DNA Microarrays: A Practical Approach

DNA microarrays, or biochips, are small glass chips embedded with ordered rows of DNA and by providing a massive parallel platform for data gathering represent a fundamental technical advance in biomedical research. Such biochips enable the use of advanced fabrication, detection, and data mining technologies that allow data gathering at an unprecedented rate. The first chapter is an introduction to the technology of DNA microarrays, emphasizing the methodological fundamentals of biochips. The next two chapters describe the use of confocal scanning in microarray detection and techniques for the efficient cloning and screening of differentially expressed genes. Chapter 4 describes assay optimization for enzymatic assays and chapter 5 antisense scanning arrays. This is followed by a chapter on the manufacture of molecular arrays using ink-jet printing technology. Chapter 7 describes gene expression analysis from cDNA microarrays and then chapter 8 covers the use of expression data in bioinformatics. Chapter 9 describes the use of active microelectronic arrays for DNA hybridization analysis and the last chapter details the use of microarray technology in pharmacogenomics. This Practical Approach book is a comprehensive overview of the new and expanding field of DNA microarray technology and will be invaluable to any researcher interested in the use of biochips.

Table of Contents:
1. Genes, genomes, and chips: Introduction; Information content of genomes; microarray analysis; Applications of microarrays; Chips and pharmacogenomics; Summary; References ; 2. Confocal scanning microscopy in microarray detection: Introduction - microarrays, fluorescence, and detection; Sample handling; Confocal scanning of microarrays; Wavelength discrimination - minimizing the background image; Detectors; Signal processing and instrument control; Instrument performance measures; Scanarray (registered trademark) confoccal microarray scanners; References ; 3. Representational differences analysis and microarray hybridization for efficient cloning and screening of differentially expressed genes: Introduction; RDA; Generation of libraries from RDA subtractions; Microarray fabrication; microarray hybridization; Differential expression screening with microarrays; Summary; References ; 4. Use of oligonucleotide arrays in enzymatic assays: assay optimization: Introduction; Fabrication of arrays; Preparation of target DNA; Hybridization to arrays; Enzyme catalysed extension reactions; Variations on protocols; References ; 5. Antisense oligonucleotide scanning arrays: Introduction; Array fabrication; Acknowledgements; References ; 6. Application of ink-jet printing technology to the manufacture of molecular arrays: Introduction; Ink-jet technology; Molecular array fabrication by synthesis; Molecular array fabrication by deposition; Conclusion; Acknowledgements; References ; 7. Gene expression analysis via cDNA microarrays of laser capture microdissected cells from fixed tissue: Ranelle C. Salunga, Hongqing Guo, Lin Luo, Anton Bittner, K. C. Joy, Jim R. Chambers, Jackson S. Wan, Michael R. Jackson, and Mark G. Erlander: Introduction; Laser capture microdissection; Generation of aRNA - first round; cDNA microarrays; Acknowledgements; References ; 8. Expression data and the bioinformatics challenges: Genes/proteins; The raw data pipeline; The reference data warehouse; The structure of molecular information; Medial lexicon and donor sample registration; Data mining an expression data mart; Conclusions; References ; 9. Active microelectronic arrays for DNA hybridization analysis: Introduction; Background on electronic array and hybridization technology; Active microelectronics array fabrication; Point mutation analysis on active electronic arrays; Microfabrication of active DNA chips; Example of single base discrimination analysis; Conclusions; References ; 10. Gene chips and microarrays: applications in disease profiles, drug target discovery, drug action and toxicity: Introduction; Methods; Results; Discussion; Acknowledgements; References ; Appendix ; Index