HGG Advances (Apr 2023)
Whole genome sequencing for USH2A-associated disease reveals several pathogenic deep-intronic variants that are amenable to splice correction
- Janine Reurink,
- Nicole Weisschuh,
- Alejandro Garanto,
- Adrian Dockery,
- L. Ingeborgh van den Born,
- Isabelle Fajardy,
- Lonneke Haer-Wigman,
- Susanne Kohl,
- Bernd Wissinger,
- G. Jane Farrar,
- Tamar Ben-Yosef,
- Fatma Kivrak Pfiffner,
- Wolfgang Berger,
- Marianna E. Weener,
- Lubica Dudakova,
- Petra Liskova,
- Dror Sharon,
- Manar Salameh,
- Ashley Offenheim,
- Elise Heon,
- Giorgia Girotto,
- Paolo Gasparini,
- Anna Morgan,
- Arthur A. Bergen,
- Jacoline B. ten Brink,
- Caroline C.W. Klaver,
- Lisbeth Tranebjærg,
- Nanna D. Rendtorff,
- Sascha Vermeer,
- Jeroen J. Smits,
- Ronald J.E. Pennings,
- Marco Aben,
- Jaap Oostrik,
- Galuh D.N. Astuti,
- Jordi Corominas Galbany,
- Hester Y. Kroes,
- Milan Phan,
- Wendy A.G. van Zelst-Stams,
- Alberta A.H.J. Thiadens,
- Joke B.G.M. Verheij,
- Mary J. van Schooneveld,
- Suzanne E. de Bruijn,
- Catherina H.Z. Li,
- Carel B. Hoyng,
- Christian Gilissen,
- Lisenka E.L.M. Vissers,
- Frans P.M. Cremers,
- Hannie Kremer,
- Erwin van Wijk,
- Susanne Roosing
Affiliations
- Janine Reurink
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Nicole Weisschuh
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
- Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Pediatrics, Amalia’s Children Hospital, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Adrian Dockery
- The School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- L. Ingeborgh van den Born
- The Rotterdam Eye Hospital, Rotterdam, the Netherlands
- Isabelle Fajardy
- Centre de Biologie Pathologie Génétique, CHU de Lille, Lille, France
- Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
- Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
- G. Jane Farrar
- The School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- Tamar Ben-Yosef
- The Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Fatma Kivrak Pfiffner
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
- Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland; Neuroscience Center Zurich, University and ETH Zurich, Zurich, Switzerland; Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
- Marianna E. Weener
- CRO Oftalmic, Moscow, Russia
- Lubica Dudakova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Petra Liskova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic; Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Dror Sharon
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Manar Salameh
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Ashley Offenheim
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Elise Heon
- Departments of Ophthalmology and Vision Sciences, The Hospital for Sick Children, The University of Toronto, Toronto, ON, Canada
- Giorgia Girotto
- Institute for Maternal and Child Health—I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Paolo Gasparini
- Institute for Maternal and Child Health—I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Anna Morgan
- Institute for Maternal and Child Health—I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
- Arthur A. Bergen
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, the Netherlands; Department of Ophthalmology, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, the Netherlands
- Jacoline B. ten Brink
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, the Netherlands
- Caroline C.W. Klaver
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Lisbeth Tranebjærg
- Department of Clinical Genetics, The Kennedy Center, Copenhagen University Hospital, 2600 Glostrup, Denmark; Institute of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Nanna D. Rendtorff
- Department of Clinical Genetics, The Kennedy Center, Copenhagen University Hospital, 2600 Glostrup, Denmark
- Sascha Vermeer
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
- Jeroen J. Smits
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Hearing & Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands; Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center of Utrecht, Utrecht, the Netherlands
- Ronald J.E. Pennings
- Hearing & Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands
- Marco Aben
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Jaap Oostrik
- Hearing & Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands
- Galuh D.N. Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University, Semarang, Indonesia
- Jordi Corominas Galbany
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Hester Y. Kroes
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center of Utrecht, Utrecht, the Netherlands
- Milan Phan
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Rijnstate Hospital, Arnhem, the Netherlands
- Wendy A.G. van Zelst-Stams
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Alberta A.H.J. Thiadens
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Joke B.G.M. Verheij
- Department of Medical Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Mary J. van Schooneveld
- Department of Ophthalmology, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, the Netherlands
- Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Catherina H.Z. Li
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
- Carel B. Hoyng
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
- Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Lisenka E.L.M. Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Frans P.M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Hannie Kremer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Hearing & Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands
- Erwin van Wijk
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Hearing & Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands; Corresponding author
- Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Corresponding author
- Journal volume & issue
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Vol. 4,
no. 2
p. 100181
Abstract
Summary: A significant number of individuals with a rare disorder such as Usher syndrome (USH) and (non-)syndromic autosomal recessive retinitis pigmentosa (arRP) remain genetically unexplained. Therefore, we assessed subjects suspected of USH2A-associated disease and no or mono-allelic USH2A variants using whole genome sequencing (WGS) followed by an improved pipeline for variant interpretation to provide a conclusive diagnosis.One hundred subjects were screened using WGS to identify causative variants in USH2A or other USH/arRP-associated genes. In addition to the existing variant interpretation pipeline, a particular focus was put on assessing splice-affecting properties of variants, both in silico and in vitro. Also structural variants were extensively addressed. For variants resulting in pseudoexon inclusion, we designed and evaluated antisense oligonucleotides (AONs) using minigene splice assays and patient-derived photoreceptor precursor cells.Biallelic variants were identified in 49 of 100 subjects, including novel splice-affecting variants and structural variants, in USH2A or arRP/USH-associated genes. Thirteen variants were shown to affect USH2A pre-mRNA splicing, including four deep-intronic USH2A variants resulting in pseudoexon inclusion, which could be corrected upon AON treatment.We have shown that WGS, combined with a thorough variant interpretation pipeline focused on assessing pre-mRNA splicing defects and structural variants, is a powerful method to provide subjects with a rare genetic condition, a (likely) conclusive genetic diagnosis. This is essential for the development of future personalized treatments and for patients to be eligible for such treatments.
