1st Edition

Biochips as Pathways to Drug Discovery

Edited By Gary Hardiman Copyright 2006
    386 Pages 14 Color & 93 B/W Illustrations
    by CRC Press

    In the fiercely competitive pharmaceutical marketplace, your organization cannot afford to spend excess dollars developing drugs that will fail to get FDA approval or have profoundly poor characteristics. Biochips as Pathways to Drug Discovery takes a comprehensive look at how the industry faces these challenges, using new technologies such as biochips to reduce the cost of drug discovery and improve drug safety. The book explores the tools and skills required at each step of the discovery process when using biochips to determine biological outcomes.

    The authors provide an in-depth review of the clinical and pharmacogenomic relevance of biochips, ChIP-chip assays, and high-throughput approaches. They discuss how biochips are used to develop biomarkers in the drug discovery process, primarily for gene expression profiling and Single Nucleotide Polymorphism (SNP) analysis. The book includes coverage of experimental theory, quality control, clinical laboratory sampling considerations, database concepts, industrial laboratory design, and the analysis of the resultant large data sets. It discusses the application of biochips to the study of malaria, toxicogenomics, and SNPs, as well as intellectual property and market overviews. The book 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.

    Written in an easily accessible style, the breadth of coverage introduces the subject to those new to the field, while the depth of coverage forms a foundation for future work. The book gives you the knowledge required to leverage the technology into bona fide discoveries.

    Daniel E. Levy, editor of the Drug Discovery Series, is the founder of DEL BioPharma, a consulting service for drug discovery programs. He also maintains a blog that explores organic chemistry.

    DNA Biochips — Past, Present, and Future: An Overview, G. Hardiman and A.A. Carmen
    Evolution and Development of Biochips
    Biochips Platforms: Comparisons and Contrasts
    Three-Dimensional HydroArrays: Novel Microarrays for Genomic and Proteomic Studies, R. Fagnani, P. Tsinberg, and T.J. Pircher
    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, K. Le Roch and E. Winzeler
    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 Cassette Transporter Expression Identified with a Global Error Assessment Model, D.M. Mutch, A. Petrov, J. B. German, G. Williamson, and M.-A. Roberts
    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: Bridging Drug Discovery and Development, A.Y. Nie, M.K. McMillian, and P.G. Lord
    Toxicogenomics Experimental Design
    Case Study: PPAR Agonist Example
    Summary and Conclusions
    The Next Generation of Automated Microarray Platforms for a Multiplexed CYP2D6 Assay, P. Kim, Y.-K. Ken Fu, V. Mahant, F. Kureshy, G. Hardiman, and J. Corbeil
    The INFINITI™ Platform
    CYP2D6 Genotyping
    Results and Discussion
    Biopsy and RNA Extraction Procedures of Muscle and Adipose Tissue for Microarray Gene-Expression Profiling, M.B.A. van Doorn, M.J.B. Kemme, M. Ouwens, E.J. van Hoogdalem, X. Liu, Q.S. Li , C.R. Jones, M.L. de Kam, J. Burggraaf, and A.F. Cohen
    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, D. Robyr
    ChIP-on-Chip: Brief History and Overview of the Method
    Yeast ChIP-on-Chip and Beyond
    ChIP-on-Chip and Biomedical Applications
    Concluding Remarks
    DNA Microarrays as Functional Genomics Tools for Cancer Drug Discovery, A. Bhattacharjee
    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
    Additional Notes

    High-Throughput Microarray Analysis, S. Sheth

    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, A. Bittner and A.A. Carmen
    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, R.M. Kliman, F. Barany, N. Cohen, and R. Favis
    Technical Considerations
    Biological Considerations
    Concluding Remarks

    Approaches for Microarray Data Validation, S.E. Ilyin

    Microarray Enterprise Information Management: What Is It and Why Is It Important? P. Morrison, P. Prakash, and S. Shams
    Importance of Systematic Data Management for Quality Assurance
    Data Management Needs at Each Step of Array Experiment
    Quality Control of Microarray Data, H. Xiao, A. Leung, and L. Yieh
    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, H. Xiao, L. Yieh, and H. Dai
    Linear Normalization
    Intensity-Dependent Normalization
    Choosing a Normalization Method
    Normalization for Oligonucleotide-Based Arrays
    Performance of Normalization
    Data Transformation
    Amplification Strategies and DNA Biochips, B. Ruggeri, L. Soverchia, M. Ubaldi, R. Ciccocioppo, and G. Hardiman
    Laser Capture Microdissection (LCM)
    Microarray Target Labeling
    Ribo-SPIA™, a Rapid Isothermal RNA Amplification Method for Gene Expression Analysis, A. Dafforn, P. Chen, G.Y. Deng, M. Herrler, D.M. Iglehart, S. Koritala, S.M. Lato, S. Pillarisetty, R. Purohit, L. Turner, M. Wang, S. Wang, and N. Kurn
    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
    Materials and Methods
    Genomics, Transcriptomics, and Proteomics: Novel Detection Technologies and Drug Discovery, P. Stafford
    Background and Introduction
    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, V.G. Norton
    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, J. Xu
    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
    L. Milne
    Microarrays: Current-Market Overview
    Microarrays: Company Profiles
    Microarrays: Future Market Directions and Hurdles

    “The authors of this volume provide an in-depth review of the clinical and pharmacogenomic relevance of biochips, ChIP-chip assays, and high-throughput approaches. … The book includes coverage of experimental theory, quality control, clinical laboratory sampling considerations, database concepts, industrial laboratory design, and the analysis of the resultant large data sets. … Written in an easily accessible style, the breadth of coverage introduces the subject to those new to the field, while the depth of coverage forms a foundation for future work.”
    — In Anticancer Research, Vol. 27, No. 3B, May/June 2007

    "This book is a must have for students who use biochips in their graduate work or others initiating efforts in these areas . . . In summary, Biochips as Pathways to Drug Discovery provides a broad yet detailed look at the use of DNA microarrays in drug discovery."

    – Matthew D. Disney, The University at Buffalo, The State University of New York, in ChemMedChem, 2008, No. 3