Technology Insight: tuning into the genetic orchestra using microarrays--limitations of DNA microarrays in clinical practice.

Scientific advances in the field of genetics and gene-expression profiling have revolutionized the concept of patient-tailored treatment. Analysis of differential gene-expression patterns across thousands of biological samples in a single experiment (as opposed to hundreds to thousands of experiments measuring the expression of one gene at a time), and extrapolation of these data to answer clinically pertinent questions such as those relating to tumor metastatic potential, can help define the best therapeutic regimens for particular patient subgroups. The use of microarrays provides a powerful technology, allowing in-depth analysis of gene-expression profiles. Currently, microarray technology is in a transition phase whereby scientific information is beginning to guide clinical practice decisions. Before microarrays qualify as a useful clinical tool, however, they must demonstrate reliability and reproducibility. The high-throughput nature of microarray experiments imposes numerous limitations, which apply to simple issues such as sample acquisition and data mining, to more controversial issues that relate to the methods of biostatistical analysis required to analyze the enormous quantities of data obtained. Methods for validating proposed gene-expression profiles and those for improving trial designs represent some of the recommendations that have been suggested. This Review focuses on the limitations of microarray analysis that are continuously being recognized, and discusses how these limitations are being addressed.