Gene expression studies using microarrays: principles, problems, and prospects

A number of mammalian genomes having been sequenced, an important next step is to catalog the expression patterns of all transcription units in health and disease by use of microarrays. Such discovery programs are crucial to our understanding of the gene networks that control developmental, physiological, and pathological processes. However, despite the excitement, the full promise of microarray technology has yet to be realized, as the superficial simplicity of the concept belies considerable problems. Microarray technology is very new; methodologies are still evolving, common standards have yet to be established, and many problems with experimental design and variability have still to be fully understood and overcome. This review will describe the time course of a microarray experiment-RNA isolation from sample, target preparation, hybridization to the microarray probe, data capture, and bioinformatic analysis. For each stage, the advantages and disadvantages of competing techniques are compared, and inherent sources of error are identified and discussed.