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Molecular characterization of NASH-HCC

We collected 80 NASH-HCCs formalin fixed paraffin-embedded (FFPE) samples from 5 different institutions. NASH was diagnosed in FFPE samples by at least two expert pathologists following a described histological algorithm (Bedossa et al., Hepatology, 2012). All NASH patients included in the study were HBV- and HCV-negative. Patients reporting alcohol consumption ≥ 20 g/day for women and 30 g/day for men, as well as patients with a known liver disease superimposed to NASH were excluded. Tumour and paired non-tumour gDNA of NASH-HCC FFPE samples was submitted to Whole Exome Sequencing (WES). Exome capture and sequencing library preparation were performed using the SureSelect Human All Exon V5, no UTR hybridization capture kit from Agilent (Target Size 50 Mb). Libraries were sequenced on an Illumina HiSeq 4000 instrument with 100-bp paired-end reads.

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The Laboratory of Translational Research in Hepatic Oncology at IDIBAPs will conform the DAC for this dataset.

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 IDIBAPS within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify IDIBAPS prior to any significant changes to the protocol for the Project. 14. The User Institution will notify IDIBAPS as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. IDIBAPS 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 IDIBAPS. 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 Spain and shall be subject to the exclusive jurisdiction of the Spanish 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
EGAS00001005222 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
EGAF00005198420 fastq.gz 9.0 GB
EGAF00005198421 fastq.gz 10.5 GB
EGAF00005198422 fastq.gz 2.3 GB
EGAF00005198423 fastq.gz 2.6 GB
EGAF00005198424 fastq.gz 2.3 GB
EGAF00005198425 fastq.gz 2.7 GB
EGAF00005198426 fastq.gz 2.7 GB
EGAF00005198427 fastq.gz 2.5 GB
EGAF00005198428 fastq.gz 2.3 GB
EGAF00005198429 fastq.gz 2.6 GB
EGAF00005198430 fastq.gz 8.7 GB
EGAF00005198431 fastq.gz 9.8 GB
EGAF00005198432 fastq.gz 9.7 GB
EGAF00005198433 fastq.gz 10.9 GB
EGAF00005198434 fastq.gz 2.8 GB
EGAF00005198435 fastq.gz 3.2 GB
EGAF00005198436 fastq.gz 9.1 GB
EGAF00005198437 fastq.gz 10.4 GB
EGAF00005198438 fastq.gz 3.0 GB
EGAF00005198439 fastq.gz 3.4 GB
EGAF00005198440 fastq.gz 7.9 GB
EGAF00005198441 fastq.gz 8.8 GB
EGAF00005198442 fastq.gz 9.3 GB
EGAF00005198443 fastq.gz 10.5 GB
EGAF00005198444 fastq.gz 2.5 GB
EGAF00005198445 fastq.gz 2.9 GB
EGAF00005198446 fastq.gz 2.7 GB
EGAF00005198447 fastq.gz 3.1 GB
EGAF00005198448 fastq.gz 8.0 GB
EGAF00005198449 fastq.gz 9.1 GB
EGAF00005198450 fastq.gz 2.5 GB
EGAF00005198451 fastq.gz 2.7 GB
EGAF00005198452 fastq.gz 2.9 GB
EGAF00005198453 fastq.gz 3.2 GB
EGAF00005198454 fastq.gz 9.6 GB
EGAF00005198455 fastq.gz 11.0 GB
EGAF00005198456 fastq.gz 9.0 GB
EGAF00005198457 fastq.gz 10.0 GB
EGAF00005198458 fastq.gz 8.7 GB
EGAF00005198459 fastq.gz 9.8 GB
EGAF00005198460 fastq.gz 8.3 GB
EGAF00005198461 fastq.gz 9.2 GB
EGAF00005198462 fastq.gz 3.2 GB
EGAF00005198463 fastq.gz 3.5 GB
EGAF00005198464 fastq.gz 10.1 GB
EGAF00005198465 fastq.gz 11.8 GB
EGAF00005198466 fastq.gz 10.4 GB
EGAF00005198467 fastq.gz 11.5 GB
EGAF00005198468 fastq.gz 3.1 GB
EGAF00005198469 fastq.gz 3.6 GB
EGAF00005198470 fastq.gz 3.5 GB
EGAF00005198471 fastq.gz 3.9 GB
EGAF00005198472 fastq.gz 9.2 GB
EGAF00005198473 fastq.gz 9.5 GB
EGAF00005198474 fastq.gz 2.6 GB
EGAF00005198475 fastq.gz 2.8 GB
EGAF00005198476 fastq.gz 3.5 GB
EGAF00005198477 fastq.gz 3.9 GB
EGAF00005198478 fastq.gz 3.0 GB
EGAF00005198479 fastq.gz 3.3 GB
EGAF00005198480 fastq.gz 11.1 GB
EGAF00005198481 fastq.gz 12.5 GB
EGAF00005198482 fastq.gz 2.5 GB
EGAF00005198483 fastq.gz 2.9 GB
EGAF00005198484 fastq.gz 10.4 GB
EGAF00005198485 fastq.gz 11.9 GB
EGAF00005198486 fastq.gz 14.9 GB
EGAF00005198487 fastq.gz 17.6 GB
EGAF00005198488 fastq.gz 3.0 GB
EGAF00005198489 fastq.gz 3.4 GB
EGAF00005198490 fastq.gz 8.9 GB
EGAF00005198491 fastq.gz 9.7 GB
EGAF00005198492 fastq.gz 3.2 GB
EGAF00005198493 fastq.gz 3.5 GB
EGAF00005198494 fastq.gz 9.5 GB
EGAF00005198495 fastq.gz 10.5 GB
EGAF00005198496 fastq.gz 3.6 GB
EGAF00005198497 fastq.gz 4.2 GB
EGAF00005198498 fastq.gz 3.3 GB
EGAF00005198499 fastq.gz 3.6 GB
EGAF00005198500 fastq.gz 8.3 GB
EGAF00005198501 fastq.gz 9.2 GB
EGAF00005198502 fastq.gz 9.1 GB
EGAF00005198503 fastq.gz 10.0 GB
EGAF00005198504 fastq.gz 3.0 GB
EGAF00005198505 fastq.gz 3.3 GB
EGAF00005198506 fastq.gz 2.8 GB
EGAF00005198507 fastq.gz 3.2 GB
EGAF00005198508 fastq.gz 10.8 GB
EGAF00005198509 fastq.gz 11.8 GB
EGAF00005198510 fastq.gz 10.5 GB
EGAF00005198511 fastq.gz 12.1 GB
EGAF00005198512 fastq.gz 3.7 GB
EGAF00005198513 fastq.gz 4.2 GB
EGAF00005198514 fastq.gz 2.6 GB
EGAF00005198515 fastq.gz 3.0 GB
EGAF00005198516 fastq.gz 10.9 GB
EGAF00005198517 fastq.gz 12.6 GB
EGAF00005198518 fastq.gz 2.8 GB
EGAF00005198519 fastq.gz 3.2 GB
EGAF00005198520 fastq.gz 9.2 GB
EGAF00005198521 fastq.gz 10.7 GB
EGAF00005198522 fastq.gz 8.5 GB
EGAF00005198523 fastq.gz 9.4 GB
EGAF00005198524 fastq.gz 3.4 GB
EGAF00005198525 fastq.gz 3.8 GB
EGAF00005198526 fastq.gz 2.5 GB
EGAF00005198527 fastq.gz 2.8 GB
EGAF00005198528 fastq.gz 10.9 GB
EGAF00005198529 fastq.gz 12.7 GB
EGAF00005198530 fastq.gz 2.3 GB
EGAF00005198531 fastq.gz 2.7 GB
EGAF00005198532 fastq.gz 8.3 GB
EGAF00005198533 fastq.gz 9.6 GB
EGAF00005198534 fastq.gz 3.4 GB
EGAF00005198535 fastq.gz 4.0 GB
EGAF00005198536 fastq.gz 11.4 GB
EGAF00005198537 fastq.gz 13.3 GB
EGAF00005198538 fastq.gz 2.8 GB
EGAF00005198539 fastq.gz 3.1 GB
EGAF00005198540 fastq.gz 3.8 GB
EGAF00005198541 fastq.gz 4.2 GB
EGAF00005198542 fastq.gz 6.5 GB
EGAF00005198543 fastq.gz 7.4 GB
EGAF00005198544 fastq.gz 10.7 GB
EGAF00005198545 fastq.gz 11.7 GB
EGAF00005198546 fastq.gz 7.1 GB
EGAF00005198547 fastq.gz 7.9 GB
EGAF00005198548 fastq.gz 3.4 GB
EGAF00005198549 fastq.gz 3.7 GB
EGAF00005198550 fastq.gz 5.9 GB
EGAF00005198551 fastq.gz 6.3 GB
132 Files (864.9 GB)