The genomic commons

Annual Review of Genomics and Human Genetics

Volumn 19, Issue , 2018, Pages 429-453

  Contreras, Jorge L ^a   Knoppers, Bartha M ^b  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^b MCGILL UNIVERSITY   (Canada)

Author keywords

Bermuda Principles; commons; data release; data sharing; ethics; GA4GH; genome; Human Genome Project; informed consent; law; privacy

Indexed keywords

BERMUDA; HUMAN; HUMAN GENOME PROJECT; INFORMED CONSENT; PATENT; PRIVACY; REVIEW; ETHICS; GENETIC PRIVACY; GENETICS; GENOMICS; INFORMATION DISSEMINATION;

ETHICS; GENETIC PRIVACY; GENETIC RESEARCH; GENOMICS; HUMAN GENOME PROJECT; HUMANS; INFORMATION DISSEMINATION; INFORMED CONSENT;

EID: 85051711299     PISSN: 15278204     EISSN: 1545293X     Source Type: Book Series    
DOI: 10.1146/annurev-genom-083117-021552     Document Type: Review

References (133)

1. 1000 Genomes Proj. Consort. 2012. An integrated map of genetic variation from 1, 092 human genomes. Nature 491:56-65
2. Abbasi J. 2017. An internationalHuman Cell Atlas consortium takes shape. J. Am. Med. Assoc. 318:685-86
3. Aboy M, Liddell K, Liddicoat J, Crespo C. 2016. Myriad's impact on gene patents. Nat. Biotechnol. 34:1119-23
4. Anderson C. 1994. NIH drops bid for gene patents. Science 263:909-10
5. Andrews LB. 2002. Genes and patent policy: rethinking intellectual property rights. Nat. Rev. Genet. 3:802-8
6. Assoc. Mol. Pathol. v. Myriad Genet, 133 S. Ct. 2107 (2013)
7. Barnett J. 2000. Cultivating the genetic commons: imperfect patent protection and the network model of innovation. San Diego Law Rev. 37:987-1067
8. Benkler Y. 2014. Between Spanish huertas and the open road: a tale of two commons? See Ref. 44, pp. 69-98
9. Boyle J. 2008. The Public Domain: Enclosing the Commons of the Mind. New Haven, CT: Yale Univ. Press
10. Burton PR, Fortier I, Knoppers BM. 2009. The global emergence of epidemiological biobanks: opportunities and challenges. In Human Genome Epidemiology: Building the Evidence for Using Genetic Information to Improve Health and Prevent Disease, ed. M Khoury, S Bedrosian, M Gwinn, J Higgins, J Ioannidis, J Little, pp. 77-99. Oxford, UK: Oxford Univ. Press. 2nd ed.
11. Caldicott F. 2013. Information: To Share or Not to Share? The Information Governance Review. London: UK Dep. Health
12. Collins F. 2010. Has the revolution arrived? Nature 464:674-75
13. Conley JM, Doerr AK, Vorhaus DB. 2010. Enabling responsible public genomics. Health Matrix 20:325-85
14. Contreras JL. 2010. Prepublication data release, latency and genome commons. Science 329:393-94
15. Contreras JL. 2011. Bermuda's legacy: policy, patents, and the design of the genome commons. Minn. J. Law Sci. Technol. 12:61-125
16. Contreras JL. 2013. Technical standards and bioinformatics. In Bioinformatics Law: Legal Issues for Computational Biology in the Post-Genome Era, ed. JL Contreras, AJ Cuticchia, pp. 113-36. Chicago: ABA
17. Contreras JL. 2014. Constructing the genome commons. See Ref. 44, pp. 99-136
18. Contreras JL. 2015. NIH's genomic data sharing policy: timing and tradeoffs. Trends Genet. 31:55-57
19. Contreras JL. 2016. Genetic property. Georgetown Law J. 105:1-54
20. Contreras JL. 2017. Leviathan in the commons: biomedical data and the state. In Governing Medical Knowledge Commons, ed. KJ Strandburg, BM Frischmann, MJ Madison, pp. 19-45. Cambridge, UK: Cambridge Univ. Press
21. Contreras JL, Deshmukh VG. 2017. Development of the personal genomics industry. In Genetics, Ethics and Education, ed. S Bouregy, EL Grigorenko, SR Latham, M Tan, pp. 284-308. Cambridge, UK: Cambridge Univ. Press
22. Contreras JL, Floratos A, Holden AH. 2013. The International Serious Adverse Events Consortium's data sharing model. Nat. Biotechnol. 31:17-19
23. Contreras JL, Reichman JH. 2015. Sharing by design: data and decentralized commons: overcoming legal and policy obstacles. Science 350:1312-14
24. Contreras JL, Vertinsky L. 2016. Pre-competition. N. C. Law Rev. 95:67-131
25. Cook-Deegan R. 1994. The Gene Wars: Science, Politics, and the Human Genome. New York: Norton
26. Cook-Deegan R, Ankeny RA, Maxson Jones K. 2017. Sharing data to build a medical information commons: from Bermuda to the Global Alliance. Annu. Rev. Genom. Hum. Genet. 18:389-415
27. Cook-Deegan R, Dedeurwaerdere T. 2006. The science commons in life science research: structure, function, and value of access to genetic diversity. Int. Soc. Sci. J. 58:299-317
28. Cook-Deegan R, McGuire AL. 2017. Moving beyond Bermuda: sharing data to build a medical information commons. Genome Res. 27:897-901
29. Counc. Can. Acad. 2015. Accessing health and health-related data in Canada: the expert panel on timely access to health and social data for health research and health system innovation. Rep., Counc. Can. Acad., Ottawa, Can.
30. Counc. Eur. 1997. Convention for the Protection of Human Rights and Dignity of the Human Being with Regard to the Application of Biology and Medicine: Convention on Human Rights and Biomedicine. Eur. Treaty Ser. 164, Counc. Eur., Strasbourg, Fr. https://www. coe. int/en/web/conventions/full-list/-/ conventions/rms/090000168007cf98
31. Counc. Eur. 2016. RecommendationCM/Rec(2016)6 of the Committee ofMinisters to member States on research on biological materials of human origin. Recomm., Counc. Eur., Strasbourg, Fr. https://search. coe. int/cm/ Pages/result-details. aspx?ObjectId=090000168064e8ff
32. Counc. Eur. 2016. Recommendation CM/Rec(2016)8 of the Committee of Ministers to the member States on the processing of personal health-related data for insurance purposes, including data resulting from genetic tests. Recomm., Counc. Eur., Strasbourg, Fr. https://search. coe. int/cm/Pages/result-details. aspx? ObjectId=09000016806b2c5f
33. Counc. Eur. 2017. Chart of signatures and ratifications of Treaty 164. Eur. Treaty Ser. 164, Counc. Eur., Strasbourg, Fr. https://www. coe. int/en/web/conventions/full-list/-/conventions/treaty/164/ signatures
34. Counc. Int. Organ. Med. Sci. (CIOMS), World Health Organ. (WHO). 2016. International Ethical Guidelines for Health-Related Research Involving Humans. Geneva: CIOMS
35. Couzin-Frankel J. 2015. Trust me, I'm a medical researcher. Science 347:501-2
36. Deverka PA, Majumder MA, Villanueva AG, Anderson M, Bakker AC, et al. 2017. Creating a data resource:What will it take to build a medical information commons? Genome Med. 9:84
37. Dove ES, Townend D, Meslin EM, Bobrow M, Littler K, et al. 2016. Ethics review for international data-intensive research. Science 351:1399-400
38. Dyke SOM, Kirby E, Shabani M, Thorogood A, Kato K, Knoppers BM. 2016. Registered access: a 'Triple-A' approach. Eur. J. Hum. Genet. 24:1676-80
39. Editorial. 2017. Empty rhetoric over data sharing slows science. Nature 546:327
40. Eur. Comm. 2017. European Open Science Cloud Summit. https://ec. europa. eu/research/index. cfm? eventcode=44D86060-FBA1-1BD1-9355822B162BB0EE&pg=events
41. Eur. Union. 1996. Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases. Dir. 96/9/EC, Eur. Union
42. Eur. Union. 2016. Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 on the Protection of Natural Persons with Regard to the Processing of Personal Data and on the Free Movement of Such Data, and repealing Directive 95/46/EC (General Data Protection Regulation). Regul. 2016/679, Eur. Union. http://eur-lex. europa. eu/legal-content/en/TXT/?uri=CELEX%3A32016R0679
43. Evans BJ. 2012. Much ado about data ownership. Harv. J. Law Technol. 25:69-130
44. Frischmann BM, Madison MJ, Strandburg KJ, eds. 2014. Governing Knowledge Commons. New York: Oxford Univ. Press
45. GAIN Collab. Res. Group. 2007. New models of collaboration in genome-wide association studies: the Genetic Association Information Network. Nat. Genet. 39:1045-51
46. Genet. Assoc. Inf. Netw. (GAIN). 2010. Data use certification agreement. https://dbgap. ncbi. nlm. nih. gov/aa/wga. cgi?view-pdf&stacc=phs000021. v1. p1
47. Genom. Engl. 2017. The 100, 000 Genomes Project. https://www. genomicsengland. co. uk/the-100000-genomes-project
48. Genome Can. 2008. Data release and resource sharing. http://www. genomecanada. ca/medias/PDF/EN/ DataReleaseandResourceSharingPolicy. pdf
49. Glob. Alliance Genom. Health (GA4GH). 2016. A federated ecosystem for sharing genomic, clinical data. Science 352:1278-80
50. Glob. Alliance Genom. Health (GA4GH). 2017. About us. https://www. ga4gh. org/aboutus
51. Glob. Alliance Genom. Health (GA4GH). 2017. GA4GH strikes formal collaborations with 15 international genomic data initiatives. https://www. ga4gh. org/news/sAhZCeJjS96QHhVPIYwwWA. article
52. Greely HT. 2007. The uneasy ethical and legal underpinnings of large-scale genomic biobanks. Annu. Rev. Genom. Hum. Genet. 8:343-64
53. Guerrini CJ, McGuire AL, Majumder MA. 2017. Myriad take two: Can genomic databases remain secret? Science 356:586-87
54. Haga SB, O'Daniel J. 2011. Public perspectives regarding data-sharing practices in genomics research. Public Health Genom. 14:319-24
55. HellerMA, EisenbergRS. 1998. Can patents deter innovation?The anticommons in biomedical research. Science 280:698-701
56. Hill JA, Smith BE, Papoulias PG, Andrews PC. 2010. ProteomeCommons. org collaborative annotation and project management resources integrated with the tranche repository. J. Proteome Res. 9:2809-11
57. Holden A. 2002. The SNP Consortium: summary of a private consortium effort to develop an applied map of the human genome. BioTechniques 32:22-26
58. Hum. Genome Organ. (HUGO). 1996. Statement on the principled conduct of genetics research. Rep., HUGO, Geneva, Switz.
59. Hum. Genome Organ. (HUGO). 2003. Statement on human genomic databases, December 2002. J. Int. Bioeth. 14:207-10
60. Int. HapMap Consort. 2003. The International HapMap Project. Nature 426:789-96
61. Int. Hum. Genome Seq. Consort. 1996. Summary of principles agreed upon at the first international strategy meeting on human genome sequencing (Bermuda, 25-28 February 1996) as reported by HUGO. http:// www. ornl. gov/sci/techresources/Human-Genome/research/bermuda. shtml
62. Int. Hum. Genome Seq. Consort. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921
63. Jasny BR. 2013. Realities of data sharing using the genome wars as case study-an historical perspective and commentary. EJP Data Sci. 2:1
64. Jensen K, Murray F. 2005. Intellectual property landscape of the human genome. Science 310:239-40
65. Joint Genome Inst. 2017. Genomes OnLine Database. Retrieved Oct. 17. https://gold. jgi. doe. gov
66. Jones KH, Laurie G, Stevens L, Dobbs C, Ford DV, Lea N. 2017. The other side of the coin: harm due to the non-use of health-related data. Int. J. Med. Inform. 97:43-51
67. Karczewski KJ, Francioli L. 2017. The genome Aggregation Database (gnomAD). MacArthur Lab, Feb. 27. https://macarthurlab. org/2017/02/27/the-genome-aggregation-database-gnomad
68. Karczewski KJ, Weisburd B, Thomas B, SolomonsonM, Ruderfer DM, et al. 2017. The ExAC browser: displaying reference data information from over 60, 000 exomes. Nucleic Acids Res. 45:D840-45
69. Kaye J, Heeney C, Hawkins N, de Vries J, Boddington P. 2009. Data sharing in genomics-re-shaping scientific practice. Nat. Rev. Genet. 10:331-35
70. Kaye J, Whitley EA, Lund D, Morrison M, Teare H, Melham K. 2014. Dynamic consent: a patient interface for twenty-first century research networks. Eur. J. Hum. Genet. 23:141-46
71. Knoppers BM. 2014. Framework for responsible sharing of genomic and health-related data. HUGO J. 8:3
72. Knoppers BM, Thorogood A. 2017. Ethics and big data in health. Curr. Opin. Syst. Biol. 4:53-57
73. Knoppers BM, Zawati MH, Kirby ES. 2012. Sampling populations of humans across the world: ELSI issues. Annu. Rev. Genom. Hum. Genet. 13:395-413
74. Laakmann AB. 2015. The new genomic semicommons. UC Irvine Law Rev. 5:1001-39
75. Landrum MJ, Lee JM, Benson M, Brown G, Chao C, et al. 2016. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 44:D862-68
76. Lee P. 2009. Toward a distributive commons in patent law. Wisc. Law Rev. 2009:917-1016
77. Lee P. 2017. Centralization, fragmentation, and replication in the genomic data commons. In Governing Medical Knowledge Commons, ed. KJ Strandburg, BM Frischmann, MJ Madison, pp. 46-73. Cambridge, UK: Cambridge Univ. Press
78. Madey v. Duke Univ., 307 F. 3d 1351 (Fed. Cir.) (2002)
79. MadisonMJ, Frischmann BM, StrandburgKJ. 2010. Constructing commons in the cultural environment. Cornell Law Rev. 95:657-709
80. Majumder MA, Cook-Deegan R, McGuire AL. 2016. Beyond our borders? Public resistance to global genomic data sharing. PLOS Biol. 14:e2000206
81. Mandl KD, Bourgeois FT. 2017. The evolution of patient diagnosis: from art to digital data-driven science. J. Am. Med. Assoc. 318:1859-60
82. Manolio TA, FowlerDM, Starita LM, HaendelMA, MacArthur DG, et al. 2017. Bedside back to bench: building bridges between basic and clinical genomic research. Cell 169:6-12
83. Maxson Jones K, Ankeny RA, Cook-Deegan R. Forthcoming. The Bermuda Triangle: the politics, principles, and pragmatics of data sharing in the history of the Human Genome Project. J. Hist. Biol. Accepted, in review
84. Mayo Collab. Serv. v. Prometheus Lab., Inc., 132 S. Ct. 1289 (2012)
85. Merck. 1995. First installment of Merck Gene Index data released to public databases: cooperative effort promises to speed scientific understanding of the human genome. Press Release, Feb. 10, Merck, Whitehouse Station, NJ. http://www. bio. net/bionet/mm/bionews/1995-February/001794. html
86. Merges RP. 1996. Property rights theory and the commons: the case of scientific research. In Scientific Innovation, Philosophy, and Public Policy, ed. EF Paul, FDMiller Jr., J Paul, pp. 145-167. Cambridge, UK: Cambridge Univ. Press
87. Meslin EM, Ibrahim Garba I. 2011. Biobanking and public health: is a human rights approach the tie that binds? Hum. Genet. 130:451-63
88. Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Verezemska O, et al. 2017. Genomes OnLine Database (GOLD) v. 6: data updates and feature enhancements. Nucleic Acids Res. 45:D446-56
89. Natl. Acad. Sci. (NAS). 2009. Ensuring the Integrity, Accessibility, and Stewardship of Research Data in the Digital Age. Washington, DC: Natl. Acad. Press
90. Natl. Cancer Inst. (NCI). 2017. The next generation cancer knowledge network. https://gdc. cancer. gov
91. Natl. Hum. Genome Res. Inst. (NHGRI). 1996. NHGRI policy regarding intellectual property of human genomic sequence. http://www. genome. gov/10000926
92. Natl. Hum. Genome Res. Inst. (NHGRI). 2003. ENCODE Project data release policy (2003-2007). http://www. genome. gov/12513440
93. Natl. Hum. Genome Res. Inst. (NHGRI). 2010. The Human Genome Project completion: frequently asked questions. http://www. genome. gov/11006943
94. Natl. Inst. Health (NIH). 2007. Policy for sharing of data obtained in NIH supported or conducted genome-wide association studies (GWAS). Not. NOT-OD-07-088, NIH, Bethesda, MD. https://grants. nih. gov/grants/guide/notice-files/NOT-OD-07-088. html
95. Natl. Inst. Health (NIH). 2012. 1000 Genomes Project data available on Amazon Cloud. News Release, Mar. 29, NIH, Bethesda, MD. http://www. nih. gov/news/health/mar2012/nhgri-29. htm
96. Natl. Inst. Health (NIH). 2014. Final NIH Genomic Data Sharing policy. 79 Fed. Reg. 51345-54
97. Natl. Inst. Health (NIH). 2017. About the All of Us Research Program. https://allofus. nih. gov/about/ about-all-us-research-program
98. Natl. Inst. Health (NIH). 2017. NIH data commons pilot phase. Fund. Announc. RM-17-026, NIH, Bethesda, MD. https://commonfund. nih. gov/sites/default/files/RM-17-026-CommonsPilotPhase. pdf
99. Natl. Res. Counc. (NRC). 1988. Mapping and Sequencing the Human Genome. Washington, DC: Natl. Acad. Press
100. Natl. Res. Counc. (NRC). 2006. Reaping the Benefits of Genomic and Proteomic Research. Washington, DC: Natl. Acad. Press
101. Natl. Res. Counc. (NRC). 2011. Toward Precision Medicine: Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease. Washington, DC: Natl. Acad. Press
102. Organ. Econ. Coop. Dev. (OECD). 2009. OECDguidelines on human biobanks and genetic research databases. Rep., OECD, Paris
103. Ossorio PN. 2011. Bodies of data: genomic data and bioscience data sharing. Soc. Res. 78:907-32
104. Ostrom E. 1990. Governing the Commons. Cambridge, UK: Cambridge Univ. Press
105. Ostrom E. 2005. Understanding Institutional Diversity. Princeton, NJ: Princeton Univ. Press
106. Ostrom E, HessC, eds. 2007. Understanding Knowledge as a Commons: From Theory to Practice. Cambridge, MA: MIT Press
107. P3G Consort., Church G, Heeney C, Hawkins N, de Vries J, et al. 2009. Public access to genome-wide data: five views on balancing research with privacy and protection. PLOS Genet. 5:e1000665
108. Paltoo DN, Rodriguez LL, Feolo M, Gillanders E, Ramos EM, et al. 2014. Data use under the NIH GWAS Data Sharing Policy and future directions. Nat. Genet. 46:934-38
109. Rai AK. 1999. Regulating scientific research: intellectual property rights and the norms of science. Northwest. Univ. Law Rev. 94:77-152
110. Reichman JH, Uhlir PF. 2003. A contractually reconstructed research commons for scientific data in a highly protectionist intellectual property environment. Law Contemp. Probl. 66:315-462
111. Reichman JH, Uhlir PF, Dedeurwaerdere T. 2016. Governing Digitally Integrated Genetic Resources, Data, and Literature: Global Intellectual Property Strategies for a Redesigned Microbial Research Commons. Cambridge, UK: Cambridge Univ. Press
112. Rhodes C. 2013. Governance of Genetic Resources: A Guide to Navigating the Complex Global Landscape. Cheltenham, UK: Edward Elgar
113. Rothstein M, Knoppers BM. 2015. Harmonizing privacy laws to enable international biobank research. J. Law Med. Ethics 43:673-74
114. Schofield PN, Epping J, Huala E, Hrabe de Angelis M, Harvey M, et al. 2010. Sustaining the data and bioresource commons. Science 330:592-93
115. Selby JV, Beal AC, Frank L. 2012. The Patient-CenteredOutcomesResearch Institute (PCORI) national priorities for research and initial research agenda. J. Am. Med. Assoc. 307:1583-84
116. Shabani M, Dove ES, Murtahg M, Knoppers BM, Borry P. 2017. Oversight of genomic data sharing: what roles for ethics and data access committees? Biopreserv. Biobank. 15:469-74
117. Sherkow JS, Greely HT. 2015. The history of patenting genetic material. Annu. Rev. Genet. 49:161-82
118. Stein LD, KnoppersBM, Campbell P, Getz G, Korbel JO. 2015. Data analysis: creating a cloud commons. Nature 523:149-51
119. Tasse AM, Kirby E, Fortier I. 2016. Developing an ethical and legal interoperability assessment process for retrospective studies. Biopreserv. Biobank. 14:249-55
120. Terry SF, Terry PF, Rauen KA, Uitto J, Bercovitich LG. 2007. Advocacy groups as research organizations: the PXE international example. Nat. Rev. Genet. 8:157-64
121. Tor. Int. Data ReleaseWorkshop Authors. 2009. Prepublication data sharing. Nature 461:168-70
122. UKDep. Health. 2017. Annual report of the Chief Medical Officer 2016: Generation Genome. Rep., UKDep. Health, London. https://www. gov. uk/government/publications/chief-medical-officer-annualreport-2016-generation-genome
123. UN. 1947. Universal Declaration of Human Rights. Declar., UN, New York. http://www. un. org/en/ universal-declaration-human-rights
124. UN. 1966. International Covenant on Economic, Social and Cultural Rights. Treaty 14531, UN, New York. https://treaties. un. org/doc/Publication/UNTS/Volume%20993/volume-993-I-14531-English. pdf
125. UN Sci. Educ. Cult. Organ. (UNESCO). 1997. The Universal Declaration on the Human Genome and Human Rights. Declar., UNESCO, Paris. http://portal. unesco. org/en/ev. php-URL-ID=13177&URL- DO=DO-TOPIC&URL-SECTION=201. html
126. US Pat. Trademark Off. 1999. Revised utility examination guidelines; request for comments. 64 Fed. Reg. 71440-42
127. Van Overwalle G. 2014. Governing genomic data: plea for an "open commons. " See Ref. 44, pp. 137-54
128. Watson JD. 1997. Genes and politics. J. Mol. Med. 75:624-36
129. Wellcome Trust. 2003. Sharing data from large-scale biological research projects: a system of tripartite responsibility. Rep., Wellcome Trust, London. http://www. genome. gov/Pages/Research/ WellcomeReport0303. pdf
130. Wellcome Trust Case Control Consort. 2007. Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature 447:661-78
131. Williams HL. 2013. Intellectual property rights and innovation: evidence from the human genome. J. Political Econ. 121:1-27
132. World Med. Assoc. 2016. WMA Declaration of Taipei on ethical considerations regarding health databases and biobanks. https://www. wma. net/policies-post/wma-declaration-of-taipei-on-ethicalconsiderations-regarding-health-databases-and-biobanks
133. Wright CF, HurlesME, FirthHV. 2016. Principle of proportionality in genomic data sharing. Nat. Rev. Genet. 17:1-2