Abstract 3609: A new innovative and robust targeted deep sequencing system: 36 hours turn round time from patient samples to the final mutation report
Authors: Pedro Mendez, Jun-Hee Yoon, Sharon Lee, James Kim, Jenny Dang, Thomas Kim, David Jablons, Il Jin Kim
Journal: Cancer Research (2016)

Abstract The emergence of next-generation sequencing (NGS) has changed the paradigm for genetic and genomic studies in many medical and life science fields. Despite its growing popularity and importance in many life science applications, several factors such as complicated sample preparation, high cost, and time-consuming data analyses may prevent NGS applications from being more widely used in clinical and research settings. Therefore, it is crucial that the current methods are improved or newly developed to become faster, more robust, and accurate in NGS applications. Targeted sequencing, focusing on small but important gene sets or genetic regions, is a very powerful approach to screen disease-related key genes. Reductions in cost and experimental time as well as availability of targeted sequencing are fueling the use of NGS for many genetic applications. We have developed a new, simple, and robust sample preparation method called ‘NextDay Seq,’ enabling us to obtain targeted deep sequencing data within the next day of sample arrival. Researchers and clinicians can obtain sequencing data within 36 hours. Our method starts with a 15 minute DNA extraction kit followed by library preparation, sequencing, and then data analysis. The NextDay Seq library preparation method directly ligates adapters to targeted genes/amplicons. This new protocol does not require restriction enzyme digestion (i.e. Ion Torrent Ampliseq) or hybridization of the target region (i.e. Illumina TruSeq). It is faster and simpler than previously referenced library preparation kits. We have also developed a new data analysis tool called DanPA: a fast, accurate, and robust NGS data analysis tool. DanPA, yet developed mainly for targeted sequencing analysis, can also be used for whole exome or genome sequencing data analysis. DanPA detects any kind of reported mutations registered in the database such as Catalogue of Somatic Mutations in Cancer (COSMIC). We have so far analyzed 866 cancer FFPE tissue samples, 431 flash-frozen tissue samples, 18 cell lines samples, and 515 other biological or synthesized (i.e. plasmids) samples using these new inventions. Our system will help clinicians in better deciding which therapeutic options (personalized medicine) or biological applications are optimal to treat patients with specific mutations. Cancer patients should have exact mutation information in a timely manner in order to select treatment options. By combining our new FFPE DNA extraction method, NextDay Seq library preparation method, and DanPA data analysis software, we are able to provide key mutation data to patients, medical doctors, and researchers within 36 hours (next day). We believe this new innovative NGS system can change the paradigm for mutation screening in clinical and research applications. Citation Format: Pedro Mendez, Jun-Hee Yoon, Sharon Lee, James Kim, Jenny Dang, Thomas Kim, David Jablons, Il Jin Kim. A new innovative and robust targeted deep sequencing system: 36 hours turn round time from patient samples to the final mutation report. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3609.