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Investigating differential diagnostic and prognostic biomarkers in primary cutaneous follicle center lymphoma and follicular lymphoma using low-coverage whole-genome sequencing

In this study, we analyzed 28 primary cutaneous follicle center lymphoma samples from 20 patients and compared the copy number profiles to a cohort of diagnostic samples of 64 nodal follicular lymphoma patients using low-coverage whole genome sequencing (lcWGS).

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Data Access Policy for "Investigating differential diagnostic and prognostic biomarkers in primary cutaneous follicle center lymphoma and follicular lymphoma using low-coverage whole-genome sequencing" project.

Data Access Policy of the HCEMM-SU Molecular Oncohematology Research Group based on EGA template. 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 HCEMM-Semmelweis University – Molecular Oncohematology Research Group 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: HCEMM-Semmelweis University – Molecular Oncohematology Research Group 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. HCEMM-Semmelweis University – Molecular Oncohematology Research Group: Research Group, located at the Semmelweis University, Department of Pathology and Experimental Cancer Research, H-1085, Budapest, Üllői út 26, Hungary. Head: Professor Csaba Bödör. 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 HCEMM-Semmelweis University – Molecular Oncohematology Research Group within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify HCEMM-Semmelweis University – Molecular Oncohematology Research Group prior to any significant changes to the protocol for the Project. 14. The User Institution will notify HCEMM-Semmelweis University – Molecular Oncohematology Research Group as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. HCEMM-Semmelweis University – Molecular Oncohematology Research 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 HCEMM-Semmelweis University – Molecular Oncohematology Research 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. 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 HCEMM-Semmelweis University – Molecular Oncohematology Research Group Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS (to be completed by the data producer before passing to applicant) Dataset reference (EGA Study ID and Dataset Details) Name of project that created the dataset Investigating differential diagnostic and prognostic biomarkers in primary cutaneous follicle center lymphoma and follicular lymphoma using low-coverage whole-genome sequencing Names of other data producers/collaborators HCEMM – SU Molecular Oncohematology Research Group, Semmelweis University, Department of Pathology and Experimental Cancer Research, Budapest, Hungary Specific limitations on areas of research Minimum protection measures required User Institution and Authorized Users cannot share the files with other external collaborators unless obtaining specific approval by the DAC. Raw Files shall not be uploaded in any other database. 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 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 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 HCEMM-Semmelweis University – Molecular Oncohematology Research 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
EGAS50000000141 Whole Genome Sequencing

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
EGAF50000063640 fastq.gz 223.4 MB
EGAF50000063641 fastq.gz 224.6 MB
EGAF50000063642 fastq.gz 211.5 MB
EGAF50000063643 fastq.gz 207.5 MB
EGAF50000063644 fastq.gz 220.3 MB
EGAF50000063645 fastq.gz 216.0 MB
EGAF50000063646 fastq.gz 193.7 MB
EGAF50000063647 fastq.gz 157.7 MB
EGAF50000063648 fastq.gz 189.0 MB
EGAF50000063649 fastq.gz 158.6 MB
EGAF50000063650 fastq.gz 298.2 MB
EGAF50000063651 fastq.gz 297.6 MB
EGAF50000063652 fastq.gz 231.2 MB
EGAF50000063653 fastq.gz 227.7 MB
EGAF50000063654 fastq.gz 183.6 MB
EGAF50000063655 fastq.gz 180.6 MB
EGAF50000063656 fastq.gz 145.3 MB
EGAF50000063657 fastq.gz 144.9 MB
EGAF50000063658 fastq.gz 192.1 MB
EGAF50000063659 fastq.gz 191.5 MB
EGAF50000063660 fastq.gz 179.0 MB
EGAF50000063661 fastq.gz 134.7 MB
EGAF50000063662 fastq.gz 176.5 MB
EGAF50000063663 fastq.gz 134.5 MB
EGAF50000063664 fastq.gz 110.1 MB
EGAF50000063665 fastq.gz 110.0 MB
EGAF50000063666 fastq.gz 122.4 MB
EGAF50000063667 fastq.gz 119.7 MB
EGAF50000063668 fastq.gz 224.6 MB
EGAF50000063669 fastq.gz 220.6 MB
EGAF50000063670 fastq.gz 170.8 MB
EGAF50000063671 fastq.gz 169.5 MB
EGAF50000063672 fastq.gz 217.1 MB
EGAF50000063673 fastq.gz 219.8 MB
EGAF50000063674 fastq.gz 165.3 MB
EGAF50000063675 fastq.gz 164.2 MB
EGAF50000063676 fastq.gz 295.0 MB
EGAF50000063677 fastq.gz 294.0 MB
EGAF50000063678 fastq.gz 115.6 MB
EGAF50000063679 fastq.gz 112.0 MB
EGAF50000063680 fastq.gz 226.0 MB
EGAF50000063681 fastq.gz 226.8 MB
EGAF50000063682 fastq.gz 222.9 MB
EGAF50000063683 fastq.gz 209.3 MB
EGAF50000063684 fastq.gz 217.5 MB
EGAF50000063685 fastq.gz 195.7 MB
EGAF50000063686 fastq.gz 212.4 MB
EGAF50000063687 fastq.gz 159.3 MB
EGAF50000063688 fastq.gz 195.6 MB
EGAF50000063689 fastq.gz 157.9 MB
EGAF50000063690 fastq.gz 189.5 MB
EGAF50000063691 fastq.gz 188.8 MB
EGAF50000063692 fastq.gz 209.6 MB
EGAF50000063693 fastq.gz 217.3 MB
EGAF50000063694 fastq.gz 266.5 MB
EGAF50000063695 fastq.gz 260.2 MB
EGAF50000063696 fastq.gz 170.7 MB
EGAF50000063697 fastq.gz 175.6 MB
EGAF50000063698 fastq.gz 217.5 MB
EGAF50000063699 fastq.gz 219.1 MB
EGAF50000063700 fastq.gz 166.4 MB
EGAF50000063701 fastq.gz 165.0 MB
EGAF50000063702 fastq.gz 151.3 MB
EGAF50000063703 fastq.gz 153.4 MB
EGAF50000063704 fastq.gz 187.2 MB
EGAF50000063705 fastq.gz 184.6 MB
EGAF50000063706 fastq.gz 234.7 MB
EGAF50000063707 fastq.gz 166.3 MB
EGAF50000063708 fastq.gz 236.6 MB
EGAF50000063709 fastq.gz 162.8 MB
EGAF50000063710 fastq.gz 216.0 MB
EGAF50000063711 fastq.gz 211.9 MB
EGAF50000063712 fastq.gz 163.8 MB
EGAF50000063713 fastq.gz 160.5 MB
EGAF50000063714 fastq.gz 191.6 MB
EGAF50000063715 fastq.gz 188.8 MB
EGAF50000063716 fastq.gz 255.2 MB
EGAF50000063717 fastq.gz 251.0 MB
EGAF50000063718 fastq.gz 188.7 MB
EGAF50000063719 fastq.gz 193.8 MB
EGAF50000063720 fastq.gz 206.8 MB
EGAF50000063721 fastq.gz 206.2 MB
EGAF50000063722 fastq.gz 160.4 MB
EGAF50000063723 fastq.gz 159.8 MB
EGAF50000063724 fastq.gz 217.5 MB
EGAF50000063725 fastq.gz 214.2 MB
EGAF50000063726 fastq.gz 179.6 MB
EGAF50000063727 fastq.gz 176.7 MB
EGAF50000063728 fastq.gz 252.4 MB
EGAF50000063729 fastq.gz 250.6 MB
EGAF50000063730 fastq.gz 123.8 MB
EGAF50000063731 fastq.gz 124.5 MB
EGAF50000063732 fastq.gz 160.8 MB
EGAF50000063733 fastq.gz 162.0 MB
EGAF50000063734 fastq.gz 137.9 MB
EGAF50000063735 fastq.gz 98.4 MB
EGAF50000063736 fastq.gz 137.7 MB
EGAF50000063737 fastq.gz 96.9 MB
EGAF50000063738 fastq.gz 214.6 MB
EGAF50000063739 fastq.gz 207.5 MB
EGAF50000063740 fastq.gz 234.3 MB
EGAF50000063741 fastq.gz 236.5 MB
EGAF50000063742 fastq.gz 181.9 MB
EGAF50000063743 fastq.gz 176.1 MB
EGAF50000063744 fastq.gz 160.9 MB
EGAF50000063745 fastq.gz 161.1 MB
EGAF50000063746 fastq.gz 231.7 MB
EGAF50000063747 fastq.gz 225.9 MB
EGAF50000063748 fastq.gz 210.6 MB
EGAF50000063749 fastq.gz 205.9 MB
EGAF50000063750 fastq.gz 206.4 MB
EGAF50000063751 fastq.gz 204.6 MB
EGAF50000063752 fastq.gz 220.5 MB
EGAF50000063753 fastq.gz 216.6 MB
EGAF50000063754 fastq.gz 215.5 MB
EGAF50000063755 fastq.gz 214.4 MB
EGAF50000063756 fastq.gz 228.0 MB
EGAF50000063757 fastq.gz 227.6 MB
EGAF50000063758 fastq.gz 219.0 MB
EGAF50000063759 fastq.gz 218.7 MB
EGAF50000063760 fastq.gz 214.4 MB
EGAF50000063761 fastq.gz 213.6 MB
EGAF50000063762 fastq.gz 238.3 MB
EGAF50000063763 fastq.gz 138.1 MB
EGAF50000063764 fastq.gz 241.3 MB
EGAF50000063765 fastq.gz 139.6 MB
EGAF50000063766 fastq.gz 271.6 MB
EGAF50000063767 fastq.gz 269.5 MB
EGAF50000063768 fastq.gz 195.8 MB
EGAF50000063769 fastq.gz 197.3 MB
EGAF50000063770 fastq.gz 240.4 MB
EGAF50000063771 fastq.gz 249.3 MB
EGAF50000063772 fastq.gz 186.8 MB
EGAF50000063773 fastq.gz 187.7 MB
EGAF50000063774 fastq.gz 157.1 MB
EGAF50000063775 fastq.gz 163.4 MB
EGAF50000063776 fastq.gz 198.9 MB
EGAF50000063777 fastq.gz 195.7 MB
EGAF50000063778 fastq.gz 212.1 MB
EGAF50000063779 fastq.gz 208.6 MB
EGAF50000063780 fastq.gz 136.2 MB
EGAF50000063781 fastq.gz 140.2 MB
EGAF50000063782 fastq.gz 172.9 MB
EGAF50000063783 fastq.gz 169.8 MB
EGAF50000063784 fastq.gz 565.7 MB
EGAF50000063785 fastq.gz 238.2 MB
EGAF50000063786 fastq.gz 239.6 MB
EGAF50000063787 fastq.gz 251.2 MB
EGAF50000063788 fastq.gz 249.8 MB
EGAF50000063789 fastq.gz 271.4 MB
EGAF50000063790 fastq.gz 276.2 MB
EGAF50000063791 fastq.gz 218.1 MB
EGAF50000063792 fastq.gz 228.7 MB
EGAF50000063793 fastq.gz 225.1 MB
EGAF50000063794 fastq.gz 224.0 MB
EGAF50000063795 fastq.gz 579.7 MB
EGAF50000063796 fastq.gz 160.9 MB
EGAF50000063797 fastq.gz 161.3 MB
EGAF50000063798 fastq.gz 247.5 MB
EGAF50000063799 fastq.gz 244.3 MB
EGAF50000063800 fastq.gz 170.9 MB
EGAF50000063801 fastq.gz 170.8 MB
EGAF50000063802 fastq.gz 255.0 MB
EGAF50000063803 fastq.gz 158.5 MB
EGAF50000063804 fastq.gz 258.0 MB
EGAF50000063805 fastq.gz 165.2 MB
EGAF50000063806 fastq.gz 244.8 MB
EGAF50000063807 fastq.gz 403.7 MB
EGAF50000063808 fastq.gz 243.5 MB
EGAF50000063809 fastq.gz 288.2 MB
EGAF50000063810 fastq.gz 294.9 MB
EGAF50000063811 fastq.gz 211.1 MB
EGAF50000063812 fastq.gz 212.3 MB
EGAF50000063813 fastq.gz 298.9 MB
EGAF50000063814 fastq.gz 296.2 MB
EGAF50000063815 fastq.gz 546.7 MB
EGAF50000063816 fastq.gz 535.0 MB
EGAF50000063817 fastq.gz 426.6 MB
EGAF50000063818 fastq.gz 415.6 MB
179 Files (37.9 GB)