Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing
- Wouter Steyaert1,36,
- Lydia Sagath1,36,
- German Demidov2,
- Vicente A. Yépez3,
- Anna Esteve-Codina4,5,
- Julien Gagneur3,6,7,
- Kornelia Ellwanger2,8,
- Ronny Derks1,
- Marjan Weiss1,
- Amber den Ouden1,
- Simone van den Heuvel1,
- Hilde Swinkels1,
- Nick Zomer1,
- Marloes Steehouwer1,
- Luke O'Gorman1,
- Galuh Astuti1,
- Kornelia Neveling1,
- Rebecca Schüle9,10,
- Jishu Xu9,
- Matthis Synofzik9,11,
- Danique Beijer9,
- Holger Hengel9,
- Ludger Schöls9,11,
- Kristl G. Claeys12,13,
- Jonathan Baets14,15,16,
- Liedewei Van de Vondel14,15,
- Alessandra Ferlini17,
- Rita Selvatici17,
- Heba Morsy18,
- Marwa Saeed Abd Elmaksoud19,
- Volker Straub20,
- Juliane Müller21,
- Veronica Pini21,
- Luke Perry21,22,
- Anna Sarkozy21,
- Irina Zaharieva21,
- Francesco Muntoni21,22,
- Enrico Bugiardini23,
- Kiran Polavarapu24,
- Rita Horvath25,
- Evan Reid26,
- Hanns Lochmüller27,28,29,
- Marco Spinazzi30,
- Marco Savarese31,32,
- Solve-RD DITF-ITHACA, Solve-RD DITF-Euro-NMD, Solve-RD DITF-RND, Solve-RD DITF-EpiCARE,
- Leslie Matalonga4,5,
- Steven Laurie4,5,
- Han G. Brunner1,33,
- Holm Graessner2,8,
- Sergi Beltran4,34,
- Stephan Ossowski2,
- Lisenka E.L.M. Vissers1,
- Christian Gilissen1,37,
- Alexander Hoischen1,35,37,
- on behalf of the Solve-RD consortium
- 1Radboud University Medical Center, Department of Human Genetics, Research Institute for Medical Innovation, 6500 HB Nijmegen, Netherlands;
- 2Universitätsklinikum Tübingen - Institut für Medizinische Genetik und angewandte Genomik, 72076 Tübingen, Germany;
- 3TUM School of Computation, Information and Technology, Technical University of Munich, 85748 Garching, Germany;
- 4Centro Nacional de Análisis Genómico (CNAG), 08028 Barcelona, Spain;
- 5Universitat de Barcelona (UB), 08007 Barcelona, Spain;
- 6Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany;
- 7Computational Health Center, Helmholtz Center Munich, 85764 Neuherberg, Germany;
- 8Center for Rare Diseases, University Hospital Tübingen, 72076 Tübingen, Germany;
- 9Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany;
- 10Division of Neurodegenerative Diseases, Department of Neurology, Heidelberg University Hospital and Faculty of Medicine, 69120 Heidelberg, Germany;
- 11German Center of Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany;
- 12Department of Neurology, University Hospitals Leuven, 3000 Leuven, Belgium;
- 13Department of Neurosciences, Laboratory for Muscle Diseases and Neuropathies, KU Leuven, and Leuven Brain Institute (LBI), 3000 Leuven, Belgium;
- 14Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium;
- 15Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, 2610 Antwerp, Belgium;
- 16Neuromuscular Reference Center, Department of Neurology, Antwerp University Hospital, 2650 Antwerp, Belgium;
- 17Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy;
- 18Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, United Kingdom;
- 19Neurology Unit, Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria 5372066, Egypt;
- 20John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, United Kingdom;
- 21Dubowitz Neuromuscular Centre, UCL Great Ormond Street Hospital, London WC1N 3JH, United Kingdom;
- 22NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, United Kingdom;
- 23Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, United Kingdom;
- 24Children's Hospital of Eastern Ontario Research Institute, University of Ottawa and Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON K1H 8L1, Canada;
- 25Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0PY, United Kingdom;
- 26Cambridge Institute for Medical Research and Department of Medical Genetics, University of Cambridge, Cambridge CB2 0XY, United Kingdom;
- 27Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, ON K1H 8M8, Canada;
- 28Brain and Mind Research Institute, University of Ottawa, Ottawa, Ontario, ON K1H 8M5, Canada;
- 29The Ottawa Hospital Research Institute, University of Ottawa, Ottawa, Ontario, ON K1Y 4E9, Canada;
- 30Department of Neurology, Centre Hospitalier Universitaire d'Angers, 49933 Angers, France;
- 31Folkhälsan Research Center, 00250 Helsinki, Uusimaa, Finland;
- 32Faculty of Medicine, University of Helsinki, 00014 University of Helsinki, Uusimaa, Finland;
- 33Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, Netherlands;
- 34Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain;
- 35Radboud University Medical Center, Department of Internal Medicine; Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), 6500 HB Nijmegen, Netherlands
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↵36 These authors contributed equally to this work.
Abstract
Solve-RD is a pan-European rare disease (RD) research program that aims to identify disease-causing genetic variants in previously undiagnosed RD families. We utilized 10-fold coverage HiFi long-read sequencing (LRS) for detecting causative structural variants (SVs), single-nucleotide variants (SNVs), insertion-deletions (indels), and short tandem repeat (STR) expansions in previously studied RD families without a clear molecular diagnosis. Our cohort includes 293 individuals from 114 genetically undiagnosed RD families selected by European Reference Network (ERN) experts. Of these, 21 families were affected by so-called “unsolvable” syndromes for which genetic causes remain unknown and for which prior testing was not a prerequisite. The remaining 93 families had at least one individual affected by a rare neurological, neuromuscular, or epilepsy disorder without a genetic diagnosis despite extensive prior testing. Clinical interpretation and orthogonal validation of variants in known disease genes yielded 12 novel genetic diagnoses due to de novo and rare inherited SNVs, indels, SVs, and STR expansions. In an additional five families, we identified a candidate disease-causing variant, including an MCF2/FGF13 fusion and a PSMA3 deletion. However, no common genetic cause was identified in any of the “unsolvable” syndromes. Taken together, we found (likely) disease-causing genetic variants in 11.8% of previously unsolved families and additional candidate disease-causing SVs in another 5.4% of these families. In conclusion, our results demonstrate the potential added value of HiFi long-read genome sequencing in undiagnosed rare diseases.
Footnotes
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↵37 These authors jointly supervised this work.
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.279414.124.
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Freely available online through the Genome Research Open Access option.
- Received March 28, 2024.
- Accepted February 21, 2025.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
