Disease-Related Biomarkers: Their Potential in Patient Screening, Prognosis, and Stratification

Table of Contents

CHAPTER 1 INTRODUCTION

• 1.1. Biomarker Definitions
• 1.2. Types of Biomarkers
  • Drug Discovery View
    • Broader View of Biomarker Types
  • Diagnostic Industry View
• 1.3. Disease-Related Biomarkers
• 1.4. Biomarkers in Drug Discovery and Development
• 1.5. Organization of the Report

CHAPTER 2 TECHNOLOGIES FOR BIOMARKER DISCOVERY AND ANALYSIS

• 2.1. Sensitivity, Specificity, and Predictive Value of Biomarker Assays
• 2.2. Pregenomic Biomarkers and Technologies
  • Enzyme and Metabolite Assays
  • Immunodiagnostics
    • Enzyme Immunoassays
  • Molecular Diagnostics
    • Target Amplification: Polymerase Chain Reaction
    • Signal Amplification Methods
• 2.3. Postgenomic Biomarkers and Technologies
  • Transcriptomics
    • Positional DNA Microarrays
      • Affymetrix Technology Platform
      • NimbleGen Process for Microarray Production
      • CombiMatrix Microarrays
      • Agilent' s Synthesized Arrays
      • Other Companies in the Microarray Market
      • Low-Density Arrays for In Vitro Diagnostic Applications
    • Encoded Particle Arrays
      • Illumina' s Encoded Particle Technology
      • Luminex' s xMAP Bead Arrays
      • Meso Scale Discovery Multi-array Formats for Immunoassays
      • Pierce' s SearchLight Proteome Arrays
      • Invitrogen' s Encoded Bead Technology
      • High Throughput Genomics' Gene Expression Assays
  • Proteomics
    • Ciphergen' s Technology
      • Biomarker Discovery
      • Assay Development
    • 2D Gel Electrophoresis
    • Differential In-gel Electrophoresis
    • Mass Spectrometry in Biomarker Discovery and Validation
      • Sample Processing
    • Metabolomics
  • Analysis of Metabolites in Biological Specimens
    • Metabolite Profiling for Biomarker Discovery
    • Potential for Metabolomics in Discovery of
    • Disease-Related Biomarkers
      • Sidebar: Disease-Related Imaging Biomarkers

CHAPTER 3 BIOMARKER ADVANCES IN SPECIFIC THERAPEUTIC AREAS

• 3.1. Cancer
  • Noncommercial Biomarker Programs
    • Nucleic Acid Programs
    • Protein Programs
      • Role of Autoimmunity in Cancer
      • Protein Biomarkers for Astrocytomas
      • Protein Biomarkers for Ovarian Cancer
      • Use of SELDI-TOF to Detect Prostate Cancer
      • Serum Peptidomics for Cancer Detection
    • Metabolomics Programs
  • Commercial Biomarker Programs
    • Nucleic Acid Programs
      • Gene Expression Tests
      • ErbB2 Gene Assay for Breast Tumors
      • PCA3 mRNA Test for Prostate Cancer
      • DNA Methylation-Based Cancer Assays
      • Use of Genomic Signatures in Cancer Diagnosis
    • Protein Programs
      • Serum-Based Biomarkers
      • Semen Test for Detecting Prostate Cancer
      • Serum Protein Panels as Cancer Biomarkers
      • Other Programs for Cancer Biomarker Identification and Development
    • Metabolomics Programs
    • Summary
• 3.2. Neurological Diseases
  • Noncommercial Programs
    • Identification of Biomarkers for Schizophrenia
    • Identification of Biomarkers for Alzheimer' s Disease
    • Identification of Molecular and Imaging Biomarkers for Parkinson' s Disease
  • Commercial Programs
• 3.3. Cardiovascular and Metabolic Diseases
  • Noncommercial Programs
    • Detection of Biomarkers for Type 2 Diabetes
  • Commercial Programs
• 3.4. Autoimmune and Inflammatory Diseases
  • Noncommercial Programs
    • Biomarker Programs for Lupus Nephritis
    • Biomarker Programs for Other Inflammatory Diseases
  • Commercial Programs
    • Biomarker Programs for Arthritis
    • Biomarker Program for Inflammatory Bowel Disease
• 3.5. Other Diseases
  • Noncommercial Programs
  • Commercial Programs

CHAPTER 4 PRECOMMERCIAL BIOMARKER DEVELOPMENT

• 4.1. PhRMA/NIH/FDA Biomarkers Consortium
• 4.2. European Union 7th Framework Biomarkers Programme
• 4.3. Other Consortia
  • International Cancer Biomarker Consortium
  • NCI' s Early Detection Research Network
  • Oncology Biomarker Qualification Initiative
  • Clinical Plasma Profiling Consortium
  • High-Risk Plaque Initiative

CHAPTER 5 MARKET CONSIDERATIONS

• 5.1. Sector-Related Efforts in Biomarker Discovery and Development
  • Role of Academia
  • Role of Pharmaceutical and Biopharmaceutical Companies
    • Confounding Issues in Biomarker Discovery
    • Biomarkers as Surrogate Endpoints
  • Role of Biotechnology Companies Specializing in Biomarker
  • Discovery
  • Role of the Diagnostics Industry
  • Regulatory Considerations
    • FDA IVDMIA Guidance
    • Regulations on Home-brew Tests
• 5.2. Summary of Recommendations to Develop Biomarker-based Tools for Cancer
  • Methods, Tools, and Resources Needed to Discover and Develop Biomarkers
  • Guidelines, Standards, Oversight, and Incentives Needed for Biomarker Development
  • Methods and Processes Needed for Clinical Evaluation and Adoption
• 5.3. Limitations in Converting Biomarkers to In Vitro Diagnostics
  • Technological Issues
  • Population Issues
  • Regulatory Issues
• 5.4. Relevant Deals
• 5.5. Deal Analysis

CHAPTER 6 CHI INSIGHT PHARMA REPORTS - DISEASE BIOMARKERS SURVEY - MARCH 2007

• 6.1. Pharmaceutical and Biopharmaceutical Company Responses
• 6.2. Diagnostics and Biomarker Discovery Company Responses
• 6.3. Overall Conclusions

CHAPTER 7 INTERVIEWS WITH DISEASE-RELATED BIOMARKER EXPERTS

• Bruce McCreedy, PhD, Metabolon
• Mark Reynolds, PhD, Gen-Probe
• Stephen Naylor, PhD, Predictive Physiology and Medicine
• Mark Chandler, PhD, Biophysical Corporation, and Ralph McDade, PhD, Rules-Based Medicine
• Emanuel Petricoin III, MD, PhD, George Mason University
• Brian Edmonds, PhD, Eli Lilly
• Deborah Neff, Pathwork Diagnostics
• Metabolomics Programs
• Summary

APPENDIX COMPANY PROFILES

• Almac Diagnostics
• Applied NeuroSolutions
• AviaraDx
• BG Medicine
• Biomarker Science
• Cambridge Theranostics Ltd
• Caprion Proteomics
• Ciphergen Biosystems
• Compugen
• Cogenics (part of Clinical Data)
• CombiMatrix Molecular Diagnostics
• Correlogic Systems
• diaDexus
• Epigenomics
• GE Healthcare
• Genizon Bioscience
• Health Discovery Corporation
• IBEX Technologies
• Illumina
• Ipsogen
• Med BioGene
• Metabolon
• Monogram Biosciences
• OncoMethylome Sciences
• Orion Genomics
• Oxford Genome Sciences
• Pathway Diagnostics
• Pathwork Diagnostics
• Phenomenome Discoveries
• Power3 Medical Products
• PPD
• Predictive Biosciences
• Predictive Physiology and Medicine
• Progenika Biopharma
• Proteome Sciences
• Proteome Systems
• ProteoSys
• Randox
• Rules-Based Medicine
• sanofi-aventis
• SIRS-Lab GmbH
• Target Discovery
• Targeted Molecular Diagnostics
• XDx

References

Company Index with Web Addresses