Gene expression by RNAseq in bronchial biopsies of asthmatics, asthma in remission and healthy subjects

Groningen Asthma Remission Study: Access to Data General principles The data in the Asthma Remission Study were generated as part of a Scientific Research collaboration between research groups of the Groningen Research Institute for Asthma and COPD (GRIAC) of the University Medical Center Groningen (UMCG) funded by GSK. The primary goal of the project was to integrate multiple biological levels of genomic data (genetic, epigenetic and gene expression) to gain a deeper understanding of the molecular mechanisms of asthma remission. The participating research groups are willing to consider applications from third party researchers for access to the anonymized data generated by the Project (this data is hereafter referred to as “Project Data”). Access to Project Data will be granted to qualified researchers for approved use and will be governed by the provisions laid out in the associated informed consent of individual data subjects for each cohort and/or of the associated ethics committee approval of the associated cohort, 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 Project Data is available by application to the Asthma Remission Study Data Access Committee. Researchers granted access to Project Data must feedback the results of their research to the Consortium, after publication in accordance with the publication policy set forth in the Data Access Agreement. Access is conditional upon availability of Project Data and on the 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. Available Project Data The following Project Data are available: Illumina 450k array methylation data from 179 subjects, RNA sequencing data from 184 subjects and miRNA sequencing data from 206 subjects. Only the following phenotype data: age, asthma status, smoking status and sex can be requested. Requests for other phenotypic information would be by arrangement with the relevant principal investigator, assuming such information is accessible in the first place, and such arrangement will be subject to all pertinent ethico-legal prohibitions, restrictions and commitments. Data Access Committee Applications for access to Project Data must be made to the Asthma Remission Study Data Access Committee (hereafter referred to as “DAC”). Data Access Procedure 1. Application for Access The handling of applications, the issue of Project Data and any associated operations, administration and audits will be performed by the University Medical Center Groningen (hereafter “UMCG”) on behalf of the Consortium. Applications for access to Project Data must be submitted using the Application Form for Access to Asthma Remission Study Data, attached hereto as 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. In cases where an application contains classified plans, know-how or trade secrets, the applicant may request the conclusion of a separate confidentiality agreement. 2. Multiple applications Applicants agree to use the Project Data for the approved purpose and project described in the application; use of the Project 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 Project Data with additional collaborators not previously approved, these additional collaborators must make a separate application for access to the Project Data. In the event two or more applications overlap, the DAC may propose the respective applicants to align their applications. 3. Assessment criteria Applications, which seek to reserve Project Data for unspecified research goals, will not be taken into consideration. Applications for access to Project 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/are employed by or legitimately affiliated with a recognized research institution that can provide institutional responsibility for appropriate research governance; ii. its proposed use of the Project Data is in accordance with and meets the objectives of the Project and the objectives of the associated cohorts and collections; iii. its proposed use of the Project Data constitutes research in the context of the individual sample donor consent process, and is likely to be understood as such by the individual sample donors; iv. it would breach any of the ethical permissions or restrictions in the consent forms for any component cohort; v. all required ethico-legal approvals, restrictions and commitments for the proposed use of the Project Data have been obtained and adhered to; vi. the proposed research has any adverse potential impact, specifically whether the proposed research could affect minorities; vii. the nature of the funding of the application and the applicant; viii. the research proposal has been peer-reviewed and, if not, whether the proposal satisfies applicable scientific standards; ix. the requested Project Data are, quantitatively and qualitatively, suitable and not excessive for the applicant’s proposed research; x. there are any similar applications pending or granted; xi. the proposed use of the Project Data has the potential to produce information that will enable identification of the individual sample donors. xii. the applicant has warranted that he/she has obtained all required ethico-legal approvals, restrictions and commitments, without limitation his/her data subject informed consent and the approval of his/her pertinent medical ethical review board, for his/her proposed use of his/her data in combination with the Project Data. 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 Consortium will make the anonymized Project Data available by means of either secure download from the data SFTP server, or courier transfer by encrypted portable hard-drive (costs for the receiving party) or a custom method agreed upon by both parties. Issue of Project Data may be subject to restrictions pursuant to data subject’s or ethics committee’s consent. Prior to issue of Project Data applicants will be subject to authentication. The issue of Project Data and the Data Access Agreement will be administered by UMCG. Data Access Conditions Access to Project Data is conditional on prior receipt by the Consortium of the Data Access Agreement attached as Appendix 2 hereto, signed and dated by the applicant(s) and the responsible employing Institution(s). Appendix 1: Application Form for Access to Asthma Remission Study Data Appendix 2: Template Data Access Agreement University Medical Center Groningen, whose address is at Hanzeplein 1, 9713 GZ Groningen, the Netherlands (hereinafter referred to as “UMCG”), acting on behalf of the Asthma Remission Study Consortium (hereafter referred to as “the Consortium”) and [insert name of the applicant institution], whose registered office is at [insert address], lawfully represented by [insert name(s) and function(s)] (hereinafter referred to as “User Institution”) in the presence of [RESEARCHER] [insert researcher’s title, name and department of Institution where the researcher is employed], the supervisor under whose responsibility the Project Data will be used (hereinafter referred to as “User”) Background: This agreement governs the terms on which access will be granted to the Project Data generated by the Project. 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: “Consortium” refers to the Asthma Remission Study Consortium, comprising the research groups of the Groningen Research Institute for Asthma and COPD (GRIAC) of the University Medical Center Groningen (UMCG) “Data Subject” refers to the person whose sample has been used to generate Project Data. “Project” refers to the Asthma Remission Study; “Project Data” refers to the Illumina 450k methylation data and RNA sequencing data generated by the Project; “Publications” refers to, without limitation, articles published in print journals, electronic journals, registers, reviews, books, posters and other written and verbal presentations of research projects; “User” refers to a researcher who has successfully applied for access to Project Data; “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 Project Data only for the advancement of scientific and medical research. 2. You agree not to use, and not to allow use of, Project Data or any part thereof for the creation of products or services for sale or for any commercial purpose, whether sold or commercially made available by You or by third parties. 3. You acknowledge that the Project Data You receive is anonymized and that the Consortium will under no circumstances provide You with any means to identify any Data Subject. You agree not to use or attempt to use Project Data to identify or contact individual 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 Data Subjects and their right to privacy. 4. You agree to disclose Project Data only to those of Your employees or hired personnel who strictly need access to it for the purpose of your approved project (hereafter referred to as “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 by the Consortium, you agree to furnish the Consortium the names of all Authorized Recipients who have gained access to Project Data. You agree that you are fully 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, UMCG, of any violations of the foregoing. 7. You represent and warrant that all required ethico-legal approvals, restrictions and commitments, without limitation, Your data subjects’ informed consent and approval of the pertinent medical ethical review board for Your proposed use of Your data in combination with the Project Data, have been obtained and adhered to. 8. In the event the Project Data is issued to You bound by 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 a Data Subject 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 Subject may bring an action before a court within the Data Subject’s jurisdiction against You. 9. You acknowledge that the Data Subject remains the person that is authorized to decide on the use of his/her Project Data and may request destruction thereof. Upon first request of the Consortium or its appointed agent, you shall destroy such Project Data in accordance with its written instructions. 10. 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. 11. 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 Asthma Remission Study Data Access Procedure. 12. You agree to use Project Data for the purpose and project described in your application (No.____________________), as approved by the Asthma Remission Study Data Access Committee; use of the Project 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. 13. When Your analyses result in newly estimated variables at an individual level (e.g. haplotypes), You agree to submit these new variables for archiving with the Consortium. This should be done no later than that the related paper is submitted for publication. 14. You accept that Project Data will be reissued from time to time, with suitable versioning. If the reissue is at the request of Data Subject(s) and/or is subject to other ethical scrutiny, You will destroy earlier versions of the Project Data. 15. You agree to destroy the Project Data after the resulting Publication has been published. You agree to abide by the terms outlined in the Consortium “Publication Policy” as set out in Schedule 1. 16. You agree to acknowledge in any work based in whole or in part on Project Data, the Publication from which the Project Data derives, the version of the Project Data and the role of the Consortium and the relevant primary collectors and their funders, as per the wording provided in the Publication Policy set forth in Schedule 1. 17. You accept that the Consortium, 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, handling or storage 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 an 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 provided to You in accordance with the written instructions of the Consortium or its appointed agent. 20. You accept that it may be necessary for the Consortium or its appointed agent to alter the terms of this agreement from time to time in order to address new concerns. In this event, the Consortium or its appointed agent will contact You to inform You 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 Asthma Remission Study Data Access Committee, if requested, on completion of Your project using the Project Data. Such report will include the data resulting from Your project using the Project Data. The Asthma Remission Study 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 Asthma Remission Study 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 EU. 23. This agreement shall be construed, interpreted and governed by the laws of the Netherlands. 24. Any dispute which cannot be solved amicably between parties shall be subject to the exclusive jurisdiction of the district court of the Northern Netherlands. Name of Applicant’s Institution: ............................................................................................................... Official address of Applicant’s Institution: ................................................................................................ ................................................................................................ Name of legal representative of Applicant’s Institution: ........................................................................... Signature: ................................................................................... Date: ............................................................ Stamp or Seal of Applicant’s Institution: ................................................................................... Name of Applicant: Signature: ................................................................................... Affiliation of Applicant with Institution: ...................................................................... Date: ............................................................ Schedule 1: Asthma Remission Study Consortium Publication Policy • Appendix 1: Application form Asthma Remission Study data • 1. Name and position of the Applicant, 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 (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 Project Data; f. timeline; g. key references.

 4. Consent and Approvals. If your proposed use of Project Data involves use of your own data, please confirm that you have obtained all approvals required by the rules and regulations of your jurisdiction, including your institution’s institutional rules, and the consent of your data subjects, for your use of your own data in the study, by ticking the following box:


 ☐ Yes, I have obtained all approvals required


 ☐ No


 5. Resources, Feasibility & Expertise 
 Please confirm that you have secured funding for your proposed use of the Project 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, I have funding to carry out the proposed research


 ☐ No
 

 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).

 • 6. Access Conditions. Please declare that you have read and agree to abide by the terms and conditions outlined in the data access agreement (which you will need to sign on approval of this project), by ticking the following box:


 ☐ Yes, I have read and agree to data access agreement


 ☐ No


 •   7. Asthma Remission Consortium Publication Policy: Publications which include analyses of data generated as part of the Asthma Remission Study, must acknowledge the Asthma Remission Study Consortium as follows: “This study makes use of data generated by the Groningen Research Institute for Asthma and COPD (GRIAC), as part of a Scientific Research Collaboration funded by GSK.”