Whole-genome sequencing data of metastatic salivary gland cancer

General principles Funded by the Radboud Oncology Fund and the Dr. C.J. Vaillant Fund, the Salivary Gland Cancer Autopsy research group (Research Group) has sequenced DNA of 17 salivary gland cancer samples of and three healthy control samples from three patients with salivary gland cancer. This research project is led by Carla M.L. van Herpen from Radboud University Medical Centre in Nijmegen, the Netherlands (“Radboudumc”). The Research Group is willing to consider applications from third party researchers for access to the DNA sequence data. Access to the data will be granted to qualified researchers for approved use and will be governed by the provisions laid out in the Data Access Procedure set forth below and the terms of the Data Access Agreement attached hereto. A qualified researcher refers to a senior investigator who is employed or legitimately affiliated with an academic, non-profit or government institution and who has a track record in the field. Access to DNA Sequencing Data is available by application to the Data Access Committee (DAC). Researchers granted access to DNA Sequencing Data must feedback the results of their research to the Research Group, after publication in accordance with the Research Group publication policy set forth in the Data Access Agreement. Access is conditional upon availability of data and on signed agreement by the researcher(s) and the responsible employing institution to abide by the policies and conditions related to publication, data ownership, data return, intellectual property rights, data disposal, ethical approval, confidentiality and commercialization referred herein. Data Available The following DNA Sequencing Data are available: Tumor samples and healthy skin germline controls were collected through autopsy. All participants died outside the hospital. Following declaration of death, their bodies were immediately transported to Radboud university medical center. Refrigeration to 2-5 °C commenced upon arrival, and was initiated within six hours after death in all patients. Samples were snap-frozen at -80°C in Tissue-Tek OCT compound (Sakura). Tumor purity was estimated on hematoxylin and eosin slides and most viable areas with highest tumor purity were annotated. For samples with sufficient viable tumor, punch biopsies of 2 mm were taken from the annotated areas for subsequent DNA isolation. Samples were homogenized with Nuclease-free water using the Qiagen TissueLyzer. Samples were purified using the QIAsymphony and DSP DNA mini kit (Qiagen). Library preparation was done using the TruSeq Nano DNA library prep kit (Illumina, 8 PCR cycles) according to manufacturers’ instructions with 50-200ng of Covaris sheared gDNA as input. Library concentrations were quantified by qPCR (KAPA) with a threshold of minimal 3nM. A total of 17 tumor samples and 3 healthy controls from three patients were whole-genome sequenced (Illumina Novaseq S4 2x150 bp V1.5) to a median coverage of 60x for tumor samples and 30x for healthy controls. Data available are FastQ-files. Data Access Committee Applications for access to DNA Sequencing Data must be made to the Data Access Committee (DAC). The DAC consists of Carla van Herpen and Gerald Verhaegh. Data Access Procedure 1. Application for Access The handling of applications, the issue of DNA Sequencing Data and any associated operations, administration and audits will be performed by the Radboudumc on behalf of the Research Group. Applications for access to DNA Sequencing Data must be submitted using the online EGA data request procedure and using the form in Appendix 1. The information disclosed in the application will be treated as confidential and will only be disclosed to the persons evaluating the application. All incoming applications will be documented, including any conjunct agreements with the applicants. Unless explicitly consented for by the applicant, this information will not be used for purposes other than evaluation of the application. 2. Multiple Applications Applicants agree to use the DNA Sequencing Data for the approved purpose and project described in the application; use of the data for a new purpose or project will require a new application and approval. The DAC will consider applications that include named collaborators, but each Institution must sign a separate Data Access Agreement. In the event an applicant wishes to share the data with additional collaborators not previously approved, these additional collaborators must make a separate application for access to the DNA Sequencing Data. In the event that two or more applications overlap, the DAC may propose the respective applicants to align their applications. 3. Assessment Criteria Applications which seek to reserve DNA Sequencing Data for unspecified research goals will not be taken into consideration. Applications for access to DNA Sequencing Data must be Specific, Measurable, Attainable, Resourced and Timely (SMART). Specifically, the DAC will assess each application to determine whether: i. it has been submitted by a qualified researcher or researchers, who is employed by or legitimately affiliated with a recognized research institution that can provide institutional responsibility for appropriate research governance; ii. the nature of the funding of the application and the applicant; iii. the research proposal has been peer-reviewed, and, if not, whether the proposal satisfies applicable scientific standards; iv. the requested data are, quantitatively and qualitatively, suitable and not excessive for the applicant’s proposed research; v. there are any similar applications pending or granted; 4. Access Decision The DAC will decide on an application within a reasonable period of time after it has received all pertinent information. If the DAC grants an application, additional agreements may be made regarding authorships along the lines set forth in the Publication Policy attached to the Data Access Agreement. Rejections of applications will be motivated. Mode of Access to Data, Restrictions and Authentication The DNA Sequencing Data will be made available through the European Genome Phenome Archive (EGA), hosted at the European Bioinformatics Institute. The issue of Project Data and the Data Access Agreement will be administered by Radboudumc. Data Access Conditions Access to DNA Sequencing Data is conditional on prior receipt by the Data Access Agreement attached as Appendix 2 hereto, signed and dated by the applicant(s) and the responsible employing Institution(s). Authors who use Project Data must: 1. Acknowledge the Salivary Gland Cancer Autopsy research group at Radboudumc using the following wording: "This study makes use of DNA sequencing data generated by the Salivary Gland Cancer Autopsy research group led by Carla M.L. van Herpen, Department of Medical Oncology, Radboudumc, Nijmegen, The Netherlands.“ Appendix 1 Application Form for Access to DNA Sequencing Data PLEASE SUBMIT COMPLETED, SIGNED AND DATED FORM BY EMAIL TO: carla.vanherpen@radboudumc.nl 1. Name and position of the Applicant(s), including employment or affiliation with any organization Please ensure that a full postal and email address is included for each applicant. 2. Title of the study In less than 30 words. 3. Research Question Please describe the study in no more than 750 words. Include: a. outline of the study design; b. an indication of the methodologies to be used; c. proposed use of the Project Data; d. preceding peer-reviews of the study (if any present); e. specific details of what you plan to do with the DNA Sequencing Data; f. timeline; g. key references. 4. Consent and Approvals Does your proposed use of DNA Sequencing Data involve use of your own data? Yes […..] No […..] If Yes, with signing this document you confirm the following: ‘I confirm that I have obtained all approvals required by the rules and regulations of my jurisdiction, including my institution’s institutional rules, and the consent of my data subjects, for my use of my own data in combination with the Project Data in the study.’ 5. Resources, Feasibility & Expertise Please confirm that you have secured funding for your proposed use of the DNA Sequencing Data and that you will carry out your research within a reasonable period of time after the granting of this application: by ticking the following box: Yes, we will □. Please describe your experience and expertise, and that of your collaborators, and how this will be applied to the proposed study (in 250 words). Please provide a list of recent publications (max. 10). Appendix 2 Data Access Agreement This agreement governs the terms on which access will be granted to the DNA Sequencing Data generated in this study. In signing this agreement, You are agreeing to be bound by the terms and conditions of access set out in this agreement. For the sake of clarity, the terms of access set out in this agreement apply both to the User and the User’s Institution (as defined below). User Institution and User are referred to within the agreement as “You” and “Your” and shall be construed accordingly. Definitions: “Project” refers to the project in which the DNA Sequencing Data were obtained. “Project Data” refers to the DNA Sequencing Data generated by the Project. “Data Subjects” refers to the persons whose sample has been used to generate Project Data. “User” refers to a researcher who has successfully applied for access to Project Data. “Publications” refers to, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. “User Institution” refers to the organization with which the User is employed, affiliated or enrolled. Terms and Conditions: In signing this Agreement: 1. You agree to use DNA Sequencing Data only for the advancement of scientific and medical research. 2. You agree not to use, and not to allow use of DNA Sequencing Data or any part thereof for the creation of products or services for sale or for any commercial purpose, whether sale by You or by third parties. 3. You agree not to use Project Data to identify or contact the Data Subjects. You agree to preserve, at all times, the confidentiality of information and Project Data. In particular, You undertake not to use, or attempt to use Project Data to compromise or otherwise infringe the confidentiality of information on the Data Subjects and their right to privacy. 4. You agree to disclose Project Data only to those of Your employees who strictly need access to it for the purpose of your approved study (Authorized Recipients), and who are bound by a duty of confidentiality which is at least as strict as provided for in this agreement. 5. You agree to ensure that any Authorized Recipient who has access to Project Data is advised of the confidentiality of Project Data. Upon request, you agree to furnish the names of all Authorized Recipients who have gained access to Project Data. You agree that You are responsible for all breaches of confidentiality and of the terms of this agreement by your Authorized Recipients. 6. You agree to store Project Data on a computer with adequate security controls that prevent unauthorized access to or loss of Project Data and to maintain appropriate control over the Project Data. You represent and warrant that You have in place, and You agree that You will keep having in place, state of the art technical and organizational security measures preventing unauthorized access and loss of Project Data or other forms of unlawful processing of Project Data, including without limitation, physical security measures, access controls, security and privacy technologies, security checks in relation to personnel, security incident response management and audit arrangements. You agree to notify forthwith the administrator of the Project, Radboudumc, of any violations of the foregoing. 7. You represent and warrant that you have obtained and adhered to all required ethico-legal approvals, restrictions and commitments, without limitation data subject consent and approval of the pertinent medical ethical review board, for Your proposed use of Your data in combination with the Project Data. 8. In the event the Project Data is issued to You subject to any Data Subject’s restrictions, you hereby assume the obligation to abide by these restrictions as Your own obligation towards the Data Subjects. You agree that Data Subjects can enforce such restrictions as well as any pertinent provisions of this agreement as third-party beneficiaries and, in the event they choose to do so, that You will not object to Data Subjects being represented by an association or other bodies if they so wish. You agree that Data Subjects who has suffered damage(s) as a result of any violation by You of pertinent provisions in this Agreement or of applicable legislation, is entitled to receive compensation from You for the damage(s) suffered. You agree that, in the event of such a violation, the Data Subjects may bring an action before a court within the Data Subject’s jurisdiction against You. 9. You agree not to attempt to link Project Data to other information or archive data available for the data sets provided to You under this agreement, even if access to that data has been formally granted to you, or it is freely available without restriction, without the required consents and approvals. You agree to retain control over Project Data, and NOT TO DISTRIBUTE (individual-level or aggregated) Project Data provided under this agreement, in any form, to any entity or individual. 10. You agree not to transfer, share or disclose Project Data, in whole or in part, to or with anybody else, whether or not he or she is affiliated with Your institution, unless he or she is a named and approved collaborator under the Data Access Procedure. 11. You agree to use Project Data for the purpose and project described in your application (nr.____________________), as approved by the Data Access Committee; use of the data for a new purpose or project or by another researcher will require a new application and approval. Substantive modification of the original application requires submission of an amendment to the original application. 12. You agree to, when analyses result in newly estimated variables at an individual level (e.g. haplotypes), submit these new variables for archiving. This should be done no later than that the related paper will be submitted for publication. 13. You accept that Project Data will be reissued from time to time, with suitable versioning. If the reissue is at the request of sample donors and/or subject to other ethical scrutiny, You will destroy earlier versions of the Project Data. 14. You agree to destroy the Project Data after the resulting paper has been published. To meet journals’ requirements for availability of Project Data for reviewers to see and readers to use, you agree to refer to the availability of the Project Data as deposited with EGA, under the terms hereof. You agree that the availability of the data resulting from your study of the Project Data for reviewers to see and readers to use is subject to this Access Policy, Procedure and this Data Access Agreement. 15. You agree to acknowledge in any work based in whole or in part on Project Data, the published paper from which the Project Data derives and the version of the data, as per the wording provided in the paragraph “Data Access Conditions”. 16. You accept that the original Project Data generators and the funders of the Project Data: a) bear no legal responsibility whatsoever for the accuracy, completeness or comprehensiveness of the Project Data; and b) accept no liability for direct, indirect, consequential or incidental, damages or losses arising from any use of Project Data by anyone, including without limitation any clinical use and any commercial use thereof, or arising from the unavailability of, or break in access to, the Project Data for whatever reason. 17. You understand and acknowledge that Project Data are protected by copyright, database right and other intellectual property and proprietary rights, and that duplication, sale, licensing or any other form of disposing or distribution or making available, of all or part of the Project Data on any media is not permitted. 18. You acknowledge that the Project Data are made available to you under this agreement on the title of unassignable, non-exclusive “loan”. You recognize that nothing in this agreement shall operate to transfer to You any rights, including but not limited to intellectual property rights and database rights, in or relating to Project Data. 19. You accept that this agreement will terminate immediately upon any breach of this agreement by You and You will be required to destroy any Project Data held. 20. You accept that it may be necessary to alter the terms of this agreement from time to time in order to address new concerns. In this event, You will be contacted and informed of any changes and You agree that Your continued use of Project Data shall be dependent on the parties entering into a new version of the agreement. 21. You agree that You will submit a report to the Data Access Committee, if requested, on completion of your study of the Project Data. Such report will include the data resulting from your study of the Project Data. The Data Access Committee agrees to treat the report and all information, data, results, and conclusions contained within such report as confidential information. 22. You accept that Project Data may be protected by and subject to national and international laws and that You are responsible for ensuring compliance with any such applicable law. The Data Access Committee reserves the right to request and inspect Your data security and management documentation to ensure the adequacy of data protection measures in countries that have no national laws comparable to that which pertain in the European Economic Area (EEA). 23. This agreement shall be construed, interpreted and governed by the laws of the Netherlands. Signed by: ……………………………………………………………. ………………………………….……………………………………. Name of Applicant: Legal representative of Applicant’s Institution: Affiliation of Applicant with Institution: Name of Applicant’s Institution: ……………………………………………………………. ……………………………………………………………………….. Place:………………………………………………….. Place:……………………………………………………………… Date:…………………………………………………… Date:……………………………..……………………………….. Stamp or Seal of Applicant’s Institution: ………………………………………………………………………..