Rapid EGFR Mutation Detection Using the Idylla Platform: Single institution experience of 1200 cases analyzed by an in-house developed pipeline and comparison with concurrent next-generation sequencing results

Abstract: Mutations in the epidermal growth factor receptor (EGFR) are the most common targetable alterations in lung adenocarcinoma. To facilitate rapid testing, we incorporated the Idylla EGFR assay as screening method prior to next generation sequencing (NGS). We describe our validation and experience using an in-house developed analysis pipeline, enhanced with a manual review algorithm. Results are compared with corresponding NGS results. In all, 1,249 samples were studied. Validation demonstrated 98.57% (69/70) concordance with the reference methods. The limit of detection varied from 2 to 5% variant allele frequency if total EGFR Cq was between 20 and 23. Of 1179 clinical cases, 23.41% were EGFR positive by Idylla. Concurrent NGS was successfully performed on 94.9% (799/842) of requests. Concordance of Idylla with NGS was 98.62% (788/799) and 98.50% (787/799) using our in-house and Idylla analysis pipelines, respectively. Discordances involved missed mutations by both assays associated with low tumor/low input. Incorporating a manual review algorithm to supplement automated calls, improved accuracy from 98.62 to 99.37% and sensitivity from 94.68% to 97.58%. Overall reporting time, from receipt of material to official clinical report, ranged from 1-3 days. We conclude that Idylla EGFR testing enables rapid and sensitive screening without compromising subsequent comprehensive NGS, when required. Automated calling, enhanced with a manual review algorithm, reduces false negative calls associated with low tumor/low input samples.