Multi-omic dataset utilized in the analysis of a phase II study of epigenetic priming followed by nivolumab in lung cancer

DATA ACCESS AGREEMENT This Data Access Agreement (“Agreement” or “DAA”), including its appendices, is to allow User Institution and its Authorized Personnel to access and use the Data from Johns Hopkins University (“Provider”) for the Project. Provider is willing to allow User Institution to access such Data from the European Genome-Phenome Archive (“EGA”) for use solely for the research purposes described in Appendix II, wherein User Institution may not use the Data for any commercial purpose. The User Institution agrees to be bound by the terms and conditions of this Agreement. This Agreement is effective as of the data of last signature below. 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 DAC: The data access committee for Multi-omic analyses from a randomized phase II study of epigenetic priming followed by nivolumab in previously treated metastatic non-small cell lung cancer, EGA DAC EGAC50000000563. The DAC is comprised of Drs. Valsamo Anagnostou, Julie Brahmer, and Stephen Baylin and can be contacted at vanagno1@jhmi.edu. Authorised Personnel: The individuals at the User Institution to whom the DAC 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 Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: The DAC and the collaborators listed in Appendix I responsible for the development, organisation, 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. Please include your Institution details here: 1. The User Institution agrees 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. 2. The User Institution agrees to preserve, at all times, the confidentiality of these Data. In particular, it undertakes 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 Institution agrees 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 agrees 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. Should User Institution inadvertently receive identifiable information or otherwise identify a subject, Recipient shall promptly notify Provider and follow Data Producer’s reasonable written instructions, which may include return or destruction of the identifiable information. 5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. Should the 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 Institution agrees 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 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 recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. Nothing herein shall authorize the User Institution to use or further disclose the Data in a manner that would violate the requirements of Data Producers under U.S. law, including 45 CFR 164.514. 8. The User Institution agrees 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 analysing these Data. 9. The User Institution agrees 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 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 agrees 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 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. 12. The User Institution will notify the DAC within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify the DAC prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the DAC 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. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 16. 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 the DAC. 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. 17. 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 Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this agreement. 19. If the Data Producer is a HIPAA Covered Entity, and if the the Data will be a Limited Data Set as defined by the Health Insurance Portability and Accountability Act of 1996 (“HIPAA”). In accordance with Section 164.514(e)(2) of the HIPAA Privacy Rule, the Data shall exclude the following direct identifiers of the individual or of relatives, employers, or household members of the individual: (i) Names; (ii) Postal address information, other than town or city, State, and zip code; (iii) Telephone numbers; (iv) Fax numbers; (v) Electronic mail addresses; (vi) Social security numbers; (vii) Medical record numbers; (viii) Health plan beneficiary numbers; (ix) Account numbers; (x) Certificate/license numbers; (xi) Vehicle identifiers and serial numbers, including license plate numbers; (xii) Device identifiers and serial numbers; (xiii) Web Universal Resource Locators (URLs); (xiv) Internet Protocol (IP) address numbers; (xv) Biometric identifiers, including finger and voice prints; and (xvi) Full face photographic images and any comparable images. If the Data being provided is coded, the Data Producer will not release, and the User Institution will not request, the key to the code. 20. The User Institution agrees to cite the publication(s) from which the Data are derived to acknowledge the version of the data and the contribution of the Data Producers in all reports or publications resulting from the use of the Data. The full citation(s) of the Data generating publication(s) and suggested acknowledgement are in Appendix IV.   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 Provider: Signature: Name: Neha Parikh, JD Title: Assistant Director, Contracts, JHU ORA Date: On behalf of the DAC, I confirm that I have read and understood this Agreement: Signature: Name: Dr. Valsamo Anagnostou Title: Associate Professor of Oncology Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) EGA study: Multi-omic analyses from a randomized phase II study of epigenetic priming followed by nivolumab in previously treated metastatic non-small cell lung cancer EGA dataset: The dataset for the study “Multi-omic analyses from a randomized phase II study of epigenetic priming followed by nivolumab in previously treated metastatic non-small cell lung cancer” includes 78 bam files from whole exome sequencing (WES) on the Illumina HiSeq2500 and 36 fastq files from RNA sequencing (RNAseq) on the Illumina HiSeq 2500 or NovaSeq 6000. The samples analyzed include 39 tumor and matched normal DNA sample pairs and 18 serial tumor samples from individuals with non-small cell lung cancer treated with either epigenetic priming followed by nivolumab or nivolumab only. Name of project that created the dataset EGA study: Multi-omic analyses from a randomized phase II study of epigenetic priming followed by nivolumab in previously treated metastatic non-small cell lung cancer Names of other data producers/collaborators Kristen A. Marrone, Blair V. Landon, Michael J. Topper, Hua-Ling Tsai, Akshaya Annapragada, Archana Balan, Noushin Niknafs, Christopher Cherry, James R. White, Zineb Belcaid, Gavin Pereira, Jaime Wehr, Vilmos Adleff, Chen Hu, Patrick Forde, Christine Hann, Ronan Kelly, David Ettinger, Benjamin Levy, Jorge Nieva, James Herman, Victor Velculescu, Valsamo Anagnostou, Stephen Baylin and Julie Brahmer Specific limitations on areas of research The User Institution agrees that it will only use these Data for Research Purposes. Use of this data by for-profit organizations is not allowed. 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 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 (500 words max) All Individuals who the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* All Individuals that should have an account created at the EGA Name of Registered User Email Job Title APPENDIX III – PUBLICATION POLICY The DAC 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. The DAC anticipates 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 0 months after these data were first made available on the relevant hosting database, unless the DAC has provided written consent to earlier submission. 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., EGAS000000000XX), and acknowledge its use in a form agreed by the User Institution with the DAC. APPENDIX IV – ACKNOWLEDGEMENT/CITATION POLICY Authorized Personnel must acknowledge the Data Producers and primary funding organizations that supported the Data Producers in all oral and written presentations, disclosures, and publications resulting from any analyses of controlled-access data obtained through this Agreement. Acknowledgments must include the EGA dataset reference number for the specific version of the dataset analyzed.