAs was higher in the DNA+RNA-NGS cohort (55.6% vs. 45.0%, p=0.21), primarily due to increased detection of rearrangements (14.3% vs. 7.5%, p=0.21). SNV/indel detection rates showed no significant difference (41.3% vs. 37.5%, p=0.65). Among rearrangement AGAs, there were no significant differences in ALK (4.8% vs. 3.8%, p=0.76), RET (1.6% vs. 1.3%, p=0.86), and METex14 skipping (1.6% vs. 2.5%, p=0.71). However, the ROS1 rearrangement detection rate was significantly higher in the DNA+RNA-NGS cohort (6.3% vs. 0%, p=0.02), attributed to the sequence characteristics of the ROS1 gene, which contains two large repetitive fragments (L1PA8A and L1PA10) in intron 31 that DNA probes often miss. Similar challenges occur with NTRK1/2/3 rearrangements, especially at intron 11 and 12 breakpoints in NTRK3, which are hard to capture with DNA probes, leading to missed detections. However, due to the low incidence of NTRK rearrangements, no cases were found in either cohort. In total, 7 (ALK, n=2; ROS1, n=3; RET, n=1; METex14 skipping, n=1) and 3 (ALK, n=3) fusion-positive patients from the DNA+RNA-NGS and DNA-NGS cohorts, respectively, received targeted therapy, with all 10 achieving favorable clinical responses. Conclusion: DNA+RNA-NGS enhances the detection rate of AGAs compared to DNA-NGS, particularly for rearrangement-related genes in patients with NSCLC. Patients with rearrangements identified by DNA+RNA-NGS who receive targeted therapy can experience significant clinical benefits, thereby improving precision diagnosis and treatment in NSCLC. Citation Format: Guohao Xia, Ping Liu, Lin Shi, Gao Ning, Ding Zhang. Comparison of DNA+RNA-NGS and DNA-NGS for detecting targetable driver gene alterations in Chinese patients with advanced NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 819.