Microarray technology: basic methodology and application in clinical research for biomarker discovery in vascular diseases.

Microarray technology is a novel tool in molecular biology, capable of quantitating hundreds or thousands of gene transcripts from a given cell or tissue sample simultaneously. A microarray has thousands of DNA fragments or oligonucleotides of known sequence arrayed in a known sequence of rows and columns on a chip. Hybridization of sample RNA that has been reverse-transcribed and labeled enables the detection and quantitation of specific transcripts. The ability to quantitate systemic gene changes in normal vs. diseased states has led to significant progress in many biomedical disciplines, including lipoprotein and atherosclerosis research, and can be used for discovery of diagnostic/prognostic and predictive biomarkers and to test the effectiveness of potential therapeutic agents. The design and analysis of microarray experiments present some unique problems to clinical medicine due to inherent issues related to biological sample procurement and processing, sensitivity and specificity of the assay, reliability and reproducibility of data, and applicability of the technology in multicenter-based clinical studies. This chapter will provide details on the methodologies that address these problems for successful microarray-based transcriptome analysis of tissues, whole blood, cell subpopulations, and cultured cells.