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Companion Diagnostics in Personalized Medicine and Cancer Therapy

  • September 2015
  • -
  • TriMark Publications
  • -
  • 249 pages

Companion diagnostics (CDx) refers to a particular clinical diagnostic test that is under evaluation and is specifically linked to a known drug therapy. This linkage could be important in the therapeutic application and clinical outcome of a drug, such as with personalized medicine for oncology patients. The molecular diagnostics field plays a vital part in personalized medicine and has greatly expanded over the past twenty years, expanding by more than 20% annually compared to most other laboratory procedures. Research will continue to produce an increased understanding of disease processes, and diagnostics manufacturers will continue to expand and refine the technology and automation needed for clinical testing. Companion diagnostics, although smaller at present, is one of the fastest growing segments in the in vitro diagnostic (IVD) market. And while the concept of a drug-diagnostic combination is not new, it has only recently started to generate interest with the move of healthcare towards pharmacogenomics. This TriMark Publications report examines the use of companion diagnostics in personalized medicine and cancer therapy. The study provides a qualitative and quantitative review of the industry, including cancer biomarker tests, pharmacogenomics tests, recurrence prediction tests, blood-based technologies, proteomics and regulatory trends. Moreover, this analysis profiles the leading companies that are developing and manufacturing companion diagnostics solutions. Each company is discussed in extensive depth with a section on its history, product line, business and marketing analysis, and a subjective commentary of the company's market position. Detailed tables and charts with sales forecasts and market share data are also included.

Table Of Contents

Companion Diagnostics in Personalized Medicine and Cancer Therapy
1. Overview 8
1.1 Statement of Report 8
1.2 Why You Should Read This Report 8
1.3 Scope of the Report 9
1.4 Objectives 10
1.5 Key Questions Answered by This Report 11
1.6 Methodology 11
1.7 Executive Summary 12

2. Companion Diagnostics: Trends and Overview 18
2.1 Stakeholders in Companion Diagnostics 18
2.2 Development of Stakeholders' Business Models for Companion Diagnostics for Personalized
Medicine 20
2.2.1 Pharmaceutical Company Business Models for Developing Companion Diagnostics Products 20
2.2.2 Diagnostic Company Business Models for Developing Companion Diagnostics Products 21
2.2.3 Life Science Company Business Models for Developing Companion Diagnostics Products 21
2.2.4 Pharmacy Benefit Management Company Business Models for Developing Companion Diagnostics Products 22
2.3 Trends in Companion Diagnostic Deals 22
2.4 Market Size of Companion Diagnostics 23
2.5 Companion Diagnostics: Industry SWOT Analysis 31
2.6 Challenges for Companion Diagnostics Development 31
2.7 Timeline for Impact of Various Segments in Companion Diagnostics 33
2.8 Use of Proteomics to Develop Individualized Tests 35

3. Companion Diagnostics: Qualitative and Quantitative Market Analysis 37
3.1 Market Analysis of Molecular Diagnostics and Companion Diagnostics 37
3.2 Costs of Companion Diagnostics in Healthcare Expenditures 38
3.3 Molecular Diagnostic Market 40
3.4 Molecular Diagnostics Technology Platforms and Their Impact on Clinical Medicine 42
3.5 Snapshot of Companion Diagnostics Industry Structure 44
3.6 The Case for Theranostics 45
3.7 Companion Diagnostics Market Analysis 46

4. Biomarker Tests Co-Developed with Cancer Therapeutics as Companion Diagnostics 48
4.1 Sector Overview 48
4.1.1 Impact of New Technology Platforms 48
4.1.2 Impact on Drug Discovery 49
4.1.3 Biomarkers as Endpoints in Drug Discovery 49
4.1.4 Targeted Therapy 50
4.2 Companion Diagnostics on the Market 51
4.3 Epidermal Growth Factor Receptor Companions 52
4.3.1 Bevacizamab (Avastin) 53
4.3.2 EGFR for CRC and Camptosar (Irinotecan) 55
4.3.2.1 Companion Diagnostic Test Developed for UGT1A1 for Irinotecan 55
4.3.2.2 Companion Diagnostic Test Developed for Bristol-Myers' SPRYCEL 55
4.3.3 EGFR Express and Erbitux (Cetuximab) 55
4.3.4 HER2 and Herceptin (Trastuzumab) 56
4.3.4.1 Siemen's Advia Centaur HER2/neu Assay 57
4.3.4.2 Companies Marketing HER2/neu Assays 58
4.3.5 Iressa and Tarceva Companion Test 58
4.3.6 Tykerb GlaxoSmithKline (GSK)) and Vectibix (Amgen) Companion Tests 58
4.3.7 EGFRx Assay 58
4.3.8 A Personalized Medicine Program for CML 60
4.4 Companions Based on Myriad's IVDMIA Technology 60
4.4.1 Myriad's BRACAnalysis Collaboration with Partners in Companion Test Development 60
4.5 Companions for Tyrosine Kinase Inhibitors: Erlotinib and Gefitinib 62
4.5.1 TheraScreen: EGFR29 62
4.5.2 The K-RAS Mutation Detection Kit 62
4.6 Irinotecan and UGT1A1 62
4.7 Gleevec (Imatinib) Companions 63
4.7.1 DakoCytomation's c-Kit (9.7) pharmDx 63
4.8 Companion Diagnostics Involving Metabolizing Enzymes 64
4.8.1 Companions for TMPT, CYP2C9 and UGT1A1 Enzymes 64
4.8.2 Companions for Aromatase Inhibitors 64
4.9 Drivers and Barriers to Companion Diagnostics 65
4.10 Partnerships with Pharma Companies to Identify Therapeutic Targets 66
4.11 Circulating Tumor Cell Assay: Prognostic and Predictive Factors for Breast Cancer 66
4.12 Companion Diagnostics Used by Clinical Service Laboratories 67
4.13 New Technologies and Products under Development 68
4.13.1 MDxHealth Epigenetic Marker as Companion for Irinotecan Therapy in Colorectal Cancer 69
4.13.2 Ventana to Collaborate with Pfizer and CST on Companion Diagnostic to Identify Lung Cancer Patients with ALK Gene Rearrangements 69
4.13.3 Abbott and Merck Collaborate to Develop Companion Diagnostic Test for Investigational Cancer
Therapy 70
4.14 Pharmacogenomics Tests 71
4.14.1 MGMT Methylation Assay 71
4.14.2 Other Pharmacogenomic Opportunities 72
4.15 Recurrence Prediction Tests 72
4.16 Monogram Biosciences HIV Personalized Platform 73
4.17 Wako LBA AFP Test for Liver Cancer 73
4.18 Future Developments for Companion Diagnostics 73
4.19 Drug Response Predictors 75

5. Business and Regulatory Trends in the Companion Biomarker Testing Sector 76
5.1 Industry Consolidation 76
5.2 Breath of Product Offering and Pricing 77
5.3 Government Regulation of Medical Devices 77
5.3.1 FDA Guidance on Drug Test Co-Development 79
5.3.2 Device Classes 80
5.3.3 Investigational Use of IVDMIAs 80
5.3.4 Post-Market Requirements 81
5.3.5 Voluntary vs. Required Submissions 81
5.3.6 Examples of Recent Voluntary Genomic Data Submissions 81
5.3.7 FDA Labeling Implications and Rules 81
5.3.8 Regulatory Activities in Companion Diagnostic Testing—Translation of Diagnostic Testing Results into Clinical Practice 82
5.4 Strategic Business and Marketing Considerations 82
5.5 Commercial Opportunities in Companion Markers 83
5.6 Moderators of Growth 85
5.6.1 Roadblocks to Integrating Companion Biomarkers into Clinical Practice 85
5.6.2 Management of Targeted Therapeutics by Third-Party Payers 86
5.7 Biotechnology Industry Trends 86
5.8 Pharmaceutical Industry Trends 86
5.9 Acquisition, License Agreement, Partnerships 87
5.10 Legal Developments 94
5.11 Sales and Marketing Strategies for Companion Diagnostic Tests 95
5.11.1 International Markets 98
5.11.2 Europe 98
5.11.3 Central and South America 99
5.11.4 Asia-Pacific 100
5.11.4.1 Japan 100
5.11.4.2 China 101
5.12 Product Commercialization 101
5.13 Reimbursement 102
5.14 Self-Referral Rules 103
5.15 Health Insurance Portability and Accountability Act 104
5.16 Clinical Laboratory Improvement Amendments (CLIA) 104
5.17 In Vitro Diagnostic Directive (IVDD) and Medical Device Regulations 105
5.18 FDA's Quality System Regulation (QSR) 106
5.19 The FDA's OIVD on IVDMIAs 106
5.20 FDA's Qualification of Cancer Biomarkers 107
5.20.1 Regulatory Perspectives of Biomarker Validation 107
5.21 Genetic Tests and Medical Records 108
5.21.1 Laws Against Genetic Discrimination 109
5.22 Global Drivers of Clinical Laboratory Testing 109
5.23 Global Outlook 110
5.24 Oncology Biomarker Qualification Initiative 111
5.25 FDA Critical Path 111
5.26 Biomarkers and FDA's Voluntary Genomic Data Submission 112
5.27 From Personalized to Predictive Medicine 112
5.28 Analysis of Cost-Effectiveness at the Individual Level 112
5.29 The Patient and Advocate Perspective: An Evolution of Influence 112
5.30 Real-World Experiences Translating the Vision of Personalized Medicine into Practice 112
5.30.1 Evolving Business Models in Companion Diagnostics and Personalized Medicine 113
5.30.2 Current Pharma/Diagnostics Business Model Examples 114
5.31 Reimbursement and Value Creation 114
5.32 What is the Role of Governmental Agencies in Driving the Adoption of Companion Diagnostics? 114
5.33 What is the Role of the Insurance Industry in Driving the Adoption of Pharmacogenomics (PGx)? 114
5.34 What is the Role of the Pharma Industry in Driving the Adoption of PGx? 115
5.35 FDA Guidance Document on Co-Development 115
5.36 What is the Role of the Diagnostic Industry in Driving the Adoption of PGx? 115
5.37 What is the Future Role of PBMs in Laboratory Services? 116

6. Companion Diagnostics and Personalized Medicine 117
6.1 Scope of This Section 117
6.2 Introduction to Companion Diagnostics and Personalized Medicine 117
6.3 Drug Metabolism, Companion Diagnostics and Personalized Medicine 124
6.4 Examples of Personalized Medicine and Companion Diagnostic Tests 127
6.5 Personalized Medicine and Companion Diagnostic Testing Product Pipeline 132
6.6 The Personalized Medicine Coalition (PMC) 134
6.7 Regulatory Trends and Guidelines in the Personalized Medicine Space 139
6.7.1 The Changing Regulatory Landscape for Personalized Medicine 140
6.8 Companion Diagnostics Play an Increasing Role in Cancer Care 142
6.9 Specific Examples of Clinical Situations where Companion Diagnostics are being Deployed 142
6.9.1 Epidermal Growth Factor Receptor Assay 143
6.9.2 Individualized Warfarin Therapy 145
6.9.3 UGT1A1 Molecular Assay for Camptosar 146
6.9.4 Response to Gleevec in Gastrointestinal Stromal Tumors (GISTs) 146
6.9.5 LabCorp and QIAGEN and Personalized Medicine for the treatment of Colorectal Cancer 146
6.9.6 LabCorp and ARCA Discovery, Inc. Personalized Medicine for Cardiovascular Disease 147
6.9.7 Roche's Metastatic Melanoma Treatment, Zelboraf (Vemurafenib) 147
6.9.8 Abbott's Companion Test for Late-Stage NSCLC Treatment Drug Xalkori (Crizotinib) 148
6.10 Diagnostic Tests for Personalized Analysis of Cancer Therapy Effectiveness 148
6.11 Value Chain 149
6.12 Impact of Companion Diagnostics/Personalized Medicine on Drug Clinical Trials 150
6.13 The Market Problem: Finding Value with Diagnostics for Personalized Medicine 151

7. Companies Entering the Companion Diagnostics Market 153
7.1 Industry Overview 153
7.1.1 20/20 GeneSystems, Inc. 155
7.1.2 Abbott Molecular, Inc. 156
7.1.3 Affymetrix, Inc. 159
7.1.4 Agendia BV 167
7.1.5 Agilent Technologies 169
7.1.6 Almac Group 170
7.1.7 Asuragen, Inc. 172
7.1.8 Aureon Laboratories, Inc. 173
7.1.9 Becton, Dickinson and Company (BD) Diagnostics—TriPath 175
7.1.10 Biodesix 176
7.1.11 Biomarker Technologies, LLC 176
7.1.12 bioMerieux, Inc. 177
7.1.13 Cepheid, Inc. 177
7.1.14 Cipher Genomics 179
7.1.15 diaDexus 179
7.1.16 DiagnoCure 180
7.1.17 EDP Biotech Corporation 183
7.1.18 Eisai Co., Ltd. 183
7.1.19 Eli Lilly and Co. 183
7.1.20 Epigenomics 184
7.1.21 Exagen Diagnostics, Inc. 185
7.1.22 Exiqon 185
7.1.23 Genomic Health, Inc. 186
7.1.24 Hologic 187
7.1.25 Halozyme Therapeutics 192
7.1.26 Ikonisys, Inc. 192
7.1.27 Illumina, Inc. 194
7.1.28 HalioDx 196
7.1.29 InterGenetics, Inc. 196
7.1.30 Johnson and Johnson 197
7.1.31 LabCorp 197
7.1.32 MolecularMD Corporation 199
7.1.33 MDxHealth 199
7.1.34 Monogram Biosciences 200
7.1.35 Myriad Genetics, Inc. 200
7.1.36 Novartis MDx 204
7.1.37 Nycomed (Takeda) 205
7.1.38 Orion Genomics 205
7.1.39 Oxford BioTherapeutics (Formerly Oxford Genome Sciences) 206
7.1.40 NanoString Technologies 207
7.1.41 QIAGEN N.V. 208
7.1.42 Roche Molecular Diagnostics 212
7.1.43 Sanko Junyaku Co., Ltd. (Eisai Co., Ltd.) 214
7.1.44 SensiGen, LLC (Sequenom Center for Molecular Medicine) 214
7.1.45 Siemens Healthcare Diagnostics, Inc. 215
7.1.46 Tosoh Biosciences Corporation 216
7.1.47 Transgenomic, Inc. 217
7.1.48 Ventana Medical Systems, Inc. 217
7.1.49 Vermillion, Inc. (Formerly Ciphergen) 219
7.1.50 Vertex Pharmaceuticals, Inc. 220

Appendix 1: FDA Guidance for Industry: Pharmacogenomic Data Submissions 221
Appendix 1.1: Introduction 221
Appendix 1.2: Background 221
Appendix 1.3: Submission Policy 222
Appendix 1.3.1: General Principles 222
Appendix 1.3.2: Specific Uses of Pharmacogenomic Data in Drug Development and Labeling 224
Appendix 1.3.3: Benefits of Voluntary Submissions to Sponsors and FDA 225
Appendix 1.4: Submission of Pharmacogenomic Data 225
Appendix 1.4.1: Submission of Pharmacogenomic Data During the IND Phase 226
Appendix 1.4.2: Submission of Pharmacogenomic Data to a New NDA, BLA or Supplement 227
Appendix 1.4.3: Submission to a Previously Approved NDA or BLA 228
Appendix 1.4.4: Compliance with 21 CFR Part 58 228
Appendix 1.4.5: Submission of Voluntary Genomic Data from Application-Independent Research 228
Appendix 1.5: Format and Content of a VGDS 229
Appendix 1.6: Process for Submitting Pharmacogenomic Data 230
Appendix 1.7: Agency Review of VGDSs 230
Appendix 2: FDA Issues Draft Companion Diagnostic Guidance 232
Appendix 3: Histochemical Markers for Cancer 234
Appendix 4: E16 Biomarkers Related to Drug or Biotechnology Product Development: Context, Structure, and Format of Qualification Submissions 235
Appendix 4.1: Introduction 235
Appendix 4.2: Background 235
Appendix 4.3: Scope 235
Appendix 4.4: General Principles 235
Appendix 4.5: Structure of Biomarker Qualification Submissions 236
Appendix 5: Selected Personalized Medicine Drugs, Treatments and Diagnostics 243
Glossary 248


INDEX OF FIGURES

Figure 2.1: Strategic and Tactical Considerations for Co-Development of Companion Diagnostics 23
Figure 2.2: Global Market for Companion Diagnostics, 2012-2019 24
Figure 2.3: Number of Companion Diagnostic Agreements, 2000-2013 25
Figure 2.4: FDA Approved Companion Drugs by Type 30
Figure 3.1: From Genetic Content to Personalized Medicine 38
Figure 3.2: Impact of Diagnostic Testing on Healthcare Decision-Making 39
Figure 3.3: Impact of Diagnostic Testing on Healthcare Spending 39
Figure 3.4: Breakout of the Molecular Diagnostics Marketplace 41
Figure 3.5: Molecular Diagnostics Market Segmentation 42
Figure 3.6: Molecular Diagnostics Market Segmentation by Technology 42
Figure 3.7: Segmentation of the Personalized Medicine Market 46
Figure 4.1: Carcinogenesis is a Multi-Step Process 54
Figure 4.2: ASCO-CAP Guidelines for HER2 Testing in Breast Cancer: Equivocal Results with IHC 56
Figure 4.3: ASCO-CAP Guidelines for HER2 Testing in Breast Cancer: Results by FISH 57
Figure 5.1: Companion Diagnostics Partnering, 2007-2013 88
Figure 5.2: Companion Diagnostics Partnering by Stage of Development, 2013 88
Figure 5.3: Companion Diagnostics Partnering by Therapeutic Area, 2013 90
Figure 6.1: U.S. Healthcare Expenditures by Category of Service, 2010 118
Figure 6.2: Representation of the Trial-and-Error or One-Dose-Fits-All Approach vs. Personalized
Medicine 118
Figure 6.3: Approaches to Personalized Medicine 120
Figure 6.4: Organizational Transformation to Support Personalized Medicine, 1998-2013 121
Figure 6.5: The Phase I and II Processes of Drug Metabolism 124
Figure 6.6: Hepatic Distribution of Human CYP450 125
Figure 6.7: Relative Contribution of CYP450 Enzymes to Drug Metabolism 125
Figure 6.8: Genetic Components Determine Drug Metabolism 126
Figure 6.9: Personalized Medicine Clinical Trials by Year, 1993-2008 131
Figure 6.10: Healthcare Value Chain 149


INDEX OF TABLES

Table 2.1: FDA Approved Companion Diagnostic Devices: In Vitro and Imaging Tools 26
Table 2.2: Personalized Medicine Industry SWOT Analysis 31
Table 2.3: Hurdles to Personalized Medicine and Companion Diagnostics Development 32
Table 2.4: Timeline of Impact in Areas of Personalized Medicine 34
Table 2.5: Impact of Personalized Medicine on Various Therapeutic Areas 35
Table 3.1: Diagnostic Facts 38
Table 3.2: Timeline for Impact of Various Molecular Diagnostics Technologies on Personalized Medicine 43
Table 3.3: Impact of Molecular Diagnostics Technologies on Therapeutic Areas in Personalized Medicine 43
Table 3.4: Challenges of Various Molecular Diagnostics Technology Platforms in Personalized Medicine 44
Table 3.5: FDA Classification of Diagnostics by Risk 46
Table 4.1: Potential Benefits of Biomarkers as Companion Diagnostics 50
Table 4.2: Utility of Biomarker as Companion Diagnostics to Drug Development 50
Table 4.3: ASCO-CAP Guidelines for HER2 Testing in Breast Cancer: How to Interpret Test Results 56
Table 4.4: Myriad BRACAnalysis CDxâ„¢ Partnerships 61
Table 4.5: Drivers of Companion Diagnostics Discovery 65
Table 4.6: Barriers to Companion Diagnostics Discovery 65
Table 4.7: Device Submission Elements for the FDA 66
Table 5.1: List and Discounted Prices for Abbott Tumor Marker Tests 77
Table 5.2: Recent Major Companion Diagnostics Deals 89
Table 5.3: Summary of Biomarker Use in the Commercialization of Novel Oncology
Pharmacotherapeutics 113
Table 5.4: Pharmacoeconomic Challenges to the Implementation of Biomarkers as Companion
Diagnostics Tests 113
Table 6.1: Timeline for Development of Companion Diagnostics 120
Table 6.2: Personalized Medicine at the Nexus Point 122
Table 6.3: Percentage of Non-Responders in Various Drug Classes 122
Table 6.4: High-Profile Drug Withdrawals from the Marketplace 123
Table 6.5: Metabolism of Drugs by Hepatic Enzymes 124
Table 6.6: Drug Metabolism Drives Drug Efficacy/Toxicity 127
Table 6.7: Population Frequency of the Various Cytochromes 127
Table 6.8: Selected List of Personalized Medicine Tests 130
Table 6.9: Personalized Medicine and Companion Diagnostics Product Pipeline 133
Table 6.10: Members of the Personalized Medicine Coalition 135
Table 6.11: Typical Response Rates in Therapeutic Areas 143
Table 6.12: Prevalence of People Taking Medications Metabolized by Liver Enzymes 144
Table 6.13: UGT1A1 Helps to Determine Risks Associated with Irinotecan 144
Table 6.14: Current Product Labels: Enzyme Metabolism 145
Table 7.1: Major Players in Companion Diagnostics Sector and Summary List of Companion Diagnostics Agreements 153
Table 7.2: Major GeneChip Instrument Products 162
Table 7.3: Major GeneChip Array and Reagent Products 163
Table 7.4: Gene Titan Products 163
Table 7.5: Gene Atlas Products 163
Table 7.6: Opportunities for Biomarkers in Cancer Diagnosis and Treatment 179

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