Outlook for DNA Microarrays: Emerging Applications and Insights on Optimizing Microarray Studies

Published by: CHI Insight Pharma Reports

Published: Jul. 1, 2002 - 160 Pages

Table of Contents

• 1.1. Overview of DNA Microarrays
  
• The Importance of mRNAs and Alternative Splicing in Microarrays: An Interview with Alon Amit
  of Compugen
  
• 1.2. Competing/Complementary Technologies to DNA Microarrays
  
• SAGE
  
• Massively Parallel Signature Sequencing and Megasort
  
• Proteomics/Protein Arrays
  
• Applying Protein Arrays in Network Biology Studies for Drug Discovery: An Interview with
  Ulrik B. Nielsen of Merrimack Pharmaceuticals
  
• 1.3. DNA Microarray Informatics
  
• Image Analysis
  
• Preprocessing and Normalization
  
• Filtering
  
• Biological Interpretation

Chapter 2. Current And Emerging Technologies: Microarrays, Other Emerging Tools, Informatics, and Applications

• 2.1. Details on DNA Microarrays
  
• cDNA Arrays
  
• Oligonucleotide Arrays
  
• Usage of cDNA Arrays vs. Oligonucleotide Arrays
  
• Universal Arrays
  
• 2.2. Other Types of Hybridization Arrays/Microfluidic Devices
  
• Microelectronic Arrays
  
• Bead-Based Arrays
  
• Microfluidic Devices
  
• 2.3. Microarray Informatics
  
• Full-Service Products
  
• Specialized Products
  
• Custom Data Analysis Companies
  
• Specialized Academic Software
  
• 2.4. Evolving Applications of Microarrays: From Drug Discovery to Diagnostics
  
• Target/Drug Discovery
  
• Systems Studies
  
• The Challenges of Building a Systems Approach: An Interview with Eric Neumann
  of Beyond Genomics
  
• Toxicogenomics
  
• Diagnostic Applications
  
• Moving Toward Clinical Subtyping of Cancer: An Interview with Douglas Ross of Applied Genomics

Chapter 3. Optimizing Results From Microarray Studies:
Key Approaches and Tools

• 3.1. Experimental Design
  
• Overview
  
• Design Workflow
  
• Conclusion
  
• 3.2. Analytics
  
• Analytics Workflow
  
• Conclusion
  
• 3.3. Informatics
  
• Part 1. Types of Information to Store
  
• Part 2. Categories of Array Software

Chapter 4. Business And Strategic Outlook: Shifting Market Dynamics

• 4.1. Overall Business Trends and Outlook
  
• Proteomewide Chips: Not So Fast?
  
• 4.2. Dealmaking Trends in Microarrays
  
• 4.3. Profiles of Selected Companies
  
• Affymetrix
  
• Agilent Technologies
  
• Amersham Biosciences (formerly Amersham Pharmacia Biotech)
  
• Axon Instruments
  
• BD Biosciences Clontech
  
• BioDiscovery
  
• Gene Logic
  
• InforMax
  
• Lion Bioscience
  
• MolecularWare
  
• OmniViz
  
• Partek
  
• Rosetta Inpharmatics/Rosetta Biosoftware
  
• Silicon Genetics
  
• Spotfire
  
• 4.4. Expert Commentaries
  
• Stanley Abramowitz, Partner, ATG Advanced Technology Group
  
• Gene Brown, Director, Expression Profiling Sciences, Genetics Institute/Wyeth-Ayerst Research
  
• Timothy Connolly, Research Scientist, Aventis Genomics Center (Cambridge, MA)
  
• David Dorris, Section Manager, Motorola Life Sciences
  
• Tom Downey, President and CEO, Partek
  
• David Finkelstein, Data Analysis Scientist, Affymetrix
  
• Sam Hicken, Director of Bioinformatics, Phase-1 Molecular Toxicology
  
• Donald J. Kessler, Product Manager for Catalog Microarrays, Agilent Technologies
  
• N. Stephen Ober, President, Beyond Genomics
  
• Alan Roter, Vice President, Informatics, Iconix Pharmaceuticals
  
• Winston K. Wong, Global Program Manager, Microarray Analysis, Stratagene
  
• Ali Zareh, Vice President of Business Development, Corimbia

Appendix A. Companies Providing Microarray-Related Tools, Services, and Software/Data

Appendix B. Recent Dealmaking Activity in DNA and Protein Microarrays

Glossary

Company Index

List of Tables and Figures

• Table 1: Some Relative Advantages and Challenges of DNA Microarrays and Protein Microarrays
  
• Table 2: Overview of Popular Array Analysis Software and Relationship to 0ther Software Categories
  
• Table 3: Overview of Portions of the Analytics Workflow Addressed by the Most Popular Array Analysis Software
  
• Table 4: Top Dealmakers in DNA-Based Arrays, 2001 (with 2002 deals through 7/1/02)
  
• Table A1: Selected Companies Offering Arrays and Related Equipment, Supplies, and Services
  
• Table A2: Selected Companies Providing Microarray-Related Software/Databases
  
• Table B1: Selected Deals in DNA Microarrays and Related Technologies, 7/1/2001-7/1/2002
  
• Table B2: Selected Deals in Protein Microarrays and Related Technologies, 7/1/2001-7/1/2002
  
• Figure 1: General Steps in Conducting Array Experiments
  
• Figure 2: Experimental Process: cDNA Arrays
  
• Figure 3: Complete Microarray Process
  
• Figure 4: Replication, Balance, and Evenness in Array Experiment Design

Abstract

• The pros and cons of protein arrays versus traditional DNA microarrays.
• How some groups are dealing with complications such as alternative splicing.
• The advancement of microarrays from pure research applications toward the clinic.
• New tools and approaches for microarray analysis.

The DNA microarray marketplace is changing rapidly. Microarrays are already widely adopted, and many use2rs are now going beyond exploratory studies. With a better understanding of what is required to get optimal results from this potentially finicky technology platform, researchers are getting more robust data from their studies, and findings with potential clinical applicability are trickling in. At the same time, several major developments are making it increasingly challenging to maintain viable business models in this arena.

Many experts believe that DNA microarrays will be used for some years to come, despite increasing competition from protein arrays. Perhaps the most promising commercial application of microarrays is their potential use as clinical diagnostics; this area will likely attract more and more players over time if this approach continues to show promise. Intriguing results are beginning to emerge from the use of DNA microarrays to classify subtypes of cancer and to guide treatment decisions. If they could be optimized further for clinical applications in classifying disease, to determine the most appropriate treatments, their market potential could be significant.

This report provides an overview of the scientific basis of microarrays, explains how to optimize results obtained from these tools, details the competitors in this market and the distinctions among their products, and analyzes and forecasts the market dynamics. The activities of approximately 100 companies are reviewed, 15 companies are profiled (with financial capsules), and 16 expert commentaries or interviews are presented. Dealmaking trends in microarrays are also discussed, based on data from CHI’s Drug Discovery and Development Deals Database.

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