DDD DATAFREEZE 2013-12-18: 1133 trios - VCF files (Ref: DDD Nature 2015)

Wellcome Trust Sanger InstituteDATA ACCESS AGREEMENTFebruary 2011 v2Application for Access to DataI would like to apply for access to the following Deciphering Developmental Disorders (DDD) data sets (tick all that apply):[Data set names/IDs: ______________ ______________ ______________ ] I - Contact and Project Information (to be submitted by applicant)A. Name of applicant (principal investigator), including affiliation and contact details.Please ensure that a full postal address and a valid institutional email are included.Name:Title:Position:Affiliation:Institutional E-mail Address:Mailing Address:B. Name of the authorised institutional representative, including affiliation and contact details.Please ensure that a full postal address and a valid institutional email are included.Name:Title:Position:Affiliation:Institutional E-mail Address:Mailing Address:C. Names of authorised personnel (within your institution*)Include the names of all investigators, collaborators and research staff who will have accessto the data in order to work on the project (see Research Project under E). Pleaseensure that a valid institutional email address for each name is included along with their jobtitle/function.*Co-investigators or collaborators at other institutions must submit a separate Application for Access to the Data.Name: (copy and paste as needed for additional personnel)Title:Position:Affiliation:Institutional E-mail Address:D. Names of authorised students (within your institution*)Include the names of all students who will have access to the data in order to workon the project (see Research Project under E). Please ensure that a valid email address foreach name is included.*Students at other institutions should not be included in this list.Name: (copy and paste as needed for additional students)Title:Position:Affiliation:Institutional E-mail Address:E. Title of project (within which data will be used)Please provide the address of the project website as well, if availableF. Research track recordInclude a list of up to 3 relevant publications of which you were an author or a co-author.G. Research Project (scientific abstract)Please provide a clear description of the project and its specific aims, including an explanation of the role the accessed data will play in answering the research question, in no more than 500words. II – Data SecurityWe ask that you provide a level of security similar to that described below when storing and using the data you have applied for.File access: Data should only be accessible to named users. Files should either have only user Unix read/write access, not group or world access, or project-specific Unix groups should be used for group access that contain only those names authorised to access the data. User IDs within groups should be reviewed at 6 monthly intervals by the applicant. Data kept on laptops should be encrypted when not in active use, either in individual encrypted files or in encrypted directories/partitions. Data should not be held on USB keys or other portable hard drives. Users may be asked to sign an agreement addressing their responsibilities with respect to access to such data. III - DATA ACCESS AGREEMENTThis Data Access Agreement governs the terms of access to the managed access datasets generated by the Wellcome Trust Sanger Institute (WTSI) and NHS Regional Genetics Services (RGS) collaborators (the “Data” as defined below). In signing this agreement, you agree to be bound by the terms and conditions of access set out therein. For the sake of clarity, the terms of access set out in this agreement apply to the User and to the User Institution(s) (as defined below).DefinitionsData: The managed access datasets of the DDD Project Data Producer(s): The WTSI and NHS RGS collaborators responsible for the development, organisation, and oversight of the Data.External Collaborator: A collaborator of the User, working for an institution other than the User Institution(s) (see below for definitions of User and User Institution(s)).Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research.Research Participant: An individual having contributed data for research purposes.Research Purposes: shall mean research that is seeking to advance the understanding of the genetic causation of the undiagnosed developmental disorder in each family.User: An applicant (principal investigator), having signed this Data Access Agreement, whose User Institution has co-signed this Data Access Agreement, both of them having received acknowledgement of its acceptance.User Institution(s): Institution(s) at which the User is employed, affiliated or enrolled. A representative of it has co-signed this Data Access Agreement with the User and received acknowledgement of its acceptance.Terms and Conditions:In signing this agreement:1. The User and the User Institution(s) agree to only use the Data for Research Purposes and specifically only for the objectives and analyses outlined in section G. “Research Project”. 2. The User and the User Institution(s) agree to preserve, at all times, the confidentiality of the Data. In particular, they undertake not to use, or attempt to use the Data to compromise or otherwise infringe the confidentiality of information on Research Participants.3. The User and the User Institution(s) agree to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking all reasonable care to limit the possibility of identification.4. The User and the User Institution(s) agree not to link or combine the Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to the User and the User Institution(s), or is freely available without restriction.5. The User and the User Institution(s) agree not to transfer or disclose the Data, in whole or part, or any material derived from the Data, to anyone not listed in section C “Names of authorised personnel” or D “Names of authorised students” of this application form, except as necessary for data safety monitoring, national audits or programme management. Should the User or the User Institution(s) wish to share the Data with an External Collaborator, the External Collaborator must complete a separate Application for Access to the Data.6. The User and the User Institution(s) agree that Genome Research Limited, the Data producers, and all other parties involved in the creation, funding or protection of the Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of the Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Recipient’s use of the Data or from the unavailability of, or break in access to, the Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data.7. The User and the User Institution(s) agree to follow the Fort Lauderdale Guidelinesincluded as Appendix I of this agreement and the Toronto Statement included as Appendix II of this agreement. This includes but is not limited to recognizing the contribution of the Data Producer(s) and including a proper acknowledgement in all reports or publications resulting from the User and the User Institutions use of the Data.8. The User and the User Institution(s) agree to follow the Publication Policy available as Appendix III of this agreement. This includes respecting the moratorium period for Data Producers to publish the first peer-review report(s) describing and analyzing the Data. The publication moratorium lasts for one year from the time at which data was first made available.9. The User and the User Institution(s) agree not to make intellectual property claims on the Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of the Data, or conclusion drawn directly from the Data.10. The User and the User Institution(s) can elect to perform further research that would add intellectual and resource capital to the data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User and the User Institution(s) agree to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006). These two policies (NIH and OECD) are included as Appendix IV and V of this agreement.11. The Data was funded by the Wellcome Trust with the charitable objective of improving health. If results arising from the User and the User Institution(s) use of the Data could provide health solutions for the benefit of people in the developing world, the User and the User Institution(s) agree to offer non-exclusive licenses to such results on a reasonable basis for use in low income and low-middle income countries (as defined by the World Bank) to any party that requests such a license solely for uses within these territories.12. The User and the User Institution(s) agree to destroy/discard the Data held, once it is no longer used for the project described in this application form, unless obligated to retain the data for archival purposes in conformity with national audits or legal requirements.13. The User and the User Institution(s) will update the List of Authorized Personnel to reflect any changes or departures in researchers, collaborators and personnel within 30 days of the changes made.14. The User and the User Institution(s) must notify the Data Producer(s) prior to any significant changes to the protocol of the User (as described in section I.G. “Research Project”). 15. The User and the User Institution(s) will notify the Data Producer(s) as soon as they become aware of a breach of the terms or conditions of this agreement.16. The User and the User Institution(s) accept that this agreement may terminate upon any breach of this agreement from the User, the User Institution(s) or any authorised personnel mentioned in section C. “Names of authorised personnel” or D. “Names of authorised students” of this application document. In this case, The User and the User Institution(s) will be required to destroy/discard any Data held, including copies and backup copies. This clause does not prevent the User and the User Institution(s) from retaining the data for archival purpose in conformity with national audits or legal requirements.17. The User and the User Institution(s) accept that it may be necessary for the Data Producer(s) or their appointed agent to alter the terms of this agreement from time to time. In this event, the Data Producer(s) or their appointed agent will contact the User and the User Institution(s) to inform them of any changes.18. If requested, the User and the User Institution(s) will allow data security and management documentation to be inspected to verify that they are complying with the terms of this agreement.19. The User and the User Institution(s) agree to distribute a copy of this agreement and explain its content to any person mentioned in section C. “Names of authorised personnel” and D. “Names of authorised students section of this application form.20. This agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this agreement or its formation) shall be construed, interpreted and governed by the laws of England and Wales and shall be subject to the exclusive jurisdiction of the English courts. I have read and agree to abide by the terms and conditions outlined in the Data Access Agreement. YES (please circle on paper copy)I have read the Appendices listed at the end of this page. YES (please circle on paper copy)Applicant:Name ____________________________(block letters)Title and position ___________________Institution _________________________Signature _____________________Authorized institutional representative:(He/she should be the same person as mentioned under Section I B. InstitutionalRepresentative of this data application document):Name ____________________________(blocks letters)Title and position ___________________Institution ________________________(name of legal entity) Signature______________________Authorized institutional representative of the Data Producer(s):I attest that the above is in conformity with the access requirements of the DDD Project:Name _____________________________ (block letters)Signature ___________________________Approval number _____________________Once completed and sent electronically to wtsidata1@sanger.ac.uk, a paper copy of this application must be faxed to +44 (0) 1223 49 6802 or mailed to Dr. Tim HubbardWellcome Trust Sanger InsituteWellcome Trust Genome CampusHinxton, CambridgeCB10 1SAUKOnly the paper copy needs to be signed. Appendices do not need to be sent back.APPENDIX I – SHARING DATA FROM LARGE-SCALE BIOLOGICAL RESEARCH PROJECTS: A SYSTEM OF TRIPARTITE RESPONSIBILTY “THE FORT LAUDERDALE GUIDELINES” (2003)APPENDIX II – “THE TORONTO STATEMENT” (2009)APPENDIX III – PUBLICATION POLICY APPENDIX IV - NIH, BEST PRACTICES FOR THE LICENSING OF GENOMIC INVENTIONS (2005)APPENDIX V - OECD, GUIDELINES FOR THE LICENSING OF GENETIC INVENTIONS (2006)APPENDIX I – SHARING DATA FROM LARGE-SCALE BIOLOGICAL RESEARCH PROJECTS: A SYSTEM OF TRIPARTITE RESPONSIBILTY “THE FORT LAUDERDALE GUIDELINES” (2003)Sharing Data from Large-scale Biological Research Projects: A System of Tripartite ResponsibilityReport of a meeting organized by the Wellcome Trust and held on 14–15 January 2003 at Fort Lauderdale, USA.IntroductionThe Wellcome Trust sponsored a meeting on 14–15 January 2003 to discuss how, at this point in the development of the field of genomics, pre-publication data release can promote the best interests of science and help to maximize the public benefit to be gained from research. About 40 people attended the meeting, among them large-scale sequence producers, sequence users including computational biologists, representatives of the major nucleotide sequence databases, journal editors, and scientists interested in other large-scale data sets. The discussion took as a given that published data are available in their entirety for any use by any investigator, and focused on issues involved in making data broadly available prior to publication. The meeting concluded that pre-publication release of sequence data by the International Human Genome Sequencing Consortium, and other sequence producers, has been of tremendous benefit to the scientific research community in general. While not all were in a position to make commitments for their funding agencies, the meeting attendees were in broad agreement that, to encourage the continuation of such benefits, the sequence producers, sequence users and the funding agencies recognize and implement a system based on ‘tripartite responsibility’.Specifically,•The meeting attendees enthusiastically reaffirmed the 1996 Bermuda Principles, which expressly called for rapid release to the public international DNA sequence databases (GenBank, EMBL, and DDBJ) of sequence assemblies of 2kb or greater by large-scale sequencing efforts and recommended that that agreement be extended to apply to all sequence data, including both the raw traces submitted to the Trace Repositories at NCBI and Ensembl and whole genome shotgun assemblies.•The attendees recommended that the principle of rapid pre-publication release should apply to other types of data from other large-scale production centers specifically established as ‘community resource projects’.•The attendees recognized that pre-publication data release might conflict with a fundamental scientific incentive – publishing the first analysis of one's own data. The attendees noted that it would not be possible to absolutely guarantee this incentive without applying restrictions that would undermine the rationale for rapid, unrestricted release of data from community resources. Nonetheless, it is essential that excellent scientists continue to be attracted to these projects. To encourage this, the scientific community should understand that pre-publication data release needs active communitywide support if it is to continue to receive widespread support from the producers. The contributions and interests of the large-scale data producers should be recognized and respected by the users of the data, and the ability of the production centres to analyse and publish their own data should be supported by their funding agencies.Community resource projectsA ‘community resource project’ is a research project specifically devised and implemented to create a set of data, reagents or other material whose primary utility will be as a resource for the broad scientific community. Recent examples of community resource projects include the International Human Genome Sequencing Consortium, the Mouse Genome Sequencing Consortium, the Mammalian Gene Collection, the SNPs Consortium, and the International HapMap Project. The products of community resource projects have, over the past several years, become increasingly important as drivers of progress in biomedical research. The scientific community will best be served if the results of community resource projects are made immediately available for free and unrestricted use by the scientific community to engage in the full range of opportunities for creative science. At the same time, it is crucial that the scientific community recognizes and respects the important contribution made by the scientists who carry out community resource projects.Tripartite sharing of responsibilityAn optimized system for generating community resources involves three constituencies within the scientific research community – resource producers, resource users, and funding agencies. Each of the three has a unique and critical role to play in ensuring the growth and development of the community resource system.A. Funding agencies. Funding agencies are the major sources of support of research projects leading to community resources and projects that depend on the availability of such resources. Funding agencies have a critical role in determining the quality and breadth of community resources through the peer review evaluation system and as the sources of scientific research policies. For these reasons funding agencies should:1.designate appropriate efforts as community resource projects, and encourage resource producers to prepare and submit Project Descriptions (see below) for publication;2.require, as a condition of funding, free and unrestricted data release from community resource projects to appropriate central and searchable public databases, and vigorously ensure that this occurs;3.encourage more investigators to serve the community through involvement in such projects. In particular, the agencies should ensure that investigators engaged in generation of such datasets have sufficient support for curation, maintenance and distribution of the data to the community, as well as resources to perform initial analyses using the resources that they have generated;4.ensure that a centralized view of existing community resource projects is available as an information source for the community;5.support central databases that will house and distribute the data in a way that prevents fragmentation of the data.B. Resource producers. Community resources are often expensive efforts. For this and other reasons, they are frequently established and supported as unique facilities. The scientists who organize and operate community resources are, accordingly, in a uniquely responsible position. The community is dependent on the success of their efforts and they often face relatively little direct competition. Resource producers should:1.when feasible, publish a Project Description. The purpose of the Project Description, which will be a new type of scientific publication, is to inform the scientific community about the resource project and to provide a citation to reference the source of the data. The Project Description should be written at the beginning of the project and describes the plans for and scope of the production and analyses that the data producer intends to undertake. It will often include a timeline for production goals and data release.2.produce data of consistently high quality;3.make the data generated by the resource immediately and freely available without restriction;4.recognize that even if the resource is occasionally used in ways that violate normal standards of scientific etiquette, this is a necessary risk set against the considerable benefits of immediate data release.C. Resource Users. Community resource data sets benefit the users enormously, giving them the opportunity to analyse the data without the need to generate it first. The data sets are, in general, much larger, richer and of higher quality than individual laboratories could normally generate. In contributing to what ideally is a symbiotic and synergistic situation, resource users should:1.appropriately cite the source of the data analysed and acknowledge the resource producers. The early publication of a Project Description, as suggested above, would provide users with an appropriate reference to cite before the data are formally published;2.recognize that the resource producers have a legitimate interest in publishing prominent peer-reviewed reports describing and analyzing the resource that they have produced (and that neither the Project Descriptions nor data deposits in databases are the equivalent of such publications);3.respect the producer’s legitimate interests as set out, e.g. in a Project Description, while being free to use the data in any creative way. There should be no restrictions on the use of the data, but the best interests of the community are served when all act responsibly to promote the highest standards of respect for the scientific contribution of others. In some cases, this might best be done by discussion or coordination with the resource producers;4.assist journals and funding agencies to play their proper roles in ensuring, through the peer review system, that the system works fairly for all constituents.Large-scale genome sequencingLarge-scale genome sequencing projects are clearly community resource projects, and serve as a well-developed example to illustrate the general principles described above. The Bermuda Principles (http://www.gene.ucl.ac.uk/hugo/bermuda.htm) were developed in 1996 by the scientists engaged in the International Human Genome Sequencing Consortium and their funding agencies, and have been the basis of a successful system for achieving rapid and open data release. Now, in 2003, the meeting attendees, recognizing the role of users as well as producers and funders in effecting a successful system, enthusiastically recommend the reaffirmation of the Bermuda Principles for continued large-scale sequencing projects, and recommend that:1.They should be extended beyond their initial application to sequence assemblies of a minimum size from BAC-based sequence projects so that they apply to rapid (i.e. as soon as possible) release of both raw and assembled sequence data, subject only to the data meeting appropriate quality assessment standards.2.Funding agencies, users and sequencing centers should all honor their obligations, as described above.Other community resource projectsIn the near future, many other large data sets will be produced as community resources.While only a few of the meeting attendees were familiar with data types other than large-scale sequences, the attendees recommended that appropriate implementation of the principles discussed should be devised for other community resource projects, such as large-scale protein structure determination or gene expression analysis. In many of these cases, the solutions, in terms of such considerations as data quality standards, data storage and dissemination modes, and producer and user interests, are only beginning to emerge. Development of effective systems for achieving the objectives of the community resource concept should be an integral component of the planning and development of such new community resources.Research materials and toolsSome of the issues involved in ensuring rapid and open access to finite resources, such as reagents, clones, cell lines and other material resources, are different from those pertaining to electronic data sets. The meeting attendees strongly encouraged the relevant funding agencies, resource producers and users to develop practical approaches to maximizing the benefit of this type of resource to the scientific community and to research.Pre-publication release of other dataBeyond community resource projects, many valuable data sets could come from other sources.Still different issues arise in the case of resources that emerge from research efforts whose primary goal is not resource generation. In such cases, contribution of the data to the public domain as a resource is more a voluntary matter. To obtain the clear benefit that would ensue from converting such data sets into community resources as rapidly as possible, incentives should be developed by the scientific community to support the voluntary release of such data prior to publication, by appropriately recognizing and protecting the interests of scientists who wish to share such pre-publication data with the community. APPENDIX II – “THE TORONTO STATEMENT” (2009)The full article, Prepublication data sharing, Nature, 461: 168-70 (2009), is available at: http://www.nature.com/nature/journal/v461/n7261/full/461168a.htmlRapid pre-publication data release should be encouraged for projects with the following attributes:● Large scale (requiring significant resources over time)● Broad utility● Creating reference data sets● Associated with community buy-inFunding agencies should facilitate the specification of data-release policies for relevant projects by:● Explicitly informing applicants of data-release requirements, especially mandatory prepublication data release● Ensuring that evaluation of data release plans is part of the peer review process● Proactively establishing analysis plans and timelines for projects releasing data pre-publication● Fostering investigator-initiated pre-publication data release● Helping to develop appropriate consent, security, access and governance mechanisms that protect research participants while encouraging pre-publication data release● Providing long-term support of databasesData producers should state their intentions and enable analyses of their data by:● Informing data users about the data being generated, data standards and quality, planned analyses, timelines, and relevant contact information, ideally through publication of a citeable marker paper near the start of the project or by provision of a citable URL at the project or funding agency website● Providing relevant metadata (e.g., questionnaires, phenotypes, environmental conditions, and laboratory methods) that will assist other researchers in reproducing and/or independently analyzing the data, while protecting interests of individuals enrolled in studies focusing on humans● Ensuring that research participants are informed that their data will be shared with other scientists in the research community● Publishing their initial global analyses, as stated in the marker paper or citable URL, in a timely fashion● Creating databases designed to archive all data (including underlying raw data) in an easily retrievable form and facilitate usage of both pre-processed and processed dataData analysts/users should freely analyze released prepublication data and act responsibly in publishing analyses of those data by:● Respecting the scientific etiquette that allows data producers to publish the first global analyses of their data set● Reading the citeable document associated with the project● Accurately and completely citing the source of prepublication data, including the version of the data set (if appropriate)● Being aware that released pre-publication data may be associated with quality issues that will be later rectified by the data producers● Contacting the data producers to discuss publication plans in the case of overlap between planned analyses● Ensuring that use of data does not harm research participants and is in conformity with ethical approvalsScientific journal editors should engage the research community about issues related to prepublication data release and provide guidance to authors and reviewers on the third-party use of pre-publication data in manuscripts APPENDIX III – PUBLICATION POLICY We are committed to the principles of rapid data release. We intend to publish the results of our analysis of this data set and do not consider its deposition into public databases to be the equivalent of such publications. We anticipate that the data set could be useful to other qualified researchers for a variety of purposes, however, some areas of work are therefore subject to a publication moratorium which will last for one year from the time at which data was first made available (please check the run submission date).The publication moratorium covers any publications (including oral communications) that describe the use of the data set for investigations related to the phenotype for which samples were selected. For research papers, this means that submission for publication should not occur until 12 months have passed since data was first made available. Researchers should make reasonable efforts to ensure that the publication of data will not have adverse effects on families included in the dataset.Please acknowledge the use of this data set as follows in any publications based on it:“The DDD study presents independent research commissioned by the Health Innovation Challenge Fund [grant number HICF-1009-003], a parallel funding partnership between the Wellcome Trust and the Department of Health, and the Wellcome Trust Sanger Institute [grant number WT098051]. The views expressed in this publication are those of the author(s) and not necessarily those of the Wellcome Trust or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network.”Please contact wtsidata1@sanger.ac.uk if you are in any doubt about the restrictions described here. APPENDIX IV - NIH, BEST PRACTICES FOR THE LICENSING OF GENOMIC INVENTIONS (2005)DEPARTMENT OF HEALTH AND HUMAN SERVICESNational Institutes of HealthBest Practices for the Licensing of Genomic Inventions: Final NoticeFederal Register / Vol. 70, No. 68 / Monday, April 11, 2005 / Notices (p18413)(for supplementary information, please see the original publication)IntroductionThe Public Health Service’s (PHS) primary mission is to acquire new knowledge through the conduct and support of biomedical research to improve the health of the American people. This mission is advanced by the intramural research efforts of government-owned and –operated laboratories and by the extramural research efforts funded through grants and contracts. PHS seeks to maximize the public benefit whenever PHS owned or funded technologies are transferred to the commercial sector. Motivated by this goal, we offer the following best practices for the licensing of government-funded genomic inventions.Genomic inventions include a wide array of technologies and materials such as cDNAs; expressed sequence tags (ESTs); haplotypes; antisense molecules; small interfering RNAs (siRNAs); fulllength genes and their expression products; as well as methods and instrumentation for the sequencing of genomes, quantification of nucleic acid molecules, detection of single nucleotide polymorphisms (SNPs), and genetic modifications. Much of the value associated with the commercial use of these technologies involves nucleic acid-based diagnostics, potential gene therapy applications, and the development of new DNA and RNAbased therapeutics.BackgroundAmong the benefits derived from PHS conducted and supported biomedical research are effective and accessible new healthcare treatments and services. Practical realization of these benefits depends on the ability and willingness of private sector partners to develop and commercialize new technologies arising from PHS conducted and funded research. For potential preventive, diagnostic, and therapeutic products, the interest of the private sector in commercializing new technologies often depends on the existence of patent protection on the technology in the United States and foreign countries.The Bayh-Dole Act of 1980 allows PHS grantees and contractors to seek patent protection on subject inventions made using Government funds and to license those inventions with the goal of promoting their utilization, commercialization, and public availability. Recipients of PHS grants and contracts have a role in implementing the requirements of the Bayh-Dole Act (https://sedison.info.nih.gov/iEdison). In 1986,Federal laboratories, including PHS research laboratories at the National Institutes of Health (NIH), the Food and Drug Administration (FDA), and the Centers for Disease Control and Prevention (CDC), were given a statutory mandate under the Federal Technology Transfer Act (P.L. 99–502) and Executive Order 12591 to ensure that new technologies developed in those laboratories were transferred to the private sector and commercialized.PHS recognizes that patenting and licensing genomic inventions presents formidable challenges for academic and government technology transfer programs because of the complexities in bringing these technologies to the marketplace in a way that balances the expansion of knowledge and direct public health benefit with the commercial needs of private interests.The following represents best practices recommendations to the intramural PHS technology transfer community as well as to universities, hospitals and other non-profit PHS funding recipients. These recommendations are not intended to constitute additional regulations, guidelines or conditions of award for any contract or grant, although they are consistent with existing policies set out in Sharing Biomedical Research Resources (http://ott.od.nih.gov/NewPages/RTguide_final.html) and Developing Sponsored Research Agreements (http://ott.od.nih.gov/spons_research.html).Patent ProtectionLike other emerging technology areas, patents directed to genomic inventions tend to issue with claims that are broad in scope. Public health-oriented technology transfer must balance the rewards of broad intellectual property protection afforded to founders of enabling genomic inventions with the benefits of fostering opportunities for those striving to improve upon those innovations.Therefore, in considering whether to seek patent protection on genomic inventions, institutional officials should consider whether significant further research and development by the private sector is required to bring the invention to practical and commercial application. Intellectual property protection should be sought when it is clear that private sector investment will be necessary to develop and make the invention widely available. By contrast, when significant further research and development investment is not required, such as with many research material and research tool technologies, best practices dictate that patent protection rarely should be sought.Best Licensing PracticesThe optimal strategy to transfer and commercialize many genomic inventions is not always apparent at early stages of technology development. As an initial step in these instances, it may be prudent to protect the intellectual property rights to the invention. As definitive commercial pathways unfold, those embodiments of an invention requiring exclusive licensing as an incentive for commercial development of products or services can be distinguished from those that would best be disseminated non-exclusively in the marketplace.Whenever possible, non-exclusive licensing should be pursued as a best practice. A non-exclusive licensing approach favors and facilitates making broad enabling technologies and research uses of inventions widely available and accessible to the scientific community. When a genomic invention represents a component part or background to a commercial development, non-exclusive freedom-tooperate licensing may provide an appropriate and sufficient complement to existing exclusive intellectual property rights.In those cases where exclusive licensing is necessary to encourage research and development by private partners, best practices dictate that exclusive licenses should be appropriately tailored to ensure expeditious development of as many aspects of the technology as possible. Specific indications, fields of use, and territories should be limited to be commensurate with the abilities and commitment of licensees to bring the technology to market expeditiously.For example, patent claims to gene sequences could be licensed exclusively in a limited field of use drawn to development of antisense molecules in therapeutic protocols. Independent of such exclusive consideration, the same intellectual property rights could be licensed non-exclusively for diagnostic testing or as a research probe to study gene expression under varying physiological conditions.License agreements should be written with developmental milestones and benchmarks to ensure that the technology is fully developed by the licensee. The timely completion of milestones and benchmarks should be monitored and enforced. Best practices provide for modification or termination of licenses when progress toward commercialization is inadequate. Negotiated sublicensing terms and provisions optimally permit fair and appropriate participation of additional parties in the technology development process.Funding recipients and the intramural technology transfer community may find these recommendations helpful in achieving the universal goal of ensuring that public health consequences are considered when negotiating licenses for genomic technologies.PHS encourages licensing policies and strategies that maximize access, as well as commercial and research utilization of the technology to benefit the public health. For this reason, PHS believes that it is important for funding recipients and the intramural technology transfer community to reserve in their license agreements the right to use the licensed technologies for their own research and educational uses, and to allow other institutions to do the same, consistent with the Research Tools Guidelines.ConclusionPHS recognizes that these recommendations generally reflect practices that may already be followed by most funding recipients and the intramural technology transfer community with regard to licensing of genomic and other technologies. PHS also acknowledges the need for flexibility in the licensing negotiation process as the requirements of individual license negotiations may vary and may not always be adaptable to these best practices.Dated: April 5, 2005.Mark L. Rohrbaugh,Director, Office of Technology Transfer,National Institutes of Health. APPENDIX V - OECD, GUIDELINES FOR THE LICENSING OF GENETIC INVENTIONS (2006)The full report, including Background, Preface and PART II: Annotations, is available at: http://www.oecd.org/dataoecd/39/38/36198812.pdfPART I: PRINCIPLES AND BEST PRACTICES FOR THE LICENSING OF GENETIC INVENTIONS A. Scope These Guidelines apply to the licensing of intellectual property rights that relate to genetic inventions used for the purpose of human healthcare. Within these Guidelines, the term “Genetic Invention” includes nucleic acids, nucleotide sequences and their expression products; transformed cell lines; vectors; as well as methods, technologies and materials for making, using or analysing such nucleic acids, nucleotide sequences, cell lines or vectors. This definition is intended to be forward looking to encompass highly related future developments. B. Principles and Best Practices 1. Licensing Generally Principles 1. A Licensing practices should foster innovation in the development of new genetic inventions related to human healthcare and should ensure that therapeutics, diagnostics and other products and services employing genetic inventions are made readily available on a reasonable basis. 1. B Licensing practices should encourage the rapid dissemination of information concerning genetic inventions. 1. C Licensing practices should provide an opportunity for licensors and licensees to obtain returns from their investment with respect to genetic inventions. 1. D Licensees and licensors should have reasonable certainty over their rights and the limitations to those rights in relation to genetic inventions.Best Practices 1.1 License agreements should permit licensees to develop and further improve the licensed genetic inventions. 1.2 License agreements should clearly set out which parties obtain, retain, receive and maintain ownership of, grant rights to and enforce intellectual property rights, including with respect to the improvements and new genetic inventions developed from the licensed technology. 1.3 Licence agreements should clearly set out which of the parties, if any, has the right to engage in collaborative research with third parties and set out the ownership of any intellectual property rights flowing from such collaborative research. 1.4 Confidentiality provisions should be carefully drafted so as to permit the dissemination of information pertaining to genetic inventions while taking into account the need to file patent applications, to protect undisclosed information and to capitalise on the inventions in the marketplace. 1.5 License agreements should not provide the licensor with exclusive control over human genetic information, including collections of such information, derived from individuals through the use of the licensed genetic invention. 1.6 Rights holders should be encouraged to agree to licensing terms and conditions that maximize the utilisation of their genetic inventions. 1.7 License agreements should clearly stipulate the duties, obligations and responsibilities of the parties and address the rights of the parties to use the improvements to the licensed genetic invention following any, including early, termination. 1.8 License agreements should define the roles and responsibilities of the parties in the commercialisation, if any, of the products and services arising from the use of the licensed genetic invention.2. Healthcare and Genetic Inventions Principles 2. A Licensing practices should seek to strike a balance between the delivery of new products and services, healthcare needs, and economic returns. 2. B Licensing practices should ensure that patients benefit from the highest applicable standards with respect to privacy, safety and good laboratory methods available pursuant to the laws of their jurisdiction or those of the jurisdiction of the service provider using the genetic invention. 2. C Licensing practices should not be used to restrict the choice of other products or services by patients and their healthcare providers. 2. D Licensing practices should encourage appropriate access to and use of genetic inventions to address unmet and urgent health needs in OECD member countries and non-member economies. Best Practices 2.1 Rights holders should broadly license genetic inventions for research and investigation purposes. 2.2 Rights holders should license genetic inventions for health applications, including diagnostic testing, on terms and conditions that seek to ensure the widest public access to, and variety of, products and services based on the inventions. 2.3 Licensing practices should permit national or local providers to use genetic inventions in order to provide healthcare services, even if the rights holder is based in another jurisdiction. 2.4 Licensing agreements relating to products and services incorporating personal health information should facilitate compliance by the licensor and the licensee with the highest applicable privacy and other relevant laws. 2.5 License agreements should not restrict access by the licensee’s researchers to databases generated from licensed genetic inventions in their efforts to develop new therapies, products or services. 2.6 License agreements should permit licensees, for example healthcare providers, to offer patients flexibility and choice with respect to the selection of the type and nature of healthcare products and services.3. Research Freedom Principles 3. A Licensing practices should increase rather than decrease access to genetic inventions for research purposes. 3. B Commercial considerations in public research activities should not unduly hinder the academic freedom of researchers. 3. C Commercial considerations in public research activities and, in particular, the need to preserve the opportunity to seek patent protection on inventions arising from these activities, should not unduly limit the ability to publish in a timely manner the results of research. 3. D Commercial considerations in public research activities should not unduly limit the educational training of students. Best Practices 3.1 License agreements should clearly delineate research areas, information and time frames in which researchers and students cannot publish or present papers or theses without violating confidentiality obligations. Licensors and licensees should inform all relevant individuals, including students, of the scope of confidentiality obligations in a timely fashion. 3.2 Licensors and licensees should educate their researchers with respect to intellectual property law, especially the effects of public disclosure on the patentability of inventions, confidentiality obligations and restrictions commonly contained in agreements. 3.3 Confidentiality provisions should provide that academic research arising pursuant to the license agreement can be freely published or disclosed, with as minimum a delay as possible, subject to the need to protect proprietary information disclosed to the licensee or arising from such research. 3.4 Delays in publications of academic research necessary, for example, for the filing of patent applications, should be limited and reasonable in the circumstances. 3.5 Confidentiality provisions in licensing agreements should be drafted as narrowly as suitable and should not prevent the possibility of reasonable disclosure in exceptional public health situations, in light of the objectives of the parties and the applicable law.4. Commercial Development Principles 4. A Foundational genetic inventions should be licensed so as to be broadly accessible. 4. B Licensing practices should be used as an effective means to create value for licensors and licensees through the development of new products and services from genetic inventions. 4. C Licensing practices should strive to overcome co-ordination problems resulting from the need to access multiple genetic inventions. Best Practices 4.1 Should several licenses be required, license agreements should include a mechanism to set a reasonable overall royalty burden for genetic invention products and services, including research tools. 4.2 License agreements should include terms that maintain low barriers for access to genetic inventions. This may mean that such agreements do not include, for example, excessive up-front fees. 4.3 License agreements should avoid reach-through rights so as to foster broad and unencumbered utilisation of the genetic invention and so as to not discourage or stifle subsequent innovations. 4.4 Private and public sector participants should develop mechanisms to decrease transaction costs in acquiring rights to use technology. 4.5 Organisations that may enter into license agreements should educate their decision-makers about the opportunities to use the least restrictive licensing practices, as appropriate, as a means to maximise the benefits from genetic inventions for society, shareholders and other stakeholders.5. Competition Principles 5. A Licensing practices pertaining to genetic inventions should foster economic growth through innovation and substantive competition, while complying with the applicable competition laws. 5. B Licensing practices should not be used to expand the breadth of exclusive rights beyond the scope of the relevant intellectual property rights. Best Practices 5.1 License agreements should avoid unduly restrictive tied-selling. 5.2 License agreements should avoid non-compete clauses in areas beyond the scope of licensed genetic invention. 5.3 License agreements relating to foundational genetic inventions should generally be non-exclusive to encourage broad access for researchers and patients and broad use of the genetic invention.