An integrated system for sample preparation and DNA sequencing is proposed. The computer controlled system will automate all steps from picking recombinant clones from agar plates to production of primary sequence data. The DNA sequencing system will eliminate all bottle necks that occur between subcloning and obtaining raw sequence data, significantly reduce both labor and reagent costs, and have a throughput of up to 250 megabases of raw DNA sequence per machine per year - more than an order-of-magnitude increase in throughput over existing technologies. The DNA sequencing system will consist of four basic hardware components - a clone picker, a microextraction module (MEM), a device for processing small volume polymerase chain reaction and cycle sequencing reactions (PCR/CS), and a capillary array electrophoresis (CAE) DNA sequencer. The DNA sequencing system will leverage the capabilities of both an existing prototype CAE instrument, which is a high throughput capillary array DNA sequencing instrument, and a colony picker, which is a functional high throughput device. In addition, major modules of the operating software have already been developed. The goals of the project are to: 1) design and construct a flow process PCR/CS device, 2) design and construct a micro-extraction module and integrate it with the clone picker, 3) evaluate improved amplification and sequencing chemistry to simplify the proposed system, and 4) integrate the chemistry and hardware and test the DNA sequencing system within a large-scale sequencing project. Development of the integrated DNA sequencing system will facilitate the completion of the DNA sequence acquisition phase of the Human Genome Project and enable the application of DNA sequencing to clinical settings for the diagnosis of human genetic diseases and the development of biopharmaceuticals.
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