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Commercial Opportunities from Biomarkers: Transforming drug discovery, clinical development and molecular diagnostics

DateMay, 2006
Pages206
Price / format€3130 / Hard Copy
€3076 / Electronic

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Abstract:
 High clinical development costs coupled with declining drug discovery success rates have meant that pharmaceutical companies must re-evaluate their drug development process in order to reduce attrition rates and remain competitive. Over the next decade biomarkers will change the way in which pharma companies determine the economic viability of their drug discovery process.
The use of biomarkers to aid the discovery of promising products will create an enhanced understanding of the clinical development process and help to facilitate the shift towards 'personalized medicine'.

'Commercial Opportunities from Biomarkers: Transforming drug discovery, clinical development and molecular diagnostics' is the latest addition to the drug discovery series, examining recent developments and applications within the biomarkers field. Using up-to-date case studies to indicate best practice strategies, this report will ensure that you are able streamline your R&D process and identify potential cost savings throughout drug discovery and development.
Regulatory changes are analyzed and recent alliances are examined, enabling you to understand the role and future of this fast-moving field.








Table of contents:
 Commercial Opportunities from Biomarkers

Executive Summary
Biomarkers in drug discovery, development and clinical diagnostics
Regulatory acceptance of biomarkers now and in the future
Fishing for new drug targets with biomarkers
Biomarkers aiding go/no go decisions
Imaging biomarkers directing clinical dosing studies
Clinical biomarkers improving trial design
Biomarkers as surrogate endpoints
Market size, collaborations and future directions

Chapter 1 Biomarkers in drug discovery,development and clinical diagnostics
Summary
Introduction
The role of biomarkers in drug discovery, preclinical, clinical development and diagnostics
Biomarkers in the drug discovery process
Safety/toxicology biomarkers
Efficacy or outcome biomarkers and surrogate endpoints
Biomarkers: challenges and opportunities

Chapter 2 Regulatory acceptance of biomarkers now and in the future
Summary
Introduction
The critical path initiative and FDA guidance
Regulatory guidance from the other major markets
Europe - the European Medicines Agency (EMEA)
Japan – the Ministry of Health and Welfare (MHLW)
Regulatory agencies working together
Other biomarker initiatives
Regulatory acceptance of a valid biomarker
Regulatory acceptance of in vitro diagnostic biomarkers
Costs and incentives for biomarker development and validation
Conclusions

Chapter 3 Fishing for new drug targets with biomarkers
Summary
Introduction
Target discovery via functional genomics
What is functional genomics?
Target discovery
New technologies in functional genomics
DNA and protein microarrays
New technologies
The genomics-derived drug pipeline
Case study – target discovery by CuraGen Corporation
The future of genomics technologies for drug target identification
Biomarker discovery via proteomics
What is proteomics?
Proteomics in biomarker development: the HUPO Project
Case studies - Biomarker development using proteomic technologies
Caprion Pharmaceuticals Inc. case study
Millennium Pharmaceuticals case study
Limitations of proteomics for biomarker discovery
Integrating ‘omics in biomarker discovery: metabonomics
What is metabonomics?
Metabonomics-based biomarker discovery – case studies
Metabolon Inc case study
Phenomenone Discoveries case study
Limitations of metabonomics
Conclusions

Chapter 4 Biomarkers aiding go/no go decisions
Summary
Introduction
Technologies for safety biomarker discovery
Toxicogenomics
Genomic biomarkers for drug-induced nephrotoxicity, genotoxicity and neutropenia
Proteomic biomarkers of drug-induced hepatotoxicity and cardiotoxicity
Metabonomic biomarkers for vasculitis and hepatotoxicity
Databases for predictive toxicogenomics
Privately held databases
Publicly held databases
Challenges and opportunities
Challenges
Opportunities
Collaboration in biomarker discovery
Conclusions

Chapter 5 Imaging biomarkers directing clinical dosing studies
Summary
Introduction
Imaging biomarkers
X-ray and computed tomography
Magnetic resonance imaging
Novel MRI imaging agents
Positron emission tomography
Molecular imaging
The role of imaging biomarkers in preclinical studies
Bioluminescence
Matrix metalloproteinase inhibition
The role of imaging biomarkers in clinical studies
Phase 1: the role of imaging biomarkers in pharmacokinetic and dosing studies
Receptor occupancy studies
PET and MRI dosing strategies for anticancer agents
Phase 2 and 3: imaging biomarkers as study endpoints
Oncology
Multiple sclerosis

Rheumatoid arthritis
Alzheimer’s disease
Go/no-go decision making
Case study – VirtualScopics
Regulatory aspects of imaging technologies
Development of molecular imaging agents
Imaging biomarkers and surrogate endpoints
Conclusions

Chapter 6 Clinical biomarkers improving trial design
Summary
Introduction
Patient enrichment in clinical trials
Patient enrichment – advantages
Patient enrichment – potential problems
Targeted cancer treatments – case studies
Herceptin case study
Gleevec case study
Iressa case study
Patient enrichment via pharmacogenomics in therapeutic areas other than cancer
Vilazodone – case study
Pharmacogenomic testing in the pharmaceutical industry – an update
Conclusions

Chapter 7 Biomarkers as surrogate endpoints
Summary
Introduction
What is a surrogate endpoint?
Benefits and drawbacks of surrogate endpoints
Benefits
Drawbacks
Surrogate endpoint validation
Effective use of surrogates and examples
Case study – FDG-PET as a surrogate endpoint in oncology studies
CA-125 as a surrogate endpoint in trials of ovarian cancer
Costs of surrogate endpoint development
Regulatory perspective on surrogate endpoints
Conclusions

Chapter 8 Market size, collaborations and future directions
Summary
Introduction
The biomarker market
Potential cost savings in drug discovery and development
Market size
Genomics and proteomics
Metabonomics
Bioinformatics
Imaging
Molecular diagnostics
Companies and their alliances in the biomarker field
Outline of key companies
Key alliances
Alliances with pharmaceutical companies
Biomarker-diagnostic company alliances
Alliances with academia
Pharma strategies for biomarkers
Current and future trends for the evaluation of disease biomarkers
Conclusions

Chapter 9 Appendix
Biomarker discovery collaborations
Bibliography
Glossary
Index
Footnotes

List of Figures
Figure 1.1: Types of biomarker and examples
Figure 1.2: Low success rate of developmental drugs
Figure 1.3: The many roles of biomarkers in drug development
Figure 2.4: Voluntary genomic data submissions: process and outcomes
Figure 2.5: The EMEA and FDA working together
Figure 2.6: Valid DNA based biomarkers of enzyme activity
Figure 2.7: Exploratory DNA based biomarkers of enzyme or transporter activity
Figure 2.8: Fit-for-purpose qualification of biomarkers
Figure 2.9: Proposed biomarker validation in preclinical drug safety assessment
Figure 3.10: Genomics, proteomics and metabonomics: what is measured?
Figure 3.11: Technologies and methods used in biomarker discovery
Figure 3.12: A timeline for the introduction of various genomics technologies
Figure 3.13: The branches of proteomics for biomarker discovery
Figure 3.14: Scientific initiatives in the Human Proteome Organisation
Figure 3.15: CellCarta®: uses for proteomic analysis
Figure 3.16: An NMR metabonomic profile of urine
Figure 3.17: Metabonomic analysis of data from patients with ALS and controls
Figure 3.18: Biomarker discovery through metabolomics
Figure 4.19: Toxicogenomics and traditional toxicology working together to provide a framework
for systems toxicology
Figure 4.20: Principal component analysis of gene expression changes following treatment with
cisplatin, gentamicin and puromycin
Figure 4.21: Principal component analysis of urine from rats treated with a vasculitis causing
compound
Figure 4.22: Database enabled predictive toxicology
Figure 4.23: Example of rank ordering candidate leads using the ToxExpress® Program
Figure 5.24: Imaging techniques and their uses
Figure 5.25: Targeted MRI imaging agents from Kereos Inc.
Figure 5.26: A PET/CT image indicating the uptake of 18F-fluoro-2-deoxy-D-glucose in a primary
cancer lesion and a lymph node (orange areas)
Figure 5.27: Whole body microPET images through a rat showing 18F-FDG distribution
Figure 5.28: The VivoVision technology from Xenogen Inc.
Figure 5.29: NIRF data from rats treated with prinomastat
Figure 5.30: PET images of the serotonin 5-HT1A¬ receptors in the brain of a healthy volunteer
before and after administration of pindolol
Figure 5.31: An MRI from a multiple sclerosis patient showing a T2 lesion
Figure 5.32: VirtualScopics’ method for tumor growth measurement
Figure 6.33: Targeted study designs
Figure 6.34: Imatinib mechanism of action in chronic myeloid leukaemia
Figure 6.35: Mechanism of action of gefinitib
Figure 6.36: Frequency of mutations by exon (EGFR tyrosine kinase domain)
Figure 6.37: The association between patients’ alleles for the serotonin transporter long/short
polymorphism and response to SSRIs
Figure 7.38: Examples of bio markers that have failed to serve as surrogate endpoints in clinical
trials
Figure 7.39: Reasons for surrogate endpoint ‘failure’
Figure 7.40: Use of surrogate endpoints in antiretroviral approvals
Figure 8.41: Potential cost savings from the use of genomic biomarkers in drug discovery and
development
Figure 8.42: Alliances between major pharmaceutical and biomarker discovery companies
Figure 8.43: Therapeutic areas represented by the major alliances of biomarker and pharmaceutical
companies
Figure 8.44: Therapeutic areas represented by biomarker patents
Figure 8.45: Cancers represented by biomarker patents 170
Figure 8.46: Estimated time to the widespread use of biomarkers in different therapeutic areas

List of Tables
Table 3.1: Investments by pharmaceutical companies in genomics companies
Table 3.2: Highlights of drug discovery and development based on genomics technologies
Table 3.3: Companies predominantly using genomic and proteomic technologies for drug
development
Table 4.4: Types of toxicogenomic biomarker
Table 4.5: Drugs extensively metabolized by CYP2C19 and CYP2D6
Table 5.6: Glucose-based imaging biomarkers for a variety of diseases
Table 5.7: Advantages of molecular imaging of whole animals for preclinical studies
Table 6.8: Comparison of targeted and untargeted study designs
Table 6.9: List of targeted cancer treatments
Table 6.10: Phase 3 trial outcome for Herceptin with and without HER2 diagnosis
Table 6.11: Examples of pharmacogenomic developments in therapeutic areas other than cancer
Table 6.12: Approval success rates for different therapeutic drug classes
Table 6.13: Currently marketed drugs that might benefit from pharmacogenomics
Table 7.14: Examples of surrogate endpoints and related clinical outcomes
Table 7.15: Sample size for Alzheimer’s disease clinical trials using volumetric MRI measures as a
surrogate endpoint
Table 7.16: Uses of CA-125 in routine clinical care
Table 8.17: Biomarker market size and forecast ($bn), 2005-2012
Table 8.18: Molecular diagnostics market size and forecast ($bn), 2005-2012
Table 8.19: Genomics-based biomarker discovery companies
Table 8.20: Proteomics-based biomarker discovery companies
Table 8.21: Metabonomics-based biomarker discovery companies
Table 8.22: Bioinformatics companies in biomarker discovery
Table 8.23: Summary of major pharmaceutical company biomarker alliances
Table 8.24: Key diagnostic-biomarker company alliances
Table 8.25: Number of patents filed by various pharma and biomarker discovery companies
Table 9.26: Biomarker discovery collaborations with major pharma
Table 9.27: Biomarker discovery collaborations with major pharma (cont.)
Table 9.28: Biomarker discovery collaborations with major pharma (cont.)
Table 9.29: Biomarker discovery collaborations with smaller pharma or biotechnology companies
Table 9.30: Biomarker discovery collaborations with smaller pharma or biotechnology companies
(cont.)
Table 9.31: Biomarker discovery alliances with academia
Table 9.32: Biomarker discovery alliances with academia (cont.)




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