DNA sequencing has seen dramatic cost reductions in recent years, while sample preparation costs have been relatively flat. The result is a `sample preparation bottleneck' apparent today will affect essentially all sequencing studies within a few years. In addition, sample input quantity requirements for standard approaches exclude important low-yield clinical sample types. The goal of this R21 project is to validate and demonstrate a practical integrated microfluidic sample preparation technology for pathogen genome sequencing that enables a significant advance in sample preparation cost, turn-around-time, and low-input capability. Integration of the entire sample preparation process in a single micro device will reduce real-world cost for high-throughput sample preparation more than 10-fold by lowering reagent consumption, the need for other consumables, capital equipment costs, hands-on time, and procedural errors. We will validate this technology on S. Aureus samples from an ongoing clinical trial, Project CLEAR, and then go on to sequence a large number of additional Project CLEAR samples.
Learning the full genome sequences of bacteria that make people sick help scientists and medical doctors discover why these bacteria cause disease, how these bacteria spread between people, and why some bacteria are resistant to antibiotic medicines. Great progress has been made in building instruments to read out DNA bases (A, C, G, T) in the genome, but it is still cumbersome to prepare patient samples to load on these machines. This proposal aims to deploy a new automated technology to streamline the preparation of samples for bacterial genome analysis.
