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Sequence data to study genomic CNVs that drive apoptotic resistance and relapses on immune checkpoint inhibitors

The dataset consists of bulk whole exome sequencing (WES) and whole genome sequencing (WGS) data from baseline and disease-progressed tumors after immune checkpoint inhibitor (ICI) treatment, derived from patients, human cell lines, and mouse models. Whole exome sequencing includes 17 clinical cases and one human cell line model with parental and acquired resistant cell lines (n = 5). Whole genome sequencing encompasses the YUMMER mouse model, including vehicle-treated controls (n = 2) and acquired resistant tumors (n = 3). The sequence reads have been aligned to hg19 and mm9 reference genomes, with mapped files (BAM) made available for analysis.

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UCLA WGS data access committee is responsible for data release to external requestors based on consent and/or National Research Ethics terms

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 XXXXX within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify XXXXX prior to any significant changes to the protocol for the Project. 14. The User Institution will notify XXXXX as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. XXXXX 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 XXXXX. 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.

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
EGAS50000001055 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
EGAF50000382304 bam 14.2 GB
EGAF50000382305 bam 10.6 GB
EGAF50000382306 bam 9.6 GB
EGAF50000382307 bam 22.2 GB
EGAF50000382308 bam 33.6 GB
EGAF50000382309 bam 19.7 GB
EGAF50000382310 bam 18.5 GB
EGAF50000382311 bam 27.5 GB
EGAF50000382312 bam 22.0 GB
EGAF50000382313 bam 20.0 GB
EGAF50000382314 bam 25.9 GB
EGAF50000382315 bam 15.0 GB
EGAF50000382316 bam 19.2 GB
EGAF50000382317 bam 13.9 GB
EGAF50000382318 bam 28.4 GB
EGAF50000382319 bam 29.8 GB
EGAF50000382320 bam 9.3 GB
EGAF50000382321 bam 7.2 GB
EGAF50000382322 bam 22.8 GB
EGAF50000382323 bam 51.1 GB
EGAF50000382324 bam 38.8 GB
EGAF50000382325 bam 34.5 GB
EGAF50000382326 bam 12.2 GB
EGAF50000382327 bam 14.1 GB
EGAF50000382328 bam 25.8 GB
EGAF50000382329 bam 26.6 GB
EGAF50000382330 bam 57.0 GB
EGAF50000382331 bam 33.3 GB
EGAF50000382332 bam 45.2 GB
EGAF50000382333 bam 52.9 GB
EGAF50000382334 bam 36.6 GB
EGAF50000382335 bam 47.8 GB
EGAF50000382336 bam 40.9 GB
EGAF50000382337 bam 44.3 GB
EGAF50000382338 bam 89.8 GB
EGAF50000382339 bam 55.5 GB
EGAF50000382340 bam 25.4 GB
EGAF50000382341 bam 21.3 GB
EGAF50000382342 bam 52.3 GB
EGAF50000382343 bam 45.4 GB
EGAF50000382344 bam 17.5 GB
EGAF50000382345 bam 16.1 GB
EGAF50000382346 bam 77.0 GB
EGAF50000382347 bam 91.7 GB
EGAF50000382348 bam 38.4 GB
EGAF50000382349 bam 51.4 GB
EGAF50000382350 bam 58.3 GB
EGAF50000382351 bam 42.7 GB
EGAF50000382352 bam 41.9 GB
EGAF50000382353 bam 60.5 GB
EGAF50000382354 bam 61.8 GB
EGAF50000382355 bam 44.9 GB
EGAF50000382356 bam 52.2 GB
EGAF50000382357 bam 51.7 GB
EGAF50000382358 bam 22.9 GB
EGAF50000382359 bam 24.9 GB
EGAF50000382360 bam 23.0 GB
EGAF50000382361 bam 22.1 GB
EGAF50000382362 bam 21.9 GB
EGAF50000382363 bam 15.5 GB
EGAF50000382364 bam 14.8 GB
EGAF50000382365 bam 18.0 GB
EGAF50000382366 bam 14.5 GB
EGAF50000382367 bam 17.2 GB
EGAF50000382368 bam 16.6 GB
EGAF50000382369 bam 12.9 GB
66 Files (2.2 TB)