Next-generation sequencing of ABCA4: High frequency of complex alleles and novel mutations in patients with retinal dystrophies from Central Europe

Ścieżyńska, Aneta; Oziębło, Dominika; Ambroziak, Anna M.; Korwin, Magdalena; Szulborski, Kamil; Krawczyński, M; Stawiński, Piotr; Szaflik, Jerzy; Szaflik, Jacek P.; Płoski, Rafał; Ołdak, Monika

doi:10.1016/j.exer.2015.11.011

Cited by 29 publications

(32 citation statements)

References 41 publications

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“…The Hungarian population was found to display a frequency of 28% among STGD patients [27]. Finally, Scieżyńska et al tested 93 unrelated Polish STGD and CRD patients and detected this allele in 33 individuals [16]. The population frequency was estimated as 0.42%.…”

Section: Discussionmentioning

confidence: 99%

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Genetic Spectrum of ABCA4-Associated Retinal Degeneration in Poland

Tracewska

Kocyła-Karczmarewicz

Rafalska

et al. 2019

Genes

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Mutations in retina-specific ATP-binding cassette transporter 4 (ABCA4) are responsible for over 95% of cases of Stargardt disease (STGD), as well as a minor proportion of retinitis pigmentosa (RP) and cone-rod dystrophy cases (CRD). Since the knowledge of the genetic causes of inherited retinal diseases (IRDs) in Poland is still scarce, the purpose of this study was to identify pathogenic ABCA4 variants in a subgroup of Polish IRD patients. We recruited 67 families with IRDs as a part of a larger study. The patients were screened with next generation sequencing using a molecular inversion probes (MIPs)-based technique targeting 108 genes involved in the pathogenesis of IRDs. All identified mutations were validated and their familial segregation was tested using Sanger sequencing. In the case of the most frequent complex allele, consisting of two variants in exon 12 and 21, familial segregation was tested using restriction fragment length polymorphism (RFLP). The most prevalent variant, a complex change c.[1622T>C;3113C>T], p.[Leu541Pro;Ala1038Val], was found in this cohort in 54% of all solved ABCA4-associated disorder cases, which is the highest frequency reported thus far. Additionally, we identified nine families displaying a pseudo-dominant mode of inheritance, indicating a high frequency of pathogenic variants within this population.

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Section: Discussionmentioning

confidence: 99%

“…Variants c.[1622T>C;3113C>T], p.[Leu541Pro;Ala1038Val] found in cis were previously described to be present in 33% of Polish patients. Population frequency was estimated to be 0.42% [16]. However, the broader context of ABCA4 mutations in Poland, especially in the case of retinitis pigmentosa patients, has never been tested.…”

Section: Introductionmentioning

confidence: 99%

Genetic Spectrum of ABCA4-Associated Retinal Degeneration in Poland

Tracewska

Kocyła-Karczmarewicz

Rafalska

et al. 2019

Genes

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“…The sole application of microarray was enough to solve 76 cases, which were not further investigated with Sanger technique. Indeed, this may have led to an underestimation of the prevalence of novel additional mutations and/or complex alleles in this cohort [28,58]. The relatively high number of unsolved cases may be related to a combination of different factors: (1) The clinical overlap of distinct genetic entities could have led to uncertainties in patients’ selection.…”

Section: Discussionmentioning

confidence: 99%

Expanding the Mutation Spectrum in ABCA4: Sixty Novel Disease Causing Variants and Their Associated Phenotype in a Large French Stargardt Cohort

Nassisi

Mohand‐Saïd

Dhaenens

et al. 2018

IJMS

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Here we report novel mutations in ABCA4 with the underlying phenotype in a large French cohort with autosomal recessive Stargardt disease. The DNA samples of 397 index subjects were analyzed in exons and flanking intronic regions of ABCA4 (NM_000350.2) by microarray analysis and direct Sanger sequencing. At the end of the screening, at least two likely pathogenic mutations were found in 302 patients (76.1%) while 95 remained unsolved: 40 (10.1%) with no variants identified, 52 (13.1%) with one heterozygous mutation, and 3 (0.7%) with at least one variant of uncertain significance (VUS). Sixty-three novel variants were identified in the cohort. Three of them were variants of uncertain significance. The other 60 mutations were classified as likely pathogenic or pathogenic, and were identified in 61 patients (15.4%). The majority of those were missense (55%) followed by frameshift and nonsense (30%), intronic (11.7%) variants, and in-frame deletions (3.3%). Only patients with variants never reported in literature were further analyzed herein. Recruited subjects underwent complete ophthalmic examination including best corrected visual acuity, kinetic and static perimetry, color vision test, full-field and multifocal electroretinography, color fundus photography, short-wavelength and near-infrared fundus autofluorescence imaging, and spectral domain optical coherence tomography. Clinical evaluation of each subject confirms the tendency that truncating mutations lead to a more severe phenotype with electroretinogram (ERG) impairment (p = 0.002) and an earlier age of onset (p = 0.037). Our study further expands the mutation spectrum in the exonic and flanking regions of ABCA4 underlying Stargardt disease.

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“…More recently, exons and splice sites have been sequenced using an amplicon tagging protocol (Zernant et al 2011;Sciezynska et al 2016), array-based hybridization (Schulz et al 2017), targeted gene-panel sequencing (Consugar et al 2015) or whole exome sequencing (Ortube et al 2014;Zhou et al 2014;Bryant et al 2018). Sequence analysis of the entire 128-kb gene and up-and downstream DNA segments was performed using next-generation sequencing platforms after enrichment of ABCA4 sequences using Raindance microdroplet-PCR target enrichment or Illumina TruSeq Custom Amplicon target enrichment (Zernant et al 2014), Haloplex-based sequence enrichment Sangermano et al 2019), or WGS (Carss et al 2017;Sangermano et al 2019).…”

Section: Introductionmentioning

confidence: 99%

Resolving the dark matter of ABCA4 for 1,054 Stargardt disease probands through integrated genomics and transcriptomics

Khan¹,

Cornelis²,

Pozo‐Valero³

et al. 2019

Preprint

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Missing heritability in human diseases represents a major challenge. Although whole-genome sequencing enables the analysis of coding and non-coding sequences, substantial costs and data storage requirements hamper its large-scale use to (re)sequence genes in genetically unsolved cases.The ABCA4 gene implicated in Stargardt disease (STGD1) has been studied extensively for 22 years, but thousands of cases remained unsolved. Therefore, single molecule molecular inversion probes were designed that enabled an automated and cost-effective sequence analysis of the complete 128-kb ABCA4 gene. Analysis of 1,054 unsolved STGD and STGD-like probands resulted in bi-allelic variations in 448 probands. Twenty-seven different causal deep-intronic variants were identified in 117 alleles. Based on in vitro splice assays, the 13 novel causal deep-intronic variants were found to result in pseudo-exon (PE) insertions (n=10) or exon elongations (n=3). 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 that were accompanied by flanking exon deletions. Structural variant analysis revealed 11 distinct deletions, two of which contained small inverted segments. Uniparental isodisomy of chromosome 1 was identified in one proband. Integrated complete gene sequencing combined with transcript analysis, identified pathogenic deep-intronic and structural variants in 26% of bi-allelic cases not solved previously by sequencing of coding regions. This strategy serves as a model study that can be applied to other inherited diseases in which only one or a few genes are involved in the majority of cases.

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Next-generation sequencing of ABCA4: High frequency of complex alleles and novel mutations in patients with retinal dystrophies from Central Europe

Cited by 29 publications

References 41 publications

Genetic Spectrum of ABCA4-Associated Retinal Degeneration in Poland

Genetic Spectrum of ABCA4-Associated Retinal Degeneration in Poland

Expanding the Mutation Spectrum in ABCA4: Sixty Novel Disease Causing Variants and Their Associated Phenotype in a Large French Stargardt Cohort

Resolving the dark matter of ABCA4 for 1,054 Stargardt disease probands through integrated genomics and transcriptomics

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