Development of A New Generation DNA Sequencer

Liu, Shaorong

Abstract

DNA sequencing using microfabricated devices has a lot of advantages; many of them are originated from a chip injector. To list a few, (1) a very narrow band is injected, (2) a uniform signal intensity profile is obtained, (3) sample volume is reduced to sub-muL and (4) extra sample cleanup is performed. However, there are two major limitations associated with microfabricated devices. (a) limited straight channel length and (b) constrained space for reservoir arrangement. A new generation DNA sequencer based a chip injector coupled with conventional capillaries is proposed. Viewed from the perspective of sequencing on a chip, the proposed scheme eliminates the two limitations. Straight channel length becomes unlimited since a capillary of any length can be coupled to a chip injector and the space for reservoirs becomes unlimited as well since many separate chip injectors can be used to host reservoirs due to the flexibility of the capillaries. Seen from the perspective of sequencing using CGE, the proposed scheme brings all advantages of a chip injector to CGE. The sequencer will consist of a 4-PMT rotary confocal scanner with 8x48-capillary arrays. Linear polyacrylamide will be optimized for sequencing separation on the proposed sequencer. Small volume sample preparation will be incorporated to reduce the sample volume and automated instrumentation will be developed to enhance the sample throughput. Through close collaboration with Genome Sequencing Centers (e.g. Genome Therapeutics Corporation), the sequencer will be developed to meet the needs of genome sequencing world. The new generation sequencer will have specifications of 24-hour operation with minimum attention, average read-length of 800-1000 bases, a run-to-run time of less than 1 hour, and a sample volume of 0.5 to 1 muL.