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 Journal Article
| Authors: | Momeni-Boroujeni, A.; Salazar, P.; Zheng, T.; Mensah, N.; Rijo, I.; Dogan, S.; Yao, J.; Moung, C.; Vanderbilt, C.; Benhamida, J.; Chang, J.; Travis, W.; Rekhtman, N.; Ladanyi, M.; Nafa, K.; Arcila, M. E. |
| Article Title: | 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, the Idylla EGFR assay was incorporated as a screening method before next-generation sequencing (NGS). Validation and experience using an in-house developed analysis pipeline, enhanced with a manual review algorithm is described. Results are compared with corresponding NGS results. In all, 1249 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 for total EGFR quantitation cycle between 20 and 23. Of the 1179 clinical cases, 23.41% were EGFR-positive by Idylla. Concurrent NGS was successfully performed on 94.9% (799/842) 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 to 3 days. Therefore, 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. © 2021 Association for Molecular Pathology and American Society for Investigative Pathology |
| Journal Title: | Journal of Molecular Diagnostics |
| Volume: | 23 |
| Issue: | 3 |
| ISSN: | 1525-1578 |
| Publisher: | Elsevier Science, Inc. |
| Date Published: | 2021-03-01 |
| Start Page: | 310 |
| End Page: | 322 |
| Language: | English |
| DOI: | 10.1016/j.jmoldx.2020.11.009 |
| PUBMED: | 33346146 |
| PROVIDER: | scopus |
| PMCID: | PMC7919857 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 1 March 2021 -- Source: Scopus |
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