Full blood mRNA sequencing of myotonic dystrophy patients before and after cognitive behavioural therapy: Access to Data
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.
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:
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
6MWT: 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.