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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MSK Authors
  1. Natasha Rekhtman
    392 Rekhtman
  2. Khedoudja Nafa
    236 Nafa
  3. Jinjuan Yao
    54 Yao
  4. Marc Ladanyi
    1278 Ladanyi
  5. William D Travis
    712 Travis
  6. Christine Gi-Yun Moung
    20 Moung
  7. Snjezana Dogan
    173 Dogan
  8. Maria Eugenia Arcila
    620 Arcila
  9. Paulo A Salazar
    35 Salazar
  10. Tao Zheng
    10 Zheng
  11. Nana Yaa Takyiwaa Mensah
    11 Mensah
  12. Ivelise A Rijo
    27 Rijo
  13. Jason Chih-Peng Chang
    111 Chang