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sWGS of OV04 PDX samples for ACN rascal study

This dataset contains 148 .bam files of shallow WGS data (~0.1X) from OV04 PDX samples. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

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Data Access policy - Brenton Lab (OV04 study)

Data Access Request Form – Brenton Lab, CRUK-CI, University of Cambridge, UK These terms and conditions govern access to and use of the managed access datasets to which the User Institution has requested access. The User Institution and User agree to be bound by these terms and conditions. Definitions: Confidential Information: means any information provided by the Data Provider relating to the Data Data: The managed access dataset(s) to which the User Institution has requested access, as detailed in Schedule B. Data Provider: THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE of The Old Schools, Trinity Lane, Cambridge CB2 1TN, United Kingdom and the Cambridge University Hospitals NHS Foundation Trust of Addenbrooke’s Hospital, Cambridge, CB2 0QQ; represented by staff of the Brenton Group at the Cancer Research UK Cambridge Institute, and contactable by email at james.brenton@cruk.cam.ac.uk or future email as updated; or future representatives as indicated in Data Access Committee(s) for the dataset(s) defined in Schedule B. Data Subject: means an individual who participated in research studies from whom the Data was derived. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Personal Data: means information and/or data about one or more living person who is the subject of personal data and who can be identified from that information, as provided under the General Data Protection Regulation (EU) 2016/679 (as amended from time to time), including but not limited to surname, initials, date of birth, address and postcodes, national insurance number, hospital number or NHS number. Project: The research project for which the User Institution has requested access to these Data, as defined in Schedule B. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. User Institution is referred to within this Agreement as “You” (and “Your” shall be construed accordingly). Data Provider will provide access to Data to the User Institution under the following Terms and Conditions: 1. You agree to preserve, at all times, the confidentiality and privacy of information and Data pertaining to Data Subjects. In particular, you undertake not to use, or attempt to use the Data to compromise or otherwise breach or infringe the confidentiality and privacy of information on Data Subjects. You agree to protect the confidentiality of Data Subjects in any Publications that you prepare by taking all reasonable care to limit the possibility of identification. You agree not to attempt to link Data to any other data source on the same samples, link the Data to any person or otherwise identify any Data Subject from the Data. 2. You agree not to transfer or disclose the Data, in whole or part, to others, except to persons within the User Institution for carrying out the Project or as reasonably necessary for Data/safety monitoring or programme management. If You wish to disclose the Data to a collaborator outside the User Institution, the third party must make a separate application for access to the Data. 3. You agree to use the Data for the advancement of medical research, and solely for the approved purpose and Project described in Schedule B and for no other purpose. 4. You agree that Data may be reissued from time to time, with suitable versioning. If the reissue is at the request of Data Subjects and/or other ethical scrutiny or concerns, you will destroy earlier versions of the Data, and upon request of Data Provider, provide written certification of such destruction. Your obligations as set out in this form pertaining to the Data and its use will continue to operate in full force and effect after Data is destroyed. 5. You agree to acknowledge in any Publication based in whole or part on the Data, the published paper(s) from which the Data derives, and the version of the Data. 6. You agree and acknowledge that the researchers of this study, the original Data creators, depositors, or copyright holders, and the Data Provider: a) bear no legal responsibility or liability for the accuracy or comprehensiveness of the Data, or from any use of the Data including further analysis or interpretation of such Data; and b) shall have no liability for any direct or indirect, consequential, or incidental damages or losses whatsoever arising out of Your use of the Data, or from the unavailability of, or lack of access to, the Data for whatever reason; and c) disclaim any and all representations, conditions or warranties (either express, implied or statutory) regarding the Data, including accuracy of the Data or that the Data corresponds with a particular description or is fit for a particular purpose. 7. You understand and acknowledge that the Data is owned by Data Provider and its collaborators and is protected by copyright, database rights and other intellectual property rights. You agree that you shall not reproduce or copy the Data, except as reasonably required to carry out the Project and for no other purpose, or sell all or any part of the Data in any circumstances. 8. You recognise that by granting You access to Data, no rights or ownership or intellectual property rights in or relating to the Data are transferred to You. 9. Upon any breach by You of the terms set out in this form, You will be required to destroy the Data in Your possession, and upon request, provide written certification to the Data Provider of such destruction. Your obligations as set out in this form pertaining to the Data and its use will continue to operate in full force and effect after Data is destroyed. 10. You accept that it may be necessary for the Data Provider to alter the terms of use of the Data from time to time. As an example, this may include specific provisions relating to the Data required by Data Provider or collaborator parties. In the event that changes are required, the Data Provider or their appointed agent will contact You to inform You of the changes and You may elect either to accept the changes or to destroy the Data in Your possession and cease its use. Your obligations as set out in this form pertaining to the Data and its use will continue to operate in full force and effect after Data is destroyed. 11. You agree that the Data is protected by and subject to applicable international laws. You are responsible for ensuring compliance with any such laws. The Data Provider reserves the right to request and inspect Your data security and management documentation to ensure the adequacy and compliance of data protection measures pertaining to storage and use of Data. 12. If the Data includes any identifiable Personal Data, You agree to: (a) take appropriate technical and organisational measures against the unauthorised or unlawful processing and/or use of the Data, any data derived from the Data and/or and all Confidential Information, against the accidental loss or destruction of, or damage to, such data and information. (b) ensure that the measures referred to in (a) shall include the measures set out in Schedule A. (c) restrict access to the Data, any data derived from the Data and all other Confidential Information to employees who strictly need access to such data and/or information to undertake the Project, and shall ensure that all such employees are reliable, and informed of the confidential nature of such data and/or information and the importance of processing it securely. (d) For the avoidance of doubt, You undertake not to disclose to a third party, whether in connection with the Project or otherwise, any data and/or information contained in or derived from the Data which constitutes Personal Data. Schedule A 1.1 You acknowledge and agree that the Data is pseudonymised Data and that You will become the Data Controller on receipt of such Data. 1.2 You will only process the Data for the purpose of carrying out the Project. 1.3 You agree that safeguards required under Article 89(1) of GDPR, and relevant conditions under the Data Protection Act 2018, are satisfied, and in particular that: (i) the processing of Data under or in connection with this Agreement is in the public interest; and (ii) if applicable, the Project has been subject to ethical review by an appropriate institutional review board or independent ethics committee. 1.4 The Data Provider does not intend to provide any information that may lead to You being able to identify any individual from whom any Data has been obtained. 1.5 You agree that You shall not analyse or make any use of any Data where it is reasonably foreseeable that such analysis or use may lead to the identification of any Data Subject or compromise the anonymity of any Data Subject in any way. 1.6 You shall notify the Data Provider immediately of any actual or suspected breach of security which involves the Data.   Schedule B Name of the applicant and co-applicant(s), including affiliations, titles and contact details. For dataset deposited at EGA, applicants must have registered accounts at EGA. Student applicants must include their supervisors as a co-applicant. Name of Registered User Email Job Title Supervisor* Title of Project (in less than 30 words) Data Requested (please indicate relevant publication(s) describing the data, accession number(s) and/or relevant links to data, and [where relevant] details of and links to the respective Data Access Committee(s) (DAC)) Research Project: Please provide a clear description of the project and its specific aims in no more than 750 words. This should include specific details of what you plan to do with the data and include key references. Brief description of the infrastructure and experience for handling the requested data securely Signature of authorized signatory of User Institution Signature: Name: Title: Date: Signature of Principal Investigator I confirm that I have read and understood the TERMS AND CONDITIONS as set forth in this DATA ACCESS REQUEST FORM. Signature: Name: Title: Date:

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
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 Located in
EGAF00005477028 1631560885948 545.9 MB
EGAF00005477029 1631560885948 805.3 MB
EGAF00005477030 1631563161020 591.9 MB
EGAF00005477031 1631562985749 944.3 MB
EGAF00005477032 1631562286166 691.0 MB
EGAF00005477033 1631562717698 582.9 MB
EGAF00005477034 1631562717697 874.2 MB
EGAF00005477035 1631579059834 816.0 MB
EGAF00005477037 bam 465.1 MB
EGAF00005477039 1631561698103 692.8 MB
EGAF00005477040 1631562717697 769.0 MB
EGAF00005477041 1631560784537 543.9 MB
EGAF00005477042 1631578327591 704.5 MB
EGAF00005477043 1631561698103 635.8 MB
EGAF00005477044 1631560954036 557.8 MB
EGAF00005477045 bam 496.6 MB
EGAF00005477046 bam 477.0 MB
EGAF00005477047 1631562206648 563.2 MB
EGAF00005477048 1631578217912 632.1 MB
EGAF00005477049 1631562286165 538.1 MB
EGAF00005477050 1631562573419 826.8 MB
EGAF00005477051 1631578217912 694.6 MB
EGAF00005477052 1631562717697 848.9 MB
EGAF00005477053 1631562286165 764.0 MB
EGAF00005477054 1631562717698 782.5 MB
EGAF00005477055 1631577376012 503.2 MB
EGAF00005477056 1631592779063 505.8 MB
EGAF00005477057 1631561374132 680.3 MB
EGAF00005477058 1631621025561 761.0 MB
EGAF00005477059 bam 463.5 MB
EGAF00005477060 1631561545083 728.9 MB
EGAF00005477061 bam 452.9 MB
EGAF00005477062 1631562798793 854.1 MB
EGAF00005477063 1631561698103 736.3 MB
EGAF00005477064 1631578643966 806.3 MB
EGAF00005477065 1631562286165 551.3 MB
EGAF00005477066 1631561698103 638.5 MB
EGAF00005477067 1631564300704 929.1 MB
EGAF00005477068 1631593102093 742.1 MB
EGAF00005477069 bam 487.5 MB
EGAF00005477070 1631578217912 683.5 MB
EGAF00005477071 1631593102093 748.9 MB
EGAF00005477072 1631567843614 782.0 MB
EGAF00005477073 1631578217912 585.7 MB
EGAF00005477074 1631578217912 718.8 MB
EGAF00005477075 1631562348273 570.3 MB
EGAF00005477076 1631561292277 555.0 MB
EGAF00005477077 1631561788269 594.9 MB
EGAF00005477078 1631562798793 616.3 MB
EGAF00005477079 1631561200156 660.3 MB
EGAF00005477080 1631577560378 602.5 MB
EGAF00005477081 1631578217912 779.1 MB
EGAF00005477082 1631561042156 610.5 MB
EGAF00005477083 1631578217911 638.3 MB
EGAF00005477084 bam 337.8 MB
EGAF00005477085 bam 433.1 MB
EGAF00005477086 1631562348273 676.7 MB
EGAF00005477087 bam 496.5 MB
EGAF00005477088 1631561698103 751.1 MB
EGAF00005477089 1631578535160 665.8 MB
EGAF00005477090 1631578217911 766.3 MB
EGAF00005477091 1631577560378 606.8 MB
EGAF00005477092 1631636527455 755.3 MB
EGAF00005477093 1631561698103 741.0 MB
EGAF00005477094 1631578217911 735.1 MB
EGAF00005477095 1631562985749 1.0 GB
EGAF00005477096 1631593010714 751.5 MB
EGAF00005477097 1631578217911 733.3 MB
EGAF00005477098 1631580317368 668.8 MB
EGAF00005477099 1631561374132 586.1 MB
EGAF00005477100 1631562206648 753.4 MB
EGAF00005477101 1631577616441 612.7 MB
EGAF00005477102 1631564300704 539.6 MB
EGAF00005477103 1631561476573 718.6 MB
EGAF00005477105 1631562861729 873.2 MB
EGAF00005477106 1631562717698 845.6 MB
EGAF00005477107 1631564300704 638.5 MB
EGAF00005477108 1631608312430 815.3 MB
EGAF00005477109 1631562717697 792.0 MB
EGAF00005477110 1631562985749 827.7 MB
EGAF00005477111 bam 498.2 MB
EGAF00005477112 1631564300704 626.4 MB
EGAF00005477113 1631562111918 755.7 MB
EGAF00005477114 bam 437.6 MB
EGAF00005477115 1631592896574 594.5 MB
EGAF00005477116 1631577560378 597.5 MB
EGAF00005477117 1631592896574 521.8 MB
EGAF00005477118 1631561374132 572.8 MB
EGAF00005477119 1631578217911 752.6 MB
EGAF00005477120 1631610484678 807.2 MB
EGAF00005477121 1631562206648 760.0 MB
EGAF00005477122 1631561200156 675.9 MB
EGAF00005477123 1631562286165 724.0 MB
EGAF00005477124 1631636045791 1.0 GB
EGAF00005477125 1631561431770 662.5 MB
EGAF00005477126 1631564300704 905.4 MB
EGAF00005477127 1631578327591 808.6 MB
EGAF00005477128 1631608312430 853.4 MB
EGAF00005477129 1631564639384 618.7 MB
EGAF00005477130 1631561698103 738.4 MB
EGAF00005477131 bam 431.1 MB
EGAF00005477132 1631562717697 840.7 MB
EGAF00005477133 1631564770560 913.5 MB
EGAF00005477134 1631593448639 940.4 MB
EGAF00005477135 1631564300704 884.9 MB
EGAF00005477136 1631561698103 679.7 MB
EGAF00005477137 1631564300704 937.2 MB
EGAF00005477138 1631562440501 767.4 MB
EGAF00005477140 1631562286165 735.5 MB
EGAF00005477141 1631562985749 1.0 GB
EGAF00005477142 1631579059834 810.9 MB
EGAF00005477143 1631594181864 821.1 MB
EGAF00005477144 bam 404.4 MB
EGAF00005477145 1631562037827 658.1 MB
EGAF00005477146 1631578217911 735.7 MB
EGAF00005477147 1631561698103 748.7 MB
EGAF00005477148 1631562286165 710.8 MB
EGAF00005477149 1631578217911 583.3 MB
EGAF00005477150 1631592896574 639.5 MB
EGAF00005477151 1631562206648 648.0 MB
EGAF00005477152 bam 492.7 MB
EGAF00005477153 1631564300704 926.1 MB
EGAF00005477154 bam 395.6 MB
EGAF00005477155 1631564770560 628.2 MB
EGAF00005477156 1631562861729 809.3 MB
EGAF00005477157 1631618213884 899.9 MB
EGAF00005477158 1631564300704 1.0 GB
EGAF00005477159 1631561879114 635.7 MB
EGAF00005477160 1631578217911 639.0 MB
EGAF00005477161 1631578643966 786.9 MB
EGAF00005477162 1631578217911 774.2 MB
EGAF00005477163 1631564300704 890.0 MB
EGAF00005477164 1631562111918 725.8 MB
EGAF00005477165 1631592896574 620.7 MB
EGAF00005477166 1631562717697 862.9 MB
EGAF00005477167 bam 432.6 MB
EGAF00005477168 1631561698103 741.5 MB
EGAF00005477169 1631578217911 742.6 MB
EGAF00005477170 bam 437.6 MB
EGAF00005477171 1631564770560 652.1 MB
EGAF00005477172 1631562717697 778.7 MB
EGAF00005477173 1631562717698 810.0 MB
EGAF00005477174 bam 440.7 MB
EGAF00005477175 1631562717697 737.9 MB
144 Files (99.7 GB)