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Whole genome sequencing of Osteosarcoma clonal evolution

Multiple large-scale genomic profiling efforts have been undertaken in osteosarcoma to define the genomic drivers of tumorigenesis, therapeutic response, and disease recurrence. The spatial and temporal intratumor heterogeneity could also play a role in promoting tumor growth and treatment resistance. Here, we conducted longitudinal whole-genome sequencing of 37 tumor samples from eight patients with osteosarcoma that relapsed or became refractory to initial therapy. We found that the chemoresistant population in recurrent osteosarcoma is subclonal at diagnosis, emerges at the time of primary resection due to selective pressure from neoadjuvant chemotherapy, and is characterized by unique oncogenic amplifications.

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MSKCC Medical Donation Program Data Access Policy

Memorial Sloan Kettering Medical Donation Program 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 MSKCC Medical Donation Program Data Access Committee 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: MSKCC Medical Donation Program Data Access Committee 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. MSKCC Medical Donation Program Data Access Committee: Memorial Sloan Kettering Cancer Center, Medical Donation Program, 1275 York Avenue, New York, NY 10065. 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 MSKCC Medical Donation Program Data Access Committee within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify the MSKCC Medical Donation Program Data Access Committee prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the MSKCC Medical Donation Program Data Access Committee as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The MSKCC Medical Donation Program 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 the MSKCC Medical Donation Program Data Access Committee. 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 the MSKCC Medical Donation Program Data Access Committee 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) EGAS00001006024 Name of project that created the dataset Sequencing of pancreatic cancer primary tumors and metastases Names of other data producers/collaborators Haochen Zhang Elias-Ramzey Karnoub Shigeaki Umeda Catilin McIntyre Akimasa Hayashi Palash Sashittal Amanda Zucker Katelyn Mullen Jungeui Hong Christine Iacobuzio-Donahue Specific limitations on areas of research None. Minimum protection measures required None. 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 The MSKCC Medical Donation Program Data Access Committee 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. The MSKCC Medical Donation Program Data Access Committee 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 12 months after these data were first made available on the relevant hosting database, unless the MSKCC Medical Donation Program Data Access Committee has provided written consent to earlier submission. 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., EGAS00001006024), and acknowledge its use in a form agreed by the User Institution with the MSKCC Medical Donation Program Data Access Committee.

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
EGAS00001007486 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
EGAF00008204327 bam 140.3 GB
EGAF00008204328 bam 190.1 GB
EGAF00008204329 bam 149.0 GB
EGAF00008204330 bam 149.3 GB
EGAF00008204331 bam 193.0 GB
EGAF00008204332 bam 146.1 GB
EGAF00008204333 bam 170.3 GB
EGAF00008204334 bam 218.4 GB
EGAF00008204335 bam 113.1 GB
EGAF00008204336 bam 97.3 GB
EGAF00008204337 bam 109.2 GB
EGAF00008204338 bam 125.9 GB
EGAF00008204339 bam 148.4 GB
EGAF00008204340 bam 153.6 GB
EGAF00008204341 bam 119.5 GB
EGAF00008204342 bam 166.0 GB
EGAF00008204343 bam 103.1 GB
EGAF00008204344 bam 105.3 GB
EGAF00008204345 bam 187.8 GB
EGAF00008204346 bam 100.4 GB
EGAF00008204347 bam 103.3 GB
EGAF00008204348 bam 113.3 GB
EGAF00008204349 bam 129.6 GB
EGAF00008204350 bam 152.1 GB
EGAF00008204351 bam 123.2 GB
EGAF00008204352 bam 137.7 GB
EGAF00008204353 bam 210.5 GB
EGAF00008204354 bam 126.3 GB
EGAF00008204355 bam 124.0 GB
EGAF00008204356 bam 198.3 GB
EGAF00008204357 bam 148.8 GB
EGAF00008204358 bam 121.1 GB
EGAF00008204359 bam 165.9 GB
EGAF00008204360 bam 100.5 GB
EGAF00008204361 bam 121.0 GB
EGAF00008204362 bam 120.0 GB
EGAF00008204363 bam 179.7 GB
37 Files (5.3 TB)