1. Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics
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Ymkje M. Hettinga, Karsten Hufendiek, Jacek P. Szaflik, Ian M. MacDonald, Isabelle Meunier, Marcela D. Mena, Kaoru Fujinami, Mubeen Khan, Eyal Banin, Elfride De Baere, G. Jane Farrar, Adrian Dockery, Rianne Miller, Tamar Ben-Yosef, Manar Salameh, L. Ingeborgh van den Born, Anna M Tracewska, Sandro Banfi, Caroline C W Klaver, John N. De Roach, Carmen Ayuso, Sabine Defoort, Damjan Glavač, Ulrich Kellner, Juliana Maria Ferraz Sallum, Claire-Marie Dhaenens, Stéphanie S. Cornelis, Bernhard H. F. Weber, Klaus Rüther, Jennifer A. Thompson, Bernard Puech, Raj Ramesar, Aurore Devos, Lisa Roberts, Herbert Jägle, Osvaldo L. Podhajcer, Hadas Newman, Bohdan Kousal, Femke Bults, Marta Del Pozo-Valero, Marc Pieterse, Laura Whelan, Xavier Zanlonghi, Alaa AlTalbishi, Francesca Simonelli, Marloes Steehouwer, Caroline Thuillier, Frans P.M. Cremers, Andrea L Vincent, Smaragda Kamakari, Ana Fakin, Anna Matynia, Dror Sharon, Ketan Mishra, Mariana Vallim Salles, Heidi Stöhr, Miriam Bauwens, Petra Liskova, Esmee H. Runhart, Buhle Ntozini, Georg Spital, Carel B. Hoyng, Takaaki Hayashi, Terri L. McLaren, Martine van Zweeden, Lubica Dudakova, Camiel J. F. Boon, Christian Gilissen, Jacquie Greenberg, Monika Ołdak, Tina M. Lamey, Yahya AlSwaiti, Alexander Hoischen, Marianthi Karali, Michael B. Gorin, Ophthalmology, ANS - Complex Trait Genetics, Khan, Mubeen, Cornelis, Stéphanie S, Pozo-Valero, Marta Del, Whelan, Laura, Runhart, Esmee H, Mishra, Ketan, Bults, Femke, Alswaiti, Yahya, Altalbishi, Alaa, De Baere, Elfride, Banfi, Sandro, Banin, Eyal, Bauwens, Miriam, Ben-Yosef, Tamar, Boon, Camiel J F, van den Born, L Ingeborgh, Defoort, Sabine, Devos, Aurore, Dockery, Adrian, Dudakova, Lubica, Fakin, Ana, Farrar, G Jane, Sallum, Juliana Maria Ferraz, Fujinami, Kaoru, Gilissen, Christian, Glavač, Damjan, Gorin, Michael B, Greenberg, Jacquie, Hayashi, Takaaki, Hettinga, Ymkje M, Hoischen, Alexander, Hoyng, Carel B, Hufendiek, Karsten, Jägle, Herbert, Kamakari, Smaragda, Karali, Marianthi, Kellner, Ulrich, Klaver, Caroline C W, Kousal, Bohdan, Lamey, Tina M, Macdonald, Ian M, Matynia, Anna, Mclaren, Terri L, Mena, Marcela D, Meunier, Isabelle, Miller, Rianne, Newman, Hada, Ntozini, Buhle, Oldak, Monika, Pieterse, Marc, Podhajcer, Osvaldo L, Puech, Bernard, Ramesar, Raj, Rüther, Klau, Salameh, Manar, Salles, Mariana Vallim, Sharon, Dror, Simonelli, Francesca, Spital, Georg, Steehouwer, Marloe, Szaflik, Jacek P, Thompson, Jennifer A, Thuillier, Caroline, Tracewska, Anna M, van Zweeden, Martine, Vincent, Andrea L, Zanlonghi, Xavier, Liskova, Petra, Stöhr, Heidi, Roach, John N De, Ayuso, Carmen, Roberts, Lisa, Weber, Bernhard H F, Dhaenens, Claire-Marie, and Cremers, Frans P M
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DEEP-INTRONIC VARIANTS ,Proband ,smMIP ,lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4] ,ABCA4 ,RPE65 ,Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12] ,Macular Degeneration ,Exon ,0302 clinical medicine ,Missing heritability problem ,purl.org/becyt/ford/3.2 [https] ,Medicine and Health Sciences ,smMIPs ,MUTATION ,Genetics (clinical) ,Genetics ,variants ,0303 health sciences ,structural ,biology ,Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6] ,Genomics ,DYSTROPHY ,Pedigree ,3. Good health ,Stargardt disease ,MATERNAL UNIPARENTAL ISODISOMY ,purl.org/becyt/ford/3 [https] ,RETINAL ,CHROMOSOME-1 ,PATIENT ,STRUCTURAL VARIANTS ,Deep sequencing ,03 medical and health sciences ,SDG 3 - Good Health and Well-being ,deep-intronic variants ,REVEALS ,medicine ,Humans ,030304 developmental biology ,REPAIR ,deep-intronic variant ,structural variants ,medicine.disease ,GENE ,Introns ,Uniparental Isodisomy ,Mutation ,030221 ophthalmology & optometry ,biology.protein ,ATP-Binding Cassette Transporters ,Transcriptome - 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. Fil: Khan, Mubeen. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Cornelis, Stéphanie S.. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Del Pozo Valero, Marta. Hospital Universitario Fundación Jiménez Díaz; España. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Whelan, Laura. Trinity College; Estados Unidos Fil: Runhart, Esmee H.. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Mishra, Ketan. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Bults, Femke. Radboud University Nijmegen Medical Centre; Países Bajos Fil: AlSwaiti, Yahya. St John of Jerusalem Eye Hospital Group; Palestina (ANP) Fil: AlTalbishi, Alaa. St John of Jerusalem Eye Hospital Group; Palestina (ANP) Fil: De Baere, Elfride. University of Ghent; Bélgica Fil: Banfi, Sandro. Seconda Universita Degli Studi Di Napoli; Italia Fil: Banin, Eyal. The Hebrew University of Jerusalem; Israel Fil: Bauwens, Miriam. University of Ghent; Bélgica Fil: Ben Yosef, Tamar. The Ruth And Bruce Rappaport Faculty Of Medicine; Israel Fil: Boon, Camiel J. F.. Leiden University. Leiden University Medical Center; Países Bajos Fil: van den Born, L. Ingeborgh. Rotterdam Ophthalmic Institute; Países Bajos Fil: Defoort, Sabine. Universite Lille; Francia Fil: Devos, Aurore. Universite Lille; Francia Fil: Dockery, Adrian. Trinity College; Estados Unidos Fil: Dudakova, Lubica. Charles University and General University Hospital; República Checa Fil: Fakin, Ana. Charles University and General University Hospital; República Checa Fil: Farrar, G. Jane. Trinity College; Estados Unidos Fil: Ferraz Sallum, Juliana Maria. Universidade Federal de Sao Paulo; Brasil Fil: Fujinami, Kaoru. UCL Institute of Ophthalmology; Reino Unido Fil: Gilissen, Christian. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Glavac, Damjan. University of Ljubljana; Eslovenia Fil: Gorin, Michael B.. University of California at Los Angeles. School of Medicine; Estados Unidos Fil: Greenberg, Jacquie. University of Cape Town; Sudáfrica Fil: Hayashi, Takaaki. The Jikei University School of Medicine; Japón Fil: Hettinga, Ymkje M.. Bartiméus Diagnostic Center for Complex Visual Disorders; Países Bajos Fil: Hoischen, Alexander. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Hoyng, Carel B.. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Hufendiek, Karsten. University Eye Hospital Hannover Medical School; Alemania Fil: Jägle, Herbert. University Regensburg; Alemania Fil: Kamakari, Smaragda. OMMA Ophthalmological Institute of Athens; Grecia Fil: Karali, Marianthi. Seconda Universita Degli Studi Di Napoli; Italia Fil: Kellner, Ulrich. No especifíca; Fil: Klaver, Caroline C. W.. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Kousal, Bohdan. Charles University and General University Hospital; República Checa Fil: Lamey, Tina M.. University of Western Australia; Australia Fil: MacDonald, Ian M.. University of Alberta; Canadá Fil: Matynia, Anna. University of California at Los Angeles. School of Medicine; Estados Unidos Fil: McLaren, Terri L.. University of Western Australia; Australia Fil: Mena, Marcela D.. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Meunier, Isabelle. Université Montpellier II; Francia Fil: Miller, Rianne. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Newman, Hadas. Universitat Tel Aviv; Israel Fil: Ntozini, Buhle. University of Cape Town; Sudáfrica Fil: Oldak, Monika. No especifíca; Fil: Pieterse, Marc. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Podhajcer, Osvaldo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Puech, Bernard. Universite Lille; Francia Fil: Ramesar, Raj. University of Cape Town; Sudáfrica Fil: Rüther, Klaus. No especifíca; Fil: Salameh, Manar. No especifíca; Fil: Salles, Mariana Vallim. Universidade de Sao Paulo; Brasil Fil: Sharon, Dror. The Hebrew University of Jerusalem; Israel Fil: Simonelli, Francesca. Seconda Universita Degli Studi Di Napoli; Italia Fil: Spital, Georg. No especifíca; Fil: Steehouwer, Marloes. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Szaflik, Jacek P.. No especifíca; Fil: Thompson, Jennifer A.. No especifíca; Fil: Thuillier, Caroline. Universite Lille; Francia Fil: Tracewska, Anna M.. No especifíca; Fil: van Zweeden, Martine. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Vincent, Andrea L.. University of Auckland; Nueva Zelanda Fil: Zanlonghi, Xavier. No especifíca; Fil: Liskova, Petra. Charles University and General University Hospital; República Checa Fil: Stöhr, Heidi. Universitat Regensburg; Alemania Fil: De Roach, John N.. University of Western Australia; Australia Fil: Ayuso, Carmen. Hospital Universitario Fundación Jiménez Díaz; España Fil: Roberts, Lisa. University of Cape Town; Sudáfrica Fil: Weber, Bernhard H. F.. Universitat Regensburg; Alemania Fil: Dhaenens, Claire Marie. Universite Lille; Francia Fil: Cremers, Frans P. M.. Radboud University Nijmegen Medical Centre; Países Bajos
- Published
- 2020
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