Gearing for automatic genomics: Automation: Genome and Functional Analyses, Methods in Microbiology (Vol. 28) edited by A.G. Craig and J.D. Hoheisel

Academic Press, 1999. $59.95 pbk (270 pages)ISBN 0 121 94860 9The emergence of structural and functional genomics has revolutionized both the conceptual approach and the experimental scale of studying life at the molecular level. The benefits of studying molecular biology at the genome scale have been evident for many years and the transition from fantasy to reality has already begun. Regardless of how enticing the fruits of a post-genome era appear, speculation and enthusiasm about conducting genome-scale analysis will only go so far in the absence of the requisite advances in the laboratory. One of the key challenges is to implement new technologies and approaches to molecular biology that allow analysis on a very large scale. The best solution to this problem is to develop and implement new technologies that miniaturize and automate many routine analyses to achieve the scale required. Attaining the automation needed to achieve ‘mega’ productivity through advances in laboratory instrumentation and methodologies is the focus of ‘Automation: Genome and Function’.Many laboratory advances in scaling and throughput have already been accomplished, permitting the dawn of the genome era. For many aspects of molecular biology, structural genomics laboratories today are conducting research on a scale that is thousands of fold higher than a decade ago. Ten years ago, the completion of 50 kb of contiguous genomic sequence was a very impressive accomplishment. Since then, dozens of microbial genomes, ranging from hundreds of kb to 5 Mb have been sequenced completely and nearly 100 genomes are forthcoming. Today’s most impressive feats are the complete sequencing of the 12 Mb Saccharomyces cerevisiae genome and 100 Mb Caenorhabditis elegans genome. Completion of even larger genomes, including the human genome, is only a few years away.The vast information generated by structural genomics and the advances in high-throughput technologies have led to an equivalent large-scale increase in gene-expression analysis. Once a fantasy for many researchers, cDNA microarray technology is now allowing investigators around the world to determine the expression of 10 000 genes simultaneously in less time than it takes to analyse a single gene’s expression by northern blot. Such genome-scale analysis could be considered the birth of functional genomics. The instrumentation and methodologies used to achieve this scale of productivity, both in structural and in functional genomics, are comprehensively detailed in this book.The forward is appropriately written by Leroy Hood, who is acutely aware of the requirements needed to achieve the high throughput necessary to conduct genome-scale analysis. He describes the challenge of gearing a modern laboratory to handle genome-scale production. He also contributes a chapter entitled ‘Deciphering Genomes Through Automated Large-scale Sequencing’. This chapter is a must read for anybody who wants to know what it takes to set up a center with the capacity of sequencing entire genomes. Ulf Pettersson introduces the book by giving a historical perspective of modern microbiology. Although this book represents the 28th volume in a series of ‘Methods in Microbiology’, not all the chapters focus on microbiology per se. For example, the chapters on automating library picking, presentation and analysis, robotic instrumentation, and integrated environments for plasmid preparations and sequencing are of more general interest. Functional genomics are also well represented, with several chapters ranging from high-throughput functional assays to computer modeling of protein function on a genomic scale. Although I was happy to see that the subject of parallel gene expression was covered in the book, it was only a brief chapter on DNA arrays for transcriptional profiling. I would have preferred greater coverage of the subject. A wide breadth of assays are presented and the focus varies from methodological to instrumentation, but the underlying automation theme of the book appears in every chapter. There is no shortage of publications about the importance of genome-scale analysis that often stress that the automation of various laboratory procedures is required to achieve this goal. It is refreshing finally to see a solution-oriented publication that describes in detail how to actually achieve automation in the laboratory.