Nanopore Based Direct BAT-25 Microsatellite Sequencing

Project Summary During this program, Electronic BioSciences, Inc. (EBS) will develop and demonstrate a complete end-to-end methodology, including sequence-targeted sample and library preparation and automated signal processing/data analysis capabilities, for targeted human genome microsatellite characterization with a specific focus on BAT-25, a well-known microsatellite biomarker associated with colon cancer. Microsatellites are simple/short repeats (1-10 nucleotides in length) that occur in tandem 5-50 times and are among the most variable types of DNA sequences in the genome. Mutations to these microsatellite regions include expansion or contraction of the repeat number, single nucleotide polymorphisms (SNPs), and/or insertions or deletions (indels), which have been documented with predisposition, onset, and/or prognosis for many types of cancer and have been associated with numerous conditions (e.g., viral infections, cardiac disease, etc.). The targeted characterization of microsatellite biomarkers represents a tractable approach (relative to whole genome sequencing) towards clinical and point-of-care diagnostics and prognostics due to the associated instrumental and consumable logistics and cost, data output/processing/management, and ease of data/results interpretation. To date, however, there is no technology presently available that is ideally suited for microsatellite characterization, which has significantly limited the understanding of microsatellites, their roles in disease states, and the development of associated assays. During this Phase I SBIR program, EBS will pave the way to quick and efficient microsatellite assessments and diagnostic/prognostic utilization through novel but simplistic methodology and technological developments.Project Narrative This program is aimed at developing a complete end-to-end system for targeted, high-accuracy, microsatellite characterization and quantification, including the associated sample/library preparation and data output/characterization. Our direct, electronic, nanopore-based, single-molecule, strand sequencing methodology will enable high accuracy, single nucleotide resolution, which is suitable for diagnostic/clinical applications. The developments and demonstrations performed during this program will lay the foundation for the development of improved targeted sequence preparation/isolation methods and the associated microsatellite research, which in turn will lead to the development of microsatellite-based clinical diagnostics and/or prognostics technologies, ultimately improving human health and personalized patient care.