Dataset for Genomic and fragmentomic landscapes of cell-free DNA in aging and disease : Alzheimer's Disease

DATA ACCESS AGREEMENT for EGA Study “Genomic and fragmentomic landscapes of cell-free DNA in aging and disease” 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 date of last signature below. We do not provide data to for-profit entities. Definitions DAC: The data access committee for “Genomic and fragmentomic landscapes of cell-free DNA in aging and disease”. The DAC is comprised of Drs. Jillian Phallen, Victor Velculescu, Robert Scharpf, and Shashikant Koul, and can be contacted at skoul3@jh.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 Institu- tion. 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 confiden- tiality 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 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 III. 8. The User Institution agrees to follow the Fort Lauderdale Guidelines (https://www.sanger.ac.uk/ wp-content/uploads/fortlauderdalereport.pdf) and the Toronto Statement (http://www.nature.com/ nature/journal/v461/n7261/full/461168a.html). 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. 9. The User Institution agrees to follow the Publication Policy in Appendix IV. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 10. 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. 11. 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) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006). 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 the DAC within 30 days of any changes or departures of Authorised Personnel. 14. The User Institution will notify the DAC prior to any significant changes to the protocol for the Project. 15. The User Institution will notify the DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 16. 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. 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 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. 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. 19. 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. 20. If the Data Producer is a HIPAA Covered Entity, and if 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. 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: Title: Date: On behalf of the DAC, I confirm that I have read and understood this Agreement: Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II – PROJECT DETAILS APPENDIX III – CITATION AND ACKNOWLEDGEMENT APPENDIX IV – PUBLICATION POLICY APPENDIX I – DATASET DETAILS Dataset reference (EGA Study and Dataset Details) EGA study “Genomic and fragmentomic landscapes of cell-free DNA in aging and disease” EGA dataset The submission for “Genomic and fragmentomic landscapes of cell-free DNA in aging and disease” includes the following datasets. The Alzheimer’s dataset contains 352 CRAM files from whole genome next-generation sequencing on the Illumina NovaSeq 6000 with 1-2x coverage. The samples analyzed include plasma samples from patients with Alzheimer’s Disease (AD), family history of AD, and patients with no neurological deficits. The MICA dataset contains 570 CRAM files from whole genome next-generation sequencing on the Illumina NovaSeq 6000 with 1-2x coverage. The samples analyzed include plasma samples from non- cancer patients in the MICA cohort. Name of project that created the dataset EGA study: Genomic and fragmentomic landscapes of cell-free DNA in aging and disease Names of other data producers/collaborators Akshaya V. Annapragada, Daniel C. Bruhm, Daniel Du, Hope Orjuela, Carter Norton, Noushin Niknafs, Sarah Short, Chris Cherry, Shashikant Koul, Jason Zavras, Keerti Boyapati, Adrianna Bartolomucci, Jacob Carey, Alessandro Leal, Bryan Chesnick, Nic Dracopoli, Jamie E. Medina, Julia Velculescu, Sofia Velculescu, Michael Noë, Nicholas A. Vulpescu, James White, Dimitrios Mathios, Vilmos Adleff, Jeff Rothstein, Satish Menon, Jeff Olson, Chris Hamm, Sarah Bacus, Zachariah H. Foda, Mette Jegstrup Villadsen, Claus L. Feltoft, Julia S. Johansen, Jillian Phallen, Robert B. Scharpf, and Victor E. Velculescu Specific limitations on areas of research The User Institution agrees that it will only use these Data for Research Purposes. 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 – CITATION AND ACKNOWLEDGEMENT 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. Citation(s) for the publication(s) from which the Data are derived: Akshaya V. Annapragada, Daniel C. Bruhm, Daniel Du, Hope Orjuela, Carter Norton, Noushin Niknafs, Sarah Short, Chris Cherry, Shashikant Koul, Jason Zavras, Keerti Boyapati, Adrianna Bartolomucci, Jacob Carey, Alessandro Leal, Bryan Chesnick, Nic Dracopoli, Jamie E. Medina, Julia Velculescu, Sofia Velculescu, Michael Noë, Nicholas A. Vulpescu, James White, Dimitrios Mathios, Vilmos Adleff, Jeff Rothstein, Satish Menon, Jeff Olson, Chris Hamm, Sarah Bacus, Zachariah H. Foda, Mette Jegstrup Villadsen, Claus L. Feltoft, Julia S. Johansen, Jillian Phallen, Robert B. Scharpf, and Victor E. Velculescu. Genomic and fragmentomic landscapes of cell-free DNA in aging and disease (manuscript in preparation, 2026). Acknowledgement of the version of the data and the contribution of the Data Producers: “This study uses data generated by The Cancer Genomics Laboratory at The Johns Hopkins University School of Medicine Sidney Kimmel Comprehensive Cancer Center as reported by Annapragada et al. 2026.” APPENDIX IV – 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.