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Genomics is transforming the pharmaceutical industry. Companies are moving from drug discovery and development based on medicinal chemistry to the design of drugs based on information provided by genomics. Virtually all of the major pharmaceutical houses have either formed partnerships with genomics firms that began to emerge in the early 1990s or have created in house genomics divisions. The aim of this TriMark Publications study is to provide in depth information on the developing market for genomics products and services. The report will include detailed market analyses and discussions of industry trends in order to assess the impact of genomics on the current and emerging pharmaceutical and diagnostic markets. Forecasts and trends were developed from interviews with industry sources, as well as from an assessment of available and emerging technologies. The report focuses on how researchers are applying new genomic approaches to drug discovery and development, and on how these technologies can be used most effectively and in a high throughput capacity. Case studies analyzing particular applications of genomic technologies to specific disease related research are provided, and future trends and developments are forecasted. Information to prepare this study was derived from interviews with product managers, marketing strategists, research executives and others. These individuals are employed at leading genomics firms or in pharmaceutical and biotechnology companies that either contract with these firms or have developed in house genomics capabilities.

1. 1. Introduction 6
2. 1.1 Statement of Report 6
3. 1.2 Objectives and Goals of Study 6
4. 1.3 Methodology 6
5. 1.4 Executive Summary 8
6. 1.4.1 Market Drivers 8
7. 1.4.2 Market Restraints 8
8. 1.4.3 Market Size and Growth Projections 8
9. 1.5 What Is a Gene? 9
10. 1.6 Gene Expression 10
11. 1.7 Genetic Variability 10
12. 1.8 The Human Genome Project (HGP) 11
13. 1.9 Gene Databases 12
14. 1.10 Sequencing and Resequencing 12
15. 1.11 RNA Interference (RNAi) 13
16. 1.12 DNA Tags 15
18. 2. Genomics Technology and Industry 16
19. 2.1 The Development of a Genomics Market 16
20. 2.1.1 Market Size and Growth Projections 16
21. 2.1.2 The U.S. Genomics Market 16
22. 2.2 DNA Microarray Technology 17
23. 2.2.1 Biochips 17
24. 2.2.2 Photolithography 17
25. 2.2.3 Instrumentation for DNA Microarray Analysis 18
26. 2.2.4 Lab-on-a-Chip 19
27. 2.2.5 DNA Microarrays 20
28. 2.3 Applications of DNA Microarrays 21
29. 2.3.1 DNA Sequence Analysis 21
30. 2.3.2 Gene Expression Analysis 28
31. 2.3.3 Effect of DNA Sequence and Gene Expression Monitoring on the Genomics Market 31
32. 2.4 Bioinformatics 32
33. 2.5 Functional Genomics 34
34. 2.5.1 Gene Knockdown 35
35. 2.5.2 Protein-Protein Interactions 36
36. 2.5.3 Bioinformatics 36
37. 2.5.4 Strategies of Functional Genomics Companies 37
38. 2.5.5 Frontiers in Functional Genomics 38
39. 2.6 Comparative Genomics 39
40. 2.7 Pharmacogenomics 39
41. 2.8 Proteomics 40
42. 2.9 Structural Genomics 40
43. 2.10 Disease Targets 41
44. 2.10.1 Paradigm Shift in Drug Development: The Evolution of Targeted Therapies 41
45. 2.10.2 Personalized Warfarin Therapy 41
47. 3. How Genomics Is Revolutionizing Healthcare 44
48. 3.1 Pharmaceutical Applications 44
49. 3.2 Diagnostics 46
50. 3.3 Toxicogenomics 50
51. 3.4 The Market for DNA Microarrays 50
52. 3.5 DNA Chip Technology Competition 50
53. 3.6 Expression Profiling 51
54. 3.7 Gene Sequencing-Advantages of Chip Array Technology 51
55. 3.8 Applied Markets for Genomics 52
56. 3.9 Genomics and the Pharmaceutical Companies 53
57. 3.10 Cancer Markets 54
58. 3.11 Agricultural Markets 55
59. 3.11.1 Plant Genomics 56
60. 3.11.2 Food Processing 57
61. 3.11.3 Animal Husbandry 57
63. 4. Proprietary Applications and Patents 59
64. 4.1 What is Patentable? 59
65. 4.2 Patents and Litigation 61
67. 5. Business Analysis 64
68. 5.1 Facilitation and Capitalization of the Convergence of Gene Expression Analysis and Proteomics 64
69. 5.2 Competition 64
70. 5.3 Market Opportunities for Functional Genomics 64
71. 5.3.1 Metabolic Profiling 64
72. 5.3.2 Anti-Fungal Targets 65
73. 5.3.3 Nutrition 66
74. 5.3.4 Crop Production 66
75. 5.4 The Highly-Competitive Nature of the Genomics Industry 68
76. 5.4.1 First-Generation Biotech 68
77. 5.4.2 Second-Generation Genomics Companies 69
78. 5.4.3 Next-Generation DNA Sequencing Companies 69
79. 5.5 Strategic Alliances 69
81. 6. Genomics Company Profiles 71
82. 6.1 Affymetrix, Inc. 71
83. 6.2 Agendia 80
84. 6.3 Agilent Technologies, Inc. 80
85. 6.4 Applied Biosystems Group 81
86. 6.5 Bayer, AG 85
87. 6.6 Biotage 85
88. 6.7 Caliper Life Sciences 85
89. 6.8 Celera Group 88
90. 6.9 Cepheid 88
91. 6.10 CLC bio 89
92. 6.11 Clinical Data, Inc. 89
93. 6.12 CuraGen Corporation 90
94. 6.13 Cytocell Ltd. 95
95. 6.14 diaDexus, Inc. 95
96. 6.15 Enzo Biochem, Inc. 97
97. 6.16 Exiqon A/S 98
98. 6.17 GE Healthcare 98
99. 6.18 Gene Link, Inc. 98
100. 6.19 Gene Logic, Inc. 98
101. 6.20 Genentech, Inc. 100
102. 6.21 Genisphere, Inc. 101
103. 6.22 Genomatix Software, Inc. 102
104. 6.23 Genomic Solutions, Inc. 102
105. 6.24 Gen-Probe, Inc. 103
106. 6.25 Harvard Bioscience, Inc. 105
107. 6.26 Helicos Biosciences Corporation 105
108. 6.27 Human Genome Sciences, Inc. 105
109. 6.28 Illumina, Inc. 107
110. 6.29 Interleukin Genetics 110
111. 6.30 LI-COR Biosciences 111
112. 6.31 Luminex Corporation 112
113. 6.32 Millennium Pharmaceuticals, Inc. 112
114. 6.33 Monogram Biosciences, Inc. 113
115. 6.34 Motorola, Inc. 115
116. 6.35 MWG Biotech AG 115
117. 6.36 Myriad Genetics, Inc. 116
118. 6.37 Nanogen, Inc. 117
119. 6.38 Nuvelo, Inc. 120
120. 6.39 Orchid Cellmark 121
121. 6.40 Pacific Biosciences, Inc. 124
122. 6.41 QIAGEN, Inc. 124
123. 6.42 Roche Diagnostics 127
124. 6.43 Sequenom, Inc. 129
125. 6.44 Third Wave Technologies, Inc. 131
126. 6.45 Verenium Corporation 133
127. 6.46 Visigen Technologies, Inc. 133
128. 6.47 Brief Profiles of Companies Marketing Personalized Genomics Products 134
129. 6.47.1 23andMe, Inc. 134
130. 6.47.2 deCODE Genetics, Inc. 134
131. 6.47.3 Navigenics, Inc. 134
132. 6.48 Brief Profiles of Other Selected Genomics Firms 135
133. 6.48.1 Aber Genomic Computing 135
134. 6.48.2 Spotfire, Inc. 135
136. 7. Genomics Challenges and Growth Factors 136
137. 7.1 Market Drivers 136
138. 7.1.1 Product Pipeline: Need for More Drug Candidates 136
139. 7.1.2 Need for Increased Research and Development Productivity 136
140. 7.2 A Genomics Market Bottleneck-Bioinformatics 136
141. 7.3 Strategic Recommendations-Market Opportunities 137
142. 7.3.1 More Comprehensive Tools Are Needed 137
143. 7.3.2 Resolving Bottlenecks in Functional Genomics Market 138
144. 7.4 Key Trends of Recent Mergers and Acquisition Deals 139
145. 7.5 Chemogenomics 139
146. 7.6 Pharmacogenomics 140
147. 7.7 Biomarkers 141
148. 7.8 Additional Genomics Market Opportunities 142
150. 8. Bioinformatics 146
151. 8.1 Types of Data and Bioinformatics Applications 146
152. 8.1.1 Validated Core Modeling Technology 147
153. 8.1.2 Broad Applicability 147
154. 8.1.3 Data Management Compliant with Industry Standards 148
155. 8.1.4 Open Architecture 148
156. 8.1.5 Ease of Use 148
157. 8.1.6 Increased Access 148
158. 8.2 Functions of Informatics Software 149
159. 8.2.1 Data Management 149
160. 8.2.2 Transformation of Data into Knowledge 149
161. 8.2.3 Collaboration Among Researchers 149
162. 8.2.4 Interface for Online Data Sources 149
163. 8.3 Target Markets for Informatics Software 149
164. 8.3.1 Pharmaceutical Companies 149
165. 8.3.2 Biotechnology Companies 150
166. 8.3.3 Academic and Government Research Institutions 150
167. 8.3.4 Agricultural, Environmental and Industrial Biotechnology Companies 150
168. 8.4 Products of Bioinformatics 150
169. 8.4.1 Sequences and Structure of Genes and Proteins 150
170. 8.4.2 3-D Molecular Structures 150
171. 8.4.3 Genome Structures and Functions 150
172. 8.4.4 Bibliographic Data 150
173. 8.5 Bioinformatics Processes 151
174. 8.6 Informatics Tools and Functionalities 151
175. 8.6.1 Sequence to Structure 151
176. 8.6.2 Lead Identification and Optimization 152
177. 8.6.3 Development and Formulation 152
178. 8.6.4 Improving Materials and Processes in the Chemicals Industry 152
179. 8.6.5 Other Materials-Based Industries 153
180. 8.7 Role of Bioinformatics in the Value Chain 154
181. 8.8 Bioinformatics Market Segments 154
182. 8.8.1 Database 154
183. 8.8.2 Hardware 154
184. 8.8.3 Software 155
185. 8.8.4 Bioinformatics Services 155
186. 8.9 Bioinformatics Business Models 155
187. 8.9.1 Changing Business Models 156
188. 8.9.2 Selected Business Strategies 157
190. Glossary 159
193. INDEX OF FIGURES
195. Figure 2.1: Major Areas of Functional Genomics and Their Relationship to Bioinformatics and Industry 36
196. Figure 8.1: Role of Bioinformatics in the Biotechnology Value Chain 154
199. INDEX OF TABLES
201. Table 2.1: Genomics Sector Global Market Size, 2001 to 2010 16
202. Table 2.2: Companies Marketing DNA Microarray Software 19
203. Table 2.3: Selected Competitors in the DNA Microarray Market 20
204. Table 2.4: Companies Offering DNA Sequencing Products 24
205. Table 2.5: Competitors in the SNP-Genotyping Segment 26
206. Table 2.6: Companies that Market MAQC-tested Gene Expression Microarrays 30
207. Table 2.7: Worldwide Market for Bioinformatics, 2005 to 2010 33
208. Table 2.8: Selected Companies Marketing New Functional Genomics Tools 38
209. Table 3.1: Genomics Pharmaceutical Market Sector Leaders and Promising Newcomers 45
210. Table 3.2: Summary of Assays for HIV Viral Load Testing 47
211. Table 3.3: Global Market for HIV Diagnostic Testing, 2000 to 2012 48
212. Table 3.4: Summary of Molecular Diagnostics Testing 49
213. Table 3.5: Global Market for Molecular Diagnostics Testing, 2000 to 2012 49
214. Table 3.6: U.S. Market for Molecular Diagnostics Testing, 2004 to 2012 49
215. Table 3.7: Applied Markets for Genomics 52
216. Table 3.8: Competitors in the Field of Identity Genomics Testing 53
217. Table 3.9: Opportunities for Molecular-Targeting Therapeutics for Cancer 54
218. Table 3.10: Emerging Companies in the Anti-Cancer Sector 54
219. Table 8.1: Data Source and Bioinformatic Investigations 147
220. Table 8.2: Bioinformatics Activities, Subactivities and Key Players 155