Aims Targeted therapies for non-small cell lung carcinoma (NSCLC) rely on the detection of specific genomic lesions, such as mutations within the epidermal growth factor receptor (EGFR) gene. The Biocartis Idylla platform and single-use EGFR mutation test cartridge is CE-IVD for use with formalin-fixed paraffin embedded (FFPE) tumour material, but can also function off-scope using extracted DNA as input material. This can expand the utility of the platform and potentially conserve valuable tissue.
Methods We sought to evaluate the performance of this system to detect known EGFR mutations using extracted DNA at different input levels. 130 next generation sequencing-characterised NSCLC cases possessing EGFR mutations that were theoretically detectable by the Idylla system were selected. Replicate analyses were performed using the Idylla EGFR test with up to three different DNA input levels (20 ng, 50 ng and 250 ng).
Results Considering only variants within the test manufacturer’s specified scope, the Idylla EGFR test generated concordant findings for 90.77% of cases at 20 ng DNA input, 98.46% at 50 ng input and 100% at 250 ng input. Analyses with discordant findings all generated control quantification cycle (CQ) values greater than 23. Very low CQ values were associated with EGFR gene amplification.
Conclusions The Idylla EGFR Mutation Test can be used at least as well with pre-extracted DNA than with direct FFPE input. In cases with control CQ >23, reanalysis with an increased DNA input should ideally be undertaken. If this is not possible, the risk of false negative calls may be mitigated by manual review of the quantitative PCR data and/or by reflexing to alternative analysis options.
- lung neoplasms
- diagnostic techniques and procedures
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Handling editor Runjan Chetty.
GG and PB contributed equally.
Contributors JG performed the lab work, collated and analysed the data, and wrote the manuscript. AS performed the lab work and contributed to the manuscript. KB performed data analysis, statistical analysis and contributed to the manuscript. GG helped supervise the project, performed data analysis and contributed to the manuscript. PB supervised the project, performed data analysis and edited the manuscript.
Funding The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.
Competing interests PB has participated in remunerated advisory board and dedicated user meetings for both Biocartis and Thermo Fisher UK. He has also delivered sponsored, but not for profit, presentations at open access meeting upon the invitation of both Biocartis and Thermo Fisher UK.
Patient consent for publication Not required.
Provenance and peer review Not commissioned; externally peer reviewed.
Data availability statement Relevant data are included in the manuscript; all raw data (were possible) are available upon request.
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