Need Help?

Paired WES and low coverage WGS of osteosarcoma

Longitudinal genome-sequencing analysis of 12 patients with metastatic or refractory osteosarcoma. The study was approved at the University Hospital Basel, following the approval of the ethical committee for mutational analysis of anonymized samples (“Ethikkommission beider Basel” ref. 274/12). Informed consent was obtained from all 12 patients. All tumor samples were evaluated by an experienced bone pathologist to confirm the diagnosis. WES and low coverage WGS are aligned against the reference genome GRCh37. More details in the associated publication.

Request Access

The file access request must be send to Pr. Daniel Baumhoer from the University Hospital Basel : daniel.baumhoer@usb.ch

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 Bone Tumor Reference Centre 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: Bone Tumor Reference Centre 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. 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 Bone Tumor Reference Centre within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Bone Tumor Reference Centre prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Bone Tumor Reference Centre as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Bone Tumor Reference Centre 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 Bone Tumor Reference Centre. 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 Bone Tumor Reference Centre 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) Name of project that created the dataset Early Evolutionary Landscape of Osteosarcoma Names of other data producers/collaborators Michal KOVAC Baptiste AMELINE Specific limitations on areas of research None Minimum protection measures required Cloud computing is prohibited. 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. If held on Laptop, USB keys or other portable hard drives, the data must be encrypted. Only individuals that have obtained authorization will have access to the data. If copies of the data are stored locally on a shared computer system or a file server, then they must be strong password and/or encryption protected so that only the authorized individual have access to it. If the computer that holds the data is backed up, the backup media must encrypted and/or stored in a physically secure location. If the data are stored on a network-accessible computer, there must be controls in place to prevent access by computer “hackers”, or contamination by viruses, malware and spyware. Network security is usually implemented by your institution’s IT department and will consist of some combination of network firewalls, network intrusion monitoring and virus scanning software. After finishing the research project for which you are requesting access or if your access approval is terminated, you must securely destroy all local copies of the data, including any backups copies. However, if necessary, you may still keep the data for archival purpose in conformity with national audits or other legal requirements. 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 Bone Tumor Reference Centre intends 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. Bone Tumor Reference Centre anticipates 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. 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 Bone Tumor Reference Centre.

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
EGAS00001005199 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
EGAF00005189446 bam 5.0 GB
EGAF00005189448 bam 6.7 GB
EGAF00005189449 bam 12.7 GB
EGAF00005189450 bam 6.5 GB
EGAF00005189451 bam 6.5 GB
EGAF00005189452 bam 8.5 GB
EGAF00005189453 bam 9.9 GB
EGAF00005189454 bam 7.8 GB
EGAF00005189455 bam 7.6 GB
EGAF00005189456 bam 9.9 GB
EGAF00005189457 bam 5.0 GB
EGAF00005189458 bam 8.5 GB
EGAF00005189459 bam 7.9 GB
EGAF00005189460 bam 20.0 GB
EGAF00005189461 bam 15.6 GB
EGAF00005189462 bam 9.4 GB
EGAF00005189463 bam 5.3 GB
EGAF00005189464 bam 10.1 GB
EGAF00005189465 bam 7.1 GB
EGAF00005189466 bam 9.8 GB
EGAF00005189467 bam 9.2 GB
EGAF00005189469 bam 9.4 GB
EGAF00005189470 bam 93.4 GB
EGAF00005189471 bam 11.4 GB
EGAF00005189472 bam 8.1 GB
EGAF00005189473 bam 6.4 GB
EGAF00005189474 bam 6.5 GB
EGAF00005189475 bam 5.5 GB
EGAF00005189476 bam 93.3 GB
EGAF00005189477 bam 19.0 GB
EGAF00005189478 bam 10.1 GB
EGAF00005189479 bam 4.8 GB
EGAF00005189480 bam 4.2 GB
EGAF00005189481 bam 6.8 GB
EGAF00005189482 bam 4.6 GB
EGAF00005189483 bam 8.9 GB
EGAF00005189484 bam 7.5 GB
EGAF00005189486 bam 7.7 GB
EGAF00005189487 bam 8.2 GB
EGAF00005189488 bam 10.3 GB
EGAF00005189489 bam 4.9 GB
EGAF00005189490 bam 19.9 GB
EGAF00005189491 bam 16.3 GB
EGAF00005189492 bam 5.1 GB
EGAF00005189493 bam 5.4 GB
EGAF00005189494 bam 7.2 GB
EGAF00005189495 bam 4.9 GB
EGAF00005189496 bam 7.3 GB
EGAF00005189497 bam 9.9 GB
EGAF00005189498 bam 10.5 GB
EGAF00005189499 bam 3.9 GB
EGAF00005189500 bam 4.6 GB
EGAF00005189501 bam 5.0 GB
EGAF00005189502 bam 18.8 GB
EGAF00005189503 bam 7.6 GB
EGAF00005189504 bam 22.1 GB
EGAF00005189505 bam 6.7 GB
EGAF00005189506 bam 5.1 GB
EGAF00005189507 bam 9.3 GB
EGAF00005189508 bam 8.3 GB
EGAF00005189509 bam 7.8 GB
EGAF00005189510 bam 5.5 GB
EGAF00005189511 bam 9.2 GB
EGAF00005189512 bam 6.3 GB
EGAF00005189513 bam 19.0 GB
EGAF00005189514 bam 23.1 GB
EGAF00005189515 bam 5.7 GB
EGAF00005189516 bam 6.0 GB
EGAF00005189517 bam 5.2 GB
EGAF00005189518 bam 18.3 GB
EGAF00005189519 bam 5.2 GB
EGAF00005189520 bam 6.3 GB
EGAF00005189521 bai 8.8 MB
EGAF00005189522 bai 8.7 MB
EGAF00005189523 bai 8.8 MB
EGAF00005189524 bai 7.1 MB
EGAF00005189525 bai 8.5 MB
EGAF00005189526 bai 7.0 MB
EGAF00005189527 bai 7.0 MB
EGAF00005189528 bai 7.1 MB
EGAF00005189529 bai 6.8 MB
EGAF00005189530 bai 8.8 MB
EGAF00005189531 bai 6.7 MB
EGAF00005189532 bai 8.8 MB
EGAF00005189533 bai 8.9 MB
EGAF00005189534 bai 7.0 MB
EGAF00005189535 bai 6.9 MB
EGAF00005189536 bai 8.2 MB
EGAF00005189538 bai 8.7 MB
EGAF00005189539 bai 8.8 MB
EGAF00005189540 bai 8.8 MB
EGAF00005189541 bai 8.8 MB
EGAF00005189542 bai 8.8 MB
EGAF00005189543 bai 8.8 MB
EGAF00005189544 bai 8.8 MB
EGAF00005189545 bai 7.8 MB
EGAF00005189546 bai 7.9 MB
EGAF00005189547 bai 8.9 MB
EGAF00005189548 bai 8.8 MB
EGAF00005189549 bai 8.7 MB
EGAF00005189550 bai 8.8 MB
EGAF00005189551 bai 8.7 MB
EGAF00005189552 bai 6.9 MB
EGAF00005189553 bai 6.9 MB
EGAF00005189554 bai 8.0 MB
EGAF00005189555 bai 6.9 MB
EGAF00005189556 bai 6.9 MB
EGAF00005189557 bai 6.9 MB
EGAF00005189558 bai 8.7 MB
EGAF00005189559 bai 7.7 MB
EGAF00005189560 bai 7.6 MB
EGAF00005189561 bai 6.8 MB
EGAF00005189562 bai 7.1 MB
EGAF00005189564 bai 7.9 MB
EGAF00005189565 bai 8.8 MB
EGAF00005189566 bai 6.9 MB
EGAF00005189567 bai 7.7 MB
EGAF00005189568 bai 7.0 MB
EGAF00005189569 bai 7.0 MB
EGAF00005189570 bai 6.8 MB
EGAF00005189571 bai 8.8 MB
EGAF00005189572 bai 7.7 MB
EGAF00005189573 bai 8.8 MB
EGAF00005189574 bai 8.8 MB
EGAF00005189575 bai 8.7 MB
EGAF00005189576 bai 6.8 MB
EGAF00005189577 bai 8.8 MB
EGAF00005189579 bai 8.8 MB
EGAF00005189580 bai 8.3 MB
EGAF00005189581 bai 8.3 MB
EGAF00005189582 bai 8.4 MB
EGAF00005189583 bai 7.4 MB
EGAF00005189584 bai 8.8 MB
EGAF00005189585 bai 7.5 MB
EGAF00005189586 bai 8.0 MB
EGAF00005189587 bai 8.1 MB
EGAF00005189588 bai 8.7 MB
EGAF00005189589 bai 8.1 MB
EGAF00005189590 bai 7.4 MB
EGAF00005189591 bai 7.0 MB
EGAF00005189592 bai 8.8 MB
EGAF00005189593 bai 8.8 MB
EGAF00005189594 bai 7.0 MB
EGAF00005189595 bai 8.8 MB
144 Files (816.2 GB)