The text concludes with a comprehensive overview of how these chips are employed from early target discovery through preclinical toxicology and on through to pharmacogenomic and proof of concept studies in humans.

Contents

DNA Biochips—Past, Present, and Future: An Overview

• Evolution and Development of Biochips
• Biochips Platforms: Comparisons and Contrasts

Three-Dimensional Hydroarrays: Novel Microarrays for Genomic and Proteomic Studies

• Three-Dimensional HydroArrays
• HydroArray Chemistry
• Example of Focus Three-Dimensional HydroArrays
• In-Vitro Diagnostic Applications
• Protein Three-Dimensional HydroArrays

Biochip in Malaria for Antiparasitic Discovery

• Malaria
• Life Cycle of the Malaria Parasite
• Short Oligonucleotide vs. Long Oligonucleotide Microarray
• Biological Relevance of Expression Profiling
• The Use of Biochips for Elucidating the Mechanism of Drug Action
• Vaccine Development

Regional Variations in Intestinal ATP-Binding Cassetter Trasporter Expression Indentified with a Global Error Assessment Model

• Global Error Assessment (GEA) Model
• Regional Variations in ABC Transporter Expression in the Intestine
• Validation 1: GEA Analysis of Microarray Data vs. Real-Time PCR
• Validation 2: GEA Analysis of Microarray Data vs. an in Silico cDNA Data Set
• Validation 3: GEA Analysis of Microarray Data vs. Protein Expression

Toxicogenomics in Drug Safety Evaluation: Toxicogenomics in Drug Safety Evaluation: Bridging Drug Discovery and Development

• Toxicogenomics Experimental Design
• Case Study: PPAR Agonist Example

The Next Generation of Automated Microarray Platforms for a Multiplexed CYP2D6 Assay

• The INFINITI™ Platform
• CYP2D6 Genotyping
• Results and Discussion

Biopsy and RNA Extraction Procedures of Muscle and Adipose Tissue for Microarray Gene-Expression Profiling

• Subjects and Methods
• Blood Sampling and Leukocyte Isolation
• RNA Extraction
• Microarray Data Analysis
• Evaluation of Gene Expression Profiles in Biopsy Tissues and White Blood Cells

Chip-on-Chip: Analysis of Genomewide Protein Binding and Posttranslational Modifications

• ChIP-on-Chip: Brief History and Overview of the Method
• Yeast ChIP-on-Chip and Beyond
• ChIP-on-Chip and Biomedical Applications

DNA Microarrays as Functional Genomics Tools for Cancer Drug Discovery

• Introduction: DNA Microarrays in Drug Discovery
• From Cancer Classification to Drug Discovery
• Hunting and Screening Approaches in Drug Discovery
• The Era of DNA Microarrays
• Impact of Mechanism-Based Studies in Cancer Drug Discovery and Development
• Future of Microarrays in System-Level Overview of Cancer and Therapeutic Intervention

High-Throughput Microarray Analysis

• Developing the HT Array
• Applications to Drug Discovery and Development
• More Successful Clinical Trials
• The Way Ahead

Laboratory Automation: Strategies for High-Volume Industrial Microarray Programs

• Benefit of Automation to Microarray Experiments
• Automation for Array Processing
• Data Collection, Analysis, and Sample Tracking
• Pitfalls of Automation

Association Studies: Practical and Theoretical Considerations for Drug Discovery, Evaluation, and Beyond

• Technical Considerations
• Biological Considerations

Approaches for Microarry Data Validation

Microarry Enterprise Information Management: What is it and Why is it Important?

• Importance of Systematic Data Management for Quality Assurance
• Data Management Needs at Each Step of Array Experiment

Quality Control of Microarray Data

• Algorithms Developed for Microarray Quality Control
• Automation of Quality Control
• Automatic Monitoring of Expression Data Improves Throughput of Data Processing and Data Quality

Microarray Data Normalization and Transformation

• Linear Normalization
• Intensity-Dependent Normalization
• Choosing a Normalization Method
• Normalization for Oligonucleotide-Based Arrays
• Performance of Normalization
• Data Transformation

Amplification Strategies and DNA Biochips

• Laser Capture Microdissection (LCM)
• Microarray Target Labeling

Ribo-Spia™, A Rapid Isothermal RNA Amplification Method for Gene Expression Analysis

• Ribo-SPIA™: A Novel Method for Global Isothermal Linear Amplification of mRNA
• Ribo-SPIA™ Protocol for Rapid Robust Amplification of Total mRNA in Small Total RNA Samples
• Accuracy, Reproducibility, and Linearity of Ribo-SPIA™ Assessed by qPCR
• Expression Analysis Using the Ribo-SPIA™ Amplification and GeneChip® Arrays
• Performance of Ribo-SPIA™-Amplified Product on Two-Color Spotted Arrays

Genomics, Transcriptomics, and Proteomics: Novel Detection Technologies and Drug Discovery

• Fostering Biological Knowledge: Cross-Discipline Data
• Unifying the Biological (Data) World
• The Legacy of Expression Arrays
• Systems Biology - Driving Drug Development through Data Integration
• Controls and Standards
• Biomarkers and the History of Genetics
• SNP Detection
• Some Detection Technologies of Interest
• NonSNP Technology: The Protein Chip, Microfluidics, and Assorted Engineering Marvels
• Microfluidics and Alternate Small-Scale Detection Devices
• Other Biomolecule Detection Methods
• SNP Detection: Major Commercial Technologies
• SNP Detection Diversity
• SNP Detection: Electronic Detection
• SNP Detection: Bead-Based
• The SNP Chip: Flow-Through Methods
• SNP Detection: Sequence-Based
• SNP Detection: Alternate Detection Methods
• SNP Technology: Analysis Software

Intellectual Property Issues for DNA Chips and Microarrays

• Overview of Patent Law Statutes and Guidelines Applied to Genomic Inventions
• IP Implications for DNA Chips and Microarrays
• Other Solutions to Promote Innovation: Free Sharing of SNP Information

Biochips: Market Drivers and Commercial Prospect

• DNA Microarrays: An Established and Expanding Business
• The Evolving Industry Landscape
• Continued Market Drivers and Commercial Prospect
• Protein Arrays: An Industry in Take-Off
• Emerging Industry LandscapeMarket Drivers and Commercial Prospects
• Biochip Industry: The Next 5 Years

A Pharmaceutical Perspective for Microarrays and Biochips: Current-Market Overview and Future Trends

• Microarrays: Current-Market Overview
• Microarrays: Company Profiles
• Microarrays: Future Market Directions and Hurdles