AUTOMATION OF STEPS IN LARGE SCALE DNA SEQUENCING

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The overall objective of this research career award is to develop new methods and tools for automated large-scale DNA sequencing. Initially, the specific aims of the award are to: Train extensively in the field of genomics via lab rotations, courses and seminars in the Department of Molecular Biotechnology. In the lab training the candidate will perform all steps of DNA sequencing via current methods. This experience combined with the candidate's electrical engineering background will be used to develop fast, efficient methods to automate certain steps in large-scale DNA sequencing procedures. Develop a prototype robot that will dispense sub-microliter to sub- nanoliter volumes of reagents for DNA sequencing reactions. A precise robotic positioning system will be designed and built to access individual wells on 384-well or 864-well microtiter plates and alternate denser formats. Investigate and develop a new, automated procedure for loading sequencing reactions onto gels from high density formats. Currently this step in large-scale DNA sequencing is performed manually but with higher density reactions this will be more problematic. Explore alternate electrophoretic formats that require no net migration. Signal processing and identification techniques will be employed to identify DNA molecules in free solution. While performing the steps of large-scale DNA sequencing in lab training during the first year of the five year SERCA program, bottlenecks in large-scale DNA sequencing procedures will be identified. The remainder of the award will be used to focus on solving these problems using new, automated techniques. Ultimately, these technological developments will increase the throughput in DNA sequencing and contribute to the sequencing of the Human Genome. Deirdre Meldrum, the candidate, received her Ph.D. in Electrical Engineering from Stanford University in 1992. At Stanford and the Jet Propulsion Laboratory, Deirdre worked extensively on robotic and controls for space structures, space robots, and computer disk drives. Her strong background in robotics, controls, dynamics, and electrical/mechanical design will be invaluable for fulfilling the goal of automating steps in large-scale DNA sequencing. Throughout the award period and beyond, Deirdre will train and work closely with the faculty in the Department of Molecular Biology while maintaining close ties with the Department of Electrical Engineering. Leroy Hood, the principle faculty advisor, is Professor and Chair of the Department of Molecular Biotechnology at the University of Washington.