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Poster Display session (Friday) (ID 65)
- Event: ELCC 2018
- Type: Poster Display session
- Presentations: 1
- Coordinates: 4/13/2018, 12:30 - 13:00, Hall 1
29P - Preliminary assessment of a targeted break-point NGS assay for ALK gene fusion detection in lung adenocarcinoma samples from Chilean patients (ID 241)
12:30 - 13:00 | Presenting Author(s): M. Freire
Lung cancer is the leading cause of cancer death in women and men. The most common mutations in lung adenocarcinoma are in EGFR and KRAS, and along with ten other genes (e.g. ALK and MET) they show a prevalence of 5% or less. As many of these mutations are clinically actionable, it is essential to know the mutation state for all of these genes. Therefore, it is necessary to evaluate multiple types of mutations (SNP, fusions, and CNV) of numerous genes in a small amount of FFPE tissue. We performed a preliminary orthogonal validation of the next generation sequencing based Oncomine Focus Assay (OFA, Thermo Fisher) for the determination of ALK gene fusion in lung adenocarcinoma samples from Chilean patients under standard clinical settings.
This work analyzed 722 lung adenocarcinoma samples from patients recruited in the NIRVANA study by an immunohistochemistry-based ALK test (Ventana) and OFA (including an ALK gene fusion breakpoint assay). Twenty-eight ALK-positive cases by Ventana ALK, OFA or both and 22 negative samples for both tests, were analyzed using a validated (in EU and China) qPCR EML4-ALK fusion gene detection kit (AmoyDx).
Using the EML4-ALK qPCR fusion kit as benchmark, both Ventana ALK and OFA have a sensitivity of 75% [CI95%:51–91]. However, OFA presents a 96% [CI95%: 80–>99] specificity vs. 88% [CI95%:69–97] for Ventana ALK. Therefore, the positive predictive value is 94% [CI95%:68–99] for OFA and 83% [CI95%:63–94] for Ventana ALK. The most commons ALK gene fusions were exon 20 and 6 of EML4.
When these techniques were compared using “real world” lung adenocarcinoma samples, OFA presented an advantage in the ability to predict positive values and was more specific than Ventana ALK test. These results indicate the need for further research to validate the use of OFA panel for the determination of these gene rearrangements.
Clinical trial identification:
NIRVANA study NCT03220230
Legal entity responsible for the study:
M. Freire, R. Lizana, L. Ramos: Currently Pfizer employee and directly involved in this research initiative. G. Sepúlveda, A. Blanco: Currently Pfizer employee and directly involved in this research initiative, through the data analysis. S. Chernilo, O. Arén: Principal Investigator in one of the centers that recruit subject to this study; involved in the results discussion and review; Pfizer funding to research center for the subjects recruitment. C. Fernández: Collaborates with one of Principal Investigator and also gives Anatomopathological support to this study; Involved in the results discussion and review; Pfizer funding to anatomopathological team for the samples analyzed. R. Armisén: Currently Pfizer employee, head of research at the center where this research was done; involved in the results discussion and review.