Over the past 3 years the Genomation Laboratory of the University of Washington (15W) and partner/subcontractor Orca Photonic Systems, Inc., havedesigned, developed, and tested ACAPELLA, an automated fluid sample handling system. This system prepares final reaction volumes of 1 to 2 microliters inside glass capillaries for reactions such as PCR, sequencing reactions, and restriction digests. Approximately 44,000 capillaries have been run through the system to test the hardware, software, and biology. Some biology tests were run in parallel with the UW Genome Center to validate the results. The testing results demonstrate that the first generation system, the ACAPELLA-1K, can process samples with high reliability, no contamination, and high quality at a rate of 1,000 samples in 8 hours. The second-generation system, the ACAPELLA-5K, has just come on-line and will process 5,000 samples in 8 hours. The 5K system available at the start of this project will include automated thermal cycling. In this advanced development project, the ACAPELLA-5K system will be enhanced to provide a contiguous, automated process stream, from initial DNA samples to the sequencer. Thermal cycling, purification, sample pooling, sample storage and archiving, will be integrated with ACAPELLA's existing sample preparation capabilities. To validate ACAPELLA technology in the operational sequencing center environment, extensive alpha- and beta-tests will be performed with NIH Genome Centers. Alpha-testing will take place in the UW Genome Center. Beta-testing will take place in the UW Genome Center, the Washington University St. Louis Genome Sequencing Center (subcontract), and the Whitehead Institute/MIT Center for Genome Research (no subcontract, volunteer with existing funds). To ensure ACAPELLA remains viable with the state-of-the-art in DNA sequencing technologies, we will assess and develop methods for direct, automated loading to capillary electrophoresis systems and microchip sequencers. Technology associated with this project will be disseminated and commercialized to bring ACAPELLA processors to the point where they can be deployed to the major genome centers on a commercial basis.