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Whole Exome sequencing data from Shwachman-Diamond syndrome bone marrow samples

This dataset includes paired WES from bone marrow samples of patients with SDS and paired bone marrow-derived fibroblasts as a germline reference. Some patients have multiple samples collected serially over time. There are 74 BAM files included in this dataset.

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Data sharing is available upon request for collaborative projects between pediatric or other institutions. Requests should be directed towards the Data Access Committee for approval.

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 Children’s Hospital Corporation d/b/a Boston Children’s Hospital (hereinafter “Boston Children’s Hospital”) 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: Boston Children’s Hospital 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, and such research is solely for teaching and academic research purposes. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. l Your Institution details here 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. This provision shall apply to Data that is in possession of Authorised Personnel. In the event that User Institution determines that returning or destroying the Data is infeasible, User Institution shall extend the protections of this Agreement to such Data and limit further uses and disclosures of such Data to only those purposes that make the return or destruction infeasible, for so long as User Institution maintains such Data. 12. The User Institution will notify Boston Children’s Hospital within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Boston Children’s Hospital, no less than five (5) days prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Boston Children’s Hospital as soon as it becomes aware, but within twenty-four (24) hours of a breach of the terms or conditions of this agreement. 15. The User Institution agrees to indemnify Boston Children’s Hospital for any liability, loss, claim, or demand arising from its use, storage or disclosure of the Data. 16. Boston Children’s Hospital 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. 17. 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 Boston Children’s Hospital. 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 in writing and the User Institution may elect to accept the changes or terminate the agreement. If the User Institution elects to accept the changes, this agreement will be amended or modified through a later written agreement, signed by both parties, and expressly referencing this agreement. 18. 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. 19. 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. 20. 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 Commonwealth of Massachusetts, United States of America.

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
EGAS00001004856 Other
EGAS00001004880 Exome 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
EGAF00004937031 bam 28.7 GB
EGAF00004937033 bam 27.4 GB
EGAF00004937034 bam 13.0 GB
EGAF00004937036 bam 11.2 GB
EGAF00004937037 bam 23.6 GB
EGAF00004937038 bam 22.7 GB
EGAF00004937039 bam 11.8 GB
EGAF00004937040 bam 21.3 GB
EGAF00004937041 bam 12.6 GB
EGAF00004937042 bam 28.2 GB
EGAF00004937497 bai 6.9 MB
EGAF00004937501 bai 6.4 MB
EGAF00004937503 bai 6.9 MB
EGAF00004937504 bai 6.4 MB
EGAF00004937505 bai 7.5 MB
EGAF00004937508 bai 7.5 MB
EGAF00004937510 bai 6.8 MB
EGAF00004937511 bai 6.3 MB
EGAF00004937513 bai 6.4 MB
EGAF00004937515 bai 6.8 MB
EGAF00004952077 bam 24.4 GB
EGAF00004952078 bam 12.9 GB
EGAF00004952079 bam 26.0 GB
EGAF00004952080 bam 25.9 GB
EGAF00004952081 bam 14.9 GB
EGAF00004952082 bam 13.0 GB
EGAF00004952083 bam 19.9 GB
EGAF00004952084 bai 6.4 MB
EGAF00004952085 bam 24.6 GB
EGAF00004952086 bam 23.1 GB
EGAF00004952087 bam 11.7 GB
EGAF00004952088 bam 8.0 GB
EGAF00004952089 bam 12.0 GB
EGAF00004952090 bam 24.6 GB
EGAF00004952091 bam 13.6 GB
EGAF00004952092 bam 25.3 GB
EGAF00004952093 bam 11.6 GB
EGAF00004952094 bam 24.8 GB
EGAF00004952095 bam 11.5 GB
EGAF00004952096 bam 8.7 GB
EGAF00004952097 bam 12.2 GB
EGAF00004952098 bam 40.4 GB
EGAF00004952099 bam 40.9 GB
EGAF00004952100 bam 13.2 GB
EGAF00004952101 bam 18.3 GB
EGAF00004952102 bam 32.7 GB
EGAF00004952103 bam 10.4 GB
EGAF00004952104 bam 37.7 GB
EGAF00004952105 bam 9.7 GB
EGAF00004952106 bam 25.4 GB
EGAF00004952107 bam 11.9 GB
EGAF00004952108 bam 24.0 GB
EGAF00004952109 bam 21.4 GB
EGAF00004952156 bai 6.4 MB
EGAF00004952162 bai 7.0 MB
EGAF00004952164 bai 6.2 MB
EGAF00004952182 bai 6.4 MB
EGAF00004952217 bai 6.7 MB
EGAF00004952220 bai 7.2 MB
EGAF00004952226 bai 6.6 MB
EGAF00004952243 bai 6.3 MB
EGAF00004952248 bai 7.2 MB
EGAF00004952291 bai 6.3 MB
EGAF00004952302 bai 6.7 MB
EGAF00004952311 bai 6.6 MB
EGAF00004952329 bai 6.4 MB
EGAF00004952343 bai 7.3 MB
EGAF00004952385 bai 6.4 MB
EGAF00004952423 bai 6.5 MB
EGAF00004952429 bai 7.0 MB
EGAF00004952436 bai 6.7 MB
EGAF00004952448 bai 7.1 MB
EGAF00004952449 bai 6.5 MB
EGAF00004952454 bai 7.4 MB
EGAF00004952461 bai 6.4 MB
EGAF00004952464 bai 6.9 MB
EGAF00004952483 bai 8.3 MB
EGAF00004952492 bai 6.6 MB
EGAF00004952494 bai 7.1 MB
EGAF00004952498 bai 7.3 MB
EGAF00004952501 bai 6.6 MB
EGAF00004952519 bai 7.2 MB
EGAF00004952578 bai 6.4 MB
EGAF00004952579 bai 6.4 MB
EGAF00004952584 bai 7.2 MB
EGAF00004955777 bam 21.5 GB
EGAF00004955778 bam 23.3 GB
EGAF00004955779 bam 39.9 GB
EGAF00004955780 bam 13.1 GB
EGAF00004955781 bam 26.7 GB
EGAF00004955782 bam 13.7 GB
EGAF00004955783 bam 20.6 GB
EGAF00004955784 bam 27.4 GB
EGAF00004955785 bam 29.6 GB
EGAF00004955786 bam 12.6 GB
EGAF00004955787 bam 23.8 GB
EGAF00004955788 bam 23.5 GB
EGAF00004955789 bam 26.5 GB
EGAF00004955790 bam 13.1 GB
EGAF00004955791 bam 21.3 GB
EGAF00004955792 bam 29.0 GB
EGAF00004955793 bam 22.0 GB
EGAF00004955794 bam 12.5 GB
EGAF00004955795 bam 21.2 GB
EGAF00004955796 bam 13.3 GB
EGAF00004955797 bam 28.9 GB
EGAF00004955798 bam 27.9 GB
EGAF00004955799 bam 19.4 GB
EGAF00004955800 bam 13.2 GB
EGAF00004955801 bam 29.7 GB
EGAF00004955802 bam 27.4 GB
EGAF00004955803 bam 26.6 GB
EGAF00004955804 bam 32.9 GB
EGAF00004955805 bam 14.5 GB
EGAF00004955806 bai 6.9 MB
EGAF00004955807 bai 6.4 MB
EGAF00004955808 bai 7.5 MB
EGAF00004955809 bai 6.5 MB
EGAF00004955810 bai 6.6 MB
119 Files (1.5 TB)