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Microarrays pp 67-93 | Cite as

Integrated Microfluidic Devices for Automated Microarray-Based Gene Expression and Genotyping Analysis

  • Robin H. Liu
  • Mike Lodes
  • H. Sho Fuji
  • David Danley
  • Andrew McShea
Part of the Integrated Analytical Systems book series (ANASYS)

Abstract

Microarray assays typically involve multistage sample processing and fluidic handling, which are generally labor-intensive and time-consuming. Automation of these processes would improve robustness, reduce run-to-run and operator-to-operator variation, and reduce costs. In this chapter, a fully integrated and self-contained microfluidic biochip device that has been developed to automate the fluidic handling steps for microarray-based gene expression or genotyping analysis is presented. The device consists of a semiconductor-based CustomArray® chip with 12,000 features and a microfluidic cartridge. The CustomArray was manufactured using a semiconductor-based in situ synthesis technology. The micro-fluidic cartridge consists of microfluidic pumps, mixers, valves, fluid channels, and reagent storage chambers. Microarray hybridization and subsequent fluidic handling and reactions (including a number of washing and labeling steps) were performed in this fully automated and miniature device before fluorescent image scanning of the microarray chip. Electrochemical micropumps were integrated in the cartridge to provide pumping of liquid solutions. A micromixing technique based on gas bubbling generated by electrochemical micropumps was developed. Low-cost check valves were implemented in the cartridge to prevent cross-talk of the stored reagents. Gene expression study of the human leukemia cell line (K562) and genotyping detection and sequencing of influenza A subtypes have been demonstrated using this integrated biochip platform. For gene expression assays, the microfluidic CustomArray device detected sample RNAs with a concentration as low as 0.375 pM. Detection was quantitative over more than three orders of magnitude. Experiment also showed that chip-to-chip variability was low indicating that the integrated microfluidic devices eliminate manual fluidic handling steps that can be a significant source of variability in genomic analysis. The genotyping results showed that the device identified influenza A hemagglutinin and neuraminidase subtypes and sequenced portions of both genes, demonstrating the potential of integrated microfluidic and microarray technology for multiple virus detection. The device provides a cost-effective solution to eliminate labor-intensive and time-consuming fluidic handling steps and allows microarray-based DNA analysis in a rapid and automated fashion.

Keywords

Check Valve Microarray Chip Hybridization Chamber Storage Chamber Fluidic Handling 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

Acknowledgment The authors thank Tai Nguyen, Kevin Schwarzkopf, Tony Siuda, Alla Petrova, Kia Peyvan, Michael Bizak, Jeff Kemper, Al Pierce, and Mike Slota for technical support and useful discussions. This work has been sponsored by DoD contract #1999011104A.

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Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Robin H. Liu
    • 1
  • Mike Lodes
    • 2
  • H. Sho Fuji
    • 2
  • David Danley
    • 2
  • Andrew McShea
    • 2
  1. 1.CombiMatrix Corporation, IncOsmetech Molecular, DiagnosticsPasadena, CAUSA
  2. 2.CombiMatrix Corp.Mukilteo

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