the intellectual property landscape of the human genome
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Kyle L. [email protected]
Slide 1/1721/10/05
The intellectual property landscape of the human genome
Kyle JensenPhD CandidateMIT Chemical Engineering
Fiona MurrayAssistant Professor Management of Technology Innovation & EntrepreneurshipMIT Sloan School of Management
Kyle L. [email protected]
Slide 2/1721/10/05
The “tragedy of the anti-commons” describes resource under-usage when many agents have rights to exclude
Tragedy of the commons Tragedy of the anti-commons
M. A. Heller, R. S. Eisenberg, Science 280, 698 (1998).
Kyle L. [email protected]
Slide 3/1721/10/05
There is some evidence for an anti-commons effect in the broader field of biotechnology
Patent
Use forward citations as a measure of
scientific progress
All publications from Nature Biotech 97-99
Patent
Patent Grant Date
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Publication
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FCjtF. Murray, S. Stern, NBER Working Paper 11465, 2005.
Kyle L. [email protected]
Slide 4/1721/10/05
Many suggest a genomic anti-commons effect exists; however, supporting evidence is limited and anecdotal
● Genomic anti-commons in a nutshell:
» IP rights, paired with exclusive licensing will increase transaction costs and
● Slow development of new medicines
● Stifle academic R&D
● Discourage downstream investment
● But, classic rationale for patent system is to promote investment, R&D
» Evidence for genomic anti-commons is ancedotal
Nuffield Council on Bioethics, The ethics ..., Tech. rep., London, UK (2002).T. Caulfield, E. Gold, M. Cho, Nat Rev Genet 1, 227 (2000)L. Andrews, Nat Rev Genet 3, 803 (2002)S. M. Thomas, M. M. Hopkins, M. Brady, Nat Biotechnol 20, 1185 (2002).M. Stott, J. Valentine, Nat Rev Drug Discov 3, 364 (2004).
Kyle L. [email protected]
Slide 5/1721/10/05
The growth in sequence-oriented IPR prompts many of the same questions for the human geome
No. sequences in Genbank No. sequences disclosedin issued US patents
1:50 scale
How much of the human genome is covered by IPR? By whom?
D. L. Wheeler, et al., Nucleic Acids Res 33 Database Issue, 39 (2005).
Kyle L. [email protected]
Slide 6/1721/10/05
To map patents to human genes we assembled a database of nucleotide sequences from issued US patents
● 686,864 sequences from Genbank
● +109,766 parsed from patent full-texts
● Only from patents with a valid sequence listing
D. L. Wheeler, et al., Nucleic Acids Res 33 Database Issue, 39 (2005).User Services, National Center for Biotechnology Information (2004). Personal communication.O. of Public Affairs, U.S. Patent and Trademark Office (2005). Personal communicationUSPTO, Patent FullText and FullPage Image Databases, http://www.uspto.gov/patft/index.html (2005).
Kyle L. [email protected]
Slide 7/1721/10/05
From this database, we extracted only sequences that are explicitly mentioned in the patent claims
● Natural language modeling using simple regular expressions
● Applicable only to claims using SEQ ID nomenclature
Kyle L. [email protected]
Slide 8/1721/10/05
An all-by-all homology search was used to determine which patented sequences correspond to human genes
Patent 1 sequences
Patent 2 sequences
Patent N sequences
USPTO Patent Sequences
796,630 sequences(82,395 claimed) from
30,048 patents
Gene 1 transcripts
NCBI RefSeq
495,772 sequences from 2,969 species
BlastnEval = 0.0>= 150 bp
Gene M transcripts
NCBI, The RefSeq Database, http://www.ncbi.nlm.nih.gov/RefSeq/ (2005).
K. D. Pruitt, T. Tatusova, D. R. Maglott, Nucleic Acids Res 33 Database Issue, 501 (2005).
Conflicts resolved by highest bit-score
X
Kyle L. [email protected]
Slide 9/1721/10/05
Our analysis show that 4,382 of the 23,688 genes in the human genome are claimed in granted U.S. patents
NCBI Map Viewer. Build 35.1 http://www.ncbi.nlm.nih.gov/mapview/ (2005).
D. Maglott, J. Ostell, K. D. Pruitt, T. Tatusova, Nucleic Acids Res 33 Database Issue, 54 (2005).
Kyle L. [email protected]
Slide 10/1721/10/05
Most genes are claimed in only a single patent; a few genes are covered by extensive IPR
Kyle L. [email protected]
Slide 11/1721/10/05
The most IP-protected genes tend to be involved in cancer and cellular processes such as signal transduction, cellular
differentiation, and cell proliferation
GeneID No. Patents Gene Name Locus Annotation
655 20 BMP7 20q13 bone morphogenetic protein 7
1029 20 CDKN2A 9p21 cyclin-dependent kinase inhibitor 2A
768 14 CA9 9p13-p12 carbonic anhydrase IX
672 14 BRCA1 17q21 breast cancer 1, early onset
6469 13 SHH 7q36 sonic hedgehog homolog
3084 13 NRG1 8p21-p12 neuregulin 1
3953 12 LEPR 1p31 leptin receptor
6004 11 RGS16 1q25-q31 regulator of G-protein signalling 16
3549 10 IHH 2q33-q35 Indian hedgehog homolog
959 10 CD40LG Xq26 CD40 ligand
7424 10 VEGFC 4q34.1-q34.3 vascular endothelial growth factor C
3557 10 IL1RN 2q14.2 interleukin 1 receptor antagonist
NCBI Map Viewer. Build 35.1 http://www.ncbi.nlm.nih.gov/mapview/ (2005).
D. Maglott, J. Ostell, K. D. Pruitt, T. Tatusova, Nucleic Acids Res 33 Database Issue, 54 (2005).
Kyle L. [email protected]
Slide 12/1721/10/05
The institutions with the most gene-oriented patents tend to be biotech or research institutes rather than larger pharmaceutical companies
No. Genes
2220
153
142
114
102
100
95
63
59
58Variations in assignee names across patents strongly effects this result. For example HGS is occasionally “Human Genome Sciences” instead of “Human Genome Sciences, Inc.” Also, this does not account formergers and acquisitions or subsidiary relationships. Assignee name standardization by EPO.
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European Patent Office, INPADOC, http://www.european-patent-office.org/inpadoc/ (2005).
Kyle L. [email protected]
Slide 13/1721/10/05
Private US-based firms tend to own the most human gene IP
Kyle L. [email protected]
Slide 14/1721/10/05
Most genes have a single rights-holder; however a handful of genes have highly fragmented IPR ownership
Kyle L. [email protected]
Slide 15/1721/10/05
Our results suggest that disease-associated genes have heavier IP coverage than others
● Of 291 known cancer genes, 131 appear “patented”
» 45% vs. 18% background rate● Significant with p-value<0.01 based on binomial distribution
» Those that are patented, are more heavily patented than expected by chance
● Significant with p-value<0.01 based on chi-squared test
● Of 1,456 genes in Online Mendelian Inheritance in ManTM database 517 are “patented”
» 35% vs. 18% background rate● Significant with p-value<0.01 based on binomial distribution
Kyle L. [email protected]
Slide 16/1721/10/05
A patent density view of disease pathways reveals the IP barrier of various targets
Huntington's disease pathway