Molecular Diagnosis of Inherited Retinal Diseases in Indigenous African Populations by Whole-Exome Sequencing

Abstract

PurposeA majority of genes associated with inherited retinal diseases (IRDs) have been identified in patients of European origin. Indigenous African populations exhibit rich genomic diversity, and evaluation of reported genetic mutations has yielded low returns so far. Our goal was to perform whole-exome sequencing (WES) to examine variants in known IRD genes in underrepresented African cohorts.MethodsWhole-exome sequencing was performed on 56 samples from 16 families with diverse IRD phenotypes that had remained undiagnosed after screening for known mutations using genotyping-based microarrays (Asper Ophthalmics). Variants in reported IRD genes were identified using WES and validated by Sanger sequencing. Custom TaqMan assays were used to screen for identified mutations in 193 unrelated indigenous Africans with IRDs.ResultsA total of 3494 variants were identified in 217 known IRD genes, leading to the identification of seven different mutations (including six novel) in six genes (RHO, PRPF3, PRPF31, ABCA4, CERKL, and PDE6B) in six distinct families. TaqMan screening in additional probands revealed identical homozygous CERKL and PDE6B variants in four more patients.ConclusionsThis is the first report of WES of patients with IRDs in indigenous African populations. Our study identified genetic defects in almost 40% of the families analyzed, significantly enhancing the molecular diagnosis of IRD in South Africa. Thus, WES of understudied cohorts seems to present an effective strategy for determining novel mutations in heterogeneous retinal diseases.

Whole-Exome Sequencing Identifies Biallelic IDH3A Variants as a Cause of Retinitis Pigmentosa Accompanied by Pseudocoloboma

“…Exome sequencing of a panel of 217 known IRD-associated genes was negative 18 , but analysis of ERDC candidate genes (http://www.erdc.info/candidateirdgenes) revealed biallelic variants in IDH3A which segregated with the disease phenotype (Figure 1). Screening of these variants in a set of 16 indigenous African families (n=56 individuals) with IRDs was negative.…”

Long-Range PCR-Based NGS Applications to Diagnose Mendelian Retinal Diseases

“…Due to the multitude of loci associated with IRDs (almost 300 loci, ), molecular diagnostics often relies on targeted enrichment and high-throughput sequencing, either whole-exome (WES) [ 3 , 4 , 5 , 6 ] or gene panels [ 5 , 6 , 7 , 8 , 9 , 10 ]. Studies have reported that diagnostic yield when using these standard methods (WES/gene panels) is typically between 50% and 76%, depending, amongst other factors, on the specific clinical subtype being investigated [ 6 , 7 , 8 , 9 , 11 , 12 , 13 , 14 ].…”

“…the variant has been found in 2 unrelated probands. 2 size of the deletion: 3999-4033 bp (NC_000001.10:g.(94507656_94507700)_ (94511700_94511710)del) 3. size of the deletion: 70,036 bp (NC_000009.11:g.2716981_2787016del).…”

De Novo Assembly-Based Analysis of RPGR Exon ORF15 in an Indigenous African Cohort Overcomes Limitations of a Standard Next-Generation Sequencing (NGS) Data Analysis Pipeline

“…In an effort to elucidate the genetic landscape of IRD among the indigenous African populations of South Africa (SA), WES was previously performed in a cohort of 16 families, and a molecular diagnosis obtained for approximately 40% through an analysis of all reported IRD genes at that time ( n = 285) [ 25 ]. Leveraging the vast genomic diversity of indigenous Africans in SA [ 26 , 27 , 28 , 29 , 30 , 31 ] yielded several novel mutations [ 25 ] and assisted the identification of a novel IRD gene [ 32 ]. Subsequently, the WES data from five unresolved families with an absence of male-to-male disease transmission were re-interrogated, confirming that ORF15 had been insufficiently captured.…”