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Whole-exome sequencing of hepatocellular carcinoma biopsies

All 122 HCC biopsies and 115 non-tumoral tissues from 114 patients were subjected to whole-exome sequencing. Whole-exome capture was performed using the SureSelectXT Clinical Research Exome (Agilent Technologies) or SureSelect Human All Exon V6+COSMIC (Agilent Technologies) platforms according to the manufacturer’s guidelines. Sequencing was performed on an Illumina HiSeq 2500 at the Genomics Facility Basel according to the manufacturer’s guidelines. Paired-end 101-bp reads were generated.

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Data access policy for MERiC

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 MERiC consortium 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 MERiC consortium 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. The MERiC consortium: The MERiC consortium is a consortium headed by Prof Michael N Hall (Biozentrum, University of Basel), Prof Markus H Heim (Department of Biomedicine, University of Basel), Prof Gerhard Christofori (Department of Biomedicine, University of Basel) and Prof Niko Beerenwinkel (Department of Biosystems Science and Engineering, ETH Zurich). 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 MERiC consortium within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify The MERiC consortium prior to any significant changes to the protocol for the Project. 14. The User Institution will notify The MERiC consortium as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The MERiC consortium 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 MERiC consortium. 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 Switzerland and shall be subject to the exclusive jurisdiction of the Swiss 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
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
EGAF00005493243 1633623526222 7.9 GB
EGAF00005493244 1633622206313 6.5 GB
EGAF00005493246 1633608424290 9.2 GB
EGAF00005493248 1633612910196 6.4 GB
EGAF00005493249 bam 14.2 GB
EGAF00005493250 1633622386338 8.1 GB
EGAF00005493251 bam 14.6 GB
EGAF00005493252 1633613804966 8.3 GB
EGAF00005493253 bam 13.7 GB
EGAF00005493254 1633631166030 13.4 GB
EGAF00005493255 1633622206313 8.6 GB
EGAF00005493256 1633622642025 11.0 GB
EGAF00005493258 1633615661613 8.0 GB
EGAF00005493260 1633619070273 9.9 GB
EGAF00005493262 1633610884934 8.3 GB
EGAF00005493264 1633615985167 7.0 GB
EGAF00005493266 bam 6.7 GB
EGAF00005493267 1633617044758 8.2 GB
EGAF00005493269 1633609483668 7.2 GB
EGAF00005493271 1633613044943 8.9 GB
EGAF00005493273 1633612744935 7.8 GB
EGAF00005493275 1633620045880 8.6 GB
EGAF00005493276 1633642462946 29.2 GB
EGAF00005493277 bam 14.8 GB
EGAF00005493280 1633611584638 7.9 GB
EGAF00005493282 1633618251988 8.6 GB
EGAF00005493283 1633625465720 8.6 GB
EGAF00005493284 1633624205909 27.2 GB
EGAF00005493285 1633617404873 7.6 GB
EGAF00005493287 1633637497088 7.5 GB
EGAF00005493294 1633614406526 7.0 GB
EGAF00005493296 1633613645387 10.7 GB
EGAF00005493298 1633609604090 8.3 GB
EGAF00005493300 1633623586564 7.3 GB
EGAF00005493302 1633616207169 13.0 GB
EGAF00005493303 1633612205018 9.1 GB
EGAF00005493304 1633635671556 13.4 GB
EGAF00005493305 1633611855813 7.1 GB
EGAF00005493307 1633612184379 9.2 GB
EGAF00005493308 1633629365781 12.9 GB
EGAF00005493309 1633624205909 6.7 GB
EGAF00005493310 1633636127869 16.1 GB
EGAF00005493311 1633613985877 6.7 GB
EGAF00005493313 1633611184697 8.2 GB
EGAF00005493315 1633635898944 8.8 GB
EGAF00005493317 1633609243996 7.0 GB
EGAF00005493318 1633611855813 7.6 GB
EGAF00005493320 1633622642025 13.1 GB
EGAF00005493321 1633612678903 7.5 GB
EGAF00005493322 1633614664839 8.8 GB
EGAF00005493324 1633620225996 8.3 GB
EGAF00005493326 1633622642025 10.8 GB
EGAF00005493328 1633614105584 7.1 GB
EGAF00005493330 1633626778420 7.1 GB
EGAF00005493332 1633610824750 8.4 GB
EGAF00005493334 1633614525091 7.1 GB
EGAF00005493336 1633613205977 6.4 GB
EGAF00005493338 1633622386338 12.0 GB
EGAF00005493340 1633634288798 7.0 GB
EGAF00005493344 1633623233901 7.2 GB
EGAF00005493346 1633621745209 8.5 GB
EGAF00005493348 1633623586564 10.4 GB
EGAF00005493350 1633613028353 7.4 GB
EGAF00005493351 1633619208083 8.2 GB
EGAF00005493353 1633630925931 9.6 GB
EGAF00005493355 1633635476813 8.4 GB
EGAF00005493357 1633616824546 9.5 GB
EGAF00005493359 1633614167444 7.6 GB
EGAF00005493361 1633627926022 8.1 GB
EGAF00005493364 1633621445536 9.6 GB
EGAF00005493366 1633623646449 8.9 GB
EGAF00005493370 1633616225470 7.4 GB
EGAF00005493374 1633609604090 8.1 GB
EGAF00005493376 1633615661613 8.2 GB
EGAF00005493379 1633613344719 9.9 GB
EGAF00005493381 1633617044758 9.8 GB
EGAF00005493384 1633615661613 8.5 GB
EGAF00005493385 1633609303788 9.5 GB
EGAF00005493388 1633637497088 9.4 GB
EGAF00005493390 1633613645387 8.4 GB
EGAF00005493393 1633624145533 9.2 GB
EGAF00005493395 1633623646449 10.1 GB
EGAF00005493397 1633613566077 9.2 GB
EGAF00005493399 1633609604090 9.3 GB
EGAF00005493400 1633610764844 8.3 GB
EGAF00005493401 1633625706367 7.4 GB
EGAF00005493402 1633623065360 8.3 GB
EGAF00005493404 1633628324206 8.9 GB
EGAF00005493408 1633622931579 7.8 GB
EGAF00005493415 1633616704593 8.3 GB
EGAF00005493417 1633621010420 20.7 GB
EGAF00005493420 1633635189625 6.3 GB
EGAF00005493422 1633608705482 9.4 GB
EGAF00005493424 1633628505125 7.3 GB
EGAF00005493426 1633622706246 7.4 GB
EGAF00005493428 1633612270539 8.4 GB
EGAF00005493430 1633608705481 8.1 GB
EGAF00005493432 1633627087139 7.0 GB
EGAF00005493434 1633629879289 7.3 GB
EGAF00005493436 1633614345603 8.0 GB
EGAF00005493438 1633614406526 7.2 GB
EGAF00005493439 1633611855814 12.9 GB
EGAF00005493441 1633623465823 11.7 GB
EGAF00005493443 1633609785489 13.0 GB
EGAF00005493445 1633628744425 10.9 GB
EGAF00005493448 1633626778420 13.5 GB
EGAF00005493451 1633626332129 12.4 GB
EGAF00005493453 1633628085004 10.7 GB
EGAF00005493455 1633620407782 11.9 GB
EGAF00005493457 1633616704593 12.9 GB
EGAF00005493459 1633625937176 12.8 GB
EGAF00005493461 1633625162494 11.2 GB
EGAF00005493463 1633613926803 12.5 GB
EGAF00005493465 1633622825886 11.1 GB
EGAF00005493467 1633623286740 12.3 GB
EGAF00005493469 1633617524772 12.2 GB
116 Files (1.1 TB)