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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
EGAS00001005073 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 bam 7.9 GB
EGAF00005493244 bam 6.5 GB
EGAF00005493245 bam 19.6 GB
EGAF00005493246 bam 9.2 GB
EGAF00005493247 bam 14.0 GB
EGAF00005493248 bam 6.4 GB
EGAF00005493249 bam 14.2 GB
EGAF00005493250 bam 8.1 GB
EGAF00005493251 bam 14.6 GB
EGAF00005493252 bam 8.3 GB
EGAF00005493253 bam 13.7 GB
EGAF00005493254 bam 13.4 GB
EGAF00005493255 bam 8.6 GB
EGAF00005493256 bam 11.0 GB
EGAF00005493257 bam 13.5 GB
EGAF00005493258 bam 8.0 GB
EGAF00005493259 bam 14.0 GB
EGAF00005493260 bam 9.9 GB
EGAF00005493261 bam 13.4 GB
EGAF00005493262 bam 8.3 GB
EGAF00005493263 bam 14.1 GB
EGAF00005493264 bam 7.0 GB
EGAF00005493265 bam 13.6 GB
EGAF00005493266 bam 6.7 GB
EGAF00005493267 bam 8.2 GB
EGAF00005493268 bam 18.1 GB
EGAF00005493269 bam 7.2 GB
EGAF00005493270 bam 13.6 GB
EGAF00005493271 bam 8.9 GB
EGAF00005493272 bam 20.3 GB
EGAF00005493273 bam 7.8 GB
EGAF00005493274 bam 13.7 GB
EGAF00005493275 bam 8.6 GB
EGAF00005493276 bam 29.2 GB
EGAF00005493277 bam 14.8 GB
EGAF00005493278 bam 15.1 GB
EGAF00005493279 bam 24.1 GB
EGAF00005493280 bam 7.9 GB
EGAF00005493281 bam 14.7 GB
EGAF00005493282 bam 8.6 GB
EGAF00005493283 bam 8.6 GB
EGAF00005493284 bam 27.2 GB
EGAF00005493285 bam 7.6 GB
EGAF00005493286 bam 13.2 GB
EGAF00005493287 bam 7.5 GB
EGAF00005493288 bam 19.5 GB
EGAF00005493289 bam 43.5 GB
EGAF00005493290 bam 13.8 GB
EGAF00005493291 bam 7.3 GB
EGAF00005493292 bam 18.9 GB
EGAF00005493293 bam 14.3 GB
EGAF00005493294 bam 7.0 GB
EGAF00005493295 bam 16.4 GB
EGAF00005493296 bam 10.7 GB
EGAF00005493297 bam 13.7 GB
EGAF00005493298 bam 8.3 GB
EGAF00005493299 bam 5.1 GB
EGAF00005493300 bam 7.3 GB
EGAF00005493301 bam 7.1 GB
EGAF00005493302 bam 13.0 GB
EGAF00005493303 bam 9.1 GB
EGAF00005493304 bam 13.4 GB
EGAF00005493305 bam 7.1 GB
EGAF00005493306 bam 23.1 GB
EGAF00005493307 bam 9.2 GB
EGAF00005493308 bam 12.9 GB
EGAF00005493309 bam 6.7 GB
EGAF00005493310 bam 16.1 GB
EGAF00005493311 bam 6.7 GB
EGAF00005493312 bam 13.6 GB
EGAF00005493313 bam 8.2 GB
EGAF00005493314 bam 16.6 GB
EGAF00005493315 bam 8.8 GB
EGAF00005493316 bam 13.8 GB
EGAF00005493317 bam 7.0 GB
EGAF00005493318 bam 7.6 GB
EGAF00005493319 bam 15.4 GB
EGAF00005493320 bam 13.1 GB
EGAF00005493321 bam 7.5 GB
EGAF00005493322 bam 8.8 GB
EGAF00005493323 bam 20.1 GB
EGAF00005493324 bam 8.3 GB
EGAF00005493325 bam 16.3 GB
EGAF00005493326 bam 10.8 GB
EGAF00005493327 bam 20.6 GB
EGAF00005493328 bam 7.1 GB
EGAF00005493329 bam 13.5 GB
EGAF00005493330 bam 7.1 GB
EGAF00005493331 bam 15.9 GB
EGAF00005493332 bam 8.4 GB
EGAF00005493333 bam 13.8 GB
EGAF00005493334 bam 7.1 GB
EGAF00005493335 bam 13.3 GB
EGAF00005493336 bam 6.4 GB
EGAF00005493337 bam 13.7 GB
EGAF00005493338 bam 12.0 GB
EGAF00005493339 bam 20.2 GB
EGAF00005493340 bam 7.0 GB
EGAF00005493341 bam 16.5 GB
EGAF00005493342 bam 13.7 GB
EGAF00005493343 bam 15.8 GB
EGAF00005493344 bam 7.2 GB
EGAF00005493345 bam 22.8 GB
EGAF00005493346 bam 8.5 GB
EGAF00005493347 bam 20.5 GB
EGAF00005493348 bam 10.4 GB
EGAF00005493349 bam 17.2 GB
EGAF00005493350 bam 7.4 GB
EGAF00005493351 bam 8.2 GB
EGAF00005493352 bam 18.8 GB
EGAF00005493353 bam 9.6 GB
EGAF00005493354 bam 14.1 GB
EGAF00005493355 bam 8.4 GB
EGAF00005493356 bam 20.5 GB
EGAF00005493357 bam 9.5 GB
EGAF00005493358 bam 15.0 GB
EGAF00005493359 bam 7.6 GB
EGAF00005493360 bam 20.1 GB
EGAF00005493361 bam 8.1 GB
EGAF00005493362 bam 22.8 GB
EGAF00005493363 bam 14.7 GB
EGAF00005493364 bam 9.6 GB
EGAF00005493365 bam 28.0 GB
EGAF00005493366 bam 8.9 GB
EGAF00005493367 bam 21.9 GB
EGAF00005493368 bam 9.1 GB
EGAF00005493369 bam 15.1 GB
EGAF00005493370 bam 7.4 GB
EGAF00005493371 bam 17.0 GB
EGAF00005493372 bam 20.7 GB
EGAF00005493373 bam 13.9 GB
EGAF00005493374 bam 8.1 GB
EGAF00005493375 bam 14.1 GB
EGAF00005493376 bam 8.2 GB
EGAF00005493377 bam 15.7 GB
EGAF00005493378 bam 15.5 GB
EGAF00005493379 bam 9.9 GB
EGAF00005493380 bam 12.7 GB
EGAF00005493381 bam 9.8 GB
EGAF00005493382 bam 14.6 GB
EGAF00005493383 bam 15.0 GB
EGAF00005493384 bam 8.5 GB
EGAF00005493385 bam 9.5 GB
EGAF00005493386 bam 15.4 GB
EGAF00005493387 bam 15.5 GB
EGAF00005493388 bam 9.4 GB
EGAF00005493389 bam 14.2 GB
EGAF00005493390 bam 8.4 GB
EGAF00005493391 bam 21.2 GB
EGAF00005493392 bam 24.0 GB
EGAF00005493393 bam 9.2 GB
EGAF00005493394 bam 15.9 GB
EGAF00005493395 bam 10.1 GB
EGAF00005493396 bam 14.3 GB
EGAF00005493397 bam 9.2 GB
EGAF00005493398 bam 14.4 GB
EGAF00005493399 bam 9.3 GB
EGAF00005493400 bam 8.3 GB
EGAF00005493401 bam 7.4 GB
EGAF00005493402 bam 8.3 GB
EGAF00005493403 bam 14.0 GB
EGAF00005493404 bam 8.9 GB
EGAF00005493405 bam 14.6 GB
EGAF00005493406 bam 9.3 GB
EGAF00005493407 bam 28.1 GB
EGAF00005493408 bam 7.8 GB
EGAF00005493409 bam 14.2 GB
EGAF00005493410 bam 12.8 GB
EGAF00005493411 bam 10.8 GB
EGAF00005493412 bam 27.2 GB
EGAF00005493413 bam 9.0 GB
EGAF00005493414 bam 19.7 GB
EGAF00005493415 bam 8.3 GB
EGAF00005493416 bam 14.4 GB
EGAF00005493417 bam 20.7 GB
EGAF00005493418 bam 8.4 GB
EGAF00005493419 bam 18.4 GB
EGAF00005493420 bam 6.3 GB
EGAF00005493421 bam 16.1 GB
EGAF00005493422 bam 9.4 GB
EGAF00005493423 bam 16.2 GB
EGAF00005493424 bam 7.3 GB
EGAF00005493425 bam 17.0 GB
EGAF00005493426 bam 7.4 GB
EGAF00005493427 bam 17.6 GB
EGAF00005493428 bam 8.4 GB
EGAF00005493429 bam 17.9 GB
EGAF00005493430 bam 8.1 GB
EGAF00005493431 bam 15.4 GB
EGAF00005493432 bam 7.0 GB
EGAF00005493433 bam 16.0 GB
EGAF00005493434 bam 7.3 GB
EGAF00005493435 bam 17.8 GB
EGAF00005493436 bam 8.0 GB
EGAF00005493437 bam 16.1 GB
EGAF00005493438 bam 7.2 GB
EGAF00005493439 bam 12.9 GB
EGAF00005493440 bam 15.1 GB
EGAF00005493441 bam 11.7 GB
EGAF00005493442 bam 14.5 GB
EGAF00005493443 bam 13.0 GB
EGAF00005493444 bam 25.1 GB
EGAF00005493445 bam 10.9 GB
EGAF00005493446 bam 26.5 GB
EGAF00005493447 bam 27.8 GB
EGAF00005493448 bam 13.5 GB
EGAF00005493449 bam 27.2 GB
EGAF00005493450 bam 28.2 GB
EGAF00005493451 bam 12.4 GB
EGAF00005493452 bam 29.8 GB
EGAF00005493453 bam 10.7 GB
EGAF00005493454 bam 25.4 GB
EGAF00005493455 bam 11.9 GB
EGAF00005493456 bam 31.3 GB
EGAF00005493457 bam 12.9 GB
EGAF00005493458 bam 30.0 GB
EGAF00005493459 bam 12.8 GB
EGAF00005493460 bam 28.8 GB
EGAF00005493461 bam 11.2 GB
EGAF00005493462 bam 31.5 GB
EGAF00005493463 bam 12.5 GB
EGAF00005493464 bam 26.2 GB
EGAF00005493465 bam 11.1 GB
EGAF00005493466 bam 30.2 GB
EGAF00005493467 bam 12.3 GB
EGAF00005493468 bam 27.8 GB
EGAF00005493469 bam 12.2 GB
EGAF00005493470 bam 30.7 GB
228 Files (3.1 TB)