WGS of tissues from members of family with germline POLD1 L474P variant

IDIBELL Access Policy

DATA ACCESS AGREEMENT BETWEEN Institut d’Investigació Biomèdica de Bellvitge “IDIBELL” (Data Producers) And XXX (User Institution) 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 ICO-IDIBELL: Catalan Institute of Oncology and Bellvitge Biomedical research Institute, Av. Gran Via de l’Hospitalet, 199-203, 08908 L'Hospitalet de Llobregat, Barcelona, Spain Authorised Personnel: The individuals at the User Institution to whom ICO-IDIBELL 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: ICO-IDIBELL 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 (Name of User Institution). The Data Producers and the User Institutions are individually referred to hereinafter as the “Party” and collectively as the “Parties”. 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 for the duration of this Agreement including any extension thereof and thereafter for a period of five (5) years following termination or expiry of this Agreement. 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. Excluded from this obligation of confidentiality shall be any Confidential Information of which the User Institution can reasonably demonstrate that it (a) was previously known to the User Institution, or (b) is, and/or becomes, publicly available during said five (5) year period through no fault of the User Institution, or (c) is independently and lawfully developed by the User Institution. This obligation of confidentiality shall not apply to any disclosure required by law, provided that the User Institution shall notify the Data Producers of any disclosure required by law in sufficient time so that the Data Producers may contest such requirement, if the Data Producers so chooses. 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. ICO-IDIBELL represents that the proper informed consent has been obtained for the Data and the transfer of the Data to the User Institution for the use by the User Institution for the purpose of the Project. 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. 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 (https://wellcome.ac.uk/sites/default/files/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. 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 ICO-IDIBELL within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify ICO-IDIBELL prior to any significant changes to the protocol for the Project. 14. The User Institution will notify ICO-IDIBELL as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Parties may terminate this agreement by written notice to the other Party. 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 ICO-IDIBELL. 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. The User Institution will provide a copy of its Ethics Committee with approval of the Project. 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. 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 Spain and shall be subject to the exclusive jurisdiction of the Spanish courts. 21. According to the General Data Protection Regulation, User Institution and ICO-IDIBELL report that the data that appears in this agreement, as well as those derived from the management thereof, will be processed only for the purpose set out on Appendix I. User Institution and ICO-IDIBELL are responsible for the veracity and accuracy of the personal data communicated and authorize their collection and processed for the described purpose. These personal data will be provided and will be kept as long as the relationship between User Institution and ICO-IDIBELL is maintained, and once it is finished, to comply with the respective legal responsibilities. Data will be transferred only when regulation requires it. User Institution and ICO-IDIBELL have the right to file a claim with the Control Authority if they consider that their rights have been violated. 22. This agreement shall enter into force on the date of the last signature hereinbelow and shall be valid for a term of one (1) year However, the obligations of confidentiality and non-use of Confidential Information by the Parties shall not be extinguished and will remain in force as indicated at clause 2. 23. The Parties may extend the term of the present Agreement, if the desired results have not been achieved by the end of the term and / or the Parties want the Agreement to be extended. In the event of an extension, the Parties shall sign an extension of the Term before its ending. The present Agreement cannot be assigned neither by virtue of any law nor by any other means, without the prior consent in writing of the ICO-IDIBELL. 24. In addition to the cases specifically regulated by the applicable legislation in force, the Agreement shall be terminated in the following cases: a. By the expiration of the contractual term agreed. b. At any time, by mutual agreement in writing. c. By the breach by a Party of any of the obligations under the Agreement, as long as such breach is not remedied within a maximum period of thirty (30) days after written request for the remedy, unless such breach is irreparable or makes impossible the fulfillment of this Agreement to the complaining Party, in which case the termination may be immediate, and in any case without prejudice to any claim for damages that may correspond to either Party. Agreed for User Institution [Name of User Institution] Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for ICO-IDIBELL Signature: Name: Dr. Gabriel Capellà Title: Director IDIBELL Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Dr. Laura Valle Title: Principal Investigator ICO-IDIBELL 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): EGAS00001006434 https://ega-archive.org/search-results.php?query=EGAS00001006434 This study aimed to estimate the influence of POLD1 L474P on somatic and germline mutagenesis. We studied the mutation rate and spectra in germline and soma in an extended family harboring the POLD1 c.1421T>C p.(Leu474Pro) pathogenic variant. The study includes WGS data for DNA extracted from blood, fibroblasts or buccal swabs from 16 family members. For 8 out of 16 family members single-cell colonies were obtained from immortalized fibroblasts and whole-genome sequenced. For 6 out of these 8 colonies additional WGS was prepared after approximately 40 passages. Study also includes WXS sequencing for 1 tumor FFPE sample and adjacent normal tissue from the individual from one family member. DNA preparation for WGS was performed with the TruSeq Nano DNA Library, and sequencing was carried out in a NovaSeq 6000 150 PE (2x150 bp). Sequencing was performed at a minimum coverage of 90 Gb (30x) for the germline studies in the family members, and at a minimum coverage of 150 Gb (50x) for the experiment with fibroblasts (P0 – P40 passages of the fibloblasts’ cultures). Sequencing was performed at Macrogen (Macrogen Inc, Seoul, South Korea). Name of project that created the dataset Extended family with germline pathogenic variant in polymerase delta provides strong evidence for recessive effect of proofreading inactivation Names of other data producers/collaborators Laura Valle (lvalle@idibell.cat) Maria A. Andrianova Vladimir B. Seplyarskiy Ana Beatriz Sánchez-Heras José Luis Soto Fyodor A. Kondrashov Alexey S. Kondrashov Georgii A. Bazykin Specific limitations on areas of research The dataset should be used to study the features of main replicative polymerases. 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 EGA Study: Dataset Accession Numbers: Dataset ID Description Technology Samples XXXXX WGS (TruSeq Nano DNA Library, NovaSeq 6000 150 PE (2x150 bp). Minimum coverage of 90 Gb (30x). Illumina NovaSeq 6000 XXX 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* Principal Investigator XXX All Individuals that should have an account created at the EGA Name of Registered User Email Job Title APPENDIX III – PUBLICATION POLICY ICO-IDIBELL 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. ICO-IDIBELL 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. 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., EGAS00001006434), and acknowledge its use in a form agreed by the User Institution with ICO-IDIBELL.