Standardized transcriptome analysis improves rare disease diagnosis in the pan-European Solve-RD consortium
Year: 2026
Type: preprint
Study design: Observational Study
Abstract: RNA sequencing (RNA-seq) provides a powerful complement to DNA sequencing for uncovering pathogenic defects affecting gene expression and splicing in individuals with genetically undiagnosed rare disorders. However, as large rare disease consortia adopt RNA-seq, challenges arise due to cohort heterogeneity, variability in tissues and sample sizes, and differences in interpretation practices. Here, we present a harmonized analytical and interpretation framework developed by the pan-European Solve-RD consortium to address these challenges. We analyzed 521 RNA-seq samples from whole blood, fibroblasts, muscle and peripheral blood mononuclear cells collected across more than 30 clinics and five European Reference Networks. Aberrant expression and splicing events were identified using OUTRIDER and FRASER 2.0 and analysed through a standardized four-level scoring framework that encompassed RNA-seq outlier reliability, phenotype relevance, variant mechanism, and segregation evidence, captured in structured reports for interpretation. Regular meetings, and collaborative “Solvathon” workshops were used to evaluate variant pathogenicity. This effort resulted in molecular diagnoses for 19 families out of 248 (7.7%) for whom DNA analyses had been inconclusive. Furthermore, three cases diagnosed using DNA analyses were confirmed, and 49 candidate events and five novel candidate disease genes were identified in the remaining families. Our results demonstrate the feasibility and impact of large-scale, standardized RNA-seq analysis in a transnational research setting. This framework provides a model for other international initiatives such as the Undiagnosed Diseases Network and ERDERA, paving the way for broader clinical implementation of transcriptome-based rare disease diagnostics.
Source: medRxiv
Authors: Vicente A. Yépez, Rebeka Luknárová, Danique Beijer, Berta Estévez-Arias, Davide Mei, Heba Morsy, Juliane S. Mueller, Kiran Polavarapu, German Demidov, Cenna Doornbos, Kornelia Ellwanger, Leon Kraß, Steven Laurie, Leslie Matalonga, Ibrahim M. Abdelrazek, Galuh Astuti, Francesca Bisulli, Felix Brechtmann, Marc Dabad, Anne-Sophie Denommé-Pichon, Minas Drakos, Zakaria Eddafir, Glòria Garrabou, Renzo Guerrini, Mridul Johari, Josua Kegele, Ozge Aksel Kilicarslan, Heike Koelbel, Ingrid H.M. Kolen, Laura Licchetta, Hanns Lochmüller, Kars Maassen, William Macken, Christian Mertes, José César Milisenda, Raffaella Minardi, Barbara Mostacci, Kornelia Neveling, Machteld M. Oud, Joohyun Park, Aurora Pujol, Andreas Roos, Lydia Sagath, Bart van der Sanden, Marco Savarese, Alba Segarra-Casas, Noor Smal, Marloes Steehouwer, Wouter Steyaert, Rachel Thompson, Mirja Thomsen, Gerben van der Vries, Carlo Wilke, Ioannis Zaganas, Sergi Beltran, Alexander Hoischen, Katja Lohmann, Daniel Natera-de Benito, Rebecca Schüle, Matthis Synofzik, Lisenka Vissers, Ana Töpf, Holm Graessner, Antonio Vitobello, Peter-Bram ’t Hoen, Anna Esteve-Codina, Julien Gagneur
Institutions: Technical University of Munich, Hertie Institute for Clinical Brain Research, University of Tübingen, Hospital Sant Joan de Déu Barcelona, Institut de Recerca Sant Joan de Déu, Meyer Children's Hospital, UCL Queen Square Institute of Neurology, University College London, Alexandria University, Great Ormond Street Hospital, Children's Hospital of Eastern Ontario, Radboud University Medical Center, Helmholtz Munich, Institut für Humangenetik, Centro Nacional de Análisis Genómico, Universitat de Barcelona, Radboud University Nijmegen, Istituto delle Scienze Neurologiche di Bologna, University of Bologna, Inserm, CHU Dijon Bourgogne, University of Crete, University Hospital of Heraklion, University of Antwerp, VIB-UAntwerp Center for Molecular Neurology, Instituto de Salud Carlos III, Centre for Biomedical Network Research on Rare Diseases, Hospital Clínic de Barcelona, Consorci Institut D'Investigacions Biomediques August Pi I Sunyer, University of Florence, University of Helsinki, The University of Western Australia, Harry Perkins Institute of Medical Research, University of Ottawa, University of Duisburg-Essen, Heidelberg University, University Hospital Heidelberg, Ottawa Hospital, uOttawa Brain and Mind Research Institute, University Medical Center Groningen, University of Groningen, Institució Catalana de Recerca i Estudis Avançats, Institut d'Investigació Biomédica de Bellvitge, BG University Hospital Bergmannsheil Bochum, Newcastle upon Tyne Hospitals NHS Foundation Trust, Hospital de Sant Pau, Institut de Recerca Sant Pau, Newcastle University, Radboud Institute for Molecular Life Sciences, University of Lübeck, German Center for Neurodegenerative Diseases
Topic: Genomics and Rare Diseases
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7128924512