Cambridge COVID-19 Single-cell PBMC

Data sharing of Single-cell multi-omic profiling of human PBMCs, including adaptive immune cell receptor sequences derived from a cross-center cohort of COVID-19, & respiratory disease patients, along with healthy controls recruited via the NIHR Cambridge Bioresource.

The NIHR BioResource Data Access Committee (DAC) will consider applications according to the Data Access Policy. Applications will be handled as they arrive, applications outside the policy will be considered by the DAC at the next committee meeting, which occur approximately every 3 months. Name of applicant and co-applicant(s), including affiliations and contact details. Please ensure that a full postal and email address is included for each applicant. PhD student applicants must include their supervisors as a co-applicant and provide their full contact details. 1 Organisation (Recipient): Name of Organisation Click here to enter text. Address Click here to enter text. 2 Applicants (Registered Users): Primary Applicant Name: Click here to enter text. Affiliation: Click here to enter text. Address : Click here to enter text. Email : Click here to enter text. Co-Applicants Name: Click here to enter text. Affiliation: Click here to enter text. Address : Click here to enter text. Email : Click here to enter text. Name: Click here to enter text. Affiliation: Click here to enter text. Address : Click here to enter text. Email : Click here to enter text.   Name: Click here to enter text. Affiliation: Click here to enter text. Address : Click here to enter text. Email : Click here to enter text. Title of Project (In less than 30 words) Click here to enter text. Genotype Data Requested Please indicate which disease and/or control genotypes you require. Click here to enter text. Research Question Please provide a clear description of the project and its specific aims in no more than 750 words. This should include specific details of what you plan to do with the data and include key references and, where applicable, the Ethics Reference Number. Ethics Reference Number Click here to enter text. Click here to enter text. Feasibility Please describe fully your experience and expertise, and that of your collaborators, and how this will be applied to the proposed study. A publication list MUST be provided for the applicant, co-applicants and PhD supervisors where PhD students have applied. The committee needs assurance of competence in handling and secure storage of datasets of this size and nature. Click here to enter text. We have read and agree to abide by the terms and conditions contained in the Data Access Agreement, which is appended to this Application for Access to Genotype and Phenotype Data. Please note that all applicants need to sign.   AGREED AND ACCEPTED by the Recipient and its Registered Users through their authorised signatories For and on behalf of the Organisation (Recipient) Name of Organisation Click here to enter text. Signed By: Print Name: Click here to enter text. Title Click here to enter text. Date: Click here to enter text. For and on behalf of Applicants (Registered Users): Applicants (Registered Users) confirm that the contents of the application above are correct and acknowledge the contents of the Data Access Agreement and agree to comply with the obligations therein. Primary Applicant Signed By: Print Name: Click here to enter text. Title Click here to enter text. Date: Click here to enter text. Co-Applicants Signed By: Print Name: Click here to enter text. Title Click here to enter text. Date: Click here to enter text.   Signed By: Print Name: Click here to enter text. Title Click here to enter text. Date: Click here to enter text. Signed By: Print Name: Click here to enter text. Title Click here to enter text. Date: Click here to enter text. WHEN SUBMITTING THIS DOCUMENT, PLEASE INCLUDE ALL PAGES OF THIS DOCUMENT INCLUDING THE DATA ACCESS AGREEMENT Please submit forms containing the original signatures to: Dr Kathy Stirrups, Project Coordinator, NIHR BioResource - Rare Diseases. Department of Haematology, University of Cambridge, NHSBT Building, Long Road, Cambridge CB2 0PT. Email: ks277@medschl.cam.ac.uk By signing below through its authorised signatory, the NIHR BioResource – Rare Diseases agrees to grant access to the Recipient and its Registered Users as identified above. Should the NIHR BioResource discover that the Recipient or any of its Registered Users have contravened any of the conditions of this agreement or made inappropriate use of the Data, then it will terminate the Agreement immediately. Signed By: Print Name: Click here to enter text. Title Click here to enter text. Date: Click here to enter text. The NIHR BioResource – Rare Disease BRIDGE Consortium complies with the requirements of the Data Protection Act 1998 with regard to the collection, storage, processing and disclosure of personal information and is committed to upholding the Act's core Data Protection Principles. Information collected under the Agreement will be used for the purposes of maintaining the Agreement, and may be used for statistical reporting. This Agreement governs the terms on which access will be granted to the genomic sequence and accompanying phenotypic data generated by the NIHR BioResource - Rare Diseases BRIDGE Consortium. In signing this Agreement, the Recipient agrees to be bound by the terms and conditions for access set out in this Agreement. For the sake of clarity, the terms of access set out in this Agreement apply both to the Registered User and the Recipient (as defined below). In response to the Recipient’s request for access to the Data, the Consortium and the Recipient agree as follows: 1. Definitions: Consortium means the BRIDGE Consortium, a topic specific working group of the NIHR BioResource – Rare Diseases, members of which can be found on the study website: https://bridgestudy.medschl.cam.ac.uk/index.shtml. Data means all and any human genetic and phenotypic data obtained from the Consortium. Data Subject means a person, who has been informed of the purpose for which the Data is held and has given his/her informed consent thereto. Intellectual Property means (i) patents, designs, trade marks and trade names (whether registered or unregistered), copyright and related rights, database rights, inventions, know-how and confidential information; (ii) all other intellectual property rights and similar or equivalent rights anywhere in the world which currently exist or are recognised in the future; and (iii) applications, extensions and renewals in relation to any such rights. Publications means, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Recipient is the organisation which has signed this Agreement. Registered User means a Researcher (or individual conducting research under the supervision of a Researcher) named in the Data Access Application form and employed by, affiliated to or enrolled at the Recipient and who is bound by the confidentiality and non-use obligations in respect of the Data and who has signed this Agreement and has received acknowledgement of its acceptance. Research shall mean research that is seeking to advance the understanding and treatment of rare diseases or work on statistical and computational methods that may be applied to such research. Details of the Researchers research interests would be supplied as part of their application. Researcher(s) shall mean an individual or individuals carrying out Research who: (a) in the case of an individual seeking access to Data has authored a relevant peer-reviewed article that the Consortium can locate on PubMed and who is still working in the field; or (b) in the case of an individual seeking access to Data held as part of a wider consortium, is a successful applicant to the consortium data access committee. 2. Purpose The Recipient agrees to use Data only for the Research, according to the consent obtained from sample donors. The Data can only be used for the approved purpose and project described in the application; use of the Data for a new purpose or project will require a new application and approval. 3. Confidentiality The Recipient agrees to preserve, at all times, the confidentiality of Data pertaining to identifiable Data Subjects. In particular, the Recipient undertakes not to use, or attempt to use the Data to deliberately compromise or otherwise infringe the confidentiality of information on Data Subjects and their right to privacy. 4. Data Protection 4.1 The Recipient agrees that it, and its Registered Users, are covered by and shall comply with the obligations contained in the Data Protection Act 1998 as amended from time to time, or equivalent national provisions no less onerous than those contained in the Data Protection Act. In particular, the Recipient and its Registered Users understand their duties under such legislation in relation to the handling of Data and the rights of Data Subjects. 4.2 The Recipient agrees that it, and its Registered Users, shall not analyse or make any use of the Data in such a way that has the potential to: (a) lead to the identification of any Data Subject; or (b) compromise the anonymity of any Data Subject in any way. 4.3 The Recipient agrees that it, and its Registered Users, shall not attempt to link the Data to other information or archive data available for the data sets provided, even if access to that data has been formally granted to you, or it is freely available without restriction, without specific permission being sought from the relevant access committees. 5. Access and Governance 5.1 The Recipient agrees that it shall take all reasonable security precautions to keep the Data confidential, such precautions to be no less onerous than those applied in respect of the Recipient’s own confidential information. 5.2 The Recipient agrees to only give access to Data, in whole or part, or any identifiable material derived from the Data, to a Registered User. The Recipient agrees that before it gives any Registered User access to Data, it shall first show the Registered User a copy of this Agreement and shall inform the Registered User that he or she must comply with the obligations contained in this Agreement and sign up to the provisions of this Agreement in the form set out at the end of this Agreement. The Recipient shall provide the Consortium with a copy of the Registered User’s acceptance form within thirty (30) days of the date of acceptance by the Registered User. 5.3 The Recipient agrees that it shall only give Registered Users that are not Researchers (including but not limited to students or new researchers to the field) access to the Data if they are supervised by a Researcher who will take responsibility for such Registered Users’ use of the Data. 5.4 The Recipient shall not transfer, copy or in any other way disclose the Data, in whole or part, or any identifiable material derived from the Data, to a Researcher who is not a Registered User. Should such Researcher wish to have access to the Data, the Recipient shall either give access in accordance with clause 5.1 above or advise the Researcher that he or she must make a separate application for access to the Consortium. 5.5 The Consortium reserves the right to request and inspect data security and management documentation to ensure the adequacy of data protection measures in countries that have no national laws comparable to that pertaining in the European Economic Area (EEA). 6. Errors The Recipient agrees to notify the Consortium of any errors detected in the Data. 7. Data reissue The Recipient accepts that Data will be reissued from time to time, with suitable versioning. If Data is reissued at the request of Data Subject(s) and/or as the result of other ethical scrutiny, the Recipient agrees to destroy all earlier versions of the Data. 8. Intellectual Property 8.1 The Recipient recognises that nothing in this Agreement shall operate to transfer to the Recipient or its Registered Users any Intellectual Property rights in or relating to the Data. 8.2 The Recipient recognises and understands that the Consortium’s BRIDGE Research Project is of a pre-competitive nature and that the results of this project will be put in the public domain. Therefore the Recipient, and its Registered Users, cannot claim inventorship on associations between sequence variants and a certain clinical condition. If the Recipient, or its Registered Users, wishes to perform functional genomics studies with the purpose of developing treatments, then the Recipient should decide whether or not arrangements for inventorship and intellectual property rights are to be made. 8.3 The Recipient agrees not to use the Data or any part thereof for the creation of products for sale or for any commercial purpose. 8.4 The Recipient understands and acknowledges that the Data is protected by copyright and other intellectual property rights, and that duplication of the Data, except as reasonably required to carry out the Research, or sale of all or part of the Data on any media is not permitted. 9. Publications 9.1 The Recipient agrees to acknowledge in any work based in whole or part on the Data, the published paper from which the Data derives, the version of the data, and the role of the Consortium and the relevant primary collectors and their funders. Suitable wording is provided in the Publications Policy given in Schedule 1. 9.2 The Recipient shall also declare in any such work that those who carried out the original analysis and collection of the Data bear no responsibility for the further analysis or interpretation of it by the Recipient. 9.3 The Recipient agrees to abide by the terms outlined in the Consortium 'Publications Policy' as set out in Schedule 1. 9.4 The Recipient agrees that it will submit a report to the Consortium Data Access Committee, if requested, on completion of the agreed purpose. The Consortium Data Access Committee will treat the report and all information, data, results, and conclusions contained within such report as confidential information belonging to the Recipient. 9.5 Where the Recipient is a member of the NIHR BioResource – Rare Disease BRIDGE Consortium, it shall comply with the terms of the BRIDGE Memorandum of Understanding which is attached as Schedule 2 as applicable. 10. Termination of Agreement 10.1 This Agreement will terminate immediately upon any breach of the provisions of this Agreement by the Recipient or its Registered Users. 10.2 The Recipient accepts that the changing ethical framework of human genetic research may lead to: (i) alteration to the provisions of this Agreement, in which case the Recipient may accept such alterations or terminate this Agreement; or (ii) the withdrawal of this Agreement in extreme circumstances. 10.3 Either party shall have the right to terminate this Agreement with immediate effect upon giving written notice of termination to the other party. 10.4 In the event that this Agreement is terminated in accordance with this Clause 10 the Recipient shall destroy any Data it or its Registered Users hold. 11. Legal statement 11.1 The Recipient acknowledges that the Consortium 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; and (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. 11.2 The Recipient understands that all the Data is protected by copyright and other intellectual property rights, such that duplication or sale of all of or part of the Data on any media is not permitted under any circumstances, except with the prior written consent of the Consortium. 12. Governing Law 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. SCHEDULE 1 Publications Policy for Recipients who are not members of the Consortium The primary purpose of the NIHR BioResource - Rare Disease BRIDGE Consortium is to discover the genetic basis of inherited Rare Diseases. Additional objectives include the development and validation of informatics and analytical solutions appropriate to the scale and nature of the project, as well as use of the data generated to answer important methodological and biological questions. The Consortium anticipates that data generated from the project will be used by others, such as required to improve the diagnosis of Rare Diseases or development of new analytical methods. A more detailed list of the Consortium aims are provided on the BRIDGE website – https://bridgestudy.medschl.cam.ac.uk/whatis.shtml Authors who use data from the project must acknowledge the BRIDGE Consortium using the following wording: “This study makes use of data generated by the NIHR BioResource - Rare Disease BRIDGE Consortium. A full list of the investigators who contributed to the generation of the data is available from http://bioresource.nihr.ac.uk/rare-diseases/rare-diseases/. Funding for the project was provided by the National Institute for Health Research in England.” The Author shall also ensure that the logos used in the heading of this Agreement are used in presentations and reports. Users should note that the Consortium bears no responsibility for the further analysis or interpretation of these data, over and above that published by the Consortium.   SCHEDULE 2 Publications Policy for Recipients who are members of the Consortium Principles:  Primary Papers are to be published by the Consortium, together with access to all Data to others via EGA  All centres contributing clinical cases will be included in the author list of the Primary Paper  The Primary Paper can be: (a) on behalf of the Consortium with Authors listed at the end of the manuscript grouped according to teams (e.g. clinical enrolment, DNA handling & sequencing, analysis, experimental studies, etc.), (b) all authors at the front with authors listed according to the “Onion Skin” model with several shared first and last authors and with remaining authors listed alphabetically  Parallel manuscripts with the Primary Papers are to be stimulated but should not “jump ahead” of the Primary Papers  If a Consortium member has credible evidence of a risk for being “scooped”, then a request can be made to publish a pre-emptive manuscript on a single candidate gene, which would precede the Primary Papers. This request will be reviewed and agreed upon by the NIHR BioResource – BRIDGE Publications Committee  Parallel manuscripts will generally have smaller authorship and author inclusion will be agreed on case-by-case basis using the more classic principles underlying authorship of original manuscripts  All manuscripts will be circulated in a timely manner by the Writing Committee to all members of the NIHR BioResource – BRIDGE Publications Committee for review and approval. The Publications Committee will generally grant permission for submission by consensus but in extreme cases a vote could be sought  All publications and communications about the project need approval from the Publications Committee. In some specific instances  A manuscript from Consortium investigators that make substantial use of primary data before the Primary Papers have been published or have made use of as yet unpublished analyses, should include at least the Consortium as an author. The Consortium authorship can appear in “expanded” or “non-expanded” form in PubMed. This is to be agreed by the Publications Committee on case-by-case basis  Manuscripts from Consortium investigators that make substantial use of primary data but after the Primary Papers have been published, should include the Consortium as an author. Whilst in principle, such studies could often be done by non-Consortium investigators without authorial attribution, considerations of early data access, plus the shared benefits of maximising consortium prominence, would generally argue in favour of including the Consortium as an author. This principle will be reviewed and “watered” down with time and ceases when the Consortium dissolves  Manuscripts from Consortium investigators that involve the further (mechanistic, physiological, molecular) follow-up of individual candidate gene signals arising from the exo-seq scan (and replication studies thereof) would not require Consortium co-authorship. Of course, future studies on e.g. regulatory regions of the same set of candidate genes will be governed by the rules to be developed by the Consortium and this will be in part be guided by the fund providers and other Consortia (e.g. Blueprint) providing access to pre-publication information.