Amplicon sequencing

DATA ACCESS AGREEMENT These terms and conditions govern access to the managed access datasets (details of which are set out in Appendix I) to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions. Definitions Data Access Committee (DAC): The group of named individuals who are responsible for approving the data to be released to bona fide external requestors. The University of Cambridge Department of Clinical Neuroscience MS genetics Data Access Committee currently consists of Stephen Sawcer (chairperson), Joanne Jones and Jyoti Khadake. GDPR means the General Data Protection Regulations. Data Controller and Data Processor have the meanings given in GDPR. Personal Data: means any Data that can be considered personal data under GDPR. Authorised Personnel: The group of bona fide individuals who have understood and agreed to the terms and conditions of this agreement and have been granted access to the Data by the DAC. This includes the User, the individuals listed in Appendix II and any other individuals subsequently approved by the DAC at the requests of the User on behalf of the User Institution. Details of the initial set of Authorised Personnel are listed in Appendix II. Data: All or any part of the managed access datasets to which the User Institution has requested access. This includes personal data, derived data and backup copies. Data Producers: The researchers and collaborators listed in Appendix I that were responsible for the development, organisation, and oversight of these Data. Project: The project for which the User Institution has requested access to these Data. A description of the Project is set out in Appendix II. 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 whose data form part of these Data. Research Purposes: Shall mean research that is seeking to advance the understanding of health or disease, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The principal investigator for the Project. User Institution: The Institution that has requested access to the Data. Consortium Collaborator: A member of the list of Authorised Personnel working at an Institution other than the User Institution who has agreed to work together with the User to undertake the research Project described in Appendix II. Like all Authorised Personnel these individuals have confirmed that they understand and will be bound by the terms and conditions set out in this agreement. Third party individual: Any individual that is not on the list of Authorised Personnel regardless of which institution they work at. Terms and Conditions 1. The User Institution and Authorised Personnel agree to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution and Authorised Personnel further agree that they will only use these Data for Research Purposes which are within the limitations set out in Appendix I. 2. The User Institution and Authorised Personnel agree to preserve, at all times, the confidentiality of these Data. In particular, they undertake not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution and Authorised Personnel agree to use at least the measures set out in Appendix I to protect these Data. 3. The User Institution and Authorised Personnel 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 Institution and Authorised Personnel agree not to link or combine these 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 Institution or Authorised Personnel or is freely available without restriction. 5. The User Institution agrees only to transfer or disclose these Data to the Authorised Personnel. The User Institution and Authorised Personnel understand that they cannot share or in any other way disclose these Data with any Third Party Individual, and that any Third Party Individual seeking access to the Data must make their own separate application for access to these Data. 6. The User Institution and Authorised Personnel agree that the Data Producers, and all other parties involved in the creation, funding or protection of these Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of these 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 these Data or from the unavailability of, or break in access to, these Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data. 7. The User Institution and Authorised Personnel agree to follow best practice with regard to disseminating their findings. This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 8. The User Institution and Authorised Personnel agree to follow the Publication Policy in Appendix III. This includes respecting any moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 9. The User Institution and Authorised Personnel agree not to make intellectual property claims on these Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of these Data, or conclusion drawn directly from these Data. 10. The User Institution and Authorised Personnel can elect to perform further research that would add intellectual and resource capital to these data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution and Authorised Personnel 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) (https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (http://www.oecd.org/science/biotech/36198812.pdf ). 11. The User Institution and Authorised Personnel confirms that they will destroy/discard the Data held by them once it is no longer needed for the Project; unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify the chairperson of the DAC (currently Stephen Sawcer) within 30 days of any changes of Authorised Personnel. 13. The User Institution will notify the chairperson of the DAC (currently Stephen Sawcer) prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the chairperson of the DAC (currently Stephen Sawcer) as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The DAC may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies, and procure all Authorised Personnel to do the same. This clause does not prevent the User Institution or Authorised Personnel from retaining these data for archival purpose in conformity with audit or legal requirements. 16. The User Institution and Authorised Personnel accept that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by any of the Data Producers. In the event that changes are required, the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. If accepted the User Institution will procure all Authorised Personnel to accept the changes. 17. If requested, the User Institution and any Authorised Personnel will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. 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. 19. The Users Institution and Authorised Personnel confirm that all users of the data will comply with their obligations under GDPR (as amended from time to time) and all other relevant laws. 20. The Users Institution and Authorised Personnel confirm that they understand their duties under GDPR in relation to the handling, processing and storage of the Data and in relation to the rights of Participants, including their responsibility to take appropriate measures to respond to requests from Participants to exercise their rights. 21. The Users Institution and Authorised Personnel acknowledge that the University of Cambridge Department of Clinical Neurosciences is the Data Controller for the Data, and that the User Institution will be the Data Controller and Data Processor for the Project. 22. The User Institution confirms that the User will distribute a copy of these terms to all the Authorised Personnel including Consortium Collaborators at other institutions and to any individuals subsequently added to the list of Authorised Personnel. The User Institution will procure that the Authorised Personnel including Consortium Collaborators and subsequently added individuals comply with the terms of this agreement, including their obligations under GDPR (as amended from time to time) and all other relevant laws. Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for the University of Cambridge Department of Clinical Neuroscience MS genetics DAC Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) Panel-based next-generation sequencing (NGS) data from 211 human subjects. The panel was designed to capture 260 SNVs in high linkage disequilibrium with multiple sclerosis susceptibility SNVs and was applied to cDNA from CD4 T cells, cDNA from CD8 T cells and genomic DNA from venous blood. NGS was carried out using PE300 reads on the Illumina MiSeq (Illumina Inc., San Diego, CA, United States). Name of project that created the dataset “Allele specific expression in lymphocyte subsets from patients with multiple sclerosis” This work was supported by the UK Medical Research Council (grant reference: G1100125) and the Cambridge NIHR Biomedical Research Centre. Names of the data producers/collaborators Maria Ban1, Wenjia Liao1, Amie Baker1, Alastair Compston1, John Thorpe1, Paul Molyneux1, Mary Fraser1, Jyoti Khadake2, Joanne Jones1, Alasdair Coles1 and Stephen Sawcer1 Affiliations: 1 University of Cambridge, Department of Clinical Neurosciences, Box 165, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0QQ, UK 2 NIHR BioResource for Translational Research, Box 299, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust Hills Road, Cambridge CB2 0QQ, UK Specific limitations on areas of research The data may only be used for ethically sound Biomedical research that complies with English law. Minimum protection measures required The data must be stored in line with General Data Protection Regulations (GDPR) and all other relevant English laws and regulations. File access: The data can be held in unencrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screen locks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. All reasonable security precautions must be employed to keep the Data confidential, such precautions to be no less onerous than those applied in respect of the User Institutions own confidential information. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number Brief abstract of the Project in which the Data will be used (300 words max) List of users All users must have an EGA account and all provided email addresses must be institutional. If PhD student users are included their supervisors must also be listed. Name of Registered User Email Job Title APPENDIX III – PUBLICATION POLICY In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS00000000029), and cite the original publication describing the data.