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The Bermuda Triangle: the Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project

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The Bermuda Triangle: the Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project Journal of the History of Biology (2018) 51:693–805 https://doi.org/10.1007/s10739-018-9538-7 The Bermuda Triangle: The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project 1,2 3 4 Kathryn Maxson Jones • Rachel A. Ankeny • Robert Cook-Deegan Published online: 2 November 2018 Ó The Author(s) 2018 Abstract The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the ‘‘community’’ of C. elegans researchers, and were introduced and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans com- munity, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health (NIH) and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner’s proposal for a nematode research program at the Laboratory of Molecular Biology (LMB) at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, The authors gratefully dedicate this article to Sir John Sulston (27 March 1942–6 March 2018), who sadly did not live to see this paper in print, but who reviewed it and contributed greatly to it. His vision for open science guided the public Human Genome Project, based on science to benefit society. He is missed. Extended author information available on the last page of the article 123 694 K. Maxson Jones et al. and conclude with observations about policy and the historiography of molecular biology. Keywords Bayh-Dole Act Á Bermuda Principles Á Big science Á Bioinformatics Á Biotechnology Á C. elegans Á Celera Genomics Á Co-production Á Community resource projects Á Data hoarding Á Data release Á Data sharing Á Databases Á DNA Databank of Japan (DDBJ) Á Department of Energy (DOE) Á DNA sequencing Á Ethical Legal and Social Implications (ELSI) Á European Bioinformatics Institute (EBI) Á GenBank Á Gene patenting Á Genetics Á Genetic mapping Á Genome commons Á Genomics Á Human Genome Project (HGP) Á Intellectual property Á Medical genetics Á Model organisms Á Molecular biology Á Moral economy of science Á National Center for Human Genome Research (NCHGR) Á National Human Genome Research Institute (NHGRI) Á National Institutes of Health (NIH) Á Nematode worm Á Open science Á Patents Á Physical mapping Á Post-genomics Á Public domain Á Reference sequence Á Science policy Á Wellcome Trust List of Acronyms ABI Applied Biosystems ACeDB A C. elegans Data Base AFM Association Franc¸aise contre les Myopathies (French Muscular Dystrophy Association) BAC Bacterial artificial chromosome BBN Bolt, Beranek, and Newman BITNET Because It’s There NETwork, or Because It’s Time NETwork BMBF Bundesministerium fu¨r Bildung und Forschung (German Federal Ministry of Education and Research) cDNA Complementary DNA CEPH Centre d’Etude du Polymorphisme Humain (Center for the Study of Human Polymorphisms, now Foundation Jean-Dausset-CEPH) CNRS Centre National de la Recherche Scientifique (French basic research agency) Consed Consensus editor Contig Contiguous DNA sequence CSHL Cold Spring Harbor Laboratory DDBJ DNA Databank of Japan DEC Declaration of Exceptional Circumstances DFG Deutsche Forschungsgemeinschaft (German basic research agency) DHGP German Human Genome Project DLR Deutsches Zentrum fu¨r Luft- und Raumfahrt (the German Aerospace Centre) DNA Deoxyribose nucleic acid DOE US Department of Energy EBI European Bioinformatics Institute 123 The Bermuda Triangle… 695 EC European Community ELSI Ethical, Legal, and Social Implications (of genomics) EMBL European Molecular Biology Laboratory ERDA Energy Research and Development Administration EST Expressed sequence tag FTP File transfer protocol FOSS Free and Open Source Software G5 The five largest HGP sequencing centers after 1999 (the Sanger Centre, Washington University in St. Louis, the Broad Institute of Harvard and MIT, the DOE Joint Genome Institute, and the Baylor College of Medicine) GBF German Research Centre for Biotechnology (in Braunschweig) GDB Genome Database (at Johns Hopkins University) GESTEC NIH Genome Science and Technology centers HGI Human Genome Initiative (of the US DOE) HGMP Human Genome Mapping Programme (of the UK MRC) HGMW Human Genome Mapping Workshop HGP Human Genome Project HGS Human Genome Sciences HHMI Howard Hughes Medical Institute HTML HyperText Markup Language HLA Human Leukocyte Antigen HUGO Human Genome Organization ICRF Imperial Cancer Research Fund (in London) IHGSC International Human Genome Sequencing Consortium IMB Institute of Molecular Biotechnology (in Jena) JGI Joint Genome Institute (of the DOE) JST Japan Science and Technology Agency (also STA) KB Kilobase (or Kb, kb) LANL Los Alamos National Laboratory LLNL Lawrence Livermore National Laboratory LMB Laboratory of Molecular Biology (University of Cambridge) MB Megabase (or Mb, mb) MBL Marine Biological Laboratory (in Woods Hole, MA) MIM Mendelian Inheritance in Man MIT Massachusetts Institute of Technology MPI Max Planck Institut fu¨r Molekulare Genetik (in Berlin) MRC UK Medical Research Council NCBI US National Center for Biotechnology Information NCHGR US National Center for Human Genome Research NCI US National Cancer Institute NHGRI US National Human Genome Research Institute NIH US National Institutes of Health NINDS US National Institute of Neurological Disorders and Stroke NLM US National Library of Medicine 123 696 K. Maxson Jones et al. NRC US National Research Council (of the National Academy of Sciences) NSF US National Science Foundation OBER Office of Biological and Environmental Research (of the DOE) OHER Office of Health and Environmental Research (of the DOE) OMIM Online Mendelian Inheritance in Man ORNL Oak Ridge National Laboratory OSRD Office of Scientific Research and Development OTA Office of Technology Assessment (of the US Congress) PCR Polymerase chain reaction PDB Protein Data Bank (at the Brookhaven National Laboratory) Phrap Phil’s revised assembly program Phred Phil’s revised editor PKD Polycystic kidney disease rDNA Recombinant DNA RIKEN Japanese Institute of Physical and Chemical Research RNA Ribonucleic acid RZPD German genomic Resource Center (at the MPI in Berlin) SAIL Stanford Artificial Intelligence Laboratory SCW Single Chromosome Workshop SNP Single nucleotide polymorphism STA Japan Science and Technology Agency (also JST) STS Science and technology studies OR sequence-tagged site (meaning apparent with context) TIGR The Institute for Genomic Research UCSF University of California at San Francisco UJAD Unpublished in Journals and Available in Databases (Stephen Hilgartner’s term) UNESCO The United Nations Educational, Scientific, and Cultural Organization USPTO United States Patent and Trademark Office USSR Union of Soviet Socialist Republics WCS Worm Community System YAC Yeast artificial chromosome Introduction The daily flow of new genomic sequence information into the public domain, generated by a global network of laboratories, became one of the signature features of the Human Genome Project (HGP). The HGP was the nonprofit and publicly funded effort that generated the first genomic reference sequences for Homo sapiens and five model organisms between 1990 and 2003 and helped to refine many key genomics technologies.1 The HGP culminated in a draft human sequence completed 1 For much of the twentieth century, genes were understood as the ‘‘expressed’’ parts of genomes, serving as the coding templates for proteins or RNA products through the genetic code. Genetics was the study of 123 The Bermuda Triangle… 697 in 2001 (Lander et al.). A more refined human reference genome was published in pieces through 2004 (International Human Genome Sequencing Consortium), with the model organism sequences all made publicly available by 2002 (Goffeau et al. 1996; Blattner et al. 1997; The C. elegans Sequencing Consortium 1998; Adams et al. 2000; Mouse Genome Sequencing Consortium 2002).2 This deluge of DNA sequence data, to which scientists and the general public had immediate access, stood in stark contrast both to the conventional sharing of data at the time of journal publication and to the restrictions that corporate sequencers were placing on their data.3 The HGP investigators from the six participant nations—the US, the UK, Germany, France, Japan, and China—gave all
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