About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
Need Help?

Shallow Whole-Genome Sequencing of Plasma ctDNA in Relapsed/Refractory Germ Cell Tumors

This dataset comprises shallow whole-genome sequencing data (~3× coverage) of circulating tumor DNA extracted from baseline and on-treatment plasma samples of patients with relapsed or refractory germ cell tumors treated with salvage high-dose chemotherapy. Libraries were generated from 20 ng of cfDNA using the KAPA Hyper Prep protocol with unique dual indexing and sequenced on an Illumina NovaSeq 6000 platform to enable genome-wide copy number and biomarker analyses associated with treatment response and clinical outcome.

Request Access

These terms and conditions govern access to the managed access datasets to which the User Institution has requested access. After the request from the User Institution, IRCCS Istituto Romagnolo per lo Studio dei Tumori "Dino Amadori" Italian Cancer Center Data Access Committee will evaluate it and the data access will be granted only after the subscription of a Data Access Agreement form that will include the following definitions and terms and conditions. Any further details about specific project, dataset or authorization will also be included in the Data Access Agreement form.

DATA ACCESS AGREEMENT TERMS & CONDITIONS These terms and conditions govern access to the managed access datasets to which the User Institution has requested access. After the request from the User Institution, IRST will evaluate it and the data access will be granted only after the subscription of a Data Access Agreement form that will include the following definitions and terms and conditions. Any further details about specific project, dataset or authorization will also be included in the Data Access Agreement form. Definitions Authorised Personnel: The individuals at the User Institution to whom IRST grants access to the Data. This includes the User and any other individuals for whom the User Institution subsequently requests access to the Data. Data: The managed access datasets to which the User Institution has requested access. Data Producers: IRST and the collaborators 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. 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: Research seeking to advance the understanding and state of the art of the specific field of interest. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. IRST: IRCCS Istituto Romagnolo per lo Studio dei Tumori “Dino Amadori” - IRST S.r.l. Terms and Conditions 1. The User Institution agrees to only use these Data for the purpose of the Project 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 the Project description. 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. 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 agree that in handling this Data it will follow an up-to-date information technology (IT) policy that must include, at a minimum, the following items: a. Logging and auditing of Access to the Data and to the computer network; b. Password protection to computer network and/or strong data encryption; c. Virus and malware protection to computers on the computer network; d. Secure backup procedure. 5. The User Institution agrees not to attempt to identify Research Participants. 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. 6. 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. 7. 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. 8. The User Institution agrees, when applicable, to follow the Fort Lauderdale Guidelines (1) and the Toronto Statement (2). 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. 9. The User Institution agrees to follow this Publication Policy: a. User Institution intends to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. IRST anticipates that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. b. User Institution respects the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. c. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur before 6 months after these data were first made available on the relevant hosting database, unless IRST has provided written consent to earlier submission. d. In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database and its accession numbers, and acknowledge its use in a form agreed by the User Institution with IRST. 10. The User Institution recognizes that nothing in this Agreement shall operate to transfer any intellectual property rights to the Data and 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. 11. 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, when applicable, the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) (3) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (4). 12. 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. 13. The User Institution will notify IRST within 30 days of any changes or departures of Authorised Personnel. 14. The User Institution will notify IRST prior to any significant changes to the protocol for the Project. 15. The User Institution will notify IRST as soon as it becomes aware of a breach of the terms or conditions of this agreement. 16. IRST 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 purposes in conformity with audit or legal requirements. 17. 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 IRST. 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. 18. 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. 19. 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. 20. 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 the laws to which the User Institution must comply and by the laws of Italy, and is subject to the exclusive jurisdiction of the courts of of the courts that will be defined by the User Institution and of the courts of Forlì (Italy). The Parties undertake to amicably settle any disputes that may arise from this agreement. In the event of disputes arising between the Parties regarding the interpretation, execution and termination of this agreement, the place of jurisdiction will be the Court of the defendant. (1)http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.pdf (2) http://www.nature.com/nature/journal/v461/n7261/full/461168a.html (3) https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf (4) http://www.oecd.org/science/biotech/36198812.pdf

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
EGAS50000001510 Whole Genome Sequencing

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
i
EGAF50000519653 fastq.gz 3.3 GB
EGAF50000519654 fastq.gz 3.0 GB
EGAF50000519655 fastq.gz 2.5 GB
EGAF50000519656 fastq.gz 3.0 GB
EGAF50000519657 fastq.gz 2.7 GB
EGAF50000519658 fastq.gz 2.8 GB
EGAF50000519659 fastq.gz 3.1 GB
EGAF50000519660 fastq.gz 2.2 GB
EGAF50000519661 fastq.gz 3.3 GB
EGAF50000519662 fastq.gz 2.7 GB
EGAF50000519663 fastq.gz 2.9 GB
EGAF50000519664 fastq.gz 2.5 GB
EGAF50000519665 fastq.gz 2.4 GB
EGAF50000519666 fastq.gz 2.3 GB
EGAF50000519667 fastq.gz 2.7 GB
EGAF50000519668 fastq.gz 2.3 GB
EGAF50000519669 fastq.gz 2.3 GB
EGAF50000519670 fastq.gz 3.3 GB
EGAF50000519671 fastq.gz 2.8 GB
EGAF50000519672 fastq.gz 2.8 GB
EGAF50000519673 fastq.gz 3.4 GB
EGAF50000519674 fastq.gz 1.9 GB
EGAF50000519675 fastq.gz 3.6 GB
EGAF50000519676 fastq.gz 2.6 GB
EGAF50000519677 fastq.gz 2.7 GB
EGAF50000519678 fastq.gz 2.3 GB
EGAF50000519679 fastq.gz 2.5 GB
EGAF50000519680 fastq.gz 2.7 GB
EGAF50000519681 fastq.gz 2.6 GB
EGAF50000519682 fastq.gz 3.1 GB
EGAF50000519683 fastq.gz 2.9 GB
EGAF50000519684 fastq.gz 2.1 GB
EGAF50000519685 fastq.gz 2.1 GB
EGAF50000519686 fastq.gz 2.7 GB
EGAF50000519687 fastq.gz 3.2 GB
EGAF50000519688 fastq.gz 2.8 GB
EGAF50000519689 fastq.gz 2.1 GB
EGAF50000519690 fastq.gz 2.8 GB
EGAF50000519691 fastq.gz 3.0 GB
EGAF50000519692 fastq.gz 3.5 GB
EGAF50000519693 fastq.gz 3.2 GB
EGAF50000519694 fastq.gz 3.1 GB
EGAF50000519695 fastq.gz 2.1 GB
EGAF50000519696 fastq.gz 3.3 GB
EGAF50000519697 fastq.gz 2.0 GB
EGAF50000519698 fastq.gz 3.6 GB
EGAF50000519699 fastq.gz 3.4 GB
EGAF50000519700 fastq.gz 3.1 GB
EGAF50000519701 fastq.gz 2.6 GB
EGAF50000519702 fastq.gz 2.8 GB
EGAF50000519703 fastq.gz 3.4 GB
EGAF50000519704 fastq.gz 2.5 GB
EGAF50000519705 fastq.gz 3.0 GB
EGAF50000519706 fastq.gz 3.5 GB
EGAF50000519707 fastq.gz 3.0 GB
EGAF50000519708 fastq.gz 3.4 GB
EGAF50000519709 fastq.gz 2.2 GB
EGAF50000519710 fastq.gz 2.5 GB
EGAF50000519711 fastq.gz 3.1 GB
EGAF50000519712 fastq.gz 2.1 GB
EGAF50000519713 fastq.gz 2.1 GB
EGAF50000519714 fastq.gz 2.5 GB
EGAF50000519715 fastq.gz 2.1 GB
EGAF50000519716 fastq.gz 2.9 GB
EGAF50000519717 fastq.gz 3.0 GB
EGAF50000519718 fastq.gz 3.5 GB
EGAF50000519719 fastq.gz 2.8 GB
EGAF50000519720 fastq.gz 3.1 GB
EGAF50000519721 fastq.gz 2.8 GB
EGAF50000519722 fastq.gz 2.1 GB
EGAF50000519723 fastq.gz 3.1 GB
EGAF50000519724 fastq.gz 3.1 GB
EGAF50000519725 fastq.gz 2.5 GB
EGAF50000519726 fastq.gz 2.6 GB
EGAF50000519727 fastq.gz 2.5 GB
EGAF50000519728 fastq.gz 3.1 GB
EGAF50000519729 fastq.gz 2.8 GB
EGAF50000519730 fastq.gz 3.1 GB
EGAF50000519731 fastq.gz 2.7 GB
EGAF50000519732 fastq.gz 2.3 GB
EGAF50000519733 fastq.gz 2.8 GB
EGAF50000519734 fastq.gz 3.1 GB
EGAF50000519735 fastq.gz 2.8 GB
EGAF50000519736 fastq.gz 2.2 GB
EGAF50000519737 fastq.gz 2.7 GB
EGAF50000519738 fastq.gz 2.6 GB
EGAF50000519739 fastq.gz 2.2 GB
EGAF50000519740 fastq.gz 3.1 GB
EGAF50000519741 fastq.gz 2.1 GB
EGAF50000519742 fastq.gz 3.2 GB
EGAF50000519743 fastq.gz 2.7 GB
EGAF50000519744 fastq.gz 2.5 GB
EGAF50000519745 fastq.gz 2.8 GB
EGAF50000519746 fastq.gz 2.9 GB
EGAF50000519747 fastq.gz 2.8 GB
EGAF50000519748 fastq.gz 2.7 GB
EGAF50000519749 fastq.gz 2.9 GB
EGAF50000519750 fastq.gz 2.8 GB
EGAF50000519751 fastq.gz 2.7 GB
EGAF50000519752 fastq.gz 2.3 GB
EGAF50000519753 fastq.gz 3.2 GB
EGAF50000519754 fastq.gz 2.9 GB
EGAF50000519755 fastq.gz 3.3 GB
EGAF50000519756 fastq.gz 2.1 GB
EGAF50000519757 fastq.gz 2.3 GB
EGAF50000519758 fastq.gz 2.6 GB
EGAF50000519759 fastq.gz 2.6 GB
EGAF50000519760 fastq.gz 2.2 GB
EGAF50000519761 fastq.gz 2.2 GB
EGAF50000519762 fastq.gz 2.5 GB
EGAF50000519763 fastq.gz 2.7 GB
EGAF50000519764 fastq.gz 2.8 GB
EGAF50000519765 fastq.gz 2.1 GB
EGAF50000519766 fastq.gz 2.8 GB
EGAF50000519767 fastq.gz 2.0 GB
EGAF50000519768 fastq.gz 2.4 GB
EGAF50000519769 fastq.gz 2.7 GB
EGAF50000519770 fastq.gz 2.5 GB
EGAF50000519771 fastq.gz 2.7 GB
EGAF50000519772 fastq.gz 2.4 GB
EGAF50000519773 fastq.gz 2.8 GB
EGAF50000519774 fastq.gz 3.2 GB
EGAF50000519775 fastq.gz 3.0 GB
EGAF50000519776 fastq.gz 2.5 GB
EGAF50000519777 fastq.gz 2.8 GB
EGAF50000519778 fastq.gz 3.5 GB
EGAF50000519779 fastq.gz 2.9 GB
EGAF50000519780 fastq.gz 2.8 GB
EGAF50000519781 fastq.gz 2.6 GB
EGAF50000519782 fastq.gz 2.4 GB
EGAF50000519783 fastq.gz 3.0 GB
EGAF50000519784 fastq.gz 3.0 GB
EGAF50000519785 fastq.gz 2.7 GB
EGAF50000519786 fastq.gz 2.9 GB
EGAF50000519787 fastq.gz 2.6 GB
EGAF50000519788 fastq.gz 2.1 GB
EGAF50000519789 fastq.gz 2.2 GB
EGAF50000519790 fastq.gz 2.7 GB
EGAF50000519791 fastq.gz 2.4 GB
EGAF50000519792 fastq.gz 2.6 GB
EGAF50000519793 fastq.gz 3.2 GB
EGAF50000519794 fastq.gz 2.8 GB
EGAF50000519795 fastq.gz 2.4 GB
EGAF50000519796 fastq.gz 3.4 GB
EGAF50000519797 fastq.gz 2.5 GB
EGAF50000519798 fastq.gz 2.1 GB
EGAF50000519799 fastq.gz 2.5 GB
EGAF50000519800 fastq.gz 2.7 GB
148 Files (403.5 GB)