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Tumour evolvability metrics predict recurrence in advanced localised prostate cancer (normal data)

There is a need for quantitative measurements of evolutionary metrics in controlled clinical trials with long term follow-up information. This is particularly true in advanced localised prostate cancer, which can recur more than a decade after diagnosis. Here we mapped genomic intra-tumour heterogeneity in 642 tumour samples from 114 patients who took part in the IMRT and DELINEATE clinical trials, for which full clinical information and 12y median follow-up was available. We concomitantly assessed phenotypic (morphological) heterogeneity using Deep Learning in 1,923 histological sections from 250 IMRT patients (fully overlapping with the genetic set). This study shows that combining genomics with AI-aided histopathology in clinical trials leads to novel clinical biomarkers. This EGA repository contains data produced from tumour samples using low coverage whole genome sequencing and a prostate cancer specific gene panel data following compression of unique molecular identifiers.

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Forecast Data Access Committee

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 Fondazione Human Technopole 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 Fondazione Human Technopole 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. 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 that it, and its Authorised Personnel, are covered by and shall comply with the obligations contained in the Data Protection Act 1998 as amended from time to time, the General Data Protection Regulation EU 2016/679 ("GDPR") (when applicable) or equivalent national provisions no less onerous then those contained in the General Data Protection Regulation EU 2016/679. In particular, the Recipient and its Registered Users understand their duties under such legislation in relation to the handling of Data and the rights of Data Subjects. 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 Fondazione Human Technopole within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify The Fondazione Human Technopole prior to any significant changes to the protocol for the Project. 14. The User Institution will notify The Fondazione Human Technopole as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The Fondazione Human Technopole 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 Fondazione Human Technopole. 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 England and Wales and shall be subject to the exclusive jurisdiction of the English courts. 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 Fondazione Human Technopole Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS (to be completed by the data producer before passing to applicant) Dataset reference (EGA Study ID and Dataset Details) EGAS00001006096 Name of project that created the dataset Tumour evolvability metrics predict recurrence in advanced localised prostate cancer (tumour data) Names of other data producers/collaborators Specific limitations on areas of research Use of the data must be related to cancer. Use of the data includes methods development research (e.g., development of software or algorithms). Minimum protection measures required The User Institution agrees that it shall take all reasonable security precautions to keep the Data confidential; to guard against unauthorised or unlawful processing of the Data;, and to prevent accidental loss or destruction of, or damage to, the Data. Such precautions to be no less onerous than those applied in respect of the Recipient’s own confidential information. 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. The internal hard drives of Laptops holding these data must be encrypted and 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 Fondazione Human Technopole 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 Fondazione Human Technopole anticipate 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 3 months after these data were first made available on the relevant hosting database, unless The Fondazione Human Technopole 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., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with The Fondazione Human Technopole.

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
EGAS00001006098 Cancer Genomics

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
EGAF00008043922 bam 54.9 GB
EGAF00008043923 bam 50.8 GB
EGAF00008043924 bam 53.9 GB
EGAF00008043925 bam 58.1 GB
EGAF00008043926 bam 53.5 GB
EGAF00008043927 bam 56.8 GB
EGAF00008043928 bam 57.8 GB
EGAF00008043929 bam 54.8 GB
EGAF00008043930 bam 63.0 GB
EGAF00008043931 bam 59.1 GB
EGAF00008043932 bam 53.5 GB
EGAF00008043933 bam 59.0 GB
EGAF00008043934 bam 59.5 GB
EGAF00008043935 bam 54.6 GB
EGAF00008043936 bam 49.9 GB
EGAF00008043937 bam 76.0 GB
EGAF00008043938 bam 56.0 GB
EGAF00008043939 bam 66.8 GB
EGAF00008043940 bam 172.8 GB
EGAF00008043941 bam 48.8 GB
EGAF00008043942 bam 53.6 GB
EGAF00008043943 bam 49.3 GB
EGAF00008043944 bam 49.7 GB
EGAF00008043945 bam 48.1 GB
EGAF00008043946 bam 59.4 GB
EGAF00008043947 bam 60.9 GB
EGAF00008043948 bam 57.1 GB
EGAF00008043949 bam 57.4 GB
EGAF00008043950 bam 62.3 GB
EGAF00008043951 bam 56.9 GB
EGAF00008043952 bam 63.9 GB
EGAF00008043953 bam 59.3 GB
EGAF00008043954 bam 59.4 GB
EGAF00008043955 bam 49.4 GB
EGAF00008043956 bam 63.6 GB
EGAF00008043957 bam 56.6 GB
EGAF00008043958 bam 56.4 GB
EGAF00008043959 bam 62.2 GB
EGAF00008043960 bam 64.9 GB
EGAF00008043961 bam 53.6 GB
EGAF00008043962 bam 50.3 GB
EGAF00008043963 bam 49.5 GB
EGAF00008043964 bam 66.9 GB
EGAF00008043965 bam 54.4 GB
EGAF00008043966 bam 55.5 GB
EGAF00008043967 bam 61.9 GB
EGAF00008043968 bam 52.8 GB
EGAF00008043969 bam 60.3 GB
EGAF00008043970 bam 48.9 GB
EGAF00008043971 bam 56.2 GB
EGAF00008043972 bam 63.7 GB
EGAF00008043973 bam 60.9 GB
EGAF00008043974 bam 58.6 GB
EGAF00008043975 bam 56.0 GB
EGAF00008043976 bam 46.2 GB
EGAF00008043977 bam 53.6 GB
EGAF00008043978 bam 52.0 GB
EGAF00008043979 bam 55.5 GB
EGAF00008043980 bam 73.3 GB
EGAF00008043981 bam 50.4 GB
EGAF00008043982 bam 68.0 GB
EGAF00008043983 bam 61.2 GB
EGAF00008043984 bam 51.5 GB
EGAF00008043985 bam 55.2 GB
EGAF00008043986 bam 46.5 GB
EGAF00008043987 bam 67.0 GB
EGAF00008043988 bam 59.6 GB
EGAF00008043989 bam 47.7 GB
EGAF00008043990 bam 57.4 GB
EGAF00008043991 bam 49.4 GB
EGAF00008043992 bam 39.7 GB
EGAF00008043993 bam 55.0 GB
EGAF00008043994 bam 56.0 GB
EGAF00008043995 bam 81.1 GB
EGAF00008043996 bam 48.6 GB
EGAF00008043997 bam 56.7 GB
EGAF00008043998 bam 60.1 GB
EGAF00008043999 bam 54.5 GB
EGAF00008044000 bam 34.0 GB
EGAF00008044001 bam 48.7 GB
EGAF00008044002 bam 69.2 GB
EGAF00008044003 bam 55.7 GB
EGAF00008044004 bam 49.5 GB
EGAF00008044005 bam 45.8 GB
EGAF00008044006 bam 61.7 GB
EGAF00008044007 bam 54.4 GB
EGAF00008044008 bam 51.1 GB
EGAF00008044009 bam 56.2 GB
EGAF00008044010 bam 56.5 GB
EGAF00008044011 bam 53.4 GB
EGAF00008044012 bam 65.5 GB
EGAF00008044013 bam 52.9 GB
EGAF00008044014 bam 49.3 GB
EGAF00008044015 bam 75.3 GB
EGAF00008044016 bam 52.1 GB
EGAF00008044017 bam 59.6 GB
EGAF00008044018 bam 75.9 GB
EGAF00008044019 bam 60.9 GB
EGAF00008044020 bam 57.9 GB
EGAF00008044021 bam 49.1 GB
100 Files (5.8 TB)