Expert guidance in managing discovery and development of disease-related biomarkersThis report focuses on disease-related biomarkers, those related to disease screening, prognosis, and stratification—more specifically, disease-related molecular biomarkers. Aspects covered include: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 Biomarker discovery has grown dramatically during the past decade, driven by: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 Disease-related biomarkers are not a new phenomenon. Early examples include blood glucose for diabetes diagnosis and management and cholesterol for cardiovascular risk. However, introduction of DNA microarrays in the mid-1990s enabled a revolution in transcriptomics and triggered a major paradigm shift in the way life scientists approached research. Subsequently, metabolomics and metabonomics, applied mainly to safety-related biomarkers originally, began to turn to disease-related biomarkers.Disease-Related Biomarkers: Their Potential in Patient Screening, Prognosis, and Stratification goes into great detail on the competitive issues in disease biomarker research and development, which, according to the results of an Insight Pharma survey of people involved, will see an increase in funding over the near future.  

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Disease-Related Biomarkers: Their Potential in Patient Screening,
Prognosis, and Stratification
Published on June 2007
Report Summary
Expert guidance in managing discovery and development of disease-related biomarkers
This report focuses on disease-related biomarkers, those related to disease screening, prognosis, and stratification—more
specifically, disease-related molecular biomarkers. Aspects covered include: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 Biomarker
discovery has grown dramatically during the past decade, driven by: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 Disease-related biomarkers are not a new phenomenon. Early examples include blood glucose for diabetes
diagnosis and management and cholesterol for cardiovascular risk. However, introduction of DNA microarrays in the mid-1990s
enabled a revolution in transcriptomics and triggered a major paradigm shift in the way life scientists approached research.
Subsequently, metabolomics and metabonomics, applied mainly to safety-related biomarkers originally, began to turn to
disease-related biomarkers.
Disease-Related Biomarkers: Their Potential in Patient Screening, Prognosis, and Stratification goes into great detail on the
competitive issues in disease biomarker research and development, which, according to the results of an Insight Pharma survey of
people involved, will see an increase in funding over the near future.
Table of Content
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
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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
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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
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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
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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
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