Miniaturized DNA Sequencer for Identification of Microbial Pathogens

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DESCRIPTION (provided by applicant): The ultimate goal of this project is to develop an extremely compact and inexpensive DNA sequence for applications in laboratory and clinical settings. The device will implement pyrosequencing on a disposable droplet based "digital microfluidic" cartridge and will be capable of sequencing 10's to 100's of nucleotides at a very low cost per run and at a low initial equipment investment. This platform will also integrate sample preparation, including DNA amplification, with sequencing to provide the integration and ease-of-use demanded of clinicians and other non-specialists who require DNA sequence data. The initial application for this capability will be microbial pathogen identification. In Phase I, a prototype was developed and the microfluidic protocols and biochemical reaction conditions for pyrosequencing were optimized. As a feasibility demonstration 20-40 base pairs within the ITS2 genetic region were sequenced for 13 different molds and yeasts which provided unambiguous identification of each isolate. In Phase II, this success will be built upon by integrating sample preparation steps including DNA concentration, DNA amplification, and template preparation into the system. The integrated system will be evaluated and compared to other commercially available solutions in terms of speed, cost and accuracy of fungal identification. Further optimization of the pyrosequencing biochemistry will be performed to enable longer read lengths on shorter time scales while retaining high accuracy. Finally, a data analysis tool will be developed to automate base calling and database queries. The final product will represent a streamlined approach to fungal species identification, integrating a number of components of the contemporary pathogen identification workflow.