Browsing by Author "Roberts, Lisa Jane"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    Open Access
    Genetic analysis of inherited retinal diseases in indigenous Southern African populations
    (2017) Roberts, Lisa Jane; Ramesar, Rajkumar; Swaroop, Anand
    Background: Inherited retinal diseases (IRDs) constitute a group of clinically and genetically heterogeneous conditions which cause degeneration of retinal photoreceptor cells and result in visual impairment. Characterisation of the genetic basis of IRD is not only beneficial for the affected families, but also contributes towards understanding of the disease pathobiology. Investigations into the molecular basis of IRDs have been ongoing in South Africa (SA) for over 30 years, however the evaluation of reported genetic mutations has yielded low returns in certain populations. Indigenous southern Africans comprise a unique population group with distinct genetic diversity, providing a valuable resource for genetic discoveries; nonetheless, this population remains largely underrepresented in genomic studies. The aim of this investigation was to characterise the underlying genetic mutations in a cohort of indigenous African IRD patients. Methods: The IRD registry in the Division of Human Genetics (University of Cape Town) was reviewed for causative mutations. Subsequently, upon identifying a mutation underlying Usher Syndrome in two indigenous African patients, an assay was designed to screen for this mutation in probands with different IRDs (n=170) and controls (n=51), and haplotype analysis was performed on mutation-positive individuals. The registry review additionally served to identify a suitable cohort for the application of next generation sequencing (NGS) technology. Whole exome sequencing (WES) was performed on genomic DNA samples from 56 individuals from 16 families. The WES data analysis strategy involved prioritisation of variants in reported and candidate IRD genes. Rare, co-segregating, pathogenic, exonic or splice variants were validated by Sanger sequencing. Custom TaqMan assays were designed to screen seven mutations, identified by WES, in 193 unrelated indigenous African probands with IRDs. Results: A homozygous founder mutation, c.6377delC in MYO7A, was identified in 43% of the indigenous African patients with Usher syndrome, which is the most common cause of deaf-blindness. Targeted WES data analysis of all known IRD genes resulted in identification of the underlying genetic defects in six distinct genes (RHO, PRPF3, PRPF31, ABCA4, CERKL, and PDE6B) in six families. Taqman screening revealed four additional probands with identical homozygous mutations in CERKL and PDE6B. An X-linked gene (RP2) mutation was subsequently identified in an affected family with semi-dominant retinitis pigmentosa. Supplementary analysis of the X-linked RPGR ORF15 mutation hotspot (not adequately covered by WES) identified two mutations in three families. A novel IRD gene, IDH3A, was found in one family by analysis of 22 putative candidate genes. The large number of variants in the remainder of the indigenous African exomes presented considerable challenges for identification of additional novel genes. Discussion: The results of this project have important implications for IRD molecular diagnostic services in SA. Using WES, a genetic diagnosis was obtained for ±73% of the indigenous African cohort, and ±70% of the causative mutations identified were novel. This outcome emphasises the superiority of NGS-based approaches over genotyping-based microarrays which screen for IRD mutations previously reported in other (mainly European-derived) populations. The unexpected identification of mutations in known X-linked genes in four families highlighted key considerations for IRD WES analysis. Cascade screening of mutations identified in this study, across larger cohorts of unrelated probands, revealed the genetic cause of IRD in additional cases and the number of indigenous African families in the registry with a genetic diagnosis was effectively doubled. Members of these families can now opt for diagnostic, carrier, or predictive testing of familial mutations. Finally, the information obtained from this research contributes towards a better understanding of the genetic architecture of IRDs in SA.
  • No Thumbnail Available
    Item
    Open Access
    Mutation analysis of important retinal candidate genes: progression from research to diagnostic service
    (2006) Roberts, Lisa Jane; Greenberg, Jacquie; Ramesar, Raj
    Approximately one third of all human inherited disease includes defects of the eye. Retinal degenerative disorders (RDDs) are a group of diseases characterised by photoreceptor cell death in the retina and consequent vision loss. The Division of Human Genetics at the University of Cape Town (UCT) has samples archived in the RDD DNA database from over 1000 South African families. The research in this Division currently involves mutation screening of retinal candidate genes, with the goal of identifying the causative genetic mutation in each of the families registered in the database, in order to facilitate future therapeutic intervention. The purpose of this study was to determine the distribution and clinical utility of mutations in important candidate genes in a subset of South African RDD patients. To this end, three important retinal candidate genes were selected and screened in appropriate patient cohorts. The mutation analysis included screening for large deletions which is a novel approach in the study of RDDs. The screening of Rhodopsin (RHO) in 61 individuals, retinitis pigmentosa 1 (RP1) in 70 individuals and retinal pigment epithelium-specific protein 65kDa (RPE65) in 87 individuals led to the identification of 10 families for whom a molecular diagnostic service can now be provided. For most families the amount of useful information available without further research is minimal, however for four of the families, therapeutic interventions may be possible, now or in the near future. In addition to the pathogenic mutations found, 17 single nucleotide polymorphisms (SNPs) were identified during this study. Furthermore, a significant association between ethnicity and the frequency of the high and low risk alleles of two of these SNPs (that may modify the phenotype of RDDs) was shown. This information may be useful in providing diagnostic or prognostic indicators in the future. The utility of RDD research should not be trivialised as it identifies families who may benefit from current interventions or be eligible for possible therapeutic trials, eliminates gene candidates in families, and is necessary for understanding the disease (which in itself is a requirement for development of therapies).