TEST:

Idylla™ GeneFusion Assay

Screening for ALK rearrangements with IHC is both reliable and cost effective. In-house testing with IHC removes reliance on send-out testing for ALK detection, effectively cutting costs and decreasing TAT. Additionally, the creation of a reflex algorithm can improve lung cancer biomarker testing processes within hospitals.

Our standard operating procedure (SOP) was updated to perform orthogonal confirmation testing for stand-alone equivocal NTRK1/2 and equivocal NTRK3 (5' failure), but to ignore equivocal NTRK3 (5' intact) and report as NTRK2/3 indeterminate. Re-verification showed no change to ALK, ROS1, RET, MET ex14, and NTRK1 results. Sensitivity of NTRK2 detection was significantly increased (80% after orthogonal testing).

She will highlight the integration of cytology and small biopsy specimens, particularly in lung and thyroid cancers, within a large cancer center. Highlights: • Evaluation of Idylla™ for rapid on-site assessment and archival aspirate smear and FFPE cell block testing • Comparison with large panel NGS assays • Data of interest to cytology labs • Review of NTRK case studies within the research of Idylla™ GeneFusion This workshop will provide insights for pathologists seeking to enhance workflows and embrace cutting-edge cytopathology techniques.

Our data confirm that MPE are suitable material for investigating fusion alterations. The Idyllaâ„¢ GeneFusion, although indicated for investigation of tissue samples, offers the possibility of performing a molecular characterization of supernatants without undertaking the entire cfRNA extraction procedure providing a rapid and reliable strategy for the detection of actionable genetic alterations.

However, NGS had a 12-day longer TAT compared to EGFR PCR. Gene fusion-panel PCR and NGS identified an additional 11.6% of patients harboring actionable alterations who may benefit from FDA-approved targeted therapies.

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.

"Biocartis Group NV...announces that four study abstracts on Idylla™ have been selected for poster presentations at the international ESMO (European Society of Molecular Oncology) congress, taking place between 20-24 October 2023 in Madrid (Spain). The studies show excellent data for the Idylla™ GeneFusion Assay and Idylla™ EGFR Mutation Assay....The first study prospectively tested lung cancer samples on the Idylla™ Platform as part of routine2 lung profiling locally and from over 60 UK hospitals....The second abstract presents the results of a multicenter study that was conducted in a routine clinical2 setting involving 12 clinical centers across Europe....The third abstract presents the results of the ORIGEN study, a multicenter study on the prevalence of EGFR gene mutations in patients with early-stage resectable non-small cell lung cancer in Spain (in collaboration with AstraZeneca Spain)."

No abstract available

We also demonstrate the need for additional reflex testing capability on larger DNA and fusion panels for a small subset of lung cancers bearing rare single-nucleotide variants, indels and fusion transcripts and secondary, post-treatment resistance mutations. A similar testing workflow could be adopted for other solid tumor types for which extensive gene/fusion variant profiles are available both in the treatment-naïve and post-therapy settings.

Clinical testing laboratories may benefit from improved understanding of strengths and limitations of different workflows. It is important to keep these in mind when reporting results.

Using commercial standards, the limit of detection of the Idylla system for the most frequent fusions and exon skipping ranges between 5 and 10 ng RNA input. These results support that the Idylla assay is a reliable and rapid option for the detection of these alterations, however a particular attention is needed for the interpretation of the expression imbalance.

Conclusions Molecular screening in non-BRAF PTC patients is useful to identify patients harboring RET fusions who may benefit from targeted therapies. As other potentially actionable gene fusions are also found in these patients, routine implementation of NGS analysis warrants a comprehensive biomarker study.

Conclusions Since results are available within 3 hours, the Idyllaâ„¢ GeneFusion Assay technology has emerged as a highly relevant time efficient upfront screening tool in FFPE samples. Moreover, detection of potentially novel fusions based on the principle of expression imbalance may be easily verified with either IHC, FISH or NGS without delaying the treatment initiation.

More importantly, the assay allows testing to be successfully completed in samples unsuitable for NGS due to low tumour burden. In conclusion, the IdyllaTM GeneFusion Assay offers a rapid, sensitive and specific method for lung sample profiling in routine practice.

The Idylla EGFR testing is an accurate and simple tool useful for the early screening of EGFR mutations. The Idylla GeneFusion is a potential screening panel with short turnaround time using a minimal amount of tissue and might be considered as a relevant complementary testing to IHC in diagnostic molecular laboratories.

DNA-only <50 gene NGS panels can identify oncogenic mutations in the majority of lung tumor cases. In contrast, FISH testing for ALK and ROS1 rearrangement is overwhelmingly negative and does not justify their use for initial testing. Instead, NGS negative lung tumor specimens can be reflexed to the Idylla GeneFusion assay, which provides results within 4 hours.

The IGFA could contribute to the rapid detection of targetable gene fusions and mutations, especially in context of rapidly growing cancers requiring urgent therapeutic choices.

UFGFA using NGS and reverse-transcriptase polymerase chain reaction approaches had an equal level of detection of gene fusion but with some technique-specific limitations. Nevertheless, UFGFA detection in routine clinical care is feasible with both systems allowing faster initiation of therapy and a broad degree of screening.

Tumor sections stored at room temperature for up to 60 days and 17 cases older than 2 years were successfully characterized. Our results suggest that the Idylla GeneFusion assay is a reliable tool to define gene fusion status and may be a valuable stand-alone diagnostic test when time efficiency is needed or NGS is not feasible.

Pan-Trk IHC has outstanding sensitivity for NTRK fusions detection, regardless of staining pattern, and can be used as an inexpensive screening test for NTRK fusions. Pan-Trk IHC has superior sensitivity compared to Idylla GeneFusion assay, especially for NTRK2 fusion detection. Interestingly, IHC+/NGS fusion- cases may have other kinase alterations, including fusions and copy number gains.

The rapid fusion assay is quick, accurate, and versatile, allowing reliable detection of ALK, ROS1, RET fusions, and MET exon 14 skipping in NSCLC, and NTRK fusions. Rapid molecular testing may expedite treatment with appropriate targeted therapies.

"Biocartis Group NV...announces the publication of nine performance study abstracts of its fully automated molecular diagnostics Idylla™ platform and assays at the annual meeting of the ‘Association for Molecular Pathology’ (AMP), a leading molecular diagnostics conference, taking place between 1-5 November in Phoenix, Arizona (US). The studies were performed by a variety of US laboratories and research institutes."

Introduction: Entrectinib and larotrectinib received tissue-agnostic FDA approvals for treatment of NTRK-rearranged cancers. The beta testing and resulting algorithm revision improved the sensitivity of detecting NTRK1 and NTRK3 fusions, and 100% specificity remained for NTRK1 fusion. Performance of standalone NTRK2 fusion detection remains poor. Applying combined NTRK2/3 fusion reporting, the assay yielded favorable performance in detecting NTRK2/3 fusions.

The performance characteristics of this assay is compatible with NGS. Due to rare false-positives by EI detection, we suggest a secondary confirmation test for fusion calls by EI only. The significant reduction in turnaround time, wide material-type acceptance, low sample amount requirements, and minimal labor make the automated gene fusion assay an attractive alternative option to NGS assays.

Taken together, these results demonstrate the clinical utility of the Idylla GeneFusion Assay for rapid, valid, and reproducible detection of the kinase fusions in lung adenocarcinoma with use of low tissue requirements in comparison to the other established testing modalities.

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We identified NTRK3 expression imbalance in one (1.1%) of 93 CCA tumours but this could not be confirmed with NGS. Our results show limited specificity of pan-TRK IHC to identify NTRK fusions. Pan-TRK IHC can thus be utilized as a screening technique for NTRK fusions in CCA, but positive samples require confirmatory testing with RNA-based methods.

MET-TKIs, capmatinib and tepotinib, for NSCLCs with METex14 marked a new step of MET-targeted therapy. METex14 alterations - point mutations/deletions/insertions/com-plex mutations lead to MET receptor decreased degradation, fol-lowed by MET signalling and tumourigenesis. The evaluation methods for METex14 include differential MET exon expression, quantitative reverse transcription polymerase chain reaction (qRT-PCR) or direct RNA sequencing.

This study showed that the IdyllaTM GeneFusion Assay might be a promising screening tool for top level MET amplification assessment in lung cancer samples. Nevertheless, even after threshold adjustment both specificity and sensitivity within different levels of MET amplification remained lower than 90%. Therefore, this test with our proposed cut-off is not suited to identify MET amplification at lower thresholds.

Ultra-fast gene fusion evaluation using NGS or RT-PCR approaches should be developed as a reflex testing for NS-NSCLC at diagnosis in order to treat these patients according to the international recommendations and guidelines.

Secondary resistance is nearly universal among NSCLC patients who receive TKIs for actionable mutations. Solvent front secondary mutations in RET (G810X) as well as activation of KRAS or MET molecular pathways have been reported to confer resistance to RET inhibitors. To our knowledge, this is the first case of a RET fusion lung cancer with resistance to a RET inhibitor mediated by transformation to small cell carcinoma.

To conclude, Idylla GeneFusion is a clinically valuable test that does not require a specific infrastructure, allowing a rapid result. The absence of alteration or the detection of expression imbalance only requires additional testing by orthogonal methods.

"Biocartis Group NV...announces the CE-marking of its fully automated Idylla™ GeneFusion Panel (CE-IVD). The Panel detects in one single cartridge ALK, ROS1, RET and METex14 skipping, a wide range of actionable targets relevant in non-small cell lung cancer (NSCLC). Designed for use in clinical laboratories, the Panel provides comprehensive testing results within 180 minutes, significantly faster than currently available testing methods which often take days or even weeks before results are available."

"This might be countered by increasing the amount of sample input. To conclude, the Idylla GeneFusion Assay has shown a clear potential in identifying NTRK fusions."

"Biocartis Group NV...announces the publication of a new study in the Journal of Molecular Diagnostics on the Idylla™ GeneFusion Assay (RUO) for rapid detection of targetable fusions involving ALK, ROS1, RET, and NTRK1/2/3 and MET exon 14 skipping mutations."

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"Our results show that kinase fusions (20/30, 67%) and most importantly targetable NTRK1 fusions (7/30, 23%) are frequent in CRCs with dMLH1/BRAFV600Ewt/MLH1ph/RASwt. NGS was the most comprehensive method in finding the fusions, of which a subset can be screened by Idylla or IHC, provided that the result is confirmed by NGS."

The GENEFUSION assay is an accurate method for rapid fusion detection in ALK, ROS1, RET, and MET exon 14 splice variants. Due to the limited number of NTRK fusion positive cases analyzed, the performance of this gene is unclear. Further evaluation of non-targeted fusions is necessary to evaluate the performance of expression imbalance.

"In our series, 20% (1/5) of MSI-H KRAS/NRAS/BRAF wt CRC were NTRK rearranged. All methodologies were optimal to detect NTRK rearrangements. Different methodologies provide complementary information about rear- rangements, being NGS the most specific."

"Idylla™ GeneFusion is an automated, reliable, ease-of- use, simple (<2 minutes hands-on time) test, and has the shortest turnaround time compared to existing diagnostic tests (3 hours turn- around time), enabling the detection of clinically relevant alterations in ALK, ROS1, RET and NTRK1/2/3 rearrangements, and MET exon 14 skipping mutation, without necessitating molecular exper- tise or infrastructure."