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

Published by: CHI Insight Pharma Reports

Published: Jun. 1, 2007 - 234 Pages

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

FIGURES

Figure 2.1. Readout from an Affymetrix DNA Microarray Experiment

Figure 2.2. Affymetrix Photolithographic Process for DNA Microarray Manufacturing

Figure 4.1. National Cancer Institute Early Detection Research Network Organization

Figure 5.1. FDA’s Schematic View of a Typical Drug-Diagnostic Development Program

Figure 6.1. Respondents by Type of Organization

Figure 6.2. Pharmaceutical and Biopharmaceutical Company Respondents by Sector

Figure 6.3. Pharmaceutical and Biopharmaceutical Company Respondents by Position

Figure 6.4. Respondents by Stage of Work

Figure 6.5. Respondents by Research Focus

Figure 6.6. Involvement with Biomarkers by Pharmaceutical and Biopharmaceutical Companies

Figure 6.7. Types of Biomarkers Used

Figure 6.8. View toward Collaboration in Biomarker Development

Figure 6.9. Experience with Novel Disease-Related Biomarkers

Figure 6.10. In-licensing or Acquisition of Novel Disease-Related Biomarkers by Pharmaceutical and Biopharmaceutical Companies

Figure 6.11. Discovery or Development of Disease-Related Biomarkers by Pharmaceutical and Biopharmaceutical Companies

Figure 6.12. Means of Biomarker Discovery or Development

Figure 6.13. Technologies Used for Biomarker Discovery

Figure 6.14. Focus of Disease-Related Biomarker Work

Figure 6.15. Expected Fiscal 2007 Budget for Disease-Related Biomarkers

Figure 6.16. Diagnostics and Biomarker Discovery Company Respondents by Sector

Figure 6.17. Involvement with Biomarkers by Diagnostics and Biomarker Discovery Companies

Figure 6.18. Diagnostics and Biomarker Discovery Company Respondents by Position

Figure 6.19. Discovery or Development of Disease-Related Biomarkers by Diagnostics and Biomarker Discovery Companies

Figure 6.20. In-licensing or Acquisition of Disease-Related Biomarkers by Diagnostics and Biomarker Discovery Companies

Figure 6.21. Therapeutic Areas of Biomarker Work

Figure 6.22. Mode of Regulatory Approval

TABLES

Table 3.1. Selected Noncommercial Biomarker Programs in Cancer

Table 3.2. Selected Commercial Biomarker Products and Programs in Cancer

Table 3.3. Selected Noncommercial Biomarker Programs in Neurology

Table 3.4. Selected Commercial Biomarker Products and Programs in Neurology

Table 3.5. Selected Noncommercial Biomarker Programs in Cardiovascular and Metabolic Diseases

Table 3.6. Selected Commercial Biomarker Products and Programs in Cardiovascular and Metabolic Diseases

Table 3.7. Selected Noncommercial Biomarker Programs in Autoimmune and Inflammatory Diseases

Table 3.8. Selected Commercial Biomarker Products and Programs in Autoimmune and Inflammatory Diseases

Table 3.9. Selected Noncommercial Programs in Other Therapeutic Areas

Table 5.1. Stages of Commercial Disease-Related Biomarker Programs

Table 5.2. Stages of Noncommercial Disease-Related Biomarker Programs

Table 5.3. Deals Involving Disease-Related Biomarkers

Table 5.4. Analysis of Deal Types

Abstract

• Historical and contextual information
• Strategies and technologies currently used for biomarker discovery and development
• Progress in biomarker discovery and development in several disease areas
• Current and future roles of consortia in disease-related biomarker discovery and development
• Market-related considerations, including the role of various sectors, competitive activity, deal activity, and regulatory factors
• Two separate surveys of individuals in (1) the pharma and biopharma sectors, and (2) biomarker discovery and diagnostic sectors. Both surveys capture attitudes, intentions, and current practices of individuals at the forefront of disease-related biomarker discovery and development.
• Profiles of 44 companies active in disease-related biomarkers
• In-depth interviews with 7 disease-related biomarker experts

• The availability of powerful new "omics" technologies
• The increasing utilization of new and untested targets in pharma
• The opportunity to replace suboptimal in vitro diagnostic assays with improved biomarkers

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