Making and Using DNA Microarrays: A Short Course at Cold Spring Harbor Laboratory

The conundrum is familiar. You are sent back in time to the Middle Ages with no artifact from the present, brought before the local ruler, and given 24 hours to prove you are indeed from the future, to impress the ruler and his advisors in some way, before you are executed in some suitably hideous fashion. What do you do?

Toying with this conundrum reveals how little we know in a practical sense about the everyday items that surround us. Can you fix your carand your computer? My guess is that few, if any, readers can do so. And so it was with some trepidation that Cold Spring Harbor Laboratory agreed to host a short course in the Fall of 1999, funded in part by the National Cancer Institute, in which students, primarily biologists, would not only print, use, and analyze DNA microarrays but would start the course by building the machines used to print the arrays. For some time, Patrick Brown and colleagues (Chu et al. 1998;DeRisi et al. 1997; Lashkari et al. 1997) at Stanford had been advocating the idea that smaller laboratories could enter the fray and hype surrounding these emerging microarray technologies by building machines rather than by buying them, a self-help philosophy that was strengthened by the Brown laboratory's web-based publication in June 1998 of the MGuide, a step-by-step guide to construct the arrayer, complete with parts list. Indeed, a number of laboratories have gone ahead and built their own machines.

Commercial vendors already offer some solutions for investigators interested in studying changes in genome-wide gene expression. Efforts by Steve Fodor and others at Affymetrix (Santa Clara, CA) in the early 1990s had led to the development of the GeneChip technology, in which relatively costly photolithographic techniques are used to …