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Performance evaluation of the Biocartis Idylla EGFR Mutation Test using pre-extracted DNA from a cohort of highly
Jack Grant1, Anne Stanley1, Kevin Balbi1
1Sarah Cannon Molecular Diagnostics, HCA Healthcare UK, London, UK.
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.
Insights
The Biocartis Idylla EGFR Mutation Test performs reliably with extracted DNA, achieving 100% concordance at 250ng input. This method offers a viable alternative to direct FFPE testing for non-small cell lung carcinoma (NSCLC) genomic analysis.
Area of Science:
- Oncology
- Molecular Diagnostics
- Genomics
Background:
- Targeted therapy for non-small cell lung carcinoma (NSCLC) requires detection of specific genomic alterations, notably epidermal growth factor receptor (EGFR) mutations.
- The Biocartis Idylla platform with its single-use EGFR mutation test cartridge is CE-IVD marked for formalin-fixed paraffin-embedded (FFPE) tissue but also supports extracted DNA input, potentially enhancing its utility and preserving tissue.
Purpose of the Study:
- To evaluate the performance of the Biocartis Idylla EGFR Mutation Test using extracted DNA at various input concentrations.
- To assess the concordance of results obtained from extracted DNA compared to direct FFPE analysis.
Main Methods:
- 130 NSCLC cases with known EGFR mutations, characterized by next-generation sequencing, were analyzed.
- The Idylla EGFR test was performed using three different DNA input levels: 20 ng, 50 ng, and 250 ng, with replicate analyses.
Main Results:
- Concordant results were achieved in 90.77% of cases at 20 ng DNA input, 98.46% at 50 ng, and 100% at 250 ng.
- Discordant findings were associated with control quantification cycle (CQ) values >23.
- Very low CQ values correlated with EGFR gene amplification.
Conclusions:
- The Idylla EGFR Mutation Test demonstrates comparable performance with pre-extracted DNA as with direct FFPE input.
- For samples with control CQ >23, reanalysis with higher DNA input is recommended.
- Mitigation strategies for potential false negatives include manual review of quantitative PCR data or alternative analysis methods.
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