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Practical Reference On Microarray Analysis, January 7, 2005
This review is from: Applying Genomic and Proteomic Microarray Technology in Drug Discovery (Hardcover)
This book details the commercial array landscape, covering the many issues surrounding the future adoption of gene expression and protein microarrays for pharmacogenomic and pharmacoproteomic applications. The author critically assesses those studies that have helped define applications in genomics and proteomics, explains gene expression microarray applications, and examines the utility of the protein microarray.
An understanding of the process used in making microarrays is fundamentally important to those interested in producing "spotted" arrays and using them properly. As this technology expands in popularity and application, industry experts must grasp the fundamental principles behind it, its strengths, and its limitations. A basic reference on the benefits of microarray technology in drug discovery, this publication offers a detailed perspective and insight into the present and future uses of this technology.
Features
Includes an extensive literature survey and comparison of microarray technology formats
Discusses the relevance and general utility of microarray technologies in the drug discovery process
Provides an in-depth discussion of important factors for successful array printing Contains protocols for printing nucleic acids and proteins and a selection of substrates and preparation of surface chemistries
Supplies an extensive review and assessment of key studies demonstrating the utility of gene expression and protein microarrays
Array technology, much like polymerase chain reaction (PCR) technique, was created to satisfy an existing need in molecular biology. PCR provided a means to amplify enough DNA to sequence genes. The first applications for arrays involved gene sequencing by hybridization (SBH) and genotyping. However, gel-based sequencing quickly supplanted the emerging SBH approach, while genotyping and mutation analysis have been slow in development. The challenge for those involved in array technology then became finding that elusive application niche, one that would demonstrate a clear, unmitigated, and thereby sustained need for the technology.
This book picks up the array technology journey from the mid-1990s with the introduction of microarray-based gene expression analysis. The global analysis of genes by microarrays has provided a fresh and exciting view of the cellular process. More importantly, it enabled others to consider similar utility in various "omic" fields. Hence, we have witnessed the emergence of protein arrays to address proteomics.
In writing this book, my aim was first to provide a detailed description and offer insight into present and future utilities for microarray technology. While arguably array-based technologies are now being adopted in diverse fields, I have placed emphasis on applications related to drug discovery. Microarrays continue to play significant and increasingly important roles in the drug discovery process.
Chapter 1 considers the respective roles as well as the many issues surrounding the future adoption of gene expression and protein microarrays for pharmacogenomic and pharmacoproteomic applications. For acceptance by the pharmaceutical and diagnostic industries, commercially validated array technology is required. Chapter 2 details the commercial microarray landscape. Chapter 3 describes alternative substrates and the preparation of various surface chemistries along with their suitability for immobilization of nucleic acids and proteins. In Chapter 4, the mechanics of microarraying are described in detail including environmental conditions, printer and pin performance, and instructions for setting up a print run. Protocols for printing nucleic acids and proteins are provided along with in-depth discussion of other important parameters such as print buffers (inks) and factors influencing print quality. I also set out to discuss the importance and provide a critical assessment of studies that helped to define applications in genomics and proteomics. In Chapter 5, gene expression microarray applications are described; Chapter 6 examines the utility of protein microarrays.
Finally, an understanding of the making of a microarray is fundamentally important to those interested in producing "spotted" arrays and properly using them. While complementary (cDNA) microarray fabrication on glass slides has been well studied, we have less experience with the attachment of oligonucleotides and the preparation of protein arrays. Moreover, additional substrates and surface chemistries that may be better suited for printing proteins are now available.
Robert (Bob) Matson, Ph.D., is a senior staff scientist in the Advanced Technology Center at Beckman Coulter, Inc., Fullerton, California. He has been involved in the development of both nucleic acid and protein array-based technology for the past 13 years. His initial introduction to array technology began in collaboration with Sir Edwin Southern in developing an in situ oligonucleotide array synthesis platform for the corporation. Later work by Dr. Matson and his research team produced some of the
first plastic microplate-based microarrays. Beckman Coulter recently launched the A2TM plate based upon the microplate "array of arrays" concept.
Prior to joining Beckman Coulter, he served in several technical management roles including: R&D director at BioProbe International, R&D director at Costar-Nuclepore, and R&D group leader, chemistry, at BioRad Lab-oratories.
Dr. Matson currently holds seven United States patents and has contributed numerous papers in peer-reviewed journals as well as chapters in several books on microarrays. He has also made many presentations in the United States and abroad on the development of microarray technology. His current interest is in automated approaches to multiplexed assay development.
Dr. Matson grew up in the San Juan Islands of Washington State and attended Western Washington University, Bellingham, where he earned his B.A. and M.S. in chemistry. He received his Ph.D. in biochemistry from Wayne State University. Following postdoctoral studies at the medical school of the University of California at Los Angeles, he served as a principal investigator with the Veterans Administration Medical Center and as an adjunct professor of biological chemistry at the medical school of the University of California at Davis. Dr. Matson also held a faculty lectureship in the department of chemistry at University of Southern California and was an assistant professor of chemistry at the University of Southern Maine, Portland. He served on the editorial boards of Applied Biochemistry and Biotechnology and the Journal of Preparative Chromatography, and is a member of the Scientific Advisory and Organizing Board of International Business Compunications' "Chips to Hits" conferences.
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