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A Study to Evaluate Denosumab in Young Patients With Primary Breast Cancer (D-Beyond)

This is a prospective, single arm phase IIa trial in which patients with early breast cancer will receive pre-operatively two doses of denosumab 120mg subcutaneously one week apart (maximum 12 days) followed by surgery. Tumor, normal breast tissue and blood samples will be collected at baseline and at surgery. Post-operative treatment will be at the discretion of the investigator.Primary objective: to determine if a short course of RANKL inhibition with denosumab can induce a decrease in tumor proliferation rates as determined by Ki67 immunohistochemistry (IHC) in newly diagnosed, early stage breast cancer in pre-menopausal women.

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Institut Jules Bordet Data Access Agreement

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 DAC-EGAC00001000748: Institut Jules Bordet Data Access Committee for EGAS00001002685 study, J.-C. Heuson Breast Cancer Translational Research Laboratory, rue Héger-Bordet 1, 1000 Bruxelles, BELGIUM Authorised Personnel: The individuals at the User Institution to whom DAC-EGAC00001000748 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: DAC-EGAC00001000748 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 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 DAC-EGAC00001000748 within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify DAC-EGAC00001000748 prior to any significant changes to the protocol for the Project. 14. The User Institution will notify DAC-EGAC00001000748 as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. DAC-EGAC00001000748 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 DAC-EGAC00001000748. 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 Belgium and shall be subject to the exclusive jurisdiction of the Belgian 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 DAC-EGAC00001000748 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) EGAS00001002685 The aim of this study was to compare the mutational landscape of breast cancer diagnosed during pregnancy (BCP) and breast cancer from age/stage non-pregnant patients (controls). We present whole genome sequencing data (Illumina HiSeq X ten platform) of tumor and matched normal tissues from 35 BCP patients and 20 controls. This work provides important novel biological insights and a unique resource to study the biology of breast cancer in young women and how pregnancy could modulate tumor biology. Name of project that created the dataset Molecular portraits of breast cancer diagnosed during pregnancy Names of other data producers/collaborators BASTIEN NGUYEN DAVID VENET CHRISTOS SOTIRIOU Specific limitations on areas of research 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 DAC-EGAC00001000748 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. DAC-EGAC00001000748 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 24 months after these data were first made available on the relevant hosting database, unless DAC-EGAC00001000748 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., EGAS00001002685), and acknowledge its use in a form agreed by the User Institution with DAC-EGAC00001000748.

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
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
EGAF00002197780 fastq.gz 2.8 GB
EGAF00002197781 fastq.gz 3.1 GB
EGAF00002197782 fastq.gz 1.5 GB
EGAF00002197783 fastq.gz 1.6 GB
EGAF00002197784 fastq.gz 1.8 GB
EGAF00002197785 fastq.gz 2.0 GB
EGAF00002197786 fastq.gz 2.0 GB
EGAF00002197787 fastq.gz 2.3 GB
EGAF00002197788 fastq.gz 1.5 GB
EGAF00002197789 fastq.gz 1.7 GB
EGAF00002197790 fastq.gz 2.0 GB
EGAF00002197791 fastq.gz 2.2 GB
EGAF00002197792 fastq.gz 2.0 GB
EGAF00002197793 fastq.gz 2.2 GB
EGAF00002197794 fastq.gz 1.8 GB
EGAF00002197795 fastq.gz 2.0 GB
EGAF00002197796 fastq.gz 1.5 GB
EGAF00002197797 fastq.gz 1.8 GB
EGAF00002197798 fastq.gz 2.0 GB
EGAF00002197799 fastq.gz 2.4 GB
EGAF00002197800 fastq.gz 1.8 GB
EGAF00002197801 fastq.gz 2.0 GB
EGAF00002197802 fastq.gz 3.6 GB
EGAF00002197803 fastq.gz 3.9 GB
EGAF00002197804 fastq.gz 2.3 GB
EGAF00002197805 fastq.gz 2.5 GB
EGAF00002197806 fastq.gz 1.7 GB
EGAF00002197807 fastq.gz 2.0 GB
EGAF00002197808 fastq.gz 3.3 GB
EGAF00002197809 fastq.gz 3.5 GB
EGAF00002197810 fastq.gz 1.9 GB
EGAF00002197811 fastq.gz 2.1 GB
EGAF00002197812 fastq.gz 2.4 GB
EGAF00002197813 fastq.gz 2.7 GB
EGAF00002197814 fastq.gz 2.6 GB
EGAF00002197815 fastq.gz 2.8 GB
EGAF00002197816 fastq.gz 1.9 GB
EGAF00002197817 fastq.gz 2.1 GB
EGAF00002197818 fastq.gz 2.3 GB
EGAF00002197819 fastq.gz 2.5 GB
EGAF00002197820 fastq.gz 1.8 GB
EGAF00002197821 fastq.gz 2.0 GB
EGAF00002197822 fastq.gz 2.3 GB
EGAF00002197823 fastq.gz 2.5 GB
EGAF00002197824 fastq.gz 946.7 MB
EGAF00002197825 fastq.gz 1.0 GB
EGAF00002197826 fastq.gz 1.6 GB
EGAF00002197827 fastq.gz 1.7 GB
EGAF00002197828 fastq.gz 1.7 GB
EGAF00002197829 fastq.gz 1.9 GB
EGAF00002197830 fastq.gz 1.4 GB
EGAF00002197831 fastq.gz 1.6 GB
EGAF00002197832 fastq.gz 2.5 GB
EGAF00002197833 fastq.gz 2.8 GB
EGAF00002197834 fastq.gz 2.1 GB
EGAF00002197835 fastq.gz 2.4 GB
EGAF00002197836 fastq.gz 1.3 GB
EGAF00002197837 fastq.gz 1.5 GB
EGAF00002197838 fastq.gz 1.9 GB
EGAF00002197839 fastq.gz 2.2 GB
EGAF00002197840 fastq.gz 758.1 MB
EGAF00002197841 fastq.gz 859.5 MB
EGAF00002197842 fastq.gz 2.2 GB
EGAF00002197843 fastq.gz 2.5 GB
EGAF00002197844 fastq.gz 1.3 GB
EGAF00002197845 fastq.gz 1.6 GB
EGAF00002197846 fastq.gz 1.8 GB
EGAF00002197847 fastq.gz 2.0 GB
EGAF00002197848 fastq.gz 1.5 GB
EGAF00002197849 fastq.gz 1.8 GB
EGAF00002197850 fastq.gz 2.3 GB
EGAF00002197851 fastq.gz 2.6 GB
EGAF00002197852 fastq.gz 1.7 GB
EGAF00002197853 fastq.gz 1.8 GB
EGAF00002197854 fastq.gz 2.1 GB
EGAF00002197855 fastq.gz 2.3 GB
EGAF00002197856 fastq.gz 1.9 GB
EGAF00002197857 fastq.gz 2.1 GB
EGAF00002197858 fastq.gz 2.2 GB
EGAF00002197859 fastq.gz 2.5 GB
EGAF00002197860 fastq.gz 2.0 GB
EGAF00002197861 fastq.gz 2.3 GB
EGAF00002197862 fastq.gz 2.3 GB
EGAF00002197863 fastq.gz 2.5 GB
EGAF00002197864 fastq.gz 27.2 GB
EGAF00002197865 fastq.gz 29.3 GB
EGAF00002197866 fastq.gz 2.5 GB
EGAF00002197867 fastq.gz 2.7 GB
EGAF00002197868 fastq.gz 2.0 GB
EGAF00002197869 fastq.gz 2.3 GB
EGAF00002197870 fastq.gz 3.1 GB
EGAF00002197871 fastq.gz 3.6 GB
EGAF00002197872 fastq.gz 2.2 GB
EGAF00002197873 fastq.gz 2.4 GB
EGAF00002197874 fastq.gz 2.1 GB
EGAF00002197875 fastq.gz 2.3 GB
EGAF00002197876 fastq.gz 2.5 GB
EGAF00002197877 fastq.gz 2.8 GB
EGAF00002197878 fastq.gz 2.2 GB
EGAF00002197879 fastq.gz 2.5 GB
EGAF00002197880 fastq.gz 16.1 GB
EGAF00002197881 fastq.gz 17.5 GB
EGAF00002197882 fastq.gz 1.5 GB
EGAF00002197883 fastq.gz 1.7 GB
EGAF00002197884 fastq.gz 1.6 GB
EGAF00002197885 fastq.gz 1.7 GB
EGAF00002197886 fastq.gz 1.8 GB
EGAF00002197887 fastq.gz 2.1 GB
EGAF00002197888 fastq.gz 1.3 GB
EGAF00002197889 fastq.gz 1.5 GB
EGAF00002197890 fastq.gz 2.0 GB
EGAF00002197891 fastq.gz 2.3 GB
EGAF00002197892 fastq.gz 1.6 GB
EGAF00002197893 fastq.gz 1.7 GB
EGAF00002197894 fastq.gz 1.8 GB
EGAF00002197895 fastq.gz 2.0 GB
EGAF00002197896 fastq.gz 2.0 GB
EGAF00002197897 fastq.gz 2.2 GB
EGAF00002197898 fastq.gz 2.1 GB
EGAF00002197899 fastq.gz 2.3 GB
EGAF00002197900 fastq.gz 2.3 GB
EGAF00002197901 fastq.gz 2.4 GB
EGAF00002197902 fastq.gz 2.0 GB
EGAF00002197903 fastq.gz 2.2 GB
EGAF00002197904 fastq.gz 1.7 GB
EGAF00002197905 fastq.gz 1.9 GB
EGAF00002197906 fastq.gz 2.5 GB
EGAF00002197907 fastq.gz 2.8 GB
EGAF00002197908 fastq.gz 1.8 GB
EGAF00002197909 fastq.gz 1.9 GB
EGAF00002197910 fastq.gz 2.0 GB
EGAF00002197911 fastq.gz 2.2 GB
EGAF00002197912 fastq.gz 2.2 GB
EGAF00002197913 fastq.gz 2.5 GB
EGAF00002197914 fastq.gz 2.2 GB
EGAF00002197915 fastq.gz 2.6 GB
EGAF00002197916 fastq.gz 1.9 GB
EGAF00002197917 fastq.gz 2.0 GB
EGAF00002197918 fastq.gz 1.9 GB
EGAF00002197919 fastq.gz 2.0 GB
EGAF00002197920 fastq.gz 1.5 GB
EGAF00002197921 fastq.gz 1.9 GB
EGAF00002197922 fastq.gz 1.8 GB
EGAF00002197923 fastq.gz 2.0 GB
144 Files (383.0 GB)