Need Help?

Genetic Basis of Hepatosplenic T Cell Lymphoma (HSTL)

Whole exome sequencing of hepatosplenic T cell lymphoma (HSTL) tumors, paired normals, and cell lines, including (1) 68 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL tumor samples, (2) 20 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL paired normal samples, and (3) 2 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL cell lines.

Request Access

Data access agreement for HSTL

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 Authorized Personnel: The individuals at the User Institution to whom DAC for Dave Lab, Duke University 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 Authorized Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: DAC for Dave Lab, Duke University and the collaborators listed in Appendix I responsible for the development, organization, 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. ? 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Non-Profit 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 Authorized 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 recognizing 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 analyzing 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 Organization 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 DAC for Dave Lab, Duke University within 30 days of any changes or departures of Authorized Personnel. 13. The User Institution will notify DAC for Dave Lab, Duke University prior to any significant changes to the protocol for the Project. 14. The User Institution will notify DAC for Dave Lab, Duke University as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. DAC for Dave Lab, Duke University 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. 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 Authorized Personnel. The User Institution will procure that the Authorized 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 England and Wales and shall be subject to the exclusive jurisdiction of the English 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 DAC for Dave Lab, Duke University 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) Study ID: EGAS00001002182 Study title: Genetic Basis of Hepatosplenic T Cell Lymphoma (HSTL) Dataset ID: EGAD00001003246 Name of project that created the dataset Genetics of hepatosplenic T cell lymphoma Names of other data producers/collaborators N/A Specific limitations on areas of research Non-profit use only. Commercial entities are forbidden from access to the data. 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 screen locks (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 – PUBLICATION POLICY DAC for Dave Lab, Duke University 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. DAC for Dave Lab, Duke University 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 3 months after these data were first made available on the relevant hosting database. 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., EGAS00001002182), and acknowledge its use in a form agreed by the User Institution with DAC for Dave Lab, Duke University.

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
EGAS00001002182 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
EGAF00001433805 bam 8.0 GB
EGAF00001433806 bam 5.3 GB
EGAF00001433807 bam 11.1 GB
EGAF00001433808 bam 17.6 GB
EGAF00001433809 bam 4.2 GB
EGAF00001433810 bam 87.9 MB
EGAF00001433811 bam 11.8 GB
EGAF00001433812 bam 18.7 GB
EGAF00001433813 bam 944.4 MB
EGAF00001433814 bam 667.7 MB
EGAF00001433815 bam 3.4 GB
EGAF00001433816 bam 53.9 GB
EGAF00001433817 bam 22.4 MB
EGAF00001433818 bam 624.0 MB
EGAF00001433819 bam 920.9 MB
EGAF00001433820 bam 2.5 GB
EGAF00001433821 bam 6.4 GB
EGAF00001433822 bam 4.5 GB
EGAF00001433823 bam 10.8 GB
EGAF00001433824 bam 541.7 MB
EGAF00001433825 bam 5.5 GB
EGAF00001433826 bam 7.6 GB
EGAF00001433827 bam 13.2 GB
EGAF00001433828 bam 15.3 GB
EGAF00001433829 bam 10.6 GB
EGAF00001433830 bam 15.3 GB
EGAF00001433831 bam 12.1 GB
EGAF00001433832 bam 13.1 GB
EGAF00001433833 bam 6.2 GB
EGAF00001433834 bam 12.6 GB
EGAF00001433835 bam 12.7 GB
EGAF00001433836 bam 9.3 GB
EGAF00001433837 bam 12.9 GB
EGAF00001433838 bam 8.7 GB
EGAF00001433839 bam 12.7 GB
EGAF00001433840 bam 14.0 GB
EGAF00001433841 bam 14.3 GB
EGAF00001433842 bam 9.9 GB
EGAF00001433843 bam 21.0 GB
EGAF00001433844 bam 13.9 GB
EGAF00001433845 bam 14.7 GB
EGAF00001433846 bam 5.8 GB
EGAF00001433847 bam 29.5 GB
EGAF00001433848 bam 13.3 GB
EGAF00001433849 bam 4.4 GB
EGAF00001433850 bam 21.1 GB
EGAF00001433851 bam 8.3 GB
EGAF00001433852 bam 18.7 GB
EGAF00001433853 bam 1.8 GB
EGAF00001433854 bam 10.2 GB
EGAF00001433855 bam 12.2 GB
EGAF00001433856 bam 5.7 GB
EGAF00001433857 bam 5.4 GB
EGAF00001433858 bam 6.4 GB
EGAF00001433859 bam 656.3 MB
EGAF00001433860 bam 9.4 GB
EGAF00001433861 bam 720.0 MB
EGAF00001433862 bam 1.9 GB
EGAF00001433863 bam 6.1 GB
EGAF00001433864 bam 3.1 GB
EGAF00001433865 bam 324.2 MB
EGAF00001433866 bam 13.0 GB
EGAF00001433867 bam 5.4 GB
EGAF00001433868 bam 4.6 GB
EGAF00001433869 bam 8.4 GB
EGAF00001433870 bam 10.4 GB
EGAF00001433871 bam 8.7 GB
EGAF00001433872 bam 6.7 GB
EGAF00001433873 bam 10.0 GB
EGAF00001433874 bam 9.5 GB
EGAF00001433875 bam 8.3 GB
EGAF00001433876 bam 7.0 GB
EGAF00001433877 bam 3.0 GB
EGAF00001433878 bam 6.5 GB
EGAF00001433879 bam 6.4 GB
EGAF00001433880 bam 5.7 GB
EGAF00001433881 bam 5.6 GB
EGAF00001433882 bam 1.9 GB
EGAF00001433883 bam 3.5 GB
EGAF00001433884 bam 1.3 GB
EGAF00001433885 bam 142.3 MB
EGAF00001433886 bam 2.8 GB
EGAF00001433887 bam 2.8 GB
EGAF00001433888 bam 1.3 GB
EGAF00001433889 bam 5.6 GB
EGAF00001433890 bam 6.7 GB
EGAF00001433891 bam 720.6 MB
EGAF00001433892 bam 9.9 GB
EGAF00001433893 bam 9.4 GB
EGAF00001433894 bam 10.4 GB
90 Files (758.3 GB)