PNNL

Abstract

Microarrays allow for deeply multiplexed analysis of biological samples. Also known as “DNA chips,” up to several hundred thousand genes can be detected with a single hybridization reaction. In the United States, several federal agencies and private environmental foundations have sponsored research investigating the ability of DNA microarrays to provide sensitive and specific multiplexed detection of the spectrum of pathogenic microorganisms that may be present in environmental samples. Because pathogens in environmental samples are expected to be in very trace quantities, the primary challenge for microarray-based detection for environmental samples is providing sufficiently labeled target materials such that they can be detected using these assays. Trace detection often requires collection of a sufficient quantity of sample, significant concentration of that sample, sample processing to remove potential interferrents, amplification and labeling of the target material and finally, endpoint detection. The purpose of this chapter will primarily focus on the challenges of multiplexed amplification and target labeling to provide sufficient material for detection on microarrays. This chapter is organized to introduce readers to concepts of DNA microarrays, published applications of microarrays, challenges from transitioning microarrays from clinical to environmental samples, target labeling strategies, and finally concluding remarks on other challenges as these deeply multiplexed assays are developed.