The Human Genome Project is rapidly developing a draft consensus sequence of the Human Genome. The immense value of this information has triggered the scale up of production rates and the incorporation of high-throughput capillary-array electrophoresis instruments. Further improvements are needed to decrease sample costs, increase automation, and improve throughput rates. This project will create an automated, integrated DNA analysis system that prepares nanoliter (nL)-scale sequencing reactions and analyzes the reactions in an ultrahigh-throughput, microchip-based DNA sequencer. The integrated system will consume about one-hundredth of the reagents used today and have a ten-fold higher throughput rate. The integrated system will consist of two main modules, a sample preparation module and an ultrahigh-throughput DNA analysis module. The sample preparation module will use arrays of 384 capillaries in cassettes to move liquids and perform biochemical reactions in 125 nL volumes. This module will automate shotgun sequencing beginning with lysed clones to produce fluorescently labeled cycle sequencing reactions for capillary or microchip analysis. The microchip-based DNA analysis module will load, run, and detect DNA samples in microchannels for sequencing and genotyping. This module will use robotics to transfer samples from microtiter plates to sample loading ports on a microchip, dock the microchip with electrodes under a detector, inject samples and separate them. The two modules will be developed simultaneously and then integrated into a complete automated sequencing system. The project will develop a series of prototypes that will be alpha-tested in the Molecular Dynamics Production Sequencing Group and then beta-tested at our collaborators at the Joint Genome Institute, the Washington University Genome Sequencing Center, and the Macromolecular Analysis Facility at the University of Wisconsin-Madison. The results of the external testing will be used to verify the system performance, refine the prototypes, and streamline the integration of this new technology into genome centers and core facilities.
