Abstract 2785: A comprehensive RNA-based assay for treatment prediction in non-small cell lung cancer patients
Authors: Kok Klaas , Wei Jaicong , Rybczynska Anna , Terpstra Martijn , Wekken Anthonie van der , Hilterman Jeroen , Schuuring Ed , Sijmons Rolf , Groen Harry , Berg Anke van den 
Published: July 2017

Abstract
Purpose: In late-stage lung cancer an increasing number of genomic aberrations is used to predict either sensitivity to, or resistance against, targeted therapies. These include gene mutations, gene fusions, amplifications and in the near future different relevant splice variants. Currently, detection of each type of aberration is carried out with different tests. We have set out to develop a novel all-in-one assay to detect the various types of aberrations, e.g. mutations, gene fusions and overexpression. The latter is assumed to be the biological marker that is underlying gene amplification.
Methods: Our assay is based on the Single Primer Enrichment Technology (SPET), allowing amplification of a target region using only a single sequence-specific primer. Our first custom-designed panel targets a comprehensive list of hotspots with therapeutic and prognostic significance in lung cancer, including EGFR, ALK, MET, KRAS, NRAS, PIK3CA, ROS1, BRAF, FGFR1 and RET. Using total RNA as input, we will be able to efficiently detect mutations, gene fusions and aberrant expression levels of selected genes. This test may also detect tumor-specific aberrations in platelets.
Results: As a proof of principle we analyzed RNA derived from 8 lung cancer-derived cell lines, from two frozen tumor biopsies, and from 10 FFPE biopsies all with confirmed genomic alterations by clinically approved assays. In total, conventional methods detected 18 small mutations, five gene fusions and three gene amplifications, that are all covered by our assay. Of these, 14 mutations, and four gene fusions were readily detected with our assay. The detection of three mutations failed because of low coverage of the target region, probably due to a less optimal design of the specific primer. One small deletion, and one gene fusion were not detected with our RNA-based assay, despite a high read coverage. Quantification of the expression level of the amplified genes is still under investigation.
Conclusion: Our preliminary data indicate this novel RNA-based assay not only efficiently identifies all crucial mutations in lung cancer cell lines, but also in small frozen and FFPE tumor biopsies of lung cancer patients. Our next goal is to test this novel method on RNA derived from platelets from cancer patients, providing a minimal invasive procedure to monitor the state of disease in those patients.
Citation Format: Klaas Kok, Jaicong Wei, Anna Rybczynska, Martijn Terpstra, Anthonie van der Wekken, Jeroen Hilterman, Ed Schuuring, Rolf Sijmons, Harry Groen, Anke van den Berg. A comprehensive RNA-based assay for treatment prediction in non-small cell lung cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2785. doi:10.1158/1538-7445.AM2017-2785