Detection of Rare Oncogenic Gene Fusions in Non-small Cell Lung Cancer Using Cytology Samples

DESCRIPTION provided by applicant In the US lung cancer will add new cases and cause deaths in Non small cell lung cancer NSCLC accounts for of lung cancer The availability of targeted therapies directed to driver oncogenes such as EGFR mutations and gene fusions e g EML ALK in recent years has transformed the management of NSCLC These advances have also created an unprecedented challenge to conduct multiple molecular testing using limited diagnostic materials In many settings of NSCLC patients present with advanced disease and are simultaneously diagnosed staged and their tumors molecularly tested for targeted therapy using fine needle aspiration FNA derived cytology specimen obtained during endobronchial ultrasound EBUS Liquid based cytology slides especially ThinPrep slides have proven superior to formalin fixed paraffin embedded FFPE cell blocks for assessing ALK gene status by DNA fluorescent in situ hybridization FISH However the number of ThinPrep slides that can be prepared from a typical EBUS FNA specimen is limited usually In order to perform multiple testing an in situ method with multiplexing capability beyond conventional FISH and immunohistochemistry IHC is needed In this Phase I study we propose to leverage the high sensitivity and multiplexing capability of a recently developed RNA in situ hybridization technology RNAscope R to develop a novel companion diagnostic algorithm that can efficiently and accurately detect multiple rare but andquot actionableandquot oncogenic gene fusions ALK ROS RET NTRK and others in NSCLC patients using FNA derived ThinPrep slides PUBLIC HEALTH RELEVANCE The current increasing use of minimally invasive diagnostic procedures in oncology poses a number of challenges to companion diagnostic testing First while the number of molecular targets to be tested is increasing on a regular basis the amount of diagnostic specimen is decreasing Second most of the molecular changes of interest are present only in small subsets of patients Therefore there is an urgent need to develop molecular diagnostic methods that have multiplexing capability beyond conventional fluorescent in situ hybridization FISH and immunohistochemistry IHC yet maintain the benefits of in situ biomarker detection In this Phase I study we propose to leverage the high sensitivity and multiplexing capability of the RNAscope RNA ISH technology to develop a novel companion diagnostic algorithm that can efficiently and accurately detect multiple rare but andquot actionableandquot oncogenic fusions in non small cell lung cancer NSCLC using limited fine needle aspiration FNA derived cytology samples