118P - Comparative analysis of DNA and RNA-based NGS for detecting MET exon 14 skipping mutation in pan-solid tumor samples

Background

The MET14 skipping mutation, prevalent in various tumors, notably in non-small cell lung cancer (NSCLC), is strongly associated with specific therapeutic targets. Our study aimed to detect MET14 skipping in pan-solid tumor samples using DNA and RNA next-generation sequencing NGS, evaluating assay sensitivity and specificity and mutation distribution across tumor types and populations.

Methods

8,049 samples were tested for MET14 skipping by DNA and RNA-based NGS in amplicon library constructs (ALC), while 7,676 samples were tested by DNA-based NGS in capture library constructs (CLC), with the analysis focusing on clinically significant mutations.

Results

In patients undergoing concurrent DNA/RNA-based NGS (ALC), 1.64% (132/8049) were positive, with lung cancer (LC) showing the highest rate at 2.12% (119/5618), followed by gastrointestinal tumors at 0.11% (3/2681). Lung sarcomatoid carcinoma had the highest MET14 skipping rate (13.6%; 3/22) among LC subtypes. The detection rates of patients with synchronized testing who tested positive by RNA or DNA-based NGS were 1.46% (123/8409) and 0.43% (36/8409), respectively. The detection rate of DNA-based NGS(CLC) was 0.55% (42/7676). Among simultaneously tested patients, 1.20% (96) of the 8,013 DNA-negative cases showed positive results on RNA testing, possibly due to probe design limitations at the Y1003 locus on the DNA level. Conversely, 9 of 36 DNA-positive cases were RNA-negative, indicating possible false-positive and false-negative problems with DNA detection. DNA NGS-based analysis showed that the splice donor site (SD) had the highest mutation rate at 28.3%. In addition, there was no significant difference in the detection rate of MET14 skipping between different tumor cell contents, sample types (e.g., pleural fluid vs. other tissues), and primary vs. metastatic foci (p>0.05). MET14 skipping was more frequent in patients aged 60 years and older (p<0.05), while there was no significant correlation between gender and detection rate.

Conclusions

RNA-based NGS is more accurate in detecting MET14 skipping mutations, and can directly recognize exons lost after transcription, independent of intronic variants, which effectively improves the accuracy of detection.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

The authors.

Funding

Has not received any funding.

Disclosure

All authors have declared no conflicts of interest.