The patenting and the enforcing of the patent rights for the DNA microarray technologies:
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| adam_text | Titel: The patenting and the enforcing of the patent rights for the DNA microarray technologies
Autor: Lindenmeir, Matthias
Jahr: 2012
CONTENTS page
The Patenting and the Enforcing of the Patent Rights for the DNA-Microarray-Technologies i
Abstract ii
Acknowledgments iii
Abbreviations iv
Contents viii
INTRODUCTION 1
The DNA-Chips in the Context of Genomics and Intellectual Property 1
A. The History of the Genome Research and the Human Genome Project (HGP) 1
B. The Evolution of the DNA-Chip 4
C. The Biotechnological Role of the DNA-Chip-Technology in Connection 5
With Bioinformatics in the Genome Research
D. The Role of the Patents and the DNA-Microarrays 6
E. A Survey of the Patent Issues 7
CHAPTER 1 8
The Scientific Background and the Industry of the DNA-Chip 8
A. The DNA-Chip 8
I. The Microfluidic and Microstructural Technologies 9
1. The In-Situ Synthesis 10
a. The Photomask-Guided Photolithography 10
b. The Maskless Photolithography 12
c. The Piezoelectric Printing Technology 13
d. The Surface Tension-Based Nucleotide Deposition 13
2. The Post-Synthetic Spot Deposition 14
a. The Site-Specific Attachment of the Pre-Synthesized Spots 14
b. The Spotting Probes on the Positively Charged Coated Glass Slides 14
c The Arrayer 15
3. The Sample Preparation 15
4. The Microarray Scanning 18
II. The Scope of the Genetic Applications of the DNA-Biochip 21
1. The Gene Expression Profiles 21
2. The Single Nucleotide Polymorphism Detection (The SNP-Detection) 25
3. The Linkage and the Gene-Mapping 27
4. The Gene Copy Number Determination 28
B. The DNA-Chip-Related Bioinformatics Tools 29
- The Data Analysis and the Interpretation -
I. The Computational DNA-Chip Data Analysis 30
II. The Comparison and the Interpretation of Acquired Data With Genebank Data 31
III. The Data Integration and the Data Management 33
C. The Options of the DN A-Chip-Technology 36
I. The Drug Discovery 37
II. The Medical Diagnostics and the Medical Treatment 42
D. The Synergies of the DNA-Chip-Technology and the Bioinformatics 45
E. The DNA-Microarray in the Economic and in the Market-Related Context 45
F. Summary and Conclusionary Remarks 50
CHAPTER 2 52
The Legal Background and the Current Status for the Genomics 52
and the Bioinformatics in Europe and the United States
Introductory Remarks 52
A. Patenting the Genomics according to European Law 54
I. Legal Sources for the European Patent Law 54
1. The TRLPS-Agreement 54
2. The EU-Directive 98/44/EC on the Genomic Inventions 55
II. The Legal Situation Concerning the Patentability and the Qualifying 57
Criteria of Patent Protection for the Genomics
1. The Patentable Subject Matter, Art. 52 (1) EPC 57
a. The Technicity-Conception 57
b. The Patent Protection for Inventions 58
- the Invention - Discovery - Dilemma
c. Patentable Genetic Inventions 59
(1.) The Concept of the Invention Concerning the Natural Compounds 59
(2.) The Legal Transfer of the Invention Concept for the Natural Compounds 60
to the Genes
(3.) Protection of Substances vs. Process-Limited-Protection 61
(4.) Clarification by the EU-Directive 98/44/EC 62
2. The Qualifying Criteria of Patent Protection for the Genomics 64
a. The Novelty, Art. 54 EPC 64
b. The Inventive Step, Art. 52 (1), Art. 56 EPC 66
c. The Industrial Application, Art. 57 EPC 69
d. Sufficient Disclosure, Art. 83 EPC 70
3. The Present European Practice for the Genomics 73
B. Patenting the Genomics according to US-Law 76
I. The Legal Background for the US-Patent Law 76
II. The Patentable Subject Matter and the Qualifying Criteria of 78
Patent Protection for the Genomics
1. The Patentable Subj ect Matter 78
- Composition of Matter - Biotechnology
2. The Qualifying Criteria of Patent Protection for the Genomics 81
a. The Novelty 82
b. The Non-Obviousness 83
c. The Utility 86
(1.) General Aspects on Chemical Compounds 86
(2.) The Present U.S. Approach on Genetic Inventions and the New 87
USPTO Utility Guidelines
(3.) The Special Issue of Patenting the ESTs and the SNPs 90
(a.) The ESTs 90
(b.) The SNPs 94
d. Enabling Disclosure 96
(1.) Enablement 96
(2.) Written Description 97
(3.) Best Mode 99
C. The Scope of Protection 100
I. The Absolute Compound or Product Protection 100
II. The Special Case of Gene Sequences 101
III. The Absolute Product Protection and DNA-Chips 104
- A Critical and Constructive View
IV. The Process Patents 109
V. The Use Patents 112
D. Patenting the Bioinformatics in Europe and the United States 115
I. The European Position 115
II. The USPTO Approach 121
E. Exclusions From Patentability 124
I. The Bounds of Patenting according to European Law 124
II. The Bounds of Patenting according to U.S.-Patent Law 128
F. The Chip-Ethics 131
I. General Considerations on Chip-Ethics and Health Policy 131
II. The Chip-Ethics on Chip-Patents 135
G. Summary and Conclusionary Remarks 139
CHAPTER 3 143
Patenting the DNA-Chips 143
A. General Views of Patenting the DNA-Chips as Genomic Inventions 143
B. The Key Points of Patenting in the Production of a DNA-Microarray 146
and the Pioneer Patents
I. The Stages From the Genome to the DNA-Microarray and Their Patentability 147
1. The DNA Types for the Probes 147
a. The Oligonucleotides 147
b. The Complementary DNA (cDNA) 148
c. The Chromosomes 148
d. The Whole Organism Genome 149
2. The Chip Fabrication 150
3. The Targeting (The Sample Preparation) 153
4. The Assaying 156
5. The Chip Reading and the Bioinformatic Software Tools 159
6. The Combinations of DNA-Microarray-Technology Elements 162
as a Content Patentable Subject Matter
II. The Patent Situation in the Field of the DNA-Microarrays 166
1. The Immunoassays as Predecessors of the DNA-Microarrays 166
2. The Pioneer Patents for the Genuine DNA-Chips 167
a. The Comparison of the Patents EP 0 373 203 168
and EP 0 619 321 on the DNA-Microarrays
(l.)EP 0 373 203 170
(2.) EP 0 619 321 170
b. The Opposition Proceedings Concerning These Pioneering Patents 171
EP 0 373 203 andEP 0 619 321 as a Preliminary Stage Before
Being Considered the Standard Patents of the DNA-Microarrays
(l.)EP 0 373 203 171
(a.) The Opponents Standpoint 172
(i.) The Prior Art 173
(ii.) The Lack of Novelty 174
(Hi.) The Lack of the Inventive Step 174
(iv.) The Background Knowledge of the Persons Skilled in the Art 175
- Analysing the Polynucleotide Sequences 175
- The Sequencing of the Polynucleotide Sequences 175
by Hybridization
- The Methods of Generating the Arrays of Oligonucleotides 176
on a Solid Support
(b.) The Opponents Conclusion 181
(c.) The Preliminary View of the Opposition Division After 181
Amending a Set of Claims of the Main Request
(i.) The Compliance With Articles 123 (2) and 123 (3)EPC 181
(ii.) The Compliance With Articles 83 and 84 EPC 182
(Hi.) The Compliance With Article 52 (2) EPC 182
(iv.) The Compliance With Articles 54 and 56 EPC 183
(v.) The Novelty 184
(vi.) The Inventive Step 184
(d.) The Preliminary Assessment by the Opposition Division 185
and the General Conclusion
(e.) The Patentee s Standpoint on the Sufficiency of Disclosure, 186
on the Novelty and on the Inventive Step
(i.) The Sufficiency of Disclosure 186
(ii.) The Novelty 189
(Hi.) The Inventive Step 189
(iv.) The Product Claims 190
(v.) The Method of the Use Claims 192
(vi.) The Method of the Manufacture Claims 192
(f.) The State of Affairs Concerning EP 0 373 203 193
in the Oral Proceedings Before the EPO
13-15* November 2001 and the Results
(i.) Article 84 EPC 193
(ii.) Articles 123 (2), (3) EPC 193
(Hi.) Article 83 EPC 194
(iv.) Articles 52 and 54 EPC 194
(v.) Article 56 EPC 195
(g.) The Results and the Current Status 195
(2.) EPO 619 321 195
C. The Recent Patents in the Field of the DNA-Microarray-Technologies 196
I. The Examples of the Issued Patents Disclosing the Typical Ideas 198
Regarding the DNA-Microarrays
1. The Arrays 198
a. USPN 5,143,854 / EP 0 476 014: Large Scale Photolithographic 198
Solid Phase Synthesis of Polypeptides and Receptor Binding
Screening Thereof
b. The Disclosures of Other Players in the Field of DNA-Microarrays 202
2. The Assays 203
a. USPN 6,309,822: Method for Comparing Copy Number 203
of Nucleic Acid Sequences YEP 0 834 576: Methods Using
Nucleic Acid Hybridization Patterns on a Matrix of Oligonu-
cleotides
b. The Disclosures of Other Players in the Field of the DNA-Microarray- 208
Related Assays
3. The Fabrication/Synthesis 209
a. USPN 6,040,193: Combinatorial Strategies for Polymer Synthesis 209
b. The Disclosures of Other Players in the Field of the DNA-Microarray 212
Fabrication and Synthesis
4. The Quality Control 213
a. USPN 6,238,862: Methods for Testing Oligonucleotide Arrays 213
b. The Disclosures of Other Players in the Field of the DNA-Microarray 216
Quality Control
5. The Reagents 217
a. USPN 6,310,189: Nucleotides and Analogs Having Photore- 217
movable Protecting Groups
b. The Disclosures of Other Players in the Field of the DNA-Microarray Reagents 221
6. The Software 222
a. USPN 6,229,911: Method and Apparatus for Providing a Bioinforma- 222
tics Database
b. The Disclosures of Other Players in the Field of the DNA-Microarray Software 229
7. The Integrated Nucleic Acid Devices 230
a. USPN 6,043,080: IntegratedNucleic Acid Diagnostic Device 230
b. The Disclosures of Other Players in the Field of the DNA-Microarray 234
Integrated Nucleic Acid Devices
8. The Array Scanner 235
a. USPN 6,225,625: Signal Detection Methods and Apparatus 235
b. The Disclosures of Other Players in the Field of the DNA-Microarray 240
Scanners
II. The Gene-Specific Patents for the DNA-Microarrays 241
1. USPN 6,511,833: Human Fatty Acid Beta-Oxidation Enzymes 241
2. USPN 6,531,315: Compositions and Methods for the Therapy and 243
Diagnosis of Lung Cancer
3. USPN 6,436,684: Isolated Human Drug-Metabolizing Proteins, Nucleic 244
Acid Molecules Encoding Human Drug-Metabolizing Proteins, and Uses
Thereof
4. The Disclosures of Other Players in the Field of the Gene-Specific 247
DNA-Microarrays
D. Summary and Conclusionary Remarks 248
CHAPTER 4 251
Enforcing the Patent Rights in the Biotechnological Field of 251
the DNA-Microarray-Related Inventions
A. The Licensing Issues 251
I. The General Issues of Licensing 251
II. The Intrinsic Biotech-Related Issues of the Licensing 254
1. The Design of a Biotech License Program and the Incentives for it 256
2. The Standard Biotech Licensing Practices for the DNA-Microarray-Technologies 259
a. The Downpayments 260
b. The Milestone Payments 260
c. The Royalties 260
d. The Cross-Licensing 262
e. The Royalty-Free Cross-Licensing 263
f. The Sub-Licensing 264
B. The Licensing of Genetic Information - A Potential Problem for 265
the Companies in the Field of the DNA-Microarray Industries -
I. The Licensing of Genes for the Probes 265
1. The Assess of the Value of the DNA-Probe Sequence 267
2. The Solution Approaches to Bypass the Patent Infringement for the Patent- 268
Owned Genetic Material
II. The Licensing of the DNA-Microarray Bioinformatics 273
1. The Intrinsic Licensing Issues for the DNA-Microarray Bioinformatics 273
2. The Extrinsic Licensing Issues for the DNA-Microarray Bioinformatics 276
C. The Value Chain Allocation in the Field of the DNA-Microarray-Technologies 279
I. The Genuine Value Chain Model for the DNA-Microarray-Technologies 280
II. The DNA-Microarray Value Chain Interrelated With the Drug Discovery 289
Pathway
III. The DNA-Microarray Value Chain Interrelated With the Specified Fields of 295
Diagnostics
D. Some Economic Facts and Impacts for the DNA-Microarray-Technologies 301
Licensing Business - The Big Players -
I. Ajfymetrix, Inc. 302
II. Incyte Corporation 307
III. Millenium Pharmaceuticals, Inc. 308
E. Summary and Conclusionary Remarks 311
CHAPTER 5 314
The Array Update of the Patent Disputes for the DNA-Microarray-Technologies 314
- Selected Legal Cases -
Introductory Remarks 314
CASES 315
A. Ajfymetrix, Inc. vs. Hyseq, Inc., and 315
Afjymetrix, Inc. vs. Synteni, Inc. and Incyte Pharmaceuticals, Inc.
I. The Background of the Parties and Their Field of Operations 315
II. The Patents at Issue 316
III. Discussion 316
IV. Concluding Remarks 323
B. Ajfymetrix, Inc. vs. PE Corporation (NY), Competitive Technologies, Inc., 323
Applera Corporation, Perseptive Biosystems, Inc.
I. The Background of the Relationships Between the Parties 323
II. The Patents at Issue 324
III. Discussion 326
IV. Concluding Remarks 327
C. Aclara Biosciences, Inc. vs. Caliper Technologies Corp. 328
I. The Background of the Legal Relationships Between the Parties 328
and Their Field of Operations
II. The Patents at Issue 329
III. Discussion 331
IV. Concluding Remarks 332
D. Invitrogen Corporation vs. Clontech Laboratories, Inc., Promega 333
Corporation, New England Biolabs Display Systems Biotech A/S
E. Invitrogen Corporation vs. Stratagene, and 335
Invitrogen Corporation vs. Incyte Genomics, Inc., and
Incyte Genomics, Inc. vs. Invitrogen Corporation
F. Nanogen, Inc. vs. Motorola, Beckman Coulter, Inc., Genometrix, Inc., 337
Massachusetts Institute of Technology, and
Nanogen, Inc. vs. CombiMatrix Corporation
G. Oxford Gene Technology, Ltd. vs. Ajfymetrix, Inc., and 339
Oxford Gene Technology, Ltd. vs. Nanogen, Inc.
H. ID Biomedical Corporation vs. Third Wave Technologies, Inc. 342
I. Summary and Conclusionary Remarks 342
Prospects 345
Deutsche Zusammenfassung 346
ANNEX 358
Bibliography 358
Cases, Statutes, Guidelines and Other Legal Sources 380
EPO Case Law of the Legal and Technical Board of Appeal 380
EPO Case Law of the Enlarged Board of Appeal 381
Germany 382
United Kingdom 382
United States of America 382
Statutes and Guidelines 385
Other Legal Sources 385
Patents 386
European Patents 386
U.S. Patents 386
PCT Patents 391
French Patents 391
Japanese Patents 391
SEC-Filings (United States Security and Exchange Commission Files) 392
Special Reports and Announcements 393
Databases 394
Tables 395
Figures 396
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| spelling | Lindenmeir, Matthias Verfasser (DE-588)1022963333 aut The patenting and the enforcing of the patent rights for the DNA microarray technologies vorgelegt von Matthias Lindenmeir 2010 [erschienen] 2012 XV, 396 S. Ill. txt rdacontent n rdamedia nc rdacarrier München, Univ., Diss., 2012 Europäisches Patentübereinkommen 1973 Oktober 5 (DE-588)4134034-6 gnd rswk-swf Patentlizenz (DE-588)4399822-7 gnd rswk-swf Patentschutz (DE-588)4173537-7 gnd rswk-swf DNS-Chip (DE-588)4721796-0 gnd rswk-swf Humangenetik (DE-588)4072653-8 gnd rswk-swf USA (DE-588)4078704-7 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content USA (DE-588)4078704-7 g Europäisches Patentübereinkommen 1973 Oktober 5 (DE-588)4134034-6 u Humangenetik (DE-588)4072653-8 s DNS-Chip (DE-588)4721796-0 s Patentschutz (DE-588)4173537-7 s Patentlizenz (DE-588)4399822-7 s DE-604 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024989471&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Lindenmeir, Matthias The patenting and the enforcing of the patent rights for the DNA microarray technologies Europäisches Patentübereinkommen 1973 Oktober 5 (DE-588)4134034-6 gnd Patentlizenz (DE-588)4399822-7 gnd Patentschutz (DE-588)4173537-7 gnd DNS-Chip (DE-588)4721796-0 gnd Humangenetik (DE-588)4072653-8 gnd |
| subject_GND | (DE-588)4134034-6 (DE-588)4399822-7 (DE-588)4173537-7 (DE-588)4721796-0 (DE-588)4072653-8 (DE-588)4078704-7 (DE-588)4113937-9 |
| title | The patenting and the enforcing of the patent rights for the DNA microarray technologies |
| title_auth | The patenting and the enforcing of the patent rights for the DNA microarray technologies |
| title_exact_search | The patenting and the enforcing of the patent rights for the DNA microarray technologies |
| title_full | The patenting and the enforcing of the patent rights for the DNA microarray technologies vorgelegt von Matthias Lindenmeir |
| title_fullStr | The patenting and the enforcing of the patent rights for the DNA microarray technologies vorgelegt von Matthias Lindenmeir |
| title_full_unstemmed | The patenting and the enforcing of the patent rights for the DNA microarray technologies vorgelegt von Matthias Lindenmeir |
| title_short | The patenting and the enforcing of the patent rights for the DNA microarray technologies |
| title_sort | the patenting and the enforcing of the patent rights for the dna microarray technologies |
| topic | Europäisches Patentübereinkommen 1973 Oktober 5 (DE-588)4134034-6 gnd Patentlizenz (DE-588)4399822-7 gnd Patentschutz (DE-588)4173537-7 gnd DNS-Chip (DE-588)4721796-0 gnd Humangenetik (DE-588)4072653-8 gnd |
| topic_facet | Europäisches Patentübereinkommen 1973 Oktober 5 Patentlizenz Patentschutz DNS-Chip Humangenetik USA Hochschulschrift |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024989471&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT lindenmeirmatthias thepatentingandtheenforcingofthepatentrightsforthednamicroarraytechnologies |