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Berlin Neuroblastoma Patient Genomic Data from Targeted Sequencing for Detection of TERT rearrangement breakpoints to monitor neuroblastoma

Our objective was to establish a liquid biopsy-based monitoring strategy for pediatric high-risk neuroblastomas that are harboring genomic TERT rearrangements at diagnosis. TERT rearrangement breakpoints are detected by a hybrid capture-based neuroblastoma DNA panel sequencing (published in PMID: 34442335) in tumor material and are reflected in cell-free tumor DNA and can serve as robust biomarkers for disease activity. Within the dataset, 5 tumors of 4 pediatric patients with a neuroblastoma were DNA sequenced. Provided are FASTQ data files, bam and bambai files, as well as breakpoint spanning and encompassing read (enspan) bam and bambai files. Sequencing bam data files are aligned to GRCh37.p13 reference genome (processed).

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DATA ACCESS AGREEMENT for neuroblastoma sequencing data provided by the Berlin Neuroblastoma Liquid Biopsy Data Access Committee (DAC) (PD Dr. Hedwig E. Deubzer, Charite).

DATA ACCESS AGREEMENT Definitions Authorised Personnel: The individuals at the User Institution to whom Berlin Neuroblastoma Liquid Biopsy Data Access Committee (main contact PD Dr. Deubzer) 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: PD Dr. Hedwig E. Deubzer 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. DAC: Berlin Neuroblastoma Liquid Biopsy Data Access Committee Main contact: principal investigator, PD Dr. Hedwig E. Deubzer: Charite Universitätsmedizin Berlin, Department of Pediatric Oncology, Augustenburger Platz 1, 13353 Berlin, Germany Alternative contact: Dr. Annabell Szymansky: Charite Universitätsmedizin Berlin, Department of Pediatric Oncology, Augustenburger Platz 1, 13353 Berlin, Germany 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 Berlin Neuroblastoma Liquid Biopsy Data Access Committee within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify the Berlin Neuroblastoma Liquid Biopsy Data Access Committee prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the Berlin Neuroblastoma Liquid Biopsy Data Access Committee as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The Berlin Neuroblastoma Liquid Biopsy Data Access Committee 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 PD Dr. Hedwig E. Deubzer. 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 Federal Republic of Germany.

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
EGAS00001007365 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
EGAF00008115767 bai 4.1 MB
EGAF00008115768 bam 959.7 MB
EGAF00008115769 bai 4.1 MB
EGAF00008115770 bai 3.6 MB
EGAF00008115771 bai 3.1 MB
EGAF00008115772 bai 3.1 MB
EGAF00008115773 bam 17.1 GB
EGAF00008115774 bam 13.5 GB
EGAF00008115775 bam 4.5 GB
EGAF00008115776 bam 3.0 GB
EGAF00008115777 bai 4.8 MB
EGAF00008115778 bai 4.7 MB
EGAF00008115779 bai 4.3 MB
EGAF00008115780 bai 3.0 MB
EGAF00008115781 bam 609.4 MB
EGAF00008115782 bam 455.3 MB
EGAF00008115783 bam 111.0 MB
EGAF00008115784 bam 46.6 MB
EGAF00008115785 fastq.gz 427.4 MB
EGAF00008115786 fastq.gz 58.8 MB
EGAF00008115787 fastq.gz 294.0 MB
EGAF00008115788 fastq.gz 2.3 GB
EGAF00008115789 fastq.gz 93.9 MB
EGAF00008115790 fastq.gz 453.8 MB
EGAF00008115791 fastq.gz 59.3 MB
EGAF00008115792 fastq.gz 313.9 MB
EGAF00008115793 fastq.gz 2.4 GB
EGAF00008115794 fastq.gz 96.8 MB
EGAF00008115795 bai 4.3 MB
EGAF00008115796 bam 3.2 GB
30 Files (49.9 GB)