SBIR Phase II: Low-cost Detection and Enrichment of Nucleic Acids by Interfacing with Commercially Available Cell Sorters

The broader impact/commercial potential of this Small Business Innovation Research (SBIR) project will be to enable affordable detection and enrichment of rare DNA or RNA molecules from a large background population. Currently, such detection is performed on expensive, dedicated instruments that have low sensitivity and are not able to enrich. The strategy is to encapsulate the fluorescently-identified target molecules in thin oil shells so that they mimic cells, and then process them on sensitive and high-throughput cell-sorting instruments that are commonly available. By offloading the detection and enrichment to such machines, all that is required by researchers is a simple tool that encapsulates the molecules in thin oil shells. Applications made possible by high sensitivity and enrichment are numerous, from rare pathogen or cell detection to target capture of uncommon mutant sequences with the goal of downstream sequencing. Between the reduced cost and expansion of capabilities, this approach is likely to become a widely adopted method. This SBIR Phase II project proposes to develop a deployable instrument that allows high-throughput, low-cost quantitation of DNA/RNA molecules in a sample by interfacing with existing flow cytometry instruments. The initial objective is to quickly engineer all the functionality desired in that final instrument into a rough alpha version. Its features will include reliable droplet generation from iteratively optimized hard-plastic microfluidic chips, and automation via an advanced fluid handling system with precise feedback control. The second objective is to build the actual beta version for customer trials. The beta version will replace most of the off-the-shelf parts with streamlined, custom engineering and focus on reducing size and cost while still improving function through more iterative chip optimization. The final objective is to use the beta instrument to optimize the protocols and reagents for several applications using customer samples and benchmarking. At the conclusion of the project, the goal is to have instruments at customer sites generating data.