Automated microfluidics for genomics

Abstract

Abstract--The Genomation Laboratory at the University of Washington is developing an automated fluid handling system called "Acapella" to prepare microliter reactions for genome analysis. The system prepares 5,000 samples in 8 hours for general-purpose chemistry analysis including DNA sequencing reaction preparation. Keywords--Automation, DNA sequencing, microfluidics, biotechnology, biomechatronics, genomics I. INTRODUCTIONMotivated by the Human Genome Project (HGP) and the biotechnology revolution, an exponential growth in genome automation has occurred over the past several years [1]. Solutions include robots that mimic manual procedures in the laboratory, automated systems that improve performance for specific tasks, to microfabricated chips that perform microfluidic analysis of DNA samples. For a review of genome automation, see [2][3]. For an introduction to DNA sequencing and the automation of it, see [4].In the Genomation Laboratory at the Univ. of Washington (http://rcs.ee.washington.edu/GNL/genomation.html) and with Orca Photonic Systems, Inc. (Redmond, WA), an automated submicroliter fluid sample preparation system called ACAPELLA is being developed. Reactions such as restriction enzyme digests, polymerase chain reactions (PCRs), and sequencing reactions are prepared in glass capillaries, one per sample, with an automated system that can process 5,000 samples in 8 hours. On-going development includes new, fully automated modules for thermal processing of capillaries, real-time DNA quantitation, and purification of DNA inside of capillaries to prepare the samples for DNA sequencing. Applications of the technology include minimal residual disease quantification and sample preparation for DNA. Preliminary work on the ACAPELLA is presented in [4][5]. This paper presents the current development on the ACAPELLA core processor and the thermal cycling module. II. SIGNIFICANCEThe goals of the ACAPELLA system are 1) to develop a very high-throughput (5000 samples in 8 hours) fluid handling system with minimal recurring labor costs, 2) to reduce by tenfold the typical DNA sample volumes for Polymerase Chain Reaction (PCR) and sequencing reactions over current practice, with a proportionate reduction in reagent costs, and 3) to develop a closed sample-processing pipeline. The core technology comprises a system capable of mixing an incoming DNA sample with appropriate reagents in a capillary under full automation.In [5] the significance of the throughput, cost reduction, process benefits, and cost/benefit analysis of the ACAPELLA system is described. In short, the system prepares small 0.5 -2 µl reaction volumes, maintains a 100 to 300 picoliter reagent dispense resolution, retains high mixing precision and quality in small volumes, and demonstrates the ability to achieve high quality, reproducible biology without contamination. The high throughput capability is competitive with large scale robotic batch processing. III. INSTRUMENTATION AND METHODSThe core ACAPELLA sample processor embodies two essential concepts:...

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