The purpose of this TriMark Publications report is to describe the specific segment of the diagnostics market that develops new technology platforms for evaluating the metabolism of therapeutic agents, or for evaluating which therapeutic regimes are most effective for a particular type of disease. The term companion diagnostic means that the particular diagnostic test under evaluation is specifically linked to a known therapeutic drug. This linkage could be important in the therapeutic application and clinical outcome of a drug (personalized medicine), or an important component of the drug development process. This report focuses on the former linkage, i.e., the use of companion diagnostic tests in personalized medicine.

1. Companion Diagnostics in Personalized Medicine and Cancer Therapy
A near-term market opportunity for cancer companion diagnostic tests exists in drug
selection for cancer therapy. Co-development of molecular diagnostics and targeted
therapeutics has already been proven to be a successful strategy in the development of
novel anti-cancer drugs. Adoption of biomarker development in clinical research provides
great opportunities to identify patient subpopulations with differential drug responses and to
uncover the underlying mechanisms. These data could help to explain if clinical trials of new
drugs are adequate, and offer the possibility of creating a clear prescription path based on
predictive biomarkers.
Buy Now: Companion Diagnostics in Personalized Medicine and Cancer
Therapy Market
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The purpose of this TriMark Publications report is to describe the specific segment of the
diagnostics market that develops new technology platforms for evaluating the metabolism
of therapeutic agents, or for evaluating which therapeutic regimes are most effective for a
particular type of disease. The term companion diagnostic means that the particular
diagnostic test under evaluation is specifically linked to a known therapeutic drug. This
linkage could be important in the therapeutic application and clinical outcome of a drug
(personalized medicine), or an important component of the drug development process. This
report focuses on the former linkage, i.e., the use of companion diagnostic tests in
personalized medicine.
TABLE OF CONTENTS
1. Overview 8
1.1 Statement of Report 8
1.2 About This Report 8
1.3 Scope of the Report 8
1.4 Objectives 9
1.5 Methodology 10
1.6 Executive Summary 11
2. Companion Diagnostics and Personalized Medicine 16
2.1 Scope of This Section 16
2.2 Introduction to Companion Diagnostics and Personalized Medicine 16
2.3 Drug Metabolism and Companion Diagnostics and Personalized Medicine 21
2.4 Examples of Personalized Medicine and Companion Diagnostic Tests 24
2.5 Personalized Medicine and Companion Diagnostic Testing Product Pipeline 27
2.6 The Personalized Medicine Coalition (PMC) 29
2.7 Regulatory Trends and Guidelines in the Personalized Medicine Space 32
2.7.1 The Changing Regulatory Landscape for Personalized Medicine 33
2.8 Companion Diagnostics Play an Increasing Role in Cancer Care 34

2. 2.9 Specific Examples of Clinical Situations where Companion Diagnostics are being
Deployed 35
2.9.1 Epidermal Growth Factor Receptor (EGFR) Assay 36
2.9.2 Individualized Warfarin Therapy 38
2.9.3 UGT1A1 Molecular Assay for Camptosar 38
2.9.4 Response to Gleevec in GIST 38
2.9.5 LabCorp, ARCA Personalized Medicine Deal for Cardiovascular Diseases 39
2.9.6 Osmetech Licenses Epidauros Biotechnologie AG CYP2D6 Biomarker to Enter
Companion
Diagnostics 39
2.10 Diagnostic Tests for Personalized Analysis of Cancer Therapy Effectiveness 39
2.11 Value Chain 40
2.12 Impact of CDx/PM on Drug Clinical Trials 41
3. Companion Diagnostics: Qualitative and Quantitative Market Analysis 43
3.1 Market Analysis of Molecular Diagnostics and Companion Diagnostics 43
3.2 Costs of Companion Diagnostics in Healthcare Expenditures 44
3.3 Molecular Diagnostic Market 45
3.4 Molecular Diagnostics Technology Platforms and Their Impact on Clinical Medicine 48
3.5 Snapshot of Companion Diagnostics Industry Structure 49
3.6 The Case for Theranostics 50
3.7 Companion Diagnostics Market Analysis-Market Survey Data Characterizing the
Qualitative and Quantitative Industry Parameters 51
4. Trends and Overview 54
4.1 Companion Diagnostics: Industry SWOT Analysis 54
4.2 Macro Trends in Companion Diagnostics 54
4.3 Challenges for Companion Diagnostics Development 58
4.4 Timeline for Impact of Various Segments in Companion Diagnostics 60
4.5 Use of Proteomics to Develop Individualized Tests 62
4.6 The Market Problem: Finding Value with Diagnostics for Personalized Medicine 63
5. Biomarker Tests Co-developed with Cancer Therapeutics as Companion
Diagnostics 64
5.1 Sector Overview 64
5.1.1 Impact of New Technology Platforms 64
5.1.2 Impact on Drug Discovery 65
5.1.3 Biomarkers as Endpoints in Drug Discovery 65
5.1.4 Targeted Therapy 66
5.2 Companion Diagnostics on the Market 67
5.3 Epidermal Growth Factor Receptor Companions 67
5.3.1 Bevacizamab (Avastin) 68
5.3.2 EGFR for Colorectal Cancer and Camptosar (Irinotecan) 69
5.3.2.1 Companion Diagnostic Test Developed for UGT1A1 for Irinotecan 69
5.3.2.2 Companion Diagnostic Test Developed for Bristol-Myers’s SPRYCEL 69
5.3.3 EGFR Express and Erbitux (Cetuximab) 69
5.3.4 HER2 and Heceptin (Trastuzumab) 70
5.3.4.1 Bayer’s Advia Centaur HER2/neu Assay 72
5.3.4.2 Companies Marketing HER2/neu Assays 72

3. 5.3.5 Iressa and Tarceva Companion Test 72
5.3.6 Tykerb (GSK), and Vectibix (Amgen) Companion Tests 72
5.3.7 EGFRx Assay 73
5.3.8 Monogram eTag 74
5.3.9 Veripath OncoDiagnostics EGFR PharmDX 74
5.3.10 NSCL Patients with EGFR Mutation 74
5.3.11 A Personalized Medicine Program for Chronic Myeloid Leukemia 74
5.4 Companions Based on Myriad’s IVDMIA Technology 74
5.4.1 Myriad’s TheraGuide 5-FU 74
5.4.2 Myriad’s BRCA Companion Dx Testing for BioMarin’s PARP Inhibitor BMN 673 75
5.5 Companions for Tyrosine Kinase Inhibitors: Erlotinib and Gefitinib 75
5.5.1 TheraScreen: EGFR29 75
5.5.2 The K-RAS Mutation Detection Kit 76
5.6 Irinotecan and UGT1A1 76
5.7 Gleevec (Imatinib) Companions 76
5.7.1 DakoCytomation’s c-Kit (9.7) pharmDx 77
5.8 Companion Diagnostics Involving Metabolizing Enzymes 77
5.8.1 Companions for TMPT, CYP2C9 and UGT1A1 Enzymes 77
5.8.2 Companions for Aromatase Inhibitors 77
5.8.3 Companions for Actos and Avandia 78
5.9 Drivers and Barriers to Companion Diagnostics 78
5.10 Partnerships with Pharma Companies to Identify Therapeutic Targets 79
5.11 Circulating Tumor Cell Assay: Prognostic and Predictive Factors for Breast Cancer 79
5.12 Companion Diagnostics Used by Clinical Service Laboratories 80
5.13 New Technologies and Products under Development 81
5.13.1 OncoMethylome 81
5.14 Pharmacogenomics Tests 81
5.14.1 MGMT Methylation Assay 81
5.14.2 Other Pharmacogenomic Opportunities 82
5.15 Recurrence Prediction Tests 83
5.16 Blood-based Technologies 83
5.16.1 Oncotech 83
5.17 Monogram Biosciences HIV Personalized Platform 84
5.18 Wako LBAAFP Test for Liver Cancer 84
5.19 Future Developments for Companion Diagnostics 85
5.20 Drug Response Predictors 85
6. Business and Regulatory Trends in the Companion Biomarker Testing Sector 87
6.1 Industry Consolidation 87
6.2 Breath of Product Offering and Pricing 88
6.3 Government Regulation of Medical Devices 88
6.3.1 FDA Guidance on Drug Test Co-development 90
6.3.2 Device Classes 90
6.3.3 Investigational Use of IVDM Assays 91
6.3.4 Post-market Requirements 91
6.3.5 Voluntary versus Required Submissions 91
6.3.6 Examples of Recent Voluntary Genomic Data Submissions 91
6.3.7 FDA Labeling Implications and Rules 92
6.3.8 Regulatory Activities in Companion Diagnostic Testing-Translation of Diagnostic

4. Testing Results into Clinical Practice 92
6.4 Strategic Business and Marketing Considerations 93
6.5 Commercial Opportunities in Companion Markers 93
6.6 Moderators of Growth 94
6.6.1 Roadblocks to Integrating Companion Biomarkers into Clinical Practice 95
6.6.2 Management of Targeted Therapeutics by Third-Party Payers 95
6.7 Biotechnology Industry Trends 95
6.8 Pharmaceutical Industry Trends 96
6.9 Acquisition, License Agreement, Partnerships 97
6.10 Legal Developments 100
6.11 Sales and Marketing Strategies for Tumor Marker Tests 102
6.11.1 International Markets 104
6.11.2 Europe 104
6.11.3 Central and South America 105
6.11.4 Asia-Pacific 105
6.12 Product Commercialization 105
6.13 Reimbursement 106
6.14 Self-Referral Rules 107
6.15 Health Insurance Portability and Accountability Act 108
6.16 Clinical Laboratory Improvement Amendments (CLIA) 108
6.17 In Vitro Diagnostic Directive (IVDD) and Medical Device Regulations 109
6.18 FDA’s Quality System Regulation (QSR) 110
6.19 FDA’S OIVD on IVDMIAs 110
6.20 FDA’s Qualification of Cancer Biomarkers 111
6.20.1 Regulatory Perspectives of Biomarker Validation 111
6.21 Genetic Tests and Medical Records 112
6.21.1 Laws against Genetic Discrimination 112
6.22 Global Drivers of Clinical Laboratory Testing 113
6.23 Global Outlook 114
6.24 Oncology Biomarker Qualification Initiative 114
6.25 FDA Critical Path 115
6.25.1 Examples of Drugs being held up due to lack of Compliance with FDA Directives 115
6.26 Biomarkers and FDA’s Voluntary Genomic Data Submission 116
6.27 From Personalized to Predictive Medicine 116
6.28 Analysis of Cost-Effectiveness at the Individual Level 116
6.29 The Patient and Advocate Perspective: An Evolution of Influence 116
6.30 Real-World Experiences Translating the Vision of Personalized Medicine into Practice
116
6.30.1 Evolving Business Models in Companion Dx and Personalized Medicine 117
6.30.2 Current Pharm/Dx Business Model Examples 118
6.31 Reimbursement and Value Creation 118
6.32 What is the Role of Governmental Agencies in Driving the Adoption of CDx? 118
6.33 What is the Role of the Insurance Industry in Driving the Adoption PGx? 118
6.34 What is the Role of the Pharma Industry in Driving the Adoption of PGx? 119
6.35 FDA Guidance Document on Co-development 119
6.36 What is the Role of the Diagnostic Industry in Driving the Adoption of PGx? 119
6.37 What is the Future Role of PBM’s in Laboratory Services? 120

5. 7. Companies Entering the Companion Diagnostics Market 121
7.1 Industry Overview 121
7.1.1 20/20 GeneSystems, Inc. 121
7.1.2 Abbott Diagnostics 121
7.1.3 Affymetrix 124
7.1.4 Agendia BV 126
7.1.5 Agensys, Inc. 127
7.1.6 Almac Group 127
7.1.7 Almac Diagnostics 128
7.1.8 AMDL, Inc. 128
7.1.9 Arcturus Bioscience, Inc. (Acquired by Molecular Devices) 130
7.1.10 Aureon Laboratories Corporation 130
7.1.11 Becton, Dickinson and Company 131
7.1.12 Beckman Coulter, Inc. 131
7.1.13 Biocode Hycel 133
7.1.14 BioCurex, Inc. 133
7.1.15 Biodesix 134
7.1.16 Biomarker Technologies, LLC 134
7.1.17 Biomedical Diagnostics, LLC 134
7.1.18 Biomerica 134
7.1.19 bioMerieux 135
7.1.20 BioModa, Inc. 135
7.1.21 Bruker Daltonics 136
7.1.22 Cangen Biotechnologies, Inc. 136
7.1.23 Caprion Proteomics 137
7.1.24 Celera Diagnostics 138
7.1.25 Cepheid 139
7.1.26 Claros Diagnostics 140
7.1.27 Clinical Data, Inc. 140
7.1.28 Ciphergen Biosystems, Inc. (Renamed Vermillion, Inc.) 142
7.1.29 Clarient, Inc. 144
7.1.30 Correlogic Systems, Inc. 145
7.1.31 CytoCore, Inc. 145
7.1.32 Cytogen Corporation 146
7.1.33 Cytyc Corporation 149
7.1.34 Dako (Formerly DakoCytomation) 150
7.1.35 DiaDexus 150
7.1.36 Digene (Acquired by Qiagen) 151
7.1.37 DiagnoCure 151
7.1.38 Diagnostic Systems Laboratories, Inc. (Acquired by Beckman Coulter) 153
7.1.39 DRG International 153
7.1.40 DxS (Acquired by Qiagen) 154
7.1.41 EDP Biotech Corporation 155
7.1.42 Epigenomics 155
7.1.43 EXACT Sciences Corporation 156
7.1.44 Exagen Diagnostics 157
7.1.45 Gene Logic, Inc. 158
7.1.46 Genesis Genomics, Inc. 159
7.1.47 Genomic Health 159

6. 7.1.48 Gen-Probe, Inc. 160
7.1.49 Health Discovery Corporation 160
7.1.50 Ikonisys, Inc. 161
7.1.51 Immunicon Corporation 161
7.1.52 Immunomedics 165
7.1.53 Incyte 166
7.1.54 InterGenetics 167
7.1.55 Ipsogen 167
7.1.56 Johnson & Johnson 167
7.1.57 LabCorp 168
7.1.58 Matritech, Inc. 169
7.1.59 Miraculins 171
7.1.60 Mitsubishi Kagaku latron 172
7.1.61 Monogram Biosciences 172
7.1.62 Myriad Genetics, Inc. 173
7.1.63 NimbleGen Systems 176
7.1.64 Northwest Biotherapeutics, Inc. 176
7.1.65 Nycomed 178
7.1.66 Oncotech, Inc. 178
7.1.67 Oncothyreon (Formerly known as Biomira) 179
7.1.68 Orion Genomics 180
7.1.69 Oxford Genome Sciences 180
7.1.70 Panacea Pharmaceuticals, Inc. 181
7.1.71 Perlegen Sciences, Inc. 181
7.1.72 Polymedco, Inc. 181
7.1.73 Power3 Medical Products 182
7.1.74 Prometheus 182
7.1.75 Proteome Systems Limited 183
7.1.76 Qiagen N.V. 183
7.1.77 Sanko Junyaku Co. Ltd. 184
7.1.78 SensiGen, LLC 184
7.1.79 SuperArray Bioscience Corporation 184
7.1.80 Third Wave Technologies, Inc. 185
7.1.81 Tosoh Biosciences 185
7.1.82 TrimGen 185
7.1.83 Upstream Biosciences, Inc. 186
7.1.84 Ventana Medical Systems, Inc. 186
7.1.85 Veridex, LLC 187
Appendix 1: FDA Guidance for Industry: Pharmacogenomic Data Submission
(March 2005) 188
I. Introduction 188
II. Background 188
III. Submission Policy 189
A. General Principles 189
B. Specific Uses of Pharmacogenomic Data in Drug Development and Labeling 191
C. Benefits of Voluntary Submissions to Sponsors and FDA 192
IV. Submission of Pharmacogenomic Data 193
A. Submission of Pharmacogenomic Data during the IND Phase 193

7. B. Submission of Pharmacogenomic Data to a New NDA, BLA, or Supplement 194
C. Submission to a Previously Approved NDA or BLA 195
D. Compliance with 21 CFR Part 58 195
E. Submission of Voluntary Genomic Data from Application-Independent Research 196
V. Format and Content of a VGDS 196
VI. Process for Submitting Pharmacogenomic Data 197
VII. Agency Review of Voluntary Genomic Data Submissions 197
Glossary 200
Appendix 2: Histochemical Markers for Cancer 201
LIST OF FIGURES
Figure 2.1: Personalizing Drug Treatment 17
Figure 2.2: Approaches to Personalized Medicine 18
Figure 2.3: The Phase I and II Processes of Drug Metabolism 21
Figure 2.4: Hepatic Distribution of Human CYP450 22
Figure 2.5: Relative Contribution of CYP450 Enzymes to Drug Metabolism 22
Figure 2.6: Genetic Components Determine Drug Metabolism 23
Figure 2.7: Personalized Medicine Drugs in Development 27
Figure 2.8: Healthcare Value Chain 41
Figure 3.1: From Genetic Content to Personalized Medicine 44
Figure 3.2: Impact of Diagnostic Testing on Healthcare Decision Making 44
Figure 3.3: Impact of Diagnostic Testing on Healthcare Spending 45
Figure 3.4: Breakout of the Molecular Diagnostics Marketplace by Country 46
Figure 3.5: Breakout of the Molecular Diagnostics Marketplace by Vendor 46
Figure 3.6: Molecular Diagnostics Market Segmentation 47
Figure 3.7: Molecular Diagnostics Market Segmentation by Technology 47
Figure 3.8: Market Survey Respondent Demographics 52
Figure 3.9: Breakout of the Respondent Pool by Affiliation 52
Figure 3.10: Segmentation of the Personalized Medicine Market 53
Figure 4.1: Personalized Medicine Market Drivers 55
Figure 4.2: Challenges in the Personalized Medicine Space 56
Figure 5.1: Carcinogenesis is a Multi-Step Process 64
Figure 5.2: ASCO-CAP Guidelines for HER2 Testing in Breast Cancer: Equivocal Results with
IHC 71
Figure 5.3: ASCO-CAP Guidelines for HER2 Testing in Breast Cancer: Results by FISH 71
Figure 5.4: MGMT Methylation Status Correlates to Survival Rate 82
LIST OF TABLES
Table 2.1: Timeline for Development of Companion Diagnostics 18
Table 2.2: Personalized Medicine at the Nexus Point 19
Table 2.3: Percentage of Non-Responders in Various Drug Classes 19
Table 2.4: High-Profile Drug Withdrawals from the Marketplace 20
Table 2.5: Metabolism of Drugs by Hepatic Enzymes 21
Table 2.6: Drug Metabolism Drives Drug Efficacy/Toxicity 24
Table 2.7: Population Frequency of the Various Cytochromes 24
Table 2.8: Selected List of Personalized Medicine Tests 26
Table 2.9: Personalized Medicine Product Pipeline 28
Table 2.10: Typical Response Rates in Therapeutic Areas 35
Table 2.11: Prevalence of People Taking Medications Metabolized by Liver Enzymes 37

8. Table 2.12: UGT1A1 Helps to Determine Risks Associated with Irinotecan 37
Table 2.13: Current Product Labels: Enzyme Metabolism 37
Table 3.1: Timeline for Impact of Various Molecular Diagnostics Technologies on
Personalized Medicine 48
Table 3.2: Impact of Molecular Diagnostics Technologies on Therapeutic Areas in
Personalized Medicine 48
Table 3.3: Challenges of Various Molecular Diagnostics Technology Platforms in Personalized
Medicine 49
Table 3.4: FDA Classification of Diagnostics by Risk 51
Table 4.1: Personalized Medicine Industry SWOT Analysis 54
Table 4.2: Market Opportunities in Personalized Medicine 57
Table 4.3: Challenges for Market Adoption of Various Personalized Medicine Tests 58
Table 4.4: Hurdles to Personalized Medicine and Companion Diagnostics Development 59
Table 4.5: Timeline of Impact in Areas of Personalized Medicine 60
Table 4.6: Impact of Personalized Medicine on Various Therapeutic Areas 61
Table 5.1: Potential Benefits of Biomarkers as Companion Diagnostics 66
Table 5.2: Utility of Biomarker as Companion Diagnostics to Drug Development 66
Table 5.3: ASCO-CAP Guidelines for HER2 Testing in Breast Cancer: How to Interpret Test
Results 70
Table 5.4: Device Submission Elements for the FDA 79
Table 6.1: List and Discounted Prices for Abbott Tumor Marker Tests 88
Table 6.2: Summary of Biomarker Use in the Commercialization of Novel Oncology
Pharmacotherapeutics 117
Table 6.3: Pharmacoeconomic Challenges to the Implementation of Biomarkers as
Companion
Diagnostic Tests 117
Table 7.1: Major Players in Companion Diagnostic Sector 121
Table 7.2: Tumor Diagnosis Immunoassay 153
Table 7.3: Tumor Diagnosis Radioimmunoassay 154
Table 7.4: Summary of Matritech’s Product Development Programs 171
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