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DNA (exome) sequencing of uveal melanoma metastases

DNA (exome) sequencing of uveal melanoma metastases.

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These terms and conditions govern access to the managed access datasets to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions.

DATA ACCESS AGREEMENT 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 Authorised Personnel: The individuals at the User Institution to whom Sahlgrenska Translational Melanoma Group (SATMEG) 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: Sahlgrenska Translational Melanoma Group (SATMEG) and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. Contact: Dr. Jonas Nilsson, group leader, principal investigator & professor Sahlgrenska Translational Melanoma Group (SATMEG) Harry Perkins Institute of Medical Research, 6 Verdun St, WA 6009, Nedlands, Perth, Australia Email: jonas.nilsson@perkins.org.au 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. 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. 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. 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 Sahlgrenska Translational Melanoma Group within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Sahlgrenska Translational Melanoma Group prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Sahlgrenska Translational Melanoma Group as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Sahlgrenska Translational Melanoma Group 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 Sahlgrenska Translational Melanoma Group. 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. In the event of a dispute arising between the Parties concerning the interpretation or execution of this Agreement, the parties shall attempt to resolve the issue amicably. If a mutually satisfactory resolution cannot be found after three (3) months, such dispute shall be submitted to the jurisdiction of the laws and courts where the defendant is legally incorporated. APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) EGA Study ID: EGASXXXXXXXXXXX. Dataset ID: EGADXXXXXXXXXXX. Dataset description: Whole genome, exome and RNA sequencing of uveal melanoma metastases, primary tumors and matched normal DNA. Name of project that created the dataset Clinical and exploratory outcomes in the PEMDAC phase 2 study of pembrolizumab and entinostat in patients with metastatic uveal melanoma Names of other data producers/collaborators Dr. Lars Ny, SATMEG, Senior Lecturer, Specialized Physician Dr. Joakim Karlsson, Bioinformatician Specific limitations on areas of research The data can only be used for cancer research. Minimum protection measures required File access: Data can be held in unencrypted files on an institutional compute system behind a secure firewall, with read and/or write access only for Authorised Personnel. Laptops holding these data should be encrypted, 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 Sahlgrenska Translational Melanoma Group intend to publish more results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. Sahlgrenska Translational Melanoma Group 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 12 months after these data were first made available on the relevant hosting database, unless Sahlgrenska Translational Melanoma Group has provided consent to earlier submission (e-mail consent is sufficient). 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., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with Sahlgrenska Translational Melanoma Group.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001005478 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00005399427 fastq.gz 2.0 GB
EGAF00005399428 fastq.gz 2.3 GB
EGAF00005399429 fastq.gz 2.3 GB
EGAF00005399430 fastq.gz 2.6 GB
EGAF00005399431 fastq.gz 2.2 GB
EGAF00005399432 fastq.gz 2.5 GB
EGAF00005399433 fastq.gz 1.9 GB
EGAF00005399434 fastq.gz 2.2 GB
EGAF00005399435 fastq.gz 2.1 GB
EGAF00005399436 fastq.gz 2.4 GB
EGAF00005399437 fastq.gz 2.4 GB
EGAF00005399438 fastq.gz 2.7 GB
EGAF00005399439 fastq.gz 2.8 GB
EGAF00005399440 fastq.gz 2.9 GB
EGAF00005399441 fastq.gz 2.7 GB
EGAF00005399442 fastq.gz 2.7 GB
EGAF00005399443 fastq.gz 2.7 GB
EGAF00005399444 fastq.gz 2.7 GB
EGAF00005399445 fastq.gz 2.6 GB
EGAF00005399446 fastq.gz 2.7 GB
EGAF00005399507 fastq.gz 512.1 MB
EGAF00005399508 fastq.gz 520.4 MB
EGAF00005399509 fastq.gz 3.0 GB
EGAF00005399510 fastq.gz 3.1 GB
EGAF00005399511 fastq.gz 632.2 MB
EGAF00005399512 fastq.gz 646.0 MB
EGAF00005399513 fastq.gz 2.4 GB
EGAF00005399514 fastq.gz 2.4 GB
EGAF00005399515 fastq.gz 1.8 GB
EGAF00005399516 fastq.gz 1.9 GB
EGAF00005399517 fastq.gz 457.6 MB
EGAF00005399518 fastq.gz 467.9 MB
EGAF00005399519 fastq.gz 519.0 MB
EGAF00005399520 fastq.gz 528.8 MB
EGAF00005399521 fastq.gz 569.2 MB
EGAF00005399522 fastq.gz 600.1 MB
EGAF00005399523 fastq.gz 1.8 GB
EGAF00005399524 fastq.gz 1.8 GB
EGAF00005399525 fastq.gz 2.5 GB
EGAF00005399526 fastq.gz 2.5 GB
EGAF00005399527 fastq.gz 1.8 MB
EGAF00005399528 fastq.gz 1.7 MB
EGAF00005399529 fastq.gz 524.3 MB
EGAF00005399530 fastq.gz 531.8 MB
EGAF00005399531 fastq.gz 1.9 GB
EGAF00005399532 fastq.gz 2.0 GB
EGAF00005399533 fastq.gz 2.6 GB
EGAF00005399534 fastq.gz 2.6 GB
EGAF00005399535 fastq.gz 2.7 GB
EGAF00005399536 fastq.gz 2.7 GB
EGAF00005399537 fastq.gz 389.9 MB
EGAF00005399538 fastq.gz 398.5 MB
EGAF00005399539 fastq.gz 402.4 MB
EGAF00005399540 fastq.gz 409.8 MB
EGAF00005399541 fastq.gz 1.5 GB
EGAF00005399542 fastq.gz 1.5 GB
EGAF00005399543 fastq.gz 1.2 GB
EGAF00005399544 fastq.gz 1.2 GB
EGAF00005399545 fastq.gz 1.8 GB
EGAF00005399546 fastq.gz 1.9 GB
EGAF00005399547 fastq.gz 2.2 GB
EGAF00005399548 fastq.gz 2.3 GB
EGAF00005399549 fastq.gz 25.6 kB
EGAF00005399550 fastq.gz 25.7 kB
EGAF00005399551 fastq.gz 1.4 GB
EGAF00005399552 fastq.gz 1.4 GB
EGAF00005399553 fastq.gz 896.0 MB
EGAF00005399554 fastq.gz 900.8 MB
EGAF00005399555 fastq.gz 921.4 MB
EGAF00005399556 fastq.gz 928.2 MB
EGAF00005399557 fastq.gz 927.8 MB
EGAF00005399558 fastq.gz 938.3 MB
EGAF00005399559 fastq.gz 1.9 GB
EGAF00005399560 fastq.gz 1.9 GB
EGAF00005399561 fastq.gz 1.5 GB
EGAF00005399562 fastq.gz 1.6 GB
EGAF00005399563 fastq.gz 1.2 GB
EGAF00005399564 fastq.gz 1.3 GB
EGAF00005399565 fastq.gz 1.9 GB
EGAF00005399566 fastq.gz 1.9 GB
EGAF00005399567 fastq.gz 869.2 MB
EGAF00005399568 fastq.gz 876.9 MB
EGAF00005399569 fastq.gz 2.2 GB
EGAF00005399570 fastq.gz 2.3 GB
EGAF00005399571 fastq.gz 1.6 GB
EGAF00005399572 fastq.gz 1.6 GB
EGAF00005399573 fastq.gz 2.1 GB
EGAF00005399574 fastq.gz 2.1 GB
EGAF00005399575 fastq.gz 865.5 MB
EGAF00005399576 fastq.gz 872.4 MB
EGAF00005399577 fastq.gz 1.8 GB
EGAF00005399578 fastq.gz 1.8 GB
EGAF00005399579 fastq.gz 2.8 GB
EGAF00005399580 fastq.gz 2.8 GB
EGAF00005399581 fastq.gz 2.6 GB
EGAF00005399582 fastq.gz 2.7 GB
EGAF00005399583 fastq.gz 2.9 GB
EGAF00005399584 fastq.gz 2.9 GB
EGAF00005399585 fastq.gz 2.9 GB
EGAF00005399586 fastq.gz 2.9 GB
EGAF00005399587 fastq.gz 2.4 GB
EGAF00005399588 fastq.gz 2.4 GB
EGAF00005399589 fastq.gz 2.7 GB
EGAF00005399590 fastq.gz 2.8 GB
EGAF00005399591 fastq.gz 3.0 GB
EGAF00005399592 fastq.gz 3.1 GB
EGAF00005399593 fastq.gz 2.6 GB
EGAF00005399594 fastq.gz 2.6 GB
EGAF00005399595 fastq.gz 1.2 GB
EGAF00005399596 fastq.gz 1.2 GB
EGAF00005399597 fastq.gz 1.4 GB
EGAF00005399598 fastq.gz 1.4 GB
EGAF00005399599 fastq.gz 1.2 GB
EGAF00005399600 fastq.gz 1.2 GB
EGAF00005399601 fastq.gz 1.2 GB
EGAF00005399602 fastq.gz 1.2 GB
EGAF00005399603 fastq.gz 1.1 GB
EGAF00005399604 fastq.gz 1.1 GB
EGAF00005399605 fastq.gz 936.3 MB
EGAF00005399606 fastq.gz 953.4 MB
EGAF00005399607 fastq.gz 1.2 GB
EGAF00005399608 fastq.gz 1.3 GB
EGAF00005399609 fastq.gz 1.4 GB
EGAF00005399610 fastq.gz 1.4 GB
EGAF00005399611 fastq.gz 1.3 GB
EGAF00005399612 fastq.gz 1.3 GB
EGAF00005399613 fastq.gz 1.3 GB
EGAF00005399614 fastq.gz 1.3 GB
EGAF00005399615 fastq.gz 1.3 GB
EGAF00005399616 fastq.gz 1.3 GB
EGAF00005399617 fastq.gz 1.4 GB
EGAF00005399618 fastq.gz 1.4 GB
EGAF00005399619 fastq.gz 1.3 GB
EGAF00005399620 fastq.gz 1.3 GB
EGAF00005399621 fastq.gz 623.0 MB
EGAF00005399622 fastq.gz 631.4 MB
EGAF00005399623 fastq.gz 90.2 MB
EGAF00005399624 fastq.gz 90.5 MB
EGAF00005399625 fastq.gz 1.2 GB
EGAF00005399626 fastq.gz 1.2 GB
EGAF00005399627 fastq.gz 991.2 MB
EGAF00005399628 fastq.gz 1.0 GB
EGAF00005399629 fastq.gz 1.2 GB
EGAF00005399630 fastq.gz 1.2 GB
EGAF00005399631 fastq.gz 2.8 GB
EGAF00005399632 fastq.gz 2.8 GB
EGAF00005399633 fastq.gz 2.6 GB
EGAF00005399634 fastq.gz 2.6 GB
EGAF00005399635 fastq.gz 2.8 GB
EGAF00005399636 fastq.gz 2.8 GB
EGAF00005399637 fastq.gz 3.4 GB
EGAF00005399638 fastq.gz 3.5 GB
EGAF00005399639 fastq.gz 3.0 GB
EGAF00005399640 fastq.gz 3.1 GB
EGAF00005399641 fastq.gz 2.6 GB
EGAF00005399642 fastq.gz 2.6 GB
EGAF00005399643 fastq.gz 2.8 GB
EGAF00005399644 fastq.gz 2.8 GB
EGAF00005399645 fastq.gz 2.7 GB
EGAF00005399646 fastq.gz 2.7 GB
EGAF00005399647 fastq.gz 2.5 GB
EGAF00005399648 fastq.gz 2.5 GB
EGAF00005399713 fastq.gz 1.1 GB
EGAF00005399714 fastq.gz 1.2 GB
EGAF00005399715 fastq.gz 92.7 MB
EGAF00005399716 fastq.gz 92.9 MB
EGAF00005399717 fastq.gz 1.3 GB
EGAF00005399718 fastq.gz 1.3 GB
EGAF00005399719 fastq.gz 968.2 MB
EGAF00005399720 fastq.gz 984.0 MB
EGAF00005399721 fastq.gz 1.2 GB
EGAF00005399722 fastq.gz 1.2 GB
EGAF00005399723 fastq.gz 1.2 GB
EGAF00005399724 fastq.gz 1.2 GB
EGAF00005399725 fastq.gz 905.5 MB
EGAF00005399726 fastq.gz 921.3 MB
EGAF00005399727 fastq.gz 1.2 GB
EGAF00005399728 fastq.gz 1.2 GB
EGAF00005399729 fastq.gz 1.3 GB
EGAF00005399730 fastq.gz 1.3 GB
EGAF00005399731 fastq.gz 1.1 GB
EGAF00005399732 fastq.gz 1.1 GB
EGAF00005399733 fastq.gz 1.4 GB
EGAF00005399734 fastq.gz 1.4 GB
EGAF00005399735 fastq.gz 1.4 GB
EGAF00005399736 fastq.gz 1.4 GB
EGAF00005399737 fastq.gz 1.3 GB
EGAF00005399738 fastq.gz 1.3 GB
EGAF00005399739 fastq.gz 598.8 MB
EGAF00005399740 fastq.gz 606.5 MB
EGAF00005399741 fastq.gz 1.2 GB
EGAF00005399742 fastq.gz 1.2 GB
EGAF00005399743 fastq.gz 1.3 GB
EGAF00005399744 fastq.gz 1.3 GB
EGAF00005399745 fastq.gz 1.2 GB
EGAF00005399746 fastq.gz 1.2 GB
EGAF00005399747 fastq.gz 1.4 GB
EGAF00005399748 fastq.gz 1.4 GB
EGAF00005399749 fastq.gz 1.7 GB
EGAF00005399750 fastq.gz 1.8 GB
EGAF00005399751 fastq.gz 1.6 GB
EGAF00005399752 fastq.gz 1.6 GB
EGAF00005399753 fastq.gz 1.5 GB
EGAF00005399754 fastq.gz 1.5 GB
EGAF00005399755 fastq.gz 1.5 GB
EGAF00005399756 fastq.gz 1.6 GB
EGAF00005399757 fastq.gz 1.6 GB
EGAF00005399758 fastq.gz 1.6 GB
EGAF00005399759 fastq.gz 1.5 GB
EGAF00005399760 fastq.gz 1.6 GB
EGAF00005399761 fastq.gz 1.6 GB
EGAF00005399762 fastq.gz 1.7 GB
EGAF00005399763 fastq.gz 1.6 GB
EGAF00005399764 fastq.gz 1.7 GB
214 Files (350.4 GB)