Detection and characterization of cancer mutations in lung cancer cells using a long-read and portable sequencer, MinION

Sequencing is the most decisive method to determine mutations in cancers. However, sequencing still requires specialized instrument and techniques, which prevents its wide-spread application for general clinical practice. Here, we demonstrate the use of a long-read and portable sequencer, MinION, for identifying somatic mutations and germline variants in the cancer-related genes. We employed cDNA amplicon sequencing covering their almost entire regions. We show mutations of varying categories can be detected, namely, base substitutions in the EGFR, KRAS and NRAS, a small deletion in EGFR, an exon skip in NF1. EML4-ALK and CCDC6-RET fusions and their precise junctions were also detected as well as five other novel gene fusions. Phasing of multiple mutations was also possible, enabling separation of the allelic background of the primary and secondary mutations. For clinical applications, we also conducted a serial dilution analysis of the template starting EGFR-mutant and wild type amplicons. Finally we applied this approach for characterizing eight clinical samples regarding genotyping their driver mutations. We found the driver mutations were precisely detected for all of the examined cases.