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The dataset for Detecting Liver Cancer Using Cell-Free DNA Fragmentomes

The dataset for Detecting Liver Cancer Using Cell-Free DNA Fragmentomes includes 444 BAM files from whole genome next-generation sequencing on the Illumina NovaSeq 6000. The samples analyzed include plasma samples from individuals with and without cancer.

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The data access policy for Detecting Liver Cancer Using Cell-Free DNA Fragmentomes

DATA ACCESS AGREEMENT for EGA Study EGAS00001007249 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 DAC: The data access committee for Detecting Liver Cancer Using Cell-Free DNA Fragmentomes, EGA DAC EGAC00001003279. Authorised Personnel: The individuals at the User Institution to whom the DAC 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 DAC 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. Please include your Institution details here: 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. Should User Institution inadvertently receive identifiable information or otherwise identify a subject, Recipient shall promptly notify Provider and follow Data Producer’s reasonable written instructions, which may include return or destruction of the identifiable information. 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 cite the publication(s) from which the Data are derived to acknowledge the version of the data and the contribution of the Data Producers in all reports or publications resulting from the use of the Data. The full citation(s) of the Data generating publication(s) and suggested acknowledgement are in Appendix III. 8. The User Institution agrees to follow the Fort Lauderdale Guidelines (https://www.sanger.ac.uk/wp-content/uploads/fortlauderdalereport.pdf) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). Nothing herein shall authorize the User Institution to use or further disclose the Data in a manner that would violate the requirements of Data Producers under U.S. law, including 45 CFR 164.514. 9. The User Institution agrees to follow the Publication Policy in Appendix IV. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 10. 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. 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 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 ). 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 the DAC within 30 days of any changes or departures of Authorised Personnel. 14. The User Institution will notify the DAC prior to any significant changes to the protocol for the Project. 15. The User Institution will notify the DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 16. The DAC 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. 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 the DAC. 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. If the Data Producer is a HIPAA Covered Entity, and if the the Data will be a Limited Data Set as defined by the Health Insurance Portability and Accountability Act of 1996 (“HIPAA”). In accordance with Section 164.514(e)(2) of the HIPAA Privacy Rule, the Data shall exclude the following direct identifiers of the individual or of relatives, employers, or household members of the individual: (i) Names; (ii) Postal address information, other than town or city, State, and zip code; (iii) Telephone numbers; (iv) Fax numbers; (v) Electronic mail addresses; (vi) Social security numbers; (vii) Medical record numbers; (viii) Health plan beneficiary numbers; (ix) Account numbers; (x) Certificate/license numbers; (xi) Vehicle identifiers and serial numbers, including license plate numbers; (xii) Device identifiers and serial numbers; (xiii) Web Universal Resource Locators (URLs); (xiv) Internet Protocol (IP) address numbers; (xv) Biometric identifiers, including finger and voice prints; and (xvi) Full face photographic images and any comparable images. If the Data being provided is coded, the Data Producer will not release, and the User Institution will not request, the key to the code.   Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for the DAC Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III – CITATION AND ACKNOWLEDGEMENT APPENDIX IV –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) EGA study accession EGAS00001007249: Detecting Liver Cancer Using Cell-Free DNA Fragmentomes EGA dataset, EGAD00001010931, for study EGAS00001007249: The dataset for Detecting Liver Cancer Using Cell-Free DNA Fragmentomes includes 444 BAM files from whole genome next-generation sequencing on the Illumina NovaSeq 6000. The samples analyzed include plasma samples from individuals with and without cancer. Name of project that created the dataset EGA study accession EGAS00001007249: Detecting Liver Cancer Using Cell-Free DNA Fragmentomes Names of other data producers/collaborators Zachariah H. Foda, Akshaya V. Annapragada, Kavya Boyapati, Daniel C. Bruhm, Nicholas A. Vulpescu, Jamie E. Medina, Dimitrios Mathios, Stephen Cristiano, Noushin Niknafs, Harry T. Luu, Michael G. Goggins, Robert A. Anders, Jing Sun, Shruti H. Meta, David L. Thomas, Gregory D. Kirk, Vilmos Adleff, Jillian Phallen, Robert B. Scharpf, Amy K. Kim, and Victor E. Velculescu Specific limitations on areas of research The User Institution agrees that it will only use these Data for Research Purposes. Minimum protection measures required File access: Data can be held in unencrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number Brief abstract of the Project in which the Data will be used (500 words max) All Individuals who the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* All Individuals that should have an account created at the EGA Name of Registered User Email Job Title   APPENDIX III – CITATION AND ACKNOWLEDGEMENT Citation(s) for the publication(s) from which the Data are derived: Foda ZH, Annapragada AV, Boyapati K, Bruhm DC, Vulpescu NA, Medina JE, Mathios D, Cristiano S, Niknafs N, Luu HT, Goggins MG, Anders RA, Sun J, Meta SH, Thomas DL, Kirk GD, Adleff V, Phallen J, Scharpf RB, Kim AK, and Velculescu VE. Detecting Liver Cancer Using Cell-Free DNA Fragmentomes. Cancer Discov. 2023 Mar 1;13(3):616-631. doi: 10.1158/2159-8290.CD-22-0659. PMID: 36399356; PMCID: PMC9975663. Acknowledgement of the version of the data and the contribution of the Data Producers: “This study uses data generated by The Cancer Genomics Laboratory at The Johns Hopkins University School of Medicine Sidney Kimmel Comprehensive Cancer Center as reported by Foda et al., Cancer Discov., 2023, PMID: 36399356.” APPENDIX IV – PUBLICATION POLICY The DAC intend 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. The DAC 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. 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 until 0 months after these data were first made available on the relevant hosting database, unless the DAC has provided written consent to earlier submission. In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS000000000XX), and acknowledge its use in a form agreed by the User Institution with the DAC.

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
EGAS00001007249 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
EGAF00008090922 bam 5.8 GB
EGAF00008090923 bam 5.4 GB
EGAF00008090924 bam 7.5 GB
EGAF00008090925 bam 6.9 GB
EGAF00008090926 bam 7.4 GB
EGAF00008090927 bam 12.0 GB
EGAF00008090928 bam 7.5 GB
EGAF00008090929 bam 12.3 GB
EGAF00008090930 bam 9.4 GB
EGAF00008090931 bam 5.8 GB
EGAF00008090932 bam 6.5 GB
EGAF00008090933 bam 6.3 GB
EGAF00008090934 bam 5.9 GB
EGAF00008090935 bam 8.6 GB
EGAF00008090936 bam 7.0 GB
EGAF00008090937 bam 9.0 GB
EGAF00008090938 bam 6.7 GB
EGAF00008090939 bam 6.6 GB
EGAF00008090940 bam 7.5 GB
EGAF00008090941 bam 7.2 GB
EGAF00008090942 bam 7.0 GB
EGAF00008090943 bam 6.5 GB
EGAF00008090944 bam 6.6 GB
EGAF00008090945 bam 8.5 GB
EGAF00008090946 bam 9.9 GB
EGAF00008090947 bam 7.8 GB
EGAF00008090948 bam 7.1 GB
EGAF00008090949 bam 10.7 GB
EGAF00008090950 bam 6.3 GB
EGAF00008090951 bam 6.7 GB
EGAF00008090952 bam 7.2 GB
EGAF00008090953 bam 8.7 GB
EGAF00008090954 bam 6.3 GB
EGAF00008090955 bam 6.1 GB
EGAF00008090956 bam 6.1 GB
EGAF00008090957 bam 5.4 GB
EGAF00008090958 bam 7.8 GB
EGAF00008090959 bam 7.5 GB
EGAF00008090960 bam 7.8 GB
EGAF00008090961 bam 8.5 GB
EGAF00008090962 bam 5.1 GB
EGAF00008090963 bam 7.8 GB
EGAF00008090964 bam 3.7 GB
EGAF00008090965 bam 6.5 GB
EGAF00008090966 bam 7.8 GB
EGAF00008090967 bam 8.0 GB
EGAF00008090968 bam 10.4 GB
EGAF00008090969 bam 8.7 GB
EGAF00008090970 bam 5.3 GB
EGAF00008090971 bam 7.6 GB
EGAF00008090972 bam 7.1 GB
EGAF00008090973 bam 6.6 GB
EGAF00008090974 bam 4.8 GB
EGAF00008090975 bam 5.3 GB
EGAF00008090976 bam 9.4 GB
EGAF00008090977 bam 8.3 GB
EGAF00008090978 bam 5.9 GB
EGAF00008090979 bam 5.8 GB
EGAF00008090980 bam 6.3 GB
EGAF00008090981 bam 6.8 GB
EGAF00008090982 bam 5.6 GB
EGAF00008090983 bam 6.6 GB
EGAF00008090984 bam 7.1 GB
EGAF00008090985 bam 6.9 GB
EGAF00008090986 bam 4.8 GB
EGAF00008090987 bam 9.4 GB
EGAF00008090988 bam 6.1 GB
EGAF00008090989 bam 5.5 GB
EGAF00008090990 bam 6.4 GB
EGAF00008090991 bam 7.4 GB
EGAF00008090992 bam 7.6 GB
EGAF00008090993 bam 7.5 GB
EGAF00008090994 bam 6.9 GB
EGAF00008090995 bam 6.1 GB
EGAF00008090996 bam 3.8 GB
EGAF00008090997 bam 4.8 GB
EGAF00008090998 bam 9.3 GB
EGAF00008090999 bam 6.2 GB
EGAF00008091000 bam 7.8 GB
EGAF00008091001 bam 8.0 GB
EGAF00008091002 bam 9.9 GB
EGAF00008091003 bam 7.9 GB
EGAF00008091004 bam 11.7 GB
EGAF00008091005 bam 10.9 GB
EGAF00008091006 bam 6.8 GB
EGAF00008091007 bam 8.0 GB
EGAF00008091008 bam 9.2 GB
EGAF00008091009 bam 6.1 GB
EGAF00008091010 bam 9.6 GB
EGAF00008091011 bam 7.2 GB
EGAF00008091012 bam 8.7 GB
EGAF00008091013 bam 7.2 GB
EGAF00008091014 bam 7.0 GB
EGAF00008091015 bam 8.5 GB
EGAF00008091016 bam 8.5 GB
EGAF00008091017 bam 9.8 GB
EGAF00008091018 bam 7.4 GB
EGAF00008091019 bam 6.7 GB
EGAF00008091020 bam 9.8 GB
EGAF00008091021 bam 8.2 GB
EGAF00008091022 bam 8.3 GB
EGAF00008091023 bam 8.3 GB
EGAF00008091024 bam 6.6 GB
EGAF00008091025 bam 8.3 GB
EGAF00008091026 bam 9.9 GB
EGAF00008091027 bam 9.1 GB
EGAF00008091028 bam 7.8 GB
EGAF00008091029 bam 5.8 GB
EGAF00008091030 bam 6.3 GB
EGAF00008091031 bam 9.0 GB
EGAF00008091032 bam 7.1 GB
EGAF00008091033 bam 7.1 GB
EGAF00008091034 bam 8.3 GB
EGAF00008091035 bam 3.8 GB
EGAF00008091036 bam 3.4 GB
EGAF00008091037 bam 8.4 GB
EGAF00008091038 bam 5.4 GB
EGAF00008091039 bam 15.9 GB
EGAF00008091040 bam 6.3 GB
EGAF00008091041 bam 7.0 GB
EGAF00008091042 bam 9.2 GB
EGAF00008091043 bam 7.1 GB
EGAF00008091044 bam 6.1 GB
EGAF00008091045 bam 4.3 GB
EGAF00008091046 bam 4.2 GB
EGAF00008091047 bam 4.2 GB
EGAF00008091048 bam 4.1 GB
EGAF00008091049 bam 4.8 GB
EGAF00008091050 bam 7.5 GB
EGAF00008091051 bam 3.9 GB
EGAF00008091052 bam 4.3 GB
EGAF00008091053 bam 2.8 GB
EGAF00008091054 bam 4.1 GB
EGAF00008091055 bam 4.8 GB
EGAF00008091056 bam 3.9 GB
EGAF00008091057 bam 8.1 GB
EGAF00008091058 bam 4.5 GB
EGAF00008091059 bam 4.3 GB
EGAF00008091060 bam 506.1 MB
EGAF00008091061 bam 6.1 GB
EGAF00008091062 bam 4.3 GB
EGAF00008091063 bam 4.4 GB
EGAF00008091064 bam 6.6 GB
EGAF00008091065 bam 4.4 GB
EGAF00008091066 bam 7.6 GB
EGAF00008091067 bam 491.8 MB
EGAF00008091068 bam 4.2 GB
EGAF00008091069 bam 3.8 GB
EGAF00008091070 bam 5.6 GB
EGAF00008091071 bam 3.9 GB
EGAF00008091072 bam 9.1 GB
151 Files (1.0 TB)