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Cancer Alliance WGS

Whole genome sequencing for individualized cancer interpretation

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Cancer Alliance Data Access Committee

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 New York Genome Center 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: New York Genome Center generated these Data in the course of a collaborative research study funded in part by International Business Machines. 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. New York Genome Center: The Institution that submitted the Data to European Genome-Phenome Archive. 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 ) and 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 New York Genome Center within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify New York Genome Center prior to any significant changes to the protocol for the Project. 14. The User Institution will notify New York Genome Center as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. New York Genome Center 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 New York Genome Center to alter the terms of this agreement from time to time. In the event that changes are required, New York Genome Center 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 require that the Authorised 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 the United States and shall be subject to the exclusive jurisdiction of the United States courts. 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 New York Genome Center Signature: Name: Title: 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): EGAS00001004013 180 Exome sequencing samples 168 RNA sequencing samples 187 Whole genome sequencing samples Name of project that created the dataset: Whole genome, exome and transcriptome analysis to guide individualized cancer interpretation. Names of other data producers/collaborators: The Data were generated by New York Genome Center in the course of a collaborative research study funded in part by International Business Machines. The following institutions collaborated in the study: Albert Einstein College of Medicine (New York) Columbia University Medical Center/New York Presbyterian Hospital Memorial Sloan Kettering Cancer Center Mount Sinai School of Medicine New York University Northwell Health The Rockefeller University The State University of New York at Stony Brook Weill Cornell Medicine Specific limitations on areas of research: Data access is limited to use for non-commercial research or academic purposes. Use for commercial purposes is prohibited. Minimum protection measures required: User Institution must follow, as a minimum standard, the NIH Best Practices for Controlled-Access Data Subject to the NIH Genomic Data Sharing Policy (https://osp.od.nih.gov/wp-content/uploads/NIH_Best_Practices_for_Controlled-Access_Data_Subject_to_the_NIH_GDS_Policy.pdf). The use of cloud computing systems must meet the data use and security standards outlined in the NIH Position Statement on Use of Cloud Computing Services for Storage and Analysis of Controlled-Access Data Subject to the NIH Genomic Data Sharing Policy (https://gds.nih.gov/pdf/NIH_Position_Statement_on_Cloud_Computing.pdf). File access: Data can be held in unencrypted files on an institutional compute system, with a role-based access system and protected behind a secure firewall. Data can be held in a cloud environment, on an encrypted filesystem, with role-based access controls and protected behind a secure firewall. Laptops holding these data should have encrypted hard drives, password protected logins and screenlocks. 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 has 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 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 New York Genome Center.

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
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
EGAF00002860420 bam 165.4 GB
EGAF00002860421 bai 9.1 MB
EGAF00002860422 bam 290.7 GB
EGAF00002860423 bai 9.8 MB
EGAF00002860424 bam 156.8 GB
EGAF00002860425 bai 9.1 MB
EGAF00002860426 bam 308.0 GB
EGAF00002860427 bai 9.7 MB
EGAF00002860428 bam 157.3 GB
EGAF00002860429 bai 9.1 MB
EGAF00002860430 bam 338.8 GB
EGAF00002860431 bai 9.7 MB
EGAF00002860432 bam 165.7 GB
EGAF00002860433 bai 9.0 MB
EGAF00002860434 bam 420.9 GB
EGAF00002860435 bai 9.9 MB
EGAF00002860436 bam 146.8 GB
EGAF00002860437 bai 9.0 MB
EGAF00002860438 bam 319.6 GB
EGAF00002860439 bai 9.5 MB
EGAF00002860440 bam 131.1 GB
EGAF00002860441 bai 8.9 MB
EGAF00002860442 bam 350.8 GB
EGAF00002860443 bai 9.5 MB
EGAF00002860444 bam 174.3 GB
EGAF00002860445 bai 9.0 MB
EGAF00002860446 bam 277.3 GB
EGAF00002860447 bai 9.2 MB
EGAF00002860448 bam 141.0 GB
EGAF00002860449 bai 8.9 MB
EGAF00002860450 bam 341.6 GB
EGAF00002860451 bai 9.4 MB
EGAF00002860452 bam 130.6 GB
EGAF00002860453 bai 8.9 MB
EGAF00002860454 bam 327.4 GB
EGAF00002860455 bai 9.4 MB
EGAF00002860456 bam 141.5 GB
EGAF00002860457 bai 8.9 MB
EGAF00002860458 bam 301.1 GB
EGAF00002860459 bai 9.3 MB
EGAF00002860460 bam 144.5 GB
EGAF00002860461 bai 8.9 MB
EGAF00002860462 bam 294.8 GB
EGAF00002860463 bai 9.3 MB
EGAF00002860464 bam 134.6 GB
EGAF00002860465 bai 8.9 MB
EGAF00002860466 bam 271.1 GB
EGAF00002860467 bai 9.4 MB
EGAF00002860468 bam 187.6 GB
EGAF00002860469 bai 9.1 MB
EGAF00002860470 bam 322.2 GB
EGAF00002860471 bai 9.4 MB
EGAF00002860472 bam 144.9 GB
EGAF00002860473 bai 8.9 MB
EGAF00002860474 bam 325.1 GB
EGAF00002860475 bai 9.4 MB
EGAF00002860476 bam 138.4 GB
EGAF00002860477 bai 8.9 MB
EGAF00002860478 bam 286.3 GB
EGAF00002860479 bai 9.5 MB
EGAF00002860480 bam 142.7 GB
EGAF00002860481 bai 8.9 MB
EGAF00002860482 bam 11.2 GB
EGAF00002860483 bai 5.4 MB
EGAF00002860484 bam 9.7 GB
EGAF00002860485 bai 5.2 MB
EGAF00002860486 bam 13.7 GB
EGAF00002860487 bai 6.5 MB
EGAF00002860488 bam 352.0 GB
EGAF00002860489 bai 9.7 MB
EGAF00002860490 bam 173.1 GB
EGAF00002860491 bai 9.0 MB
EGAF00002860492 bam 338.9 GB
EGAF00002860493 bai 9.7 MB
EGAF00002860494 bam 205.6 GB
EGAF00002860495 bai 9.2 MB
EGAF00002860496 bam 382.0 GB
EGAF00002860497 bai 9.7 MB
EGAF00002860498 bam 201.8 GB
EGAF00002860499 bai 9.1 MB
EGAF00002860500 bam 391.4 GB
EGAF00002860501 bai 10.0 MB
EGAF00002860502 bam 272.6 GB
EGAF00002860503 bai 9.5 MB
EGAF00002860504 bam 413.3 GB
EGAF00002860505 bai 9.9 MB
EGAF00002860506 bam 234.9 GB
EGAF00002860507 bai 9.2 MB
EGAF00002860508 bam 298.3 GB
EGAF00002860509 bai 9.3 MB
EGAF00002860510 bam 146.0 GB
EGAF00002860511 bai 8.9 MB
EGAF00002860512 bam 306.3 GB
EGAF00002860513 bai 9.4 MB
EGAF00002860514 bam 150.7 GB
EGAF00002860515 bai 8.9 MB
EGAF00002860516 bam 271.1 GB
EGAF00002860517 bai 9.3 MB
EGAF00002860518 bam 151.9 GB
EGAF00002860519 bai 8.9 MB
EGAF00002860520 bam 319.5 GB
EGAF00002860521 bai 9.5 MB
EGAF00002860522 bam 11.5 GB
EGAF00002860523 bai 6.2 MB
EGAF00002860524 bam 9.1 GB
EGAF00002860525 bai 5.6 MB
EGAF00002860526 bam 12.0 GB
EGAF00002860527 bai 5.6 MB
EGAF00002860528 bam 9.8 GB
EGAF00002860529 bai 5.2 MB
EGAF00002860530 bam 9.7 GB
EGAF00002860531 bai 5.2 MB
EGAF00002860532 bam 11.3 GB
EGAF00002860533 bai 5.6 MB
EGAF00002860534 bam 10.8 GB
EGAF00002860535 bai 5.4 MB
EGAF00002860536 bam 11.1 GB
EGAF00002860537 bai 5.8 MB
EGAF00002860538 bam 10.9 GB
EGAF00002860539 bai 5.3 MB
EGAF00002860540 bam 11.0 GB
EGAF00002860541 bai 5.3 MB
EGAF00002860542 bam 10.6 GB
EGAF00002860543 bai 5.0 MB
EGAF00002860544 bam 9.8 GB
EGAF00002860545 bai 4.7 MB
EGAF00002860546 bam 9.6 GB
EGAF00002860547 bai 5.6 MB
EGAF00002860548 bam 10.5 GB
EGAF00002860549 bai 6.4 MB
EGAF00002860550 bam 10.1 GB
EGAF00002860551 bai 6.1 MB
EGAF00002860552 bam 10.8 GB
EGAF00002860553 bai 6.1 MB
EGAF00002860554 bam 12.0 GB
EGAF00002860555 bai 5.5 MB
EGAF00002860556 bam 138.5 GB
EGAF00002860557 bai 8.9 MB
EGAF00002860558 bam 373.1 GB
EGAF00002860559 bai 9.7 MB
EGAF00002860560 bam 162.0 GB
EGAF00002860561 bai 9.0 MB
EGAF00002860562 bam 307.8 GB
EGAF00002860563 bai 9.4 MB
EGAF00002860564 bam 232.6 GB
EGAF00002860565 bai 9.2 MB
EGAF00002860566 bam 358.6 GB
EGAF00002860567 bai 9.6 MB
EGAF00002860568 bam 189.2 GB
EGAF00002860569 bai 9.1 MB
EGAF00002860570 bam 322.8 GB
EGAF00002860571 bai 9.4 MB
EGAF00002860572 bam 159.7 GB
EGAF00002860573 bai 9.0 MB
EGAF00002860574 bam 333.8 GB
EGAF00002860575 bai 9.5 MB
EGAF00002860576 bam 174.0 GB
EGAF00002860577 bai 9.0 MB
EGAF00002860578 bam 360.0 GB
EGAF00002860579 bai 9.6 MB
EGAF00002860580 bam 210.8 GB
EGAF00002860581 bai 9.1 MB
EGAF00002860582 bam 331.2 GB
EGAF00002860583 bai 9.6 MB
EGAF00002860584 bam 197.0 GB
EGAF00002860585 bai 9.1 MB
EGAF00002860586 bam 353.8 GB
EGAF00002860587 bai 9.5 MB
EGAF00002860588 bam 161.7 GB
EGAF00002860589 bai 9.0 MB
EGAF00002860590 bam 10.4 GB
EGAF00002860591 bai 5.8 MB
EGAF00002860592 bam 10.1 GB
EGAF00002860593 bai 5.7 MB
EGAF00002860624 bam 420.0 GB
EGAF00002860625 bai 9.7 MB
EGAF00002860626 bam 177.0 GB
EGAF00002860627 bai 9.0 MB
EGAF00002860628 bam 337.7 GB
EGAF00002860629 bai 9.6 MB
EGAF00002860630 bam 194.0 GB
EGAF00002860631 bai 9.0 MB
EGAF00002860632 bam 233.7 GB
EGAF00002860633 bai 9.1 MB
EGAF00002860634 bam 148.8 GB
EGAF00002860635 bai 8.9 MB
EGAF00002860636 bam 318.3 GB
EGAF00002860637 bai 9.2 MB
EGAF00002860638 bam 135.7 GB
EGAF00002860639 bai 8.9 MB
EGAF00002860640 bam 370.5 GB
EGAF00002860641 bai 9.7 MB
EGAF00002860642 bam 163.8 GB
EGAF00002860643 bai 9.0 MB
EGAF00002860644 bam 440.9 GB
EGAF00002860645 bai 9.9 MB
EGAF00002860646 bam 232.3 GB
EGAF00002860647 bai 9.2 MB
EGAF00002860648 bam 409.6 GB
EGAF00002860649 bai 9.8 MB
EGAF00002860650 bam 149.4 GB
EGAF00002860651 bai 9.0 MB
EGAF00002860652 bam 330.2 GB
EGAF00002860653 bai 9.5 MB
EGAF00002860654 bam 162.4 GB
EGAF00002860655 bai 9.0 MB
EGAF00002860656 bam 318.1 GB
EGAF00002860657 bai 9.5 MB
EGAF00002860846 bam 150.5 GB
EGAF00002860847 bai 8.9 MB
EGAF00002860848 bam 311.2 GB
EGAF00002860849 bai 9.5 MB
EGAF00002860850 bam 157.9 GB
EGAF00002860851 bai 9.0 MB
EGAF00002860852 bam 319.6 GB
EGAF00002860853 bai 9.4 MB
EGAF00002860854 bam 146.4 GB
EGAF00002860855 bai 8.9 MB
EGAF00002860856 bam 338.2 GB
EGAF00002860857 bai 9.6 MB
EGAF00002860858 bam 168.9 GB
EGAF00002860859 bai 9.0 MB
EGAF00002860860 bam 350.6 GB
EGAF00002860861 bai 9.6 MB
EGAF00002860862 bam 196.4 GB
EGAF00002860863 bai 9.0 MB
EGAF00002860864 bam 304.1 GB
EGAF00002860865 bai 9.4 MB
EGAF00002860866 bam 166.2 GB
EGAF00002860867 bai 9.0 MB
EGAF00002860868 bam 323.2 GB
EGAF00002860869 bai 9.8 MB
232 Files (23.9 TB)