Fully Integrated Miniature Device for Automated Gene Expression DNA Microarray Processing

A DNA microarray with 12 000 features was integrated with a microfluidic cartridge to automate the fluidic handling steps required to carry out a gene expression study of the human leukemia cell line (K562). The fully integrated microfluidic device consists of microfluidic pumps/mixers, fluid channels, reagent chambers, and a DNA microarray silicon chip. 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 into the cartridge to provide pumping of liquid solutions. The device was completely self-contained: no external pressure sources, fluid storage, mechanical pumps, mixers, or valves were necessary for fluid manipulation, thus eliminating possible sample contamination and simplifying device operation. Fluidic experiments were performed to study the on-chip washing efficiency and uniformity. A single-color transcriptional analysis of K562 cells with a series of calibration controls (spiked-in controls) to characterize this new platform with regard to sensitivity, specificity, and dynamic range was performed. The device detected sample RNAs with a concentration as low as 0.375 pM. Experiment also showed that the performance of the integrated microfluidic device is comparable with the conventional hybridization chambers with manual operations, indicating that the on-chip fluidic handling (washing and reaction) is highly efficient and can be automated with no loss of performance. The device provides a cost-effective solution to eliminate laborintensive and time-consuming fluidic handling steps in genomic analysis. Microarrays have become a widely used technology for studying mRNA levels and examining gene expression in biological samples. Investigators rely on data produced by microarray experiments to assess changes in gene expression levels among various experimental tissues and treatments. The applications of microarrays for gene expression profiling 1 include pathway dissection, 2 drug evaluation, 3,4 discovery of gene function, 5 classification of clinical samples, 6-8 and investigation of splicing events, 9 among many others. There are various microarray technologies and numerous commercially available sources of microarrays. Microarrays can be produced either by physical deposition of presynthesized DNA 1,