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The dataset for "ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma”

The dataset for the study “ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma” includes 169 bam files from whole genome sequencing on the Illumina NovaSeq6000 platform. The samples analyzed include tumor (n=28) and normal (n=28) DNA samples, and serial plasma cfDNA (n=113) samples from 28 individuals with resectable diffuse pleural mesothelioma, treated with nivolumab or nivolumab plus ipilimumab on the NCT03918252 trial.

Request Access

DUO:0000018
version: 2021-02-23

not for profit, non commercial use only

This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.

DUO:0000021
version: 2021-02-23

ethics approval required

This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval.

DUO:0000026
version: 2021-02-23

user specific restriction

This data use modifier indicates that use is limited to use by approved users.

DUO:0000027
version: 2021-02-23

project specific restriction

This data use modifier indicates that use is limited to use within an approved project.

Policy for EGA study entitled: “ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma”

This Data Access Agreement (“Agreement” or “DAA”), including its appendices, is to allow User Institution and its Authorized Personnel to access and use the Data from Johns Hopkins University (“Provider”) for the Project. Provider is willing to allow User Institution to access such Data from the European Genome-Phenome Archive (“EGA”) for use solely for the research purposes described in Appendix II, wherein User Institution may not use the Data for any commercial purpose. The User Institution agrees to be bound by the terms and conditions of this Agreement. This Agreement is effective as of the data of last signature below. 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 DAC: The data access committee for “ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma”, EGA DAC EGAC50000000706. The DAC is comprised of Dr. Valsamo Anagnostou and can be contacted at vanagno1@jhmi.edu. Authorised Personnel: The individuals at the User Institution to whom the DAC 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: The DAC 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. Please include 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. Should User Institution inadvertently receive identifiable information or otherwise identify a subject, Recipient shall promptly notify Provider and follow Data Producer’s reasonable written instructions, which may include return or destruction of the identifiable information. 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. Nothing herein shall authorize the User Institution to use or further disclose the Data in a manner that would violate the requirements of Data Producers under U.S. law, including 45 CFR 164.514. 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 DAC within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify the DAC prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The DAC 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 DAC. 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. If the Data Producer is a HIPAA Covered Entity, and if the the Data will be a Limited Data Set as defined by the Health Insurance Portability and Accountability Act of 1996 (“HIPAA”). In accordance with Section 164.514(e)(2) of the HIPAA Privacy Rule, the Data shall exclude the following direct identifiers of the individual or of relatives, employers, or household members of the individual: (i) Names; (ii) Postal address information, other than town or city, State, and zip code; (iii) Telephone numbers; (iv) Fax numbers; (v) Electronic mail addresses; (vi) Social security numbers; (vii) Medical record numbers; (viii) Health plan beneficiary numbers; (ix) Account numbers; (x) Certificate/license numbers; (xi) Vehicle identifiers and serial numbers, including license plate numbers; (xii) Device identifiers and serial numbers; (xiii) Web Universal Resource Locators (URLs); (xiv) Internet Protocol (IP) address numbers; (xv) Biometric identifiers, including finger and voice prints; and (xvi) Full face photographic images and any comparable images. If the Data being provided is coded, the Data Producer will not release, and the User Institution will not request, the key to the code. 20. The User Institution agrees to cite the publication(s) from which the Data are derived to acknowledge the version of the data and the contribution of the Data Producers in all reports or publications resulting from the use of the Data. The full citation(s) of the Data generating publication(s) and suggested acknowledgement are in Appendix IV.   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 Provider: Signature: Name: Neha Parikh, JD Title: Assistant Director, Contracts, JHU ORA Date: On behalf of the DAC, I confirm that I have read and understood this Agreement: Signature: Name: Dr. Valsamo Anagnostou Title: Associate Professor of Oncology Date:

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
EGAS50000001195 Cancer Genomics

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 Quality Report
Located in
EGAF00008865186 bam 98.9 GB
EGAF00008865188 bam 113.3 GB
EGAF00008865195 bam 109.4 GB
EGAF00008865197 bam 105.4 GB
EGAF00008865198 bam 107.6 GB
EGAF00008866557 bam 100.9 GB
EGAF00008866558 bam 84.3 GB
EGAF00008866559 bam 77.8 GB
EGAF00008866560 bam 117.0 GB
EGAF00008866561 bam 84.0 GB
EGAF00008866562 bam 107.1 GB
EGAF00008866563 bam 107.6 GB
EGAF00008866564 bam 105.1 GB
EGAF00008866565 bam 104.9 GB
EGAF00008866566 bam 98.2 GB
EGAF00008866567 bam 304.2 GB
EGAF00008867342 bam 55.1 GB
EGAF00008867345 bam 96.0 GB
EGAF00008867346 bam 86.6 GB
EGAF00008867349 bam 92.9 GB
EGAF00008867350 bam 99.1 GB
EGAF00008867351 bam 52.0 GB
EGAF00008867352 bam 120.6 GB
EGAF00008867353 bam 96.0 GB
EGAF00008867354 bam 115.1 GB
EGAF00008867356 bam 102.0 GB
EGAF00008867358 bam 91.2 GB
EGAF00008867359 bam 91.9 GB
EGAF00008867361 bam 93.8 GB
EGAF00008867362 bam 107.6 GB
EGAF00008867363 bam 52.4 GB
EGAF00008867364 bam 107.8 GB
EGAF00008867365 bam 104.6 GB
EGAF00008867366 bam 100.4 GB
EGAF00008867367 bam 97.5 GB
EGAF00008867368 bam 112.2 GB
EGAF00008867369 bam 254.6 GB
EGAF00008867370 bam 56.8 GB
EGAF00008867376 bam 301.7 GB
EGAF00008867377 bam 95.4 GB
EGAF00008867378 bam 286.2 GB
EGAF00008867379 bam 52.0 GB
EGAF00008867425 bam 273.3 GB
EGAF00008867447 bam 98.4 GB
EGAF00008868436 bam 52.3 GB
EGAF00008868437 bam 50.9 GB
EGAF00008868439 bam 52.7 GB
EGAF00008869742 bam 56.0 GB
EGAF00008869743 bam 99.0 GB
EGAF00008869744 bam 100.9 GB
EGAF00008869746 bam 102.2 GB
EGAF00008869747 bam 107.6 GB
EGAF00008869748 bam 47.8 GB
EGAF00008869749 bam 81.3 GB
EGAF00008869750 bam 90.5 GB
EGAF00008869751 bam 94.6 GB
EGAF00008869752 bam 110.9 GB
EGAF00008869760 bam 58.5 GB
EGAF00008869761 bam 76.6 GB
EGAF00008869762 bam 80.9 GB
EGAF00008869763 bam 91.6 GB
EGAF00008869771 bam 106.2 GB
EGAF00008869772 bam 102.4 GB
EGAF00008869773 bam 98.7 GB
EGAF00008869774 bam 115.3 GB
EGAF00008869775 bam 107.4 GB
EGAF00008869776 bam 92.5 GB
EGAF00008869781 bam 49.7 GB
EGAF00008869782 bam 102.3 GB
EGAF00008869783 bam 49.3 GB
EGAF00008869785 bam 114.1 GB
EGAF00008869793 bam 290.2 GB
EGAF00008869794 bam 100.5 GB
EGAF00008869796 bam 287.6 GB
EGAF00008869797 bam 110.0 GB
EGAF00008869802 bam 94.8 GB
EGAF00008869808 bam 107.3 GB
EGAF00008869809 bam 99.8 GB
EGAF00008869810 bam 292.0 GB
EGAF00008869811 bam 101.5 GB
EGAF00008869812 bam 219.2 GB
EGAF00008869813 bam 100.0 GB
EGAF00008869819 bam 269.0 GB
EGAF00008869820 bam 259.3 GB
EGAF00008869831 bam 263.3 GB
EGAF00008869853 bam 89.4 GB
EGAF00008869854 bam 105.9 GB
EGAF00008869855 bam 106.5 GB
EGAF00008870293 bam 105.9 GB
EGAF00008870294 bam 98.8 GB
EGAF00008870295 bam 279.7 GB
EGAF00008870296 bam 114.3 GB
EGAF00008870298 bam 260.3 GB
EGAF00008870299 bam 98.1 GB
EGAF00008870300 bam 269.3 GB
EGAF00008870310 bam 92.1 GB
EGAF00008870311 bam 102.1 GB
EGAF00008870320 bam 110.1 GB
EGAF00008870325 bam 98.7 GB
EGAF00008870336 bam 100.0 GB
EGAF00008870337 bam 312.2 GB
EGAF00008870338 bam 316.9 GB
EGAF00008870339 bam 106.9 GB
EGAF00008870340 bam 105.9 GB
EGAF00008870348 bam 68.6 GB
EGAF00008870356 bam 90.3 GB
EGAF00008870357 bam 89.1 GB
EGAF00008870358 bam 96.0 GB
EGAF00008870360 bam 51.5 GB
EGAF00008870361 bam 95.5 GB
EGAF00008870368 bam 82.8 GB
EGAF00008870370 bam 86.8 GB
EGAF00008870371 bam 91.1 GB
EGAF00008870385 bam 103.7 GB
EGAF00008870388 bam 109.5 GB
EGAF00008870389 bam 62.5 GB
EGAF00008870390 bam 111.2 GB
EGAF00008870391 bam 98.2 GB
EGAF00008870392 bam 86.1 GB
EGAF00008870396 bam 82.8 GB
EGAF00008870411 bam 93.1 GB
EGAF00008870412 bam 96.5 GB
EGAF00008870413 bam 55.7 GB
EGAF00008870414 bam 77.7 GB
EGAF00008870415 bam 87.5 GB
EGAF00008870416 bam 55.2 GB
EGAF00008870417 bam 85.8 GB
EGAF00008870418 bam 107.5 GB
EGAF00008870419 bam 88.0 GB
EGAF00008870420 bam 109.1 GB
EGAF00008870421 bam 99.9 GB
EGAF00008870424 bam 71.7 GB
EGAF00008870425 bam 100.2 GB
EGAF00008870447 bam 86.0 GB
EGAF00008870453 bam 257.2 GB
EGAF00008870462 bam 85.8 GB
EGAF00008870472 bam 328.5 GB
EGAF00008870506 bam 105.0 GB
EGAF00008870510 bam 100.6 GB
EGAF00008870518 bam 115.8 GB
EGAF00008870544 bam 108.5 GB
EGAF00008870570 bam 97.0 GB
EGAF00008870619 bam 356.3 GB
EGAF00008870643 bam 111.5 GB
EGAF00008870660 bam 90.7 GB
EGAF00008870748 bam 160.3 GB
EGAF00008870755 bam 99.6 GB
EGAF00008870875 bam 104.4 GB
EGAF00008870910 bam 267.9 GB
EGAF00008870918 bam 215.7 GB
EGAF00008871042 bam 70.3 GB
EGAF00008871080 bam 319.8 GB
EGAF00008871127 bam 115.0 GB
EGAF00008871180 bam 92.5 GB
EGAF00008871251 bam 100.4 GB
EGAF00008871256 bam 195.6 GB
EGAF00008871259 bam 336.9 GB
EGAF00008871302 bam 88.4 GB
EGAF00008871305 bam 101.3 GB
EGAF00008871389 bam 104.2 GB
EGAF00008871989 bam 53.3 GB
EGAF00008871990 bam 78.4 GB
EGAF00008871991 bam 99.6 GB
EGAF00008872080 bam 291.4 GB
EGAF00008872081 bam 350.9 GB
EGAF00008872232 bam 77.4 GB
EGAF00008872233 bam 84.9 GB
EGAF00008872235 bam 118.1 GB
EGAF00008872236 bam 84.6 GB
169 Files (20.9 TB)