A rapid Loop-Mediated Isothermal Amplification (LAMP) test for the detection of somatic variants, p.L858R and p.E746_A750del, in non-small cell lung cancer patients: comparison with real-time PCR and NGS

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Background Identifying tumour-derived somatic variants in the EGFR gene is crucial for making treatment decisions in NSCLC patients. The analytical performance and clinical utility of a new LAMP-based portable system for detecting the most frequent somatic variants, p.L858R and p.E746_A750del, using DNA from FFPE samples of NSCLC patients, was evaluated against the reference standards, NGS and real-time PCR. Methods This study was non-interventional conducted at the National Center of Oncology in Baku, Azerbaijan following a non-probability purposive sampling, using DNA (n=44) from FFPE samples. The analytical performance of the LAMP test was evaluated for each somatic variant, p.L858R and p.E746_A750del, using Receiver Operating Characteristic curve analysis. In addition, a questionnaire was developed for healthcare professionals (n=20) to assess the utility of integrating the new LAMP portable system in clinical practice. Results The new LAMP test generated results within one hour, demonstrating a 95.45% accuracy in detecting the p.L858R variant compared to real-time PCR and NGS. For the exon 19 deletion, specifically the p.E746_A750del variant, the test achieved 100% accuracy with NGS. Specificity with real-time PCR was 100%; however, sensitivity could not be determined, as PCR does not identify which exon 19 deletion was detected. Additionally, the questionnaire revealed unanimous agreement among healthcare professionals and successfully assessed the usefulness of new LAMP portable system, to be integrated as a first diagnostic tool in clinical practice by reducing time, costs and accelerating treatment decisions in NSCLC patients that are positive for the analysed genetic variants. Conclusions The study demonstrates outstanding analytical performance of the new LAMP portable system, highlighting its utility for integration into clinical practice. Particularly beneficial in low-resource settings, this system provides significant value for clinical decision-making in NSCLC patients with positive results, optimizing treatment decisions while saving both time and costs. To our knowledge, this is the first LAMP portable system for oncology applications that can accurately detect somatic variants in the EGFR gene.

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