Long read transcriptomes of DM1 patients

We expect a to-the-point but comprehensive plan for use, which is aimed at the advancement of scientific and medical research. When publishing based on this data, you agree to acknowledge all those as outlined in the data access policy. Under no circumstance anything from this dataset may be shared with others that are not mentioned in the application. The access request form can be found as an appendix to the data access policy document.

General principles Funded by the eRARE program, the ReCognitION consortium (hereinafter also referred to as the “Project”, “Consortium” or “ReCognitION”) has sequenced total blood RNA of 31 myotonic dystrophy type 1 (DM1) patients from four different European centers. The Project is led by Baziel van Engelen and Peter-Bram ‘t Hoen from Radboud University Medical Centre in Nijmegen, the Netherlands (“Radboudumc”). The primary goal of ReCognitION is to identify biomarkers for clinical response to cognitive behavioral therapy (CBT) in DM1. The Consortium is willing to consider applications from third party researchers for access to the anonymized sequence, genotype and phenotype data generated by the Project. See also the Project website: https://optimistic-dm.eu/recognition/. 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 ReCognitION Data Access Committee. Researchers granted access to Project Data must feedback the results of their research to ReCognitION, after publication in accordance with the ReCognitION 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 Project Data are available: Full blood mRNA sequencing data: Blood drawn within the framework of the OPTIMISTIC trial (https://pubmed.ncbi.nlm.nih.gov/26002596/ and https://pubmed.ncbi.nlm.nih.gov/29934199/) was collected in Tempus tubes and stored at X degrees for 5-6 years. RNA was isolated using the Tempus Spin RNA Isolation Kit (Applied Biosystems/Thermo Fisher Scientific) according to manufacturer’s instructions. The concentration and RNA Integrity Number (RIN) was checked using Fragment Analyzer (Thermo Fisher Scientific). The mean RIN value was 8.9 and all were > 7.5. Hemoglobin mRNA was depleted using the Globinclear kit (Thermo Fisher Scientific). Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (Illumina) according to manufacturer’s instructions for a polyA mRNA workflow using UMI-indexed adapters. The size distribution (between 300 and 500 bp) was confirmed using Fragment Analyzer. 150 bp paired end sequencing was performed with a NovaSeq6000 machine (Illumina) at a library concentration of 1.1 nM, generating >30 M read pairs per sample. Data available are fastq-files to which UMIs have been appended to the read names. Collected also during the OPTIMISTIC trial are the following genotype and patient characteristic data: AgeBaseline: age of the patient at the start of the trial (years) ePAL: estimated progenitor allele length V2Mode: modal CTG-repeat length at baseline CTGDiagnostic: CTG repeat length at diagnosis VariantRepeats: whether patient had a variant repeat (all 0=no variant repeat) Collected also during the OPTIMISTIC trial is the following phenotype data, consisting of clinical outcome measures at baseline and after 10 months of CBT: DM1ActivC: DM1ActivC MDHI: Myotonic Dystrophy Health Index INQOLQol: Individualized Neuromuscular Quality of Life Questionnaire. Domain: quality of life ASBQ: Adult Social Behavioral Questionnaire ICQ: Illness Cognition Questionnaire. Subscale: acceptance IMQ: Illness Management Questionnaire CISactivity: Checklist Individual Strength. Subscale: activity SMWT: Six-minute walk test L5ENMO: Activity during the 5 least active hours of the day (negative control) M5ENMO: Activity during the 5 most active hours of the day MeanENMO: Accelerometery, mean of euclidian norm minus one PreBORG: Borg Scale measurement after SMWT FDSS: Fatigue and Daytime Sleepiness Scale CISFatigue: Checklist Individual Strength. Subscale: fatigue JFCS: Jacobsen Fatigue Catastrophizing Scale TMT: Trail Making Test (TMTB/TMTA) StroopInterference: Stroop colour-word interference score ((60 - stroopCardIIIErrors/60) / stroopCardIIITime /(60 - stroopCardIIErrors)/60) / stroopCardIITime McGillPain: McGILL Pain Questionnaire: short version BDIFs: Beck Depression Inventory: fast screen SSLD: Social Support: Discrepancies SSLI: Social Support: Interactions SSLN: Social Support: Negative Interactions AEScScore: Apathy Evaluation Scale: clinical version Data Access Committee Applications for access to Project Data must be made to the ReCognitION Data Access Committee (DAC). The ReCognitION DAC consists of Baziel van Engelen, Peter-Bram ‘t Hoen, Guillaume Bassez, Benedikt Schoser and Grainne Gorman. 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 Radboudumc on behalf of the Consortium. Applications for Access to Project 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. The research topic of the applications which have been granted will be published on the website of the Project. Applications which have not been granted will not be published. 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 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 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 ReCognitION 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 recognised 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 ReCognitION 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 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. In the event the applicant(s)’ proposed use of Project Data involves use of his/their your own data the applicant has warranted that he has obtained all required ethico-legal approvals, restrictions and commitments, without limitation his data subject consent and approval of his pertinent medical ethical review board, for his proposed use of his data in combination with the Project Data, as appropriate. 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 pseudonymised Project Data available through the European Genome Phenome Archive (EGA), hosted at the European Bioinformatics Institute. Issue of Project Data may be subject to restrictions pursuant to data subject’s or ethics committee’s consent. The issue of Project Data and the Data Access Agreement will be administered by Radboudumc. 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). Authors who use Project Data must: 1. Acknowledge the ReCognitION Consortium using the following wording: "This study makes use of data generated by the ReCognitION Consortium. A full list of the investigators is available from https://optimistic-dm.eu/recognition/. Funding for the project was provided by E-rare 3 - JTC2018 to the ReCognitION consortium.“ 2. Acknowledge, by reference, the trial that the samples and Project Data have been derived from: Okkersen K, Jimenez-Moreno C, Wenninger S, Daidj F, Glennon J, Cumming S, Littleford R, Monckton DG, Lochmüller H, Catt M, Faber CG, Hapca A, Donnan PT, Gorman G, Bassez G, Schoser B, Knoop H, Treweek S, van Engelen BGM; OPTIMISTIC consortium. Cognitive behavioural therapy with optional graded exercise therapy in patients with severe fatigue with myotonic dystrophy type 1: a multicentre, single-blind, randomised trial. Lancet Neurol. 2018 Aug;17(8):671-680. doi: 10.1016/S1474-4422(18)30203-5. Epub 2018 Jun 19. PMID: 29934199. 3. Cite the relevant primary ReCognitION publication by van Cruchten, van As, van Engelen and ‘t Hoen (details of which can be found on the project website: https://optimistic-dm.eu/recognition/).