P2.03b-080 A Comprehensive Test of Cancer Treatment-Related Genes for the Clinical Samples of Non-Small Cell Lung Cancer (NSCLC): Topic: Biomarkers

Abstract

Molecular targeted therapies are one of the key drugs for NSCLC. For all advanced NCSLC patients to receive precise molecular targeted therapies, mutation analysis should be comprehensively analyzed from tissue and/or cytological samples with high sensitivity and cost-effectiveness. To satisfy these requirements, we established a system called MINtS(Mutation Investigation System using a Next-generation Sequencer). According to our basic data, by deep sequencing, MINtS enables us to detect genetic alterations from the clinical specimens of which cancer cell content is just over 1%. The lists of mutations are EGFR, KRAS, BRAF, HER2, and ALK/RET/ROS1 fusion genes. We report the data analyzed from the clinical cytological and tissue samples using MINtS. MINtS adapted amplicon sequencing strategy. For the EGFR, KRAS, BRAF and HER2 genes, the target regions are amplified by the multiplex PCR. For the ALK, RET and ROS1 fusion genes as well as OAZ1 housekeeping gene (internal control), the targets are amplified by the multiplex RT-PCR. The index sequences were then added for discriminating samples derived from different patients. Amplified fragments from multiple samples are combined, and run on a Next generation Sequencer. According to the index sequences, the sequencing reads obtained were de-multiplexed for each sample. Using MINtS system, we analyzed 65 tissue samples that were obtained surgically, and 76 cytological specimens that were obtained by bronchial brushing or pleural effusions from NSCLC patients. Our preliminary data indicated that mutations for EGFR, KRAS, BRAF, and HER2 were detected from DNA, and the test detected mutations from samples with cancer cell content > 1% with specificity and sensitivity >0.99. Fusion genes were detected from mRNA, and the test were considered to detect them from samples with cancer cell content >1%. Among 141samples, 140samples were successfully analyzed. EGFR mutations in 36 samples (25.5%), KRAS mutations in 10 samples (7%), BRAF mutations in 5 samples (3.5%), and HER2 mutations in 5 samples (3.5%). Regarding fusion genes, ALK fusion gene were 2 samples (1.4%), RET fusion gene were 2 samples (1.4%), and ROS fusion gene was 1 sample (0.7%). MINtS could analyze from both tissue and cytological samples. MINtS tests >100 samples in a single run. This fulfills clinical requirement of a high throughput testing at an affordable unit price; 30US dollars per sample. MINtS provides a protoytpe of mutation test applicable to cancers originating from organs other than lung, and may be also adaptable to liquid biopsy.