DNA Microarrays: A Practical Approach/Microarray Biochip Technology/DNA Arrays: Methods and Protocols.
Microarray Biochip Technology. Mark Schena, ed. Natick, MA: Eaton Publishing, 2000, 298 pp., $45.95. ISBN 1-881299-37-6.
DNA Arrays: Methods and Protocols. Jang B. Rampal, ed. Totowa, NJ: Humana Press, 2001, 264 pp., $89.50. ISBN 0-89603-822-X.
Although all three texts address the topic of microarrays, each has a different focus. The first two are edited by Mark Schena, one of the pioneers in the field of DNA microarrays, whereas the last, and newest, text is edited by Jang Rampal of the Beckman Coulter microarray group. DNA Microarrays: A Practical Approach focuses on methods and procedures that would be used by someone just entering the field of DNA microarrays. It joins the well-known "Practical Approach Series' of publications familiar to many in biomedical sciences. By contrast, Microarray Biochip Technology discusses the technology behind the major instruments and procedures used for DNA microarray analysis and is from Eaton, the publisher of BioTechniques. Finally, DNA Arrays: Methods and Protocols is the most recent publication and joins a rapidly expanding series, "Methods in Molecular Biology'. Although this text contains both procedures and technology assessment, most chapters are not as extensive as those in the books edited by Schena. Although all three books offer insights into this rapidly expanding field, each provides the reader with a different perspective that would satisfy unique needs.
DNA Microarrays: A Practical Approach. Several workers who have made substantial advances in DNA microarrays contributed to this 10-chapter book. Its major theme is providing practical information (some in a recipe format) that illustrates how to perform DNA microarray analyses. The first chapter is an overview of selected techniques and recipes and is cowritten by the Editor and R.W. Davis, another pioneer in the use of microarrays. Chapter 2, authored by an early developer of confocal scanners, addresses issues with confocal laser fluorescence scanning of arrays prepared on glass slides.
The next three chapters discuss less-recognized applications of microarrays, such as representational differential analysis, use of oligonucleotide arrays for detection of single nucleotide polymorphisms, and selection of antisense oligomers (the latter two by E. Southern and colleagues). Incyte s ink-jet technology, developed to synthesize (in situ) oligonucleotide-based arrays, although not commercially available, is summarized in Chapter 6. By contrast, D. Erlander and colleagues (Chapter 7) describe in detail the step-by-step procedures involved in the use of laser capture microdissected cells from formalin-fixed tissue and the subsequent expression results from custom cDNA arrays printed with a commercial robotic workstation (Beckman Biomek 2000). They clearly illustrate that expensive printing stations are not needed to work in the microarray field.
Chapter 8 summarizes genomic sequence manipulation and data mining methods. Unfortunately, procedures to collect, process, or analyze the enormous volume of raw results flooding out of a typical DNA microarray are not treated in this chapter or elsewhere in this book. This is a major deficiency in an otherwise excellent text devoted to practical aspects of DNA microarrays. Chap ter 9 presents the use of variable electric voltages to manipulate DNA samples on arrays as developed by M. Heller and colleagues at Nanogen. Finally, some future applications are illustrated in Chapter 10. Notably missing from this book was a chapter on the use of the Affymetrix GeneChip[R] as well as a section on experimental design and interpretation of results.
In summary, for those just entering this exciting experimental field, this is a valuable book to have on the shelf and gives much practical information to the do-it-yourselfer.
Microarray Biochip Technology. This 13-chapter book focuses on the principles and technologies used by companies and investigators in the field of DNA microarrays. Although experimental methods are absent, there is an abundance of practical information supported by explanations of procedures and concepts used in DNA microarrays.
Four chapters summarize the various array preparation procedures available to those wanting to create their own microarrays. These include the dominant spotting or "quilling" approach (Chapters 2 and 4), "ring-and-pin" technique (Chapter 3), and piezoelectric dispensing (Chapter 11). Two commercialized DNA array technologies are also discussed: the Flow-Thru[TM] chip from Gene Logic (Chapter 5) and the Affymetrix GeneChip, created using photolithography (Chapter 6).
The discussion of Incyte's proprietary Gene Expression Microarray (GEM[TM]) in Chapter 7 provides some additional explanations for creating arrays and manipulation of expression array data that integrate nicely with the following chapter. Chapter 8 provides a thorough explanation of various data analysis and interpretation methods, which are extensively reviewed by S. Shams and colleagues at BioDiscovery. Understanding this chapter is essential if one is to fully utilize any of the approaches available for data analysis or for interpretation of the deluge of raw data collected from DNA microarray chips. Here there is almost no overlap with Chapter 8 from DNA Microarrays: A Practical Approach on gene expression analysis.
Chapter 9 describes some commercial products for the preparation and use of microarrays, and Chapter 10 presents an alternative labeling system (MICROMAX[TM]) developed by NEN to provide ultrahigh sensitivity. Issues surrounding fluorescent scanning of microarrays (e.g., confocal scanning lasers vs CCD cameras, uses, and detection limits) are addressed in Chapter 13 by D. Wellis and colleagues from a leading scanner manufacturer (Axon); their discussion is congruent with those in Chapter 2 of DNA Microarrays: A Practical Approach. Finally, an extensive list of suppliers is included that contains detailed information plus website addresses. What is lacking here are chapters on mass spectroscopy-based analysis (e.g., DNA MassArray[TM] from Sequenom) and protein arrays, which have evolved rapidly since the publication of this book a year ago. These two topics would be great additions to a second edition of this otherwise superb book.
DNA Arrays: Methods and Protocols. This 17-chapter text is the most recently published of these three books and represents a more "centrist" approach. The editor has combined text-based summaries of DNA microarrays with abbreviated methods chapters, which differentiates this text from the other two reviewed here.
Chapter 1, by E. Southern, provides some historical perspective of DNA microarrays. This is followed by a description in Chapter 2 of gel-immobilized arrays by another pioneer in DNA microarrays, A. Mirzabekov. Sequencing-by-hybridization methods developed at HySeq are discussed in Chapter 3 by R. and 5. Drmanac, who use the proprietary HyChip[TM] DNA microarray as their example; corresponding recipes and specific procedures are provided in Chapter 11. Methods to synthesize the photolytic precursor compounds that are used to create the Affymetrix GeneChip are described in Chapter 5, although it is doubtful that many readers will have the necessary or game synthesis skills or resources to prepare these compounds.
Chapter 9 nicely provides recipes and protocols to perform expression analysis with the Affymetrix GeneChip. Use of the GeneChip is considered by some to be an easy entry point into use of DNA microarrays. For example, when used for the first round of expression analysis, the GeneChip will likely identify dozens of candidate gene sequences from the tens of thousands of gene sequences present on the chip. This smaller collection of candidate sequences identified from GeneChips can then be used to create custom "secondary" cDNA arrays for more targeted studies, as indicated in the next two chapters. Missing from this fine chapter, unfortunately, were approaches or procedures to process, validate, and analyze the primary data from the GeneChip.
Chapters 7 and 8 concisely describe how to create custom microarrays (using oligonucleotides or cDNA fragments) in the laboratory. Specific instructions for use of a proprietary ink-jet system to create an oligonucleotide-based glass array via phosphoramidite coupling are included. Chapter 7 also briefly addresses how to assess the imprecision of the array deposited on the glass slide, which is a major weak point in current microarray analysis. Chapter 8 details the use of the Beckman Biomek 2000 liquid-handling workstation to create cDNA arrays that are contact printed on glass slides. By contrast, this chapter provides much more detail on the use of the Biomek to print arrays than is described in Chapter 7 of DNA Microarrays: A Practical Approach.
This reviewer expected that DNA Arrays: Methods and Protocols would have the most current material, based on its publication date. Although true for most of this book, the information in Chapter 12, unfortunately, is virtually unchanged from that found in Chapter 5 of DNA Microarrays: A Practical Approach. In particular, with only minor changes, the majority of figures, the table, and the incorporation example are virtually identical to the material published 2 years earlier. This was clearly an opportunity missed to demonstrate the evolution in methodology.
The last portion of this book examines two applications (one diagnostic and one research). The diagnostic application (Chapter 13) uses ink-jet-created microarrays (prepared at MicroFab Technologies) to determine HLA genotypes, whereas gene expression analysis of yeast, using 70mer oligonucleotides printed on glass arrays, is presented in Chapter 14. Details of the actual procedures are more complete in Chapter 14 than in Chapter 13.
Chapter 15 addresses the use of bioinformatics and more sophisticated interpretation methods to process microarray data. Written by 5. Shams from BioDiscovery, it is similar to the chapter (Chapter 8) that he and his colleagues wrote for Microarray Biochip Technology. This chapter is shorter, however, and not as thorough (13 vs 33 pages) as the older chapter. Finally, Chapter 16 briefly discusses confocal scanning of microarrays and duplicates, to a lesser degree, material available in Chapter 2 of DNA Microarrays: A Practical Approach and Chapter 13 of Microarray Biochip Technology.
In summary, all three texts are excellent references to help the reader become acquainted with the field of microarrays. Clinical and research scientists entering the world of microarray analysis should consider what format they will be using when selecting one of these texts. For those who want to print their own microarrays, DNA Microarrays: A Practical Approach is probably the best reference. If the GeneChip is to be used, then DNA Arrays: Methods and Protocols contains the definitive section. Meanwhile, Microarray Biochip Technology provides much useful background information for printing microarrays or using GeneChips and includes thorough coverage of data processing and analysis.
As expected with any rapidly evolving field, many advances have been made in the field of DNA microarrays. One tool to supplement the information in these texts would be the "Virtual Appendix' of nonvendor websites, which could be consulted for the latest information (http://www.mpiz-koeln.mpg.de/~weisshaa/Adis/DNA-array-links. html; http://industry.ebi.ac.uk/~alan/MicroArray/; and http://www.protocol-online.net/molbio/DNA/dna_microarray.htm). Alternatively, the next editions could include electronic media that contain the procedures, protocols, and websites.
Theodore E. Mifflin
Department of Pathology
University of Virginia
Charlottesville, VA 22908