Targeted sequencing and in vitro splice assays shed light on ABCA4-associated retinopathies missing heritability
Citation:
Corradi Z, Khan M, Hitti-Malin R, Mishra K, Whelan L, Cornelis SS; ABCA4-Study Group; Hoyng CB, Kämpjärvi K, Klaver CCW, Liskova P, Stohr H, Weber BHF, Banfi S, Farrar GJ, Sharon D, Zernant J, Allikmets R, Dhaenens CM, Cremers FPM. Targeted sequencing and in vitro splice assays shed light on ABCA4-associated retinopathies missing heritability. HGG Adv. 2023 Sep 12;4(4):100237Download Item:
Abstract:
The ABCA4 gene is the most frequently mutated Mendelian retinopathy-associated gene. Biallelic variants lead to a variety of pheno types, however, for thousands of cases the underlying variants remain unknown. Here, we aim to shed further light on the missing her itability of ABCA4-associated retinopathy by analyzing a large cohort of macular dystrophy probands. A total of 858 probands were
collected from 26 centers, of whom 722 carried no or one pathogenic ABCA4 variant, while 136 cases carried two ABCA4 alleles, one
of which was a frequent mild variant, suggesting that deep-intronic variants (DIVs) or other cis-modifiers might have been missed. After
single molecule molecular inversion probes (smMIPs)-based sequencing of the complete 128-kb ABCA4 locus, the effect of putative
splice variants was assessed in vitro by midigene splice assays in HEK293T cells. The breakpoints of copy number variants (CNVs)
were determined by junction PCR and Sanger sequencing. ABCA4 sequence analysis solved 207 of 520 (39.8%) naive or unsolved cases
and 70 of 202 (34.7%) monoallelic cases, while additional causal variants were identified in 54 of 136 (39.7%) probands carrying two
variants. Seven novel DIVs and six novel non-canonical splice site variants were detected in a total of 35 alleles and characterized,
including the c.6283-321C>G variant leading to a complex splicing defect. Additionally, four novel CNVs were identified and charac terized in five alleles. These results confirm that smMIPs-based sequencing of the complete ABCA4 gene provides a cost-effective method
to genetically solve retinopathy cases and that several rare structural and splice altering defects remain undiscovered in Stargardt disease
cases
Author's Homepage:
http://people.tcd.ie/gjfarrar
Author: Farrar, Gwyneth
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Human Genetics and Genomics Advances;4;
4;
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Stargardt disease, ABCA4 gene, retinal degenerationDOI:
http://dx.doi.org/10.1016/j.xhgg.2023.100237Metadata
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