Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics

Mubeen Khan^{1

2}, Stéphanie S Cornelis^{1

2}, Marta Del Pozo-Valero^{1

3}, Laura Whelan⁴, Esmee H Runhart^{2

5}, Ketan Mishra^{1

2}, Femke Bults¹, Yahya AlSwaiti⁶, Alaa AlTalbishi⁶, Elfride De Baere⁷, Sandro Banfi⁸, Eyal Banin⁹, Miriam Bauwens⁷, Tamar Ben-Yosef¹⁰, Camiel J F Boon^{11

12}, L Ingeborgh van den Born^{13

14}, Sabine Defoort¹⁵, Aurore Devos¹⁶, Adrian Dockery⁴, Lubica Dudakova¹⁷, Ana Fakin¹⁸, G Jane Farrar⁴, Juliana Maria Ferraz Sallum^{19

20}, Kaoru Fujinami^{21

22

23

24}, Christian Gilissen^{1

25}, Damjan Glavač²⁶, Michael B Gorin^{27

28}, Jacquie Greenberg²⁹, Takaaki Hayashi³⁰, Ymkje M Hettinga³¹, Alexander Hoischen¹, Carel B Hoyng^{2

5}, Karsten Hufendiek³², Herbert Jägle³³, Smaragda Kamakari³⁴, Marianthi Karali⁸, Ulrich Kellner^{35

36}, Caroline C W Klaver^{5

37

38}, Bohdan Kousal^{17

39}, Tina M Lamey^{40

41}, Ian M MacDonald⁴², Anna Matynia^{27

28}, Terri L McLaren^{40

41}, Marcela D Mena⁴³, Isabelle Meunier⁴⁴, Rianne Miller¹, Hadas Newman^{45

46}, Buhle Ntozini²⁹, Monika Oldak⁴⁷, Marc Pieterse¹, Osvaldo L Podhajcer⁴³, Bernard Puech¹⁵, Raj Ramesar²⁹, Klaus Rüther⁴⁸, Manar Salameh⁶, Mariana Vallim Salles^{19

20}, Dror Sharon⁹, Francesca Simonelli⁴⁹, Georg Spital⁵⁰, Marloes Steehouwer¹, Jacek P Szaflik⁵¹, Jennifer A Thompson⁴¹, Caroline Thuillier⁵², Anna M Tracewska⁵³, Martine van Zweeden¹, Andrea L Vincent^{54

55}, Xavier Zanlonghi⁵⁶, Petra Liskova^{17

39}, Heidi Stöhr⁵⁷, John N De Roach^{40

41}, Carmen Ayuso³, Lisa Roberts²⁹, Bernhard H F Weber⁵⁷, Claire-Marie Dhaenens^#^{1

16}, Frans P M Cremers^#^{58

59}

Affiliations

¹ Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
² Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
³ Department of Genetics, IIS-Fundación Jiménez Díaz, CIBERER, Madrid, Spain.
⁴ The School of Genetics & Microbiology, Trinity College Dublin, Dublin, Ireland.
⁵ Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.
⁶ St John of Jerusalem Eye Hospital Group, East Jerusalem, Palestine.
⁷ Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
⁸ Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples and Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.
⁹ Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
¹⁰ Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
¹¹ Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands.
¹² Department of Ophthalmology, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
¹³ The Rotterdam Eye Hospital, Rotterdam, The Netherlands.
¹⁴ The Rotterdam Ophthalmic Institute, Rotterdam, The Netherlands.
¹⁵ Service d'exploration de la vision et neuro-ophtalmologie, Centre Hospitalier Universitaire de Lille, Lille, France.
¹⁶ Univ. Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000, Lille, France.
¹⁷ 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.
¹⁸ Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia.
¹⁹ Department of Ophthalmology and Visual Sciences, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
²⁰ Instituto de Genética Ocular, São Paulo, SP, Brazil.
²¹ UCL Institute of Ophthalmology, London, UK.
²² Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.
²³ Graduate School of Health Management, Keio University, Tokyo, Japan.
²⁴ Moorfields Eye Hospital, London, UK.
²⁵ Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
²⁶ Department of Molecular Genetics, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia.
²⁷ Department of Ophthalmology, David Geffen School of Medicine, Stein Eye Institute, University of California-Los Angeles, Los Angeles, CA, USA.
²⁸ Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA.
²⁹ 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.
³⁰ Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan.
³¹ Bartiméus Diagnostic Center for Complex Visual Disorders, Zeist, The Netherlands.
³² University Eye Hospital Hannover Medical School, Hannover, Germany.
³³ Department of Ophthalmology, University Hospital, University Regensburg, Regensburg, Germany.
³⁴ Ophthalmic Genetics Unit, OMMA Ophthalmological Institute of Athens, Athens, Greece.
³⁵ Rare Retinal Disease Center, AugenZentrum Siegburg, MVZ ADTC Siegburg GmbH, Siegburg, Germany.
³⁶ RetinaScience, Bonn, Germany.
³⁷ Department of Ophthalmology, Erasmus Medical Centre, Rotterdam, The Netherlands.
³⁸ Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands.
³⁹ Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.
⁴⁰ Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, WA, Australia.
⁴¹ Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA, Australia.
⁴² Departments of Ophthalmology and Medical Genetics, University of Alberta, Edmonton, AB, Canada.
⁴³ Laboratory of Molecular and Cellular Therapy, Fundacion Instituto Leloir-CONICET, Buenos Aires, Argentina.
⁴⁴ Institut des Neurosciences de Montpellier, INSERM, Université de Montpellier, Montpellier, France.
⁴⁵ Department of Ophthalmology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
⁴⁶ Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
⁴⁷ Department of Histology and Embryology, Medical University of Warsaw, Warsaw, Poland.
⁴⁸ Augenarztpraxis, Dorotheenstraße, Berlin, Germany.
⁴⁹ Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy.
⁵⁰ Department of Ophthalmology, St. Franziskus-Hospital, Münster, Germany.
⁵¹ Department of Ophthalmology, Medical University of Warsaw SPKSO Ophthalmic University Hospital, Warsaw, Poland.
⁵² CHU Lille, Institut de Génétique Médicale, Lille, France.
⁵³ DNA Analysis Unit, ŁUKASIEWICZ Research Network-PORT Polish Center for Technology Development, Wroclaw, Poland.
⁵⁴ Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, The University of Auckland, Grafton, Auckland, New Zealand.
⁵⁵ Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand.
⁵⁶ Centre de Compétence Maladie Rare, Clinique Jules Verne, Nantes, France.
⁵⁷ Institute of Human Genetics, University of Regensburg, Regensburg, Germany.
⁵⁸ Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands. frans.cremers@radboudumc.nl.
⁵⁹ Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands. frans.cremers@radboudumc.nl.

^# Contributed equally.

PMID: 32307445
DOI: 10.1038/s41436-020-0787-4

Free article

Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics

Mubeen Khan et al. Genet Med. 2020 Jul.

Free article

. 2020 Jul;22(7):1235-1246.

doi: 10.1038/s41436-020-0787-4. Epub 2020 Apr 20.

Authors

Affiliations

¹ Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
² Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
³ Department of Genetics, IIS-Fundación Jiménez Díaz, CIBERER, Madrid, Spain.
⁴ The School of Genetics & Microbiology, Trinity College Dublin, Dublin, Ireland.
⁵ Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.
⁶ St John of Jerusalem Eye Hospital Group, East Jerusalem, Palestine.
⁷ Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
⁸ Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples and Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.
⁹ Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
¹⁰ Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
¹¹ Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands.
¹² Department of Ophthalmology, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
¹³ The Rotterdam Eye Hospital, Rotterdam, The Netherlands.
¹⁴ The Rotterdam Ophthalmic Institute, Rotterdam, The Netherlands.
¹⁵ Service d'exploration de la vision et neuro-ophtalmologie, Centre Hospitalier Universitaire de Lille, Lille, France.
¹⁶ Univ. Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000, Lille, France.
¹⁷ 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.
¹⁸ Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia.
¹⁹ Department of Ophthalmology and Visual Sciences, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
²⁰ Instituto de Genética Ocular, São Paulo, SP, Brazil.
²¹ UCL Institute of Ophthalmology, London, UK.
²² Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.
²³ Graduate School of Health Management, Keio University, Tokyo, Japan.
²⁴ Moorfields Eye Hospital, London, UK.
²⁵ Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
²⁶ Department of Molecular Genetics, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia.
²⁷ Department of Ophthalmology, David Geffen School of Medicine, Stein Eye Institute, University of California-Los Angeles, Los Angeles, CA, USA.
²⁸ Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA.
²⁹ 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.
³⁰ Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan.
³¹ Bartiméus Diagnostic Center for Complex Visual Disorders, Zeist, The Netherlands.
³² University Eye Hospital Hannover Medical School, Hannover, Germany.
³³ Department of Ophthalmology, University Hospital, University Regensburg, Regensburg, Germany.
³⁴ Ophthalmic Genetics Unit, OMMA Ophthalmological Institute of Athens, Athens, Greece.
³⁵ Rare Retinal Disease Center, AugenZentrum Siegburg, MVZ ADTC Siegburg GmbH, Siegburg, Germany.
³⁶ RetinaScience, Bonn, Germany.
³⁷ Department of Ophthalmology, Erasmus Medical Centre, Rotterdam, The Netherlands.
³⁸ Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands.
³⁹ Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.
⁴⁰ Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, WA, Australia.
⁴¹ Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA, Australia.
⁴² Departments of Ophthalmology and Medical Genetics, University of Alberta, Edmonton, AB, Canada.
⁴³ Laboratory of Molecular and Cellular Therapy, Fundacion Instituto Leloir-CONICET, Buenos Aires, Argentina.
⁴⁴ Institut des Neurosciences de Montpellier, INSERM, Université de Montpellier, Montpellier, France.
⁴⁵ Department of Ophthalmology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
⁴⁶ Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
⁴⁷ Department of Histology and Embryology, Medical University of Warsaw, Warsaw, Poland.
⁴⁸ Augenarztpraxis, Dorotheenstraße, Berlin, Germany.
⁴⁹ Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy.
⁵⁰ Department of Ophthalmology, St. Franziskus-Hospital, Münster, Germany.
⁵¹ Department of Ophthalmology, Medical University of Warsaw SPKSO Ophthalmic University Hospital, Warsaw, Poland.
⁵² CHU Lille, Institut de Génétique Médicale, Lille, France.
⁵³ DNA Analysis Unit, ŁUKASIEWICZ Research Network-PORT Polish Center for Technology Development, Wroclaw, Poland.
⁵⁴ Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, The University of Auckland, Grafton, Auckland, New Zealand.
⁵⁵ Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand.
⁵⁶ Centre de Compétence Maladie Rare, Clinique Jules Verne, Nantes, France.
⁵⁷ Institute of Human Genetics, University of Regensburg, Regensburg, Germany.
⁵⁸ Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands. frans.cremers@radboudumc.nl.
⁵⁹ Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands. frans.cremers@radboudumc.nl.

^# Contributed equally.

PMID: 32307445
DOI: 10.1038/s41436-020-0787-4

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.

Keywords: ABCA4; Stargardt disease; deep-intronic variants; smMIPs; structural variants.

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References

1. Carss KJ, Arno G, Erwood M, et al. Comprehensive rare variant analysis via whole-genome sequencing to determine the molecular pathology of inherited retinal disease. Am J Hum Genet. 2017;100:75–90.
1. Blacharski PA, Newsome DA. Bilateral macular holes after Nd:YAG laser posterior capsulotomy. Am J Ophthalmol. 1988;105:417–418.
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1. Sangermano R, Khan M, Cornelis SS, et al. ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease. Genome Res. 2018;28:100–110. - PubMed - PMC
1. Khan M, Cornelis SS, Khan MI, et al. Cost-effective molecular inversion probe-based ABCA4 sequencing reveals deep-intronic variants in Stargardt disease. Hum Mutat. 2019;40:1749–1759.

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Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics

Affiliations

Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics

Authors

Affiliations

Abstract

References

Publication types

MeSH terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources

Medical