Technical Issues Involved in Obtaining Reliable Data from Microarray Experiments

Microarrays show great promise in advancing the understanding of many biological phenomena, including toxicity and effectiveness of the many products regulated by the U.S. Food and Drug Administration. In addition, devices based on the microarray technology have the potential to individualize diagnosis and treatment of disease, as well as monitor efficacy of treatment regimens. To realize these expectations, reliable and reproducible measurements are essential. Currently, there are no generally accepted standards for performing and analyzing a microarray study. Without such quality assurance standards among the microarray community, it will be difficult to move this technology into the regulatory framework where it holds such promise. Here, we describe observations and approaches undertaken at the NCTR Center for Functional Genomics to examine and optimize steps in the complex microarray procedure with the aim of decreasing variability in order to generate reliable data. These observations illustrate some of the subtle technical issues that can easily be overlooked in microarray experiments. Among the factors that can influence microarray experiments are microarray printing procedures, oligonucleotide characteristics, RNA quality, and environmental factors. REGULATORY RESEARCH PERSPECTIVES Volume 6, Issue 1 March 2006 DHHS/FDA/Jefferson Labs National Center for Toxicological Research Impact on Public Health