Multicenter evaluation of an automated, multiplex, RNA-based molecular assay for detection of ALK, ROS1, RET fusions and MET exon 14 skipping in NSCLC

Virchows Arch. 2024 Apr;484(4):677-686. doi: 10.1007/s00428-024-03778-9. Epub 2024 Mar 16.


The current study assessed the performance of the fully automated RT-PCR-based Idylla™ GeneFusion Assay, which simultaneously covers the advanced non-small cell lung carcinoma (aNSCLC) actionable ALK, ROS1, RET, and MET exon 14 rearrangements, in a routine clinical setting involving 12 European clinical centers. The Idylla™ GeneFusion Assay detects fusions using fusion-specific as well as expression imbalance detection, the latter enabling detection of uncommon fusions not covered by fusion-specific assays. In total, 326 archival aNSCLC formalin-fixed paraffin-embedded (FFPE) samples were included of which 44% were resected specimen, 46% tissue biopsies, and 9% cytological specimen. With a total of 179 biomarker-positive cases (i.e., 85 ALK, 33 ROS1, 20 RET fusions and 41 MET exon 14 skipping), this is one of the largest fusion-positive datasets ever tested. The results of the Idylla™ GeneFusion Assay were compared with earlier results of routine reference technologies including fluorescence in situ hybridization, immunohistochemistry, reverse-transcription polymerase chain reaction, and next-generation sequencing, establishing a high sensitivity/specificity of 96.1%/99.6% for ALK, 96.7%/99.0% for ROS1, 100%/99.3% for RET fusion, and 92.5%/99.6% for MET exon 14 skipping, and a low failure rate (0.9%). The Idylla™ GeneFusion Assay was found to be a reliable, sensitive, and specific tool for routine detection of ALK, ROS1, RET fusions and MET exon 14 skipping. Given its short turnaround time of about 3 h, it is a time-efficient upfront screening tool in FFPE samples, supporting rapid clinical decision making. Moreover, expression-imbalance-based detection of potentially novel fusions may be easily verified with other routine technologies without delaying treatment initiation.

Keywords: ALK fusion; MET exon 14 skipping; RET fusion; ROS1 fusion; Idylla; NSCLC.

Publication types

  • Multicenter Study
  • Evaluation Study

MeSH terms

  • Anaplastic Lymphoma Kinase* / genetics
  • Biomarkers, Tumor / analysis
  • Biomarkers, Tumor / genetics
  • Carcinoma, Non-Small-Cell Lung* / genetics
  • Carcinoma, Non-Small-Cell Lung* / pathology
  • Exons* / genetics
  • Gene Rearrangement
  • Humans
  • In Situ Hybridization, Fluorescence / methods
  • Lung Neoplasms* / genetics
  • Lung Neoplasms* / pathology
  • Multiplex Polymerase Chain Reaction
  • Oncogene Proteins, Fusion* / genetics
  • Protein-Tyrosine Kinases* / genetics
  • Proto-Oncogene Proteins c-met* / genetics
  • Proto-Oncogene Proteins c-ret* / genetics
  • Proto-Oncogene Proteins* / genetics


  • ROS1 protein, human
  • Proto-Oncogene Proteins c-ret
  • Anaplastic Lymphoma Kinase
  • RET protein, human
  • ALK protein, human
  • Protein-Tyrosine Kinases
  • Proto-Oncogene Proteins c-met
  • MET protein, human
  • Proto-Oncogene Proteins
  • Oncogene Proteins, Fusion
  • Biomarkers, Tumor