edited by B. R. Jordan Springer-Verlag (2001) 140 pages. ISBN 3-540-41508-4£31.50/$49
Much has been written about DNA microarray technology in recent years. But,for the complete novice, gathering enough information to be able to plan and conduct one's own experiments remains a great challenge. DNA microarrays are now widely used and are increasingly the method of choice for investigating changes in gene expression, and so a guide to the different systems and to data acquisition and analysis techniques would be very welcome. Jordan has assembled a collection of articles aiming to do just that. Part of the Springer `Principles and Practice' series, the book begins with an historical overview, following the development from Hans Lehrach's colony filters to Affymetrix's oligonucleotide chips. Separate chapters are dedicated to different microarray platforms: cDNA arrays on glass slides; nylon membranes for radioactive or calorimetric detection; and Affymetrix oligonucleotide chips. Each system is explained in detail, complete with protocols and figures of example results including considerations regarding experimental strategy and possible pitfalls.
A separate chapter tackles the issues of data analysis and data mining. Microarray experiments fulfil their promise only if the `red and green spots'are translated into expression levels in a correct and meaningful way. To obtain biological knowledge from the vast amount of data, skillful application of data mining tools is required. The authors manage to give an easy-to-understand introduction to this complex subject and highlight both the potential and the limitations of currently available methods. With numerous references to original articles, the difficult subject of cluster analysis is well explained. The authors also give a detailed description of Expression Profiler, a software tool that has been developed by the authors at EBI.
The final chapter offers a perspective on future developments, speculating that most laboratories will use commercially available microarray platforms rather than investing time into establishing their own systems. The competition for commercial systems can come only from a large microarray consortium that distributes standardised arrays to academic labs. The need for standardised sets of cDNA clones, preferably covering whole genomes, as well as centralised data repositories is also stressed.
While the book offers a comprehensive source of information, a little too much space is devoted to arrays spotted onto nylon membranes. Although low-density spotting can be useful as a complementary method, cDNA microarrays on glass slides are the most commonly used method. The authors themselves predict that future use of microarrays will mainly consist of commercially available (possibly glassbased) systems. Researchers no longer need to expend precious time and resources figuring out the difficult task of making their own arrays. As the technology comes of age, considerations of experimental strategy, data analysis and reproducibility become the main issues.
This book offers an overview of currently available technology and is clearly very useful as an introduction to the field. However, advances in this fast-moving field are too frequent to be covered in detail. Additional information, in particular about novel developments in spotting technology,hybridisation protocols and data processing, has to be acquired by following the recent literature or accessing sources on the internet.
The editor concludes that “expression measurement is here to stay” - this book can help us to make the most of it.