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Genomic analysis of pancreatic neuroendocrine tumour with MEN1, ATRX, or DAXX mutations

This dataset includes 52 samples from 19 individuals with pancreatic neuroendocrine tumours. These samples were analyzed using RNA-sequencing, whole-exome sequencing, shallow (~0.3x) whole-genome sequencing, and a 21-gene panel targeted capture sequencing. Everything was sequenced using the Illumina HiSeq and is provided in BAM or FASTQ format.

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Access to data generated by UHN is made available by completing the data access agreement for review by the data access committee and will be granted to qualified investigators for appropriate use.

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 the Data Access Committee (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 Principal Investigator 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. University Health Network: The University Health Network (UHN) is the largest clinical and research hospital in Canada. UHN is affiliated with the University of Toronto and is a member of the Toronto Academic Health Science Network. 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 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. 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. 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 province of Ontario and PHIPA. 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 The Data Access Committee Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY

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
EGAS00001004239 Cancer Genomics

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
EGAF00003448758 fastq.gz 352.5 MB
EGAF00003448759 fastq.gz 370.2 MB
EGAF00003448760 fastq.gz 348.2 MB
EGAF00003448761 fastq.gz 363.2 MB
EGAF00003448762 fastq.gz 345.6 MB
EGAF00003448763 fastq.gz 331.6 MB
EGAF00003448764 fastq.gz 344.5 MB
EGAF00003448765 fastq.gz 360.9 MB
EGAF00003448766 fastq.gz 321.6 MB
EGAF00003448767 fastq.gz 336.7 MB
EGAF00003448768 bam 1.1 GB
EGAF00003448769 bam 1.2 GB
EGAF00003448770 bam 1.5 GB
EGAF00003448771 bam 17.0 GB
EGAF00003448772 bam 26.1 GB
EGAF00003448773 fastq.gz 14.4 GB
EGAF00003448774 fastq.gz 13.5 GB
EGAF00003448775 fastq.gz 2.7 GB
EGAF00003448776 fastq.gz 2.7 GB
EGAF00003448777 fastq.gz 18.8 GB
EGAF00003448778 fastq.gz 18.6 GB
EGAF00003448779 fastq.gz 7.3 GB
EGAF00003448780 fastq.gz 7.1 GB
EGAF00003448782 fastq.gz 9.9 GB
EGAF00003448783 bam 25.5 GB
EGAF00003448784 bam 26.7 GB
EGAF00003448785 fastq.gz 10.1 GB
EGAF00003448786 fastq.gz 9.9 GB
EGAF00003448787 fastq.gz 12.2 GB
EGAF00003448788 fastq.gz 12.1 GB
EGAF00003448789 fastq.gz 15.3 GB
EGAF00003448790 fastq.gz 4.4 GB
EGAF00003448791 fastq.gz 2.0 GB
EGAF00003448792 fastq.gz 1.9 GB
EGAF00003448793 bam 1.3 GB
EGAF00003448794 fastq.gz 2.5 GB
EGAF00003448795 fastq.gz 2.5 GB
EGAF00003448796 fastq.gz 345.8 MB
EGAF00003448797 fastq.gz 329.4 MB
EGAF00003448798 bam 1.2 GB
EGAF00003448799 bam 1.5 GB
EGAF00003448800 fastq.gz 307.9 MB
EGAF00003448801 fastq.gz 323.7 MB
EGAF00003448802 fastq.gz 334.7 MB
EGAF00003448803 fastq.gz 350.0 MB
EGAF00003448804 fastq.gz 468.1 MB
EGAF00003448805 fastq.gz 450.0 MB
EGAF00003448806 fastq.gz 319.7 MB
EGAF00003448807 fastq.gz 334.1 MB
EGAF00003448808 bam 1.2 GB
EGAF00003448809 bam 1.1 GB
EGAF00003448810 bam 1.1 GB
EGAF00003448811 fastq.gz 384.2 MB
EGAF00003448812 fastq.gz 368.2 MB
EGAF00003448813 fastq.gz 340.0 MB
EGAF00003448814 fastq.gz 354.8 MB
EGAF00003448815 fastq.gz 371.5 MB
EGAF00003448816 fastq.gz 356.4 MB
EGAF00003448817 fastq.gz 339.8 MB
EGAF00003448818 fastq.gz 325.0 MB
EGAF00003448819 fastq.gz 362.2 MB
EGAF00003448820 fastq.gz 378.2 MB
EGAF00003448821 bam 1.2 GB
EGAF00003448822 bam 1.6 GB
EGAF00003448823 bam 1.2 GB
EGAF00003448824 bam 1.1 GB
EGAF00003448825 bam 976.5 MB
EGAF00003448826 bam 1.0 GB
EGAF00003448827 bam 1.0 GB
EGAF00003448828 bam 1.2 GB
EGAF00003448829 bam 1.4 GB
EGAF00003448830 bam 1.2 GB
EGAF00003448831 bam 1.2 GB
EGAF00003448832 bam 1.3 GB
EGAF00003448833 bam 1.3 GB
EGAF00003448834 bam 1.2 GB
76 Files (301.9 GB)