WES CRAM files of HUG-CEL Covid-19 Genomics Study

This project generated a high-coverage WES dataset of 400+ admixed Brazilians with Covid-19 extreme phenotypes from recovered nonagenarians and centenarians to deceased adults. The phase 1 includes BAM files from 415 individuals.

This agreement governs the terms on which access will be granted to the sequencing data generated by HUG-CELL regarding Brazil Genomics Data of the Project “SARS-CoV-2 host genetics and Covid-19 outcomes in admixed Brazilian with extreme phenotypes” 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 and User has requested access. In signing this agreement, the User Institution and User agree to be bound by these terms and conditions. For the sake of clarity, the terms of access set out in this agreement apply both to the User and the User Institution (terms in red are defined below). List of Appendices APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY Definitions Authorised Personnel: The individuals at the User Institution to whom HUG-CELL grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorized Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: HUG-CELL and the collaborators listed in Appendix I responsible for the development, organization, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. 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 genetics and genomics, 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(s): The Institution that has requested access to the Data. HUG-CELL: Human Genome and Stem Cell Research Center at the Biosciences Institute – University of São Paulo, Brazil. In Portuguese: Centro de Estudos sobre o Genoma Humano e Células Tronco do Instituto de Biociências, Universidade de São Paulo, Brasil. 1. The User and User Institution agree to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use these Data for Research Purposes which are within the limitations (if any) set out in Appendix I. To clarify, The User and User Institution agree not to use the Data for the creation of products for sale or for any commercial purpose. 2. The User and User Institution agree to preserve, always, the confidentiality of these Data. In particular, the User and User Institution 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 agrees to use at least the measures set out in Appendix I to protect these Data. 3. The User and User Institution 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 User Institution 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 is freely available without restriction. 5. The User and User Institution agree only to transfer or disclose these Data, in whole or part, or any material derived from these Data to the Authorized Personnel. Should the User and User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 6. The User and User Institution agree that the Data Producers, the original data creators, depositors or copyright holders, or the funders of the data, 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; c) bear no responsibility for the further analysis or interpretation of these Data. 7. The User and User Institution understand and acknowledge that the Data is protected by copyright and other intellectual property rights, and that duplication, except as reasonably required to carry out the Project and respective Research Purposes with the Data, or sale of all or part of the Data on any media is not permitted. 8. The User Institution agrees to follow the Fort Lauderdale Guidelines (http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.pdf ) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognizing the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 9. The User and User Institution agree to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analyzing these Data. 10. The User and User Institution 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. 11. The User and User Institution 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 and User Institution must notify HUG-CELL Data Access Committee, who can sign non-disclosure agreement and approve proposals upon reasonable requests. The User and User Institution 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 ). 12. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 13. The User Institution will notify HUG-CELL within 30 days of any changes or departures of Authorized Personnel. 14. The User Institution will notify HUG-CELL prior to any changes to the protocol for the Project that involve usage of the Data provided. 15. The User Institution will notify HUG-CELL as soon as it becomes aware of a breach of the terms or conditions of this agreement. 16. HUG-CELL 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. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 17. The User Institution accepts 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 Data Producers other than HUG-CELL. If 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. 18. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorized Personnel. The User Institution will procure that the Authorized Personnel comply with the terms of this agreement. 19. 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. APPENDIX I – DATASET DETAILS (to be completed by the data producer before passing to applicant) Dataset reference (EGA Study ID and Dataset Details) EGA Study ID: EGAS00001006376 This project generated a high-coverage WES dataset of 400+ admixed Brazilians with Covid-19 extreme phenotypes from recovered nonagenarians and centenarians to deceased adults. The phase 1 includes BAM files from 415 individuals. Name of project that created the dataset Whole-exome sequencing of a cohort of admixed Brazilians with extreme phenotypes of Covid-19. Names of other data producers/collaborators Mateus Vidigal de Castro Mayana Zatz Michel Satya Naslavsky Marília Oliveira Scliar Erick da Cruz Castelli Ricardo Nonaka Maria Rita Passos-Bueno Jaqueline Wang Specific limitations on areas of research There are no specific limitations on areas of research. Minimum protection measures required File access: 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 screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. APPENDIX III – PUBLICATION POLICY The primary purpose of HUG-CELL Covid-19 Genomics Study is describing genomic features related to resistance or susceptibility to Covid-19 in the Brazilian population. It comprehends medical-related analyses such as distribution of variants of clinical relevance associated to monogenic and multifactorial phenotypes. In addition, studies on population genomics, evolution and admixture are explored by HUG-CELL researchers and collaborators, as defined by Data Access Committee (entitled HUG-CELL Covid-19 Genomics Committee). HUG-CELL, regarding HUG-CELL Covid-19 Genomics Study, intend to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. HUG-CELL anticipate that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur until 3 months after these data were first made available on the relevant hosting database, unless HUG-CELL through the appointed HUG-CELL Covid-19 Genomics Committee has provided written consent to earlier submission. At least 30 days prior to submitting data on monogenic or multifactorial phenotypes shared or used as described by this agreement, present the intended publication containing results and invite HUG-CELL researchers to co-author the submission, which might be accepted or not, pending confirmation in each case. In addition, collaborations are welcome and encouraged. If HUG-CELL researchers participate in methods, discussion, manuscript writing, or other activities involving the research proposed by the User, co-authorship must take place in any publication derived from use of the Data shared and described by this agreement. Authors who use data from the project must acknowledge HUG-CELL using the following wording "This study makes use of data generated by HUG-CELL”. The User and User Institution agree cite the flagship HUG-CELL Covid-19 Genomics Study whole-exome dataset publication (10.3389/fimmu.2022.975918). 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., EGAS00001006376), and acknowledge its use in a form agreed by the User and User Institution with HUG-CELL.