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Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics
M. Khan, SS. Cornelis, MD. Pozo-Valero, L. Whelan, EH. Runhart, K. Mishra, F. Bults, Y. AlSwaiti, A. AlTalbishi, E. De Baere, S. Banfi, E. Banin, M. Bauwens, T. Ben-Yosef, CJF. Boon, LI. van den Born, S. Defoort, A. Devos, A. Dockery, L....
Jazyk angličtina Země Spojené státy americké
Typ dokumentu časopisecké články, práce podpořená grantem
NLK
ProQuest Central
od 2011-01-01 do 2021-12-31
Health & Medicine (ProQuest)
od 2011-01-01 do 2021-12-31
Elsevier Open Access Journals
od 1998-11-01 do Před 1 rokem
ROAD: Directory of Open Access Scholarly Resources
od 1998
- MeSH
- ABC transportéry genetika MeSH
- genomika MeSH
- introny MeSH
- lidé MeSH
- makulární degenerace * genetika MeSH
- mutace MeSH
- rodokmen MeSH
- Stargardtova nemoc MeSH
- transkriptom * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
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.
Augenarztpraxis Dorotheenstraße Berlin Germany
Bartiméus Diagnostic Center for Complex Visual Disorders Zeist The Netherlands
Center for Medical Genetics Ghent Ghent University and Ghent University Hospital Ghent Belgium
Centre de Compétence Maladie Rare Clinique Jules Verne Nantes France
CHU Lille Institut de Génétique Médicale Lille France
Department of Epidemiology Erasmus Medical Centre Rotterdam The Netherlands
Department of Genetics IIS Fundación Jiménez Díaz CIBERER Madrid Spain
Department of Histology and Embryology Medical University of Warsaw Warsaw Poland
Department of Human Genetics Radboud University Medical Center Nijmegen The Netherlands
Department of Molecular Genetics Institute of Pathology University of Ljubljana Ljubljana Slovenia
Department of Ophthalmology Amsterdam University Medical Centers Amsterdam The Netherlands
Department of Ophthalmology Erasmus Medical Centre Rotterdam The Netherlands
Department of Ophthalmology Leiden University Medical Center Leiden The Netherlands
Department of Ophthalmology Radboud University Medical Center Nijmegen The Netherlands
Department of Ophthalmology St Franziskus Hospital Münster Germany
Department of Ophthalmology Tel Aviv Sourasky Medical Center Tel Aviv Israel
Department of Ophthalmology The Jikei University School of Medicine Tokyo Japan
Department of Ophthalmology University Hospital University Regensburg Regensburg Germany
Departments of Ophthalmology and Medical Genetics University of Alberta Edmonton AB Canada
Eye Department Greenlane Clinical Centre Auckland District Health Board Auckland New Zealand
Eye Hospital University Medical Centre Ljubljana Ljubljana Slovenia
Graduate School of Health Management Keio University Tokyo Japan
Institut des Neurosciences de Montpellier INSERM Université de Montpellier Montpellier France
Institute of Human Genetics University of Regensburg Regensburg Germany
Instituto de Genética Ocular São Paulo SP Brazil
Moorfields Eye Hospital London UK
Ophthalmic Genetics Unit OMMA Ophthalmological Institute of Athens Athens Greece
Rare Retinal Disease Center AugenZentrum Siegburg MVZ ADTC Siegburg GmbH Siegburg Germany
Ruth and Bruce Rappaport Faculty of Medicine Technion Israel Institute of Technology Haifa Israel
Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel
St John of Jerusalem Eye Hospital Group East Jerusalem Palestine
The Rotterdam Eye Hospital Rotterdam The Netherlands
The Rotterdam Ophthalmic Institute Rotterdam The Netherlands
The School of Genetics and Microbiology Trinity College Dublin Dublin Ireland
UCL Institute of Ophthalmology London UK
Univ Lille Inserm CHU Lille U1172 LilNCog Lille Neuroscience and Cognition F 59000 Lille France
University Eye Hospital Hannover Medical School Hannover Germany
Citace poskytuje Crossref.org
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