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Dataset for white blood cell and cell-free DNA analyses for detection of residual disease in gastric cancew

The dataset for white blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer includes 169 bam files from targeted deep sequencing on the Illumina HiSeq2500. The samples analyzed include genomic DNA from white blood cells and cell-free DNA from longitudinal blood collections of patients with gastric cancer.

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These terms and conditions govern access to the following managed access dataset: White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer (EGAS00001004114).

DATA ACCESS AGREEMENT for EGA Study EGAS00001004114 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 White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer, EGA DAC EGAC00001001435. 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 follow the Fort Lauderdale Guidelines ( ) and the Toronto Statement ( 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. 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. 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) ( ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) ( ). 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 DAC within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify the DAC prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. 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. 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 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. 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. 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 –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) EGA study accession EGAS00001004114: White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer EGA dataset for study EGAS00001004114: The dataset for White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer includes 169 bam files from targeted deep sequencing on the Illumina HiSeq2500. The samples analyzed include genomic DNA from white blood cells and cell-free DNA from longitudinal blood collections of patients with gastric cancer. Name of project that created the dataset EGA study accession EGAS00001004114: White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer Names of other data producers/collaborators Alessandro Leal, Nicole C. T. van Grieken, Doreen N. Palsgrove, Jillian Phallen, Jamie E. Medina, Carolyn Hruban, Mark A. M. Broeckaert, Valsamo Anagnostou, Vilmos Adleff, Daniel C. Bruhm, Jenna V. Canzoniero, Jacob Fiksel, Marianne Nordsmark, Fabienne A. R. M. Warmerdam, Henk M. W. Verheul, Dick Johan van Spronsen, Laurens V. Beerepoot, Maud M. Geenen, Johanneke E. A. Portielje, Edwin P. M. Jansen, Johanna van Sandick, Elma Meershoek-Klein Kranenbarg, Hanneke W. M. van Laarhoven, Donald L. van der Peet, Cornelis J. H. van de Velde, Marcel Verheij, Remond Fijneman, Robert B. Scharpf, Gerrit A. Meijer, Annemieke Cats, 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 – 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
EGAS00001004114 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
EGAF00003090480 bam 2.2 GB
EGAF00003090481 bam 3.4 GB
EGAF00003090482 bam 3.0 GB
EGAF00003090483 bam 3.5 GB
EGAF00003090484 bam 3.2 GB
EGAF00003090485 bam 2.9 GB
EGAF00003090926 bam 3.0 GB
EGAF00003090927 bam 2.5 GB
EGAF00003090928 bam 3.1 GB
EGAF00003090929 bam 2.1 GB
EGAF00003090930 bam 2.1 GB
EGAF00003090931 bam 3.4 GB
EGAF00003090932 bam 3.2 GB
EGAF00003090933 bam 3.3 GB
EGAF00003090934 bam 2.7 GB
EGAF00003090935 bam 2.9 GB
EGAF00003090936 bam 4.9 GB
EGAF00003090937 bam 3.3 GB
EGAF00003090938 bam 3.2 GB
EGAF00003090939 bam 3.0 GB
EGAF00003090940 bam 3.5 GB
EGAF00003090941 bam 3.1 GB
EGAF00003090942 bam 3.2 GB
EGAF00003090943 bam 3.1 GB
EGAF00003090944 bam 3.8 GB
EGAF00003090945 bam 3.1 GB
EGAF00003090946 bam 2.7 GB
EGAF00003090947 bam 3.5 GB
EGAF00003090948 bam 3.5 GB
EGAF00003090949 bam 3.4 GB
EGAF00003090950 bam 3.2 GB
EGAF00003090951 bam 2.8 GB
EGAF00003090952 bam 2.3 GB
EGAF00003090953 bam 2.6 GB
EGAF00003090954 bam 5.4 GB
EGAF00003090955 bam 1.9 GB
EGAF00003090956 bam 2.7 GB
EGAF00003090957 bam 3.3 GB
EGAF00003090958 bam 3.0 GB
EGAF00003090959 bam 2.3 GB
EGAF00003090960 bam 2.8 GB
EGAF00003090961 bam 3.0 GB
EGAF00003090962 bam 3.1 GB
EGAF00003090963 bam 3.2 GB
EGAF00003090964 bam 2.7 GB
EGAF00003090965 bam 3.3 GB
EGAF00003090966 bam 3.2 GB
EGAF00003090967 bam 3.6 GB
EGAF00003090968 bam 3.7 GB
EGAF00003090969 bam 4.0 GB
EGAF00003090970 bam 3.2 GB
EGAF00003090971 bam 3.2 GB
EGAF00003090972 bam 3.3 GB
EGAF00003090973 bam 3.2 GB
EGAF00003090975 bam 2.3 GB
EGAF00003090976 bam 3.3 GB
EGAF00003090977 bam 2.9 GB
EGAF00003090978 bam 3.6 GB
EGAF00003090979 bam 2.5 GB
EGAF00003090980 bam 3.4 GB
EGAF00003090981 bam 2.3 GB
EGAF00003090982 bam 2.4 GB
EGAF00003090983 bam 4.6 GB
EGAF00003090984 bam 3.5 GB
EGAF00003090985 bam 310.4 MB
EGAF00003090986 bam 2.4 GB
EGAF00003090987 bam 3.3 GB
EGAF00003090988 bam 2.4 GB
EGAF00003090989 bam 2.6 GB
EGAF00003090990 bam 2.0 GB
EGAF00003090991 bam 2.9 GB
EGAF00003090992 bam 3.1 GB
EGAF00003090993 bam 3.6 GB
EGAF00003090994 bam 3.2 GB
EGAF00003090995 bam 3.1 GB
EGAF00003090996 bam 2.9 GB
EGAF00003090997 bam 3.3 GB
EGAF00003090998 bam 2.4 GB
EGAF00003090999 bam 2.4 GB
EGAF00003091000 bam 2.8 GB
EGAF00003091001 bam 2.4 GB
EGAF00003091002 bam 4.3 GB
EGAF00003091003 bam 3.7 GB
EGAF00003091004 bam 2.9 GB
EGAF00003091005 bam 3.3 GB
EGAF00003091006 bam 2.7 GB
EGAF00003091007 bam 2.5 GB
EGAF00003091008 bam 2.0 GB
EGAF00003091009 bam 3.6 GB
EGAF00003091010 bam 3.8 GB
EGAF00003091011 bam 3.2 GB
EGAF00003091012 bam 2.3 GB
EGAF00003091013 bam 2.7 GB
EGAF00003091014 bam 2.4 GB
EGAF00003091015 bam 2.6 GB
EGAF00003091016 bam 2.4 GB
EGAF00003091017 bam 4.0 GB
EGAF00003091018 bam 4.0 GB
EGAF00003091019 bam 5.0 GB
EGAF00003091020 bam 4.5 GB
EGAF00003091021 bam 2.8 GB
EGAF00003091022 bam 2.7 GB
EGAF00003091023 bam 2.6 GB
EGAF00003091024 bam 3.4 GB
EGAF00003091025 bam 3.2 GB
EGAF00003091026 bam 3.4 GB
EGAF00003091027 bam 4.1 GB
EGAF00003091028 bam 3.8 GB
EGAF00003091029 bam 3.2 GB
EGAF00003091030 bam 3.1 GB
EGAF00003091031 bam 3.2 GB
EGAF00003091032 bam 3.3 GB
EGAF00003091033 bam 4.2 GB
EGAF00003091034 bam 4.6 GB
EGAF00003091035 bam 3.1 GB
EGAF00003091036 bam 3.3 GB
EGAF00003091037 bam 3.2 GB
EGAF00003091038 bam 3.5 GB
EGAF00003091039 bam 2.9 GB
EGAF00003091040 bam 3.0 GB
EGAF00003091041 bam 2.3 GB
EGAF00003091042 bam 3.8 GB
EGAF00003091043 bam 3.2 GB
EGAF00003091044 bam 2.5 GB
EGAF00003091045 bam 3.6 GB
EGAF00003091046 bam 3.1 GB
EGAF00003091047 bam 3.5 GB
EGAF00003091048 bam 527.6 MB
EGAF00003091049 bam 5.3 GB
EGAF00003091050 bam 4.9 GB
EGAF00003091051 bam 2.8 GB
EGAF00003091052 bam 3.1 GB
EGAF00003091053 bam 2.2 GB
EGAF00003091054 bam 2.3 GB
EGAF00003091055 bam 2.8 GB
EGAF00003091056 bam 3.4 GB
EGAF00003091057 bam 3.4 GB
EGAF00003091058 bam 2.8 GB
EGAF00003091059 bam 3.6 GB
EGAF00003091060 bam 2.7 GB
EGAF00003091061 bam 3.6 GB
EGAF00003091062 bam 3.1 GB
EGAF00003091063 bam 3.0 GB
EGAF00003091064 bam 2.5 GB
EGAF00003091065 bam 2.6 GB
EGAF00003091066 bam 2.5 GB
EGAF00003091067 bam 3.1 GB
EGAF00003091068 bam 3.2 GB
EGAF00003091069 bam 2.9 GB
EGAF00003091070 bam 3.1 GB
EGAF00003091071 bam 3.4 GB
EGAF00003091073 bam 2.2 GB
EGAF00003091074 bam 3.4 GB
EGAF00003091075 bam 3.1 GB
EGAF00003091076 bam 2.8 GB
EGAF00003091077 bam 2.2 GB
EGAF00003091078 bam 3.8 GB
EGAF00003091079 bam 1.8 GB
EGAF00003091080 bam 2.1 GB
EGAF00003091081 bam 2.7 GB
EGAF00003091082 bam 4.3 GB
EGAF00003091083 bam 2.6 GB
EGAF00003091084 bam 3.4 GB
EGAF00003091085 bam 2.9 GB
EGAF00003091086 bam 2.8 GB
EGAF00003091087 bam 4.0 GB
EGAF00003091088 bam 3.2 GB
167 Files (514.5 GB)