Claire-Marie Dhaenens1,2, Frans P M Cremers3,4, Mubeen Khan1,5, Stéphanie S Cornelis1,5, Marta Del Pozo-Valero1,6, Laura Whelan7, Esmee H Runhart5,8, Ketan Mishra1,5, Femke Bults1, Yahya AlSwaiti9, Alaa AlTalbishi9, Elfride De Baere10, Sandro Banfi11, Eyal Banin12, Miriam Bauwens10, Tamar Ben-Yosef13, Camiel J F Boon14,15, L Ingeborgh van den Born16,17, Sabine Defoort18, Aurore Devos2, Adrian Dockery7, Lubica Dudakova19, Ana Fakin20, G Jane Farrar7, Juliana Maria Ferraz Sallum21,22, Kaoru Fujinami23,24,25,26, Christian Gilissen1,27, Damjan Glavač28, Michael B Gorin29,30, Jacquie Greenberg31, Takaaki Hayashi32, Ymkje M Hettinga33, Alexander Hoischen1, Carel B Hoyng5,8, Karsten Hufendiek34, Herbert Jägle35, Smaragda Kamakari36, Marianthi Karali11, Ulrich Kellner37,38, Caroline C W Klaver8,39,40, Bohdan Kousal19,41, Tina M Lamey42,43, Ian M MacDonald44, Anna Matynia29,30, Terri L McLaren42,43, Marcela D Mena45, Isabelle Meunier46, Rianne Miller1, Hadas Newman47,48, Buhle Ntozini31, Monika Oldak49, Marc Pieterse1, Osvaldo L Podhajcer45, Bernard Puech18, Raj Ramesar31, Klaus Rüther50, Manar Salameh9, Mariana Vallim Salles21,22, Dror Sharon12, Francesca Simonelli51, Georg Spital52, Marloes Steehouwer1, Jacek P Szaflik53, Jennifer A Thompson43, Caroline Thuillier54, Anna M Tracewska55, Martine van Zweeden1, Andrea L Vincent56,57, Xavier Zanlonghi58, Petra Liskova19,41, Heidi Stöhr59, John N De Roach42,43, Carmen Ayuso6, Lisa Roberts31, Bernhard H F Weber59. 1. Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands. 2. Univ. Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000, Lille, France. 3. Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands. frans.cremers@radboudumc.nl. 4. Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands. frans.cremers@radboudumc.nl. 5. Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands. 6. Department of Genetics, IIS-Fundación Jiménez Díaz, CIBERER, Madrid, Spain. 7. The School of Genetics & Microbiology, Trinity College Dublin, Dublin, Ireland. 8. Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands. 9. St John of Jerusalem Eye Hospital Group, East Jerusalem, Palestine. 10. Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium. 11. Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples and Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy. 12. Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel. 13. Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel. 14. Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands. 15. Department of Ophthalmology, Amsterdam University Medical Centers, Amsterdam, The Netherlands. 16. The Rotterdam Eye Hospital, Rotterdam, The Netherlands. 17. The Rotterdam Ophthalmic Institute, Rotterdam, The Netherlands. 18. Service d'exploration de la vision et neuro-ophtalmologie, Centre Hospitalier Universitaire de Lille, Lille, France. 19. Research Unit for Rare Diseases, Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic. 20. Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia. 21. Department of Ophthalmology and Visual Sciences, Universidade Federal de São Paulo, São Paulo, SP, Brazil. 22. Instituto de Genética Ocular, São Paulo, SP, Brazil. 23. UCL Institute of Ophthalmology, London, UK. 24. Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan. 25. Graduate School of Health Management, Keio University, Tokyo, Japan. 26. Moorfields Eye Hospital, London, UK. 27. Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands. 28. Department of Molecular Genetics, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia. 29. Department of Ophthalmology, David Geffen School of Medicine, Stein Eye Institute, University of California-Los Angeles, Los Angeles, CA, USA. 30. Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA. 31. University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. 32. Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan. 33. Bartiméus Diagnostic Center for Complex Visual Disorders, Zeist, The Netherlands. 34. University Eye Hospital Hannover Medical School, Hannover, Germany. 35. Department of Ophthalmology, University Hospital, University Regensburg, Regensburg, Germany. 36. Ophthalmic Genetics Unit, OMMA Ophthalmological Institute of Athens, Athens, Greece. 37. Rare Retinal Disease Center, AugenZentrum Siegburg, MVZ ADTC Siegburg GmbH, Siegburg, Germany. 38. RetinaScience, Bonn, Germany. 39. Department of Ophthalmology, Erasmus Medical Centre, Rotterdam, The Netherlands. 40. Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands. 41. Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic. 42. Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, WA, Australia. 43. Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA, Australia. 44. Departments of Ophthalmology and Medical Genetics, University of Alberta, Edmonton, AB, Canada. 45. Laboratory of Molecular and Cellular Therapy, Fundacion Instituto Leloir-CONICET, Buenos Aires, Argentina. 46. Institut des Neurosciences de Montpellier, INSERM, Université de Montpellier, Montpellier, France. 47. Department of Ophthalmology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel. 48. Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. 49. Department of Histology and Embryology, Medical University of Warsaw, Warsaw, Poland. 50. Augenarztpraxis, Dorotheenstraße, Berlin, Germany. 51. Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy. 52. Department of Ophthalmology, St. Franziskus-Hospital, Münster, Germany. 53. Department of Ophthalmology, Medical University of Warsaw SPKSO Ophthalmic University Hospital, Warsaw, Poland. 54. CHU Lille, Institut de Génétique Médicale, Lille, France. 55. DNA Analysis Unit, ŁUKASIEWICZ Research Network-PORT Polish Center for Technology Development, Wroclaw, Poland. 56. Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, The University of Auckland, Grafton, Auckland, New Zealand. 57. Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand. 58. Centre de Compétence Maladie Rare, Clinique Jules Verne, Nantes, France. 59. Institute of Human Genetics, University of Regensburg, Regensburg, Germany.
Abstract
PURPOSE: Missing heritability in human diseases represents a major challenge, and this is particularly true for ABCA4-associated Stargardt disease (STGD1). We aimed to elucidate the genomic and transcriptomic variation in 1054 unsolved STGD and STGD-like probands. METHODS: Sequencing of the complete 128-kb ABCA4 gene was performed using single-molecule molecular inversion probes (smMIPs), based on a semiautomated and cost-effective method. Structural variants (SVs) were identified using relative read coverage analyses and putative splice defects were studied using in vitro assays. RESULTS: In 448 biallelic probands 14 known and 13 novel deep-intronic variants were found, resulting in pseudoexon (PE) insertions or exon elongations in 105 alleles. Intriguingly, intron 13 variants c.1938-621G>A and c.1938-514G>A resulted in dual PE insertions consisting of the same upstream, but different downstream PEs. The intron 44 variant c.6148-84A>T resulted in two PE insertions and flanking exon deletions. Eleven distinct large deletions were found, two of which contained small inverted segments. Uniparental isodisomy of chromosome 1 was identified in one proband. CONCLUSION: Deep sequencing of ABCA4 and midigene-based splice assays allowed the identification of SVs and causal deep-intronic variants in 25% of biallelic STGD1 cases, which represents a model study that can be applied to other inherited diseases.
PURPOSE: Missing heritability in human diseases represents a major challenge, and this is particularly true for ABCA4-associated Stargardt disease (STGD1). We aimed to elucidate the genomic and transcriptomic variation in 1054 unsolved STGD and STGD-like probands. METHODS: Sequencing of the complete 128-kb ABCA4 gene was performed using single-molecule molecular inversion probes (smMIPs), based on a semiautomated and cost-effective method. Structural variants (SVs) were identified using relative read coverage analyses and putative splice defects were studied using in vitro assays. RESULTS: In 448 biallelic probands 14 known and 13 novel deep-intronic variants were found, resulting in pseudoexon (PE) insertions or exon elongations in 105 alleles. Intriguingly, intron 13 variants c.1938-621G>A and c.1938-514G>A resulted in dual PE insertions consisting of the same upstream, but different downstream PEs. The intron 44 variant c.6148-84A>T resulted in two PE insertions and flanking exon deletions. Eleven distinct large deletions were found, two of which contained small inverted segments. Uniparental isodisomy of chromosome 1 was identified in one proband. CONCLUSION: Deep sequencing of ABCA4 and midigene-based splice assays allowed the identification of SVs and causal deep-intronic variants in 25% of biallelic STGD1 cases, which represents a model study that can be applied to other inherited diseases.
Authors: Esmee H Runhart; Mubeen Khan; Stéphanie S Cornelis; Susanne Roosing; Marta Del Pozo-Valero; Tina M Lamey; Petra Liskova; Lisa Roberts; Heidi Stöhr; Caroline C W Klaver; Carel B Hoyng; Frans P M Cremers; Claire-Marie Dhaenens Journal: JAMA Ophthalmol Date: 2020-10-01 Impact factor: 7.389
Authors: Nathaniel K Mullin; Andrew P Voigt; Jessica A Cooke; Laura R Bohrer; Erin R Burnight; Edwin M Stone; Robert F Mullins; Budd A Tucker Journal: Prog Retin Eye Res Date: 2020-10-29 Impact factor: 21.198
Authors: Tomasz Z Tomkiewicz; Nuria Suárez-Herrera; Frans P M Cremers; Rob W J Collin; Alejandro Garanto Journal: Int J Mol Sci Date: 2021-04-28 Impact factor: 5.923
Authors: Marcela D Mena; Angélica A Moresco; Sofía H Vidal; Diana Aguilar-Cortes; María G Obregon; Adriana C Fandiño; Juan M Sendoya; Andrea S Llera; Osvaldo L Podhajcer Journal: Front Genet Date: 2021-03-26 Impact factor: 4.599
Authors: Anna M Tracewska; Beata Kocyła-Karczmarewicz; Agnieszka Rafalska; Joanna Murawska; Joanna Jakubaszko-Jabłónska; Małgorzata Rydzanicz; Piotr Stawiński; Elżbieta Ciara; Beata S Lipska-Ziętkiewicz; Muhammad Imran Khan; Frans P M Cremers; Rafał Płoski; Krystyna H Chrzanowska Journal: Mol Vis Date: 2021-07-16 Impact factor: 2.367
Authors: Janine Reurink; Adrian Dockery; Dominika Oziębło; G Jane Farrar; Monika Ołdak; Jacoline B Ten Brink; Arthur A Bergen; Tuula Rinne; Helger G Yntema; Ronald J E Pennings; L Ingeborgh van den Born; Marco Aben; Jaap Oostrik; Hanka Venselaar; Astrid S Plomp; M Imran Khan; Erwin van Wijk; Frans P M Cremers; Susanne Roosing; Hannie Kremer Journal: Int J Mol Sci Date: 2021-06-15 Impact factor: 5.923
Authors: Peter Gergics; Cathy Smith; Hironori Bando; Alexander A L Jorge; Denise Rockstroh-Lippold; Sebastian A Vishnopolska; Frederic Castinetti; Mariam Maksutova; Luciani Renata Silveira Carvalho; Julia Hoppmann; Julián Martínez Mayer; Frédérique Albarel; Debora Braslavsky; Ana Keselman; Ignacio Bergadá; Marcelo A Martí; Alexandru Saveanu; Anne Barlier; Rami Abou Jamra; Michael H Guo; Andrew Dauber; Marilena Nakaguma; Berenice B Mendonca; Sajini N Jayakody; A Bilge Ozel; Qing Fang; Qianyi Ma; Jun Z Li; Thierry Brue; María Ines Pérez Millán; Ivo J P Arnhold; Roland Pfaeffle; Jacob O Kitzman; Sally A Camper Journal: Am J Hum Genet Date: 2021-07-15 Impact factor: 11.025