Artículo
Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics
Khan, Mubeen; Cornelis, Stéphanie S.; Del Pozo Valero, Marta; 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; Ferraz Sallum, Juliana Maria; Fujinami, Kaoru; Gilissen, Christian; Glavac, 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, Hadas; Ntozini, Buhle; Oldak, Monika; Pieterse, Marc; Podhajcer, Osvaldo Luis
; Puech, Bernard; Ramesar, Raj; Rüther, Klaus; Salameh, Manar; Salles, Mariana Vallim; Sharon, Dror; Simonelli, Francesca; Spital, Georg; Steehouwer, Marloes; Szaflik, Jacek P.; Thompson, Jennifer A.; Thuillier, Caroline; Tracewska, Anna M.; van Zweeden, Martine; Vincent, Andrea L.; Zanlonghi, Xavier; Liskova, Petra; Stöhr, Heidi; De Roach, John N.; Ayuso, Carmen; Roberts, Lisa; Weber, Bernhard H. F.; Dhaenens, Claire Marie; Cremers, Frans P. M.
Fecha de publicación:
07/2020
Editorial:
Lippincott Williams
Revista:
Genetics In Medicine
ISSN:
1098-3600
e-ISSN:
1530-0366
Idioma:
Inglés
Tipo de recurso:
Artículo publicado
Clasificación temática:
Resumen
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.
Palabras clave:
ABCA4
,
DEEP-INTRONIC VARIANTS
,
SMMIPS
,
STARGARDT DISEASE
,
STRUCTURAL VARIANTS
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Articulos(IIBBA)
Articulos de INST.DE INVEST.BIOQUIMICAS DE BS.AS(I)
Articulos de INST.DE INVEST.BIOQUIMICAS DE BS.AS(I)
Citación
Khan, Mubeen; Cornelis, Stéphanie S.; Del Pozo Valero, Marta; Whelan, Laura; Runhart, Esmee H.; et al.; Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics; Lippincott Williams; Genetics In Medicine; 22; 7; 7-2020; 1235-1246
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