Abstract 6499: The landscape of MET exon 14 skipping mutations in non-small cell lung cancer patients identified by next-generation sequencing

Abstract

Abstract Background: MET exon 14 skipping mutations (METex14) account for approximately 0.9%-4% in patients with non-small cell lung cancer (NSCLC). The primary detection methods are DNA and RNA-based next-generation sequencing (NGS). However, the effect of amplicon-based library construction (ALC) and capture-based library construction (CLC) on the detection characteristics of METex14 during the NGS process is not yet fully understood. Here we described the landscape of METex14 in NSCLC patients, as identified by NGS using two different library construction methods. Methods: A total of 6811 samples with NSCLC were enrolled in this study, including 3839 samples performed by DNA-based NGS with CLC, 64 samples performed by RNA-based NGS with CLC and 2908 samples performed by the synchronous DNA-based and RNA-based NGS with ALC. Only the pathogenic mutations and likely pathogenic mutations in clinical significance were rolled into our analysis. Results: The ranking of different methods, as determined by the positive rates for METex14, was RNA-based NGS with ALC (71/2908, 2.44%), RNA-based NGS with CLC (1/64, 1.56%), DNA-based NGS with CLC (54/3839, 1.41%) and DNA-based NGS with ALC (14/2908, 0.48%). Out of 2908 samples performed by the synchronous DNA-based and RNA-based NGS with ALC, 73 samples (2.51%) had METex14 detected at either the DNA or RNA level. METex14 were only detected at the RNA level in 59 patients, while they were only detected at the DNA level in 2 patients. This might be due to the limited probe design at DNA level and the Y1003 site which could not be detected at RNA level. As revealed by DNA-based NGS, the mutation forms causing METex14 include point mutations, indels, and large segment duplications. And the highest mutation rate is in the splice donor site (30.9%), the lowest is observed at position Y1003 (2.9%). Additionally, METex14 is more prevalent in patients over 60 years of age in Chinese NSCLC, with a statistically significant difference (P=0.0043). Conclusion: RNA-based detection of MET 14 skipping yielded a higher detection rate compared to DNA-based NGS, regardless of ALC or CLC. Combining DNA and RNA analysis is more suitable for detecting MET exon 14 skipping and increases the positive rate. Citation Format: Chen Shi, Gao Ning, Zong Qinglan. The landscape of MET exon 14 skipping mutations in non-small cell lung cancer patients identified by next-generation sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6499.