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Updated: Feb 10, 2026

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
Published on: August 24, 2017
Idylla assay and next generation sequencing: an integrated EGFR mutational testing algorithm
Caterina De Luca1, Alessandra G Rappa2, Gianluca Gragnano1
1Department of Public Health, University of Naples Federico II, Naples, Italy.
Aims:
Any reference laboratory testing non-small cell lung cancer samples for predictive biomarkers needs to develop and validate a wide range of different molecular techniques, each with a specific time requirement and application. Updated international guidelines suggest that next generation sequencing (NGS) to be the initial procedure. However, in a non-negligible subset of cases, library generation may fail or amplicon coverage may be insufficient. In these NGS 'invalid' cases, the Idylla system may represent a viable option for rapid epidermal growth factor receptor (EGFR) genotyping.
Methods:
This retrospective study included 68 archival DNA samples previously processed by Ion Torrent NGS assay. Out of these, 43 cases, including 24 EGFR mutant samples, had a valid NGS result, whereas 25/68 (37%) were invalid. All samples were retested by directly pipetting the DNA inside the EGFR Idylla assay cartridge.
Results:
In all 43 cases with a valid NGS result, Idylla confirmed the EGFR mutational status. In particular, 24/24 (100%) of EGFR mutant samples as detected by NGS were confirmed by Idylla. Moreover, a large portion of cases (20/25; 80%) whose assessment by NGS was invalid were adequately processed by Idylla. Noteworthy, in 4/25 (16%) of cases, Idylla detected actionable EGFR mutations.
Conclusions:
Idylla assay could be very useful to quickly process cases for which NGS does not allow genotyping.
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