A microchannel electrophoresis DNA sequencing system

Last year, the Joint Genome Institute was the third leading sequencing group in the world with over 20 million bases of human DNA finished. The goal of the human genome project is to sequence the 3 billion bases of human DNA sequence by 2003. In order to increase the DNA sequencing throughput of the Joint Genome Institute, we have developed a microchannel electrophoresis system. One critical new and unique element of this system is a process for production of 96 and 384 microchannels on bonded glass substrates up to 14 x 58 cm. In order to utilize these instruments for DNA production sequencing, we have been evaluating and implementing software to convert raw electropherograms into called DNA bases with an associated probability of error. Our original intent was to utilize the DNA base calling software known as Plan and Phred developed by the University of Washington. In our tests and evaluations of this software applied to microchannel data, we observed that the electropherograms are of a different statistical and underlying signal structure compared to slab gels. We have modified Plan and Phred to improve base calling performance for the microchannel data. In this paper, we will present 1) the microchannel DNA sequencing system and show the advantages compared to current slab gel and capillary systems. 2) The signal processing modules needed for DNA base calling including correction of multiple wavelength channels, signal averaging, non-uniform sampling, variable DNA mobility, and peak shape and spreading effects. 3) A comparison of the DNA base signatures in the raw data of microchannels vs. slab gels including some simple modeling results. This will be propagated through the base calling software to show the impact on DNA sequencing