261 research outputs found
Common ABCA4 mutations in South Africans: frequencies, pathogenicity and genotype-phenotype correlations
No full textStargardt disease (STGD), a juvenile-onset form of macular dystrophy resulting in a severe reduction of central vision, may be inherited in either an autosomal recessive or autosomal dominant manner. To date the only gene found to be involved with the autosomal recessive form is ABCA4. Mutations in this gene are associated not only with STGD, but with other autosomal recessive retinal diseases. Due to the numerous mutations detected in ABCA4 and their associated phenotypic heterogeneity, a genotype-phenotype model has been proposed based on the amount of ABCA4 protein activity. Research in the Division of Human Genetics at the University of Cape Town (UCT) has suggested possible ABCA4 founder mutations underlying STGD in the South African Caucasian Afrikaner population and has identified seven (C1490Y, R602W, IVS38-10T>C, L2027F, V256V, G863A, and R152X) common mutations. In a cohort of patients affected with an ABCA4-associated retinopathy (AAR) a total of 36% were identified as having various bi-allelic combinations of the seven mutations.In the current study, SNaPshot PCR, allele-specific PCR (AS-PCR) and denaturing high performance liquid chromatography (dHPLC) analysis were used to screen for the seven mutations in a patient cohort and a control cohort. A high detection rate of bi-allelic disease-causing mutations in total of 28/72 patients (i.e. 38.89% were fully characterised) confirmed the designed assay to be a viable screening tool, which could be employed in a diagnostic setting. The detection of 12 heterozygotes in the Caucasian control samples (n = 269; 169 of which were specifically Afrikaner) resulted in an estimated background frequency of 4.46 per 100 individuals. This could be used by counsellors to discuss carrier risks with patients and their family members. Bioinformatic tools (PolyPhen, SIFT, PMUT, PANTHER PSEC, ESEfinder, and the BDGP Splice Site Prediction programme) revealed the predicted pathogenicity of the seven mutations to be as follows (in order of decreasing pathogenicity): C1490Y, R602W, V256V, R152X, G863A, L2027F, and IVS38-10T>C. Statistical analysis (using the Kruskal-Wallis test and the Wilcoxon Rank Sum test) showed no significant12effect of mutation combination on phenotype (i.e. AOO/severity as a measure of clinical outcome).To improve the understanding of the genotype-phenotype correlation a larger cohort of South African STGD patients with the same common mutations in various combinations and the availability of sufficient clinical data, is required. Further investigations into the genotype-phenotype correlation, combined with the information on the pathogenicity of the mutations, could result in increased understanding regarding the impact of each mutation, thus enhancing the clinical utility of identifying ABCA4 mutations
Towards identifying the ADRP gene in a large South African family with retinitis pigmentosa
No full textBibliography: leaves 162-190.The present study was initiated with the aim of elucidating the molecular genetic basis of the RP phenotype segregating in a large SA family of British origin. The family is one of the largest pedigrees from which DNA is archived in the Department, and the pedigree structure and ADRP phenotype will be discussed in detail in chapter two
The story of Anna P. : as told by herself
No full textIncludes bibliographical references (leaves 152-153).This is a book about the fragility of memory and identity, and the nature of time. It has three parts reflecting the past, present and future of a woman, Anna P, who lives on an island off the coast of Italy but can no longer remember how she got there. She comes from South Africa but has almost no memories of the place or people there, and no attachment to them. The only person she has any relationship with is a sex worker whom she pays by the hour. Her life is meaningless. She has abusive encounters with unknown men, clearly repetitions of traumatic events in the past, during which she dissociates. It is not clear whether she occasionally kills these men or not. It is only when she begins to connect emotionally with a slightly retarded child, and her self begins to coagulate around a tiny centre core of meaning, that she finds some value in herself, some place which she will not allow to be abused. Through connection with another person, she comes into an ethical relationship with the world
Elucidation of bipolar disorder : a convergent approach using genetics and imaging
No full textThe aims were to determine whether variants, within ten selected candidate genes, have an association with BPD and whether any relationship exists between these variants and brain imaging volumes in subjects with BPD. The objectives were to i) select a list of BPD candidate genes, ii) identify a cohort of individuals from the BPD registry, iii) genotype the candidate genes using a polymerase chain reaction (PCR) based technology, iv) analyse the genotyping data with the appropriate statistical methods, and v) obtain brain imaging data and perform the appropriate statistical analysis
Genomics of Lynch syndrome and Constitutional mismatch repair deficiency syndrome
No full textIntroduction: The mismatch repair system plays an important role in maintaining the genome integrity as it functions to correct mismatches during DNA replication. Heterozygous mutations in one of the mismatch repair (MMR) genes e.g. MLH1, MSH2, MSH6 and PMS2 cause the dominant adult cancer syndrome termed Lynch syndrome (or hereditary non-polyposis colorectal cancer). In our South African cohort, the MLH1 exon 13 c.1528C>T mutation is the most common Lynch syndrome-causing variant in the Mixed Ancestry population. Recently, a patient homozygous for this mutation, diagnosed with Constitutional mismatch repair deficiency (CMMR-D) syndrome was described within this extended cohort. CMMRD syndrome results in an increased predisposition to a range of cancers, most commonly brain and hematological tumours in early childhood. The aims of this thesis were: (i) to determine the rate of extra-colonic cancers in the cohort of Lynch syndrome families in our colorectal cancer registry, (ii) to determine if MLH1 c.1528C>T is a founder mutation, and (iii) to focus on the CMMR-D syndrome as a branch of Lynch syndrome and to potentially use the hypermutability-status in CMMR-D to understand the diverse carcinogenesis in Lynch syndrome. Methods: The registry consisting of Lynch syndrome families was interrogated and analysed to address the aim (i). Haplotype analysis was performed using microsatellite markers around the MHL1 c.1528C>T mutation to determine founder effect for aim (ii). For aim (iii) whole exome sequencing was also performed in a Lynch/ CMMR-D syndrome family in order to investigate the extent of hypermutability in CMMR-D syndrome, and to develop a working hypothesis for carcinogenesis in CMMR-D and Lynch syndromes. Results: From the analysis of the registry it was noted that 396 individuals carried a disease-causing mutation in either MLH1 or MSH2; females have a relatively later age of onset (for cancer) than males and MLH1 mutation carriers develop cancers relatively earlier in life than in individuals with MSH2 mutations. The most common extra-colonic cancers were endometrial and breast in females; in males small bowel cancer was most common, after CRC. The cohort study revealed a large founder effect with the MLH1 c.1528C>T mutation, with the most common inferred (disease-associated) haplotype found in 25 of the 30 subjects tested; the disease-associated haplotype was not present in controls. The mutation aging analysis traced the mutation to be ~225 years old. The WES investigation of the nuclear family within which the CMMR-D patient, including acquired and germline mutations in tissues from the child with CMMR-D, revealed a range of pathways including the extracellular matrix, WNT signaling, TGFβ and p53 as acquiring significant numbers of variants as a result of the MMR deficiency. Discussion and Conclusion: The results which are indicative of the need to improve the Lynch syndrome mutation testing and management for all patients, also suggests the need to develop surveillance programs for extra-colonic cancers, which will improve compliance and disease-free survival. WES investigation of the nuclear family containing a child with CMMR-D point to the potential involvement of a range of pathways associated with cancer development which may be indirectly invoked in the process of tumorigenesis by the wide range of variants acquired as a result of mismatch repair deficiency. It is likely that some of these processes are also involved in the emergence of extracolonic cancers in individuals affected with Lynch syndrome (i.e. heterozygous for mutations in MMR genes)
An investigation into factors which have an impact on access to and utilisation of the genetic and endoscopic surveillance clinic offered to high-risk members of known Lynch families
No full textIncludes bibliographical references (leaves 257-302).The Genetic and Endoscopic Surveillance Clinic provides predictive testing and life-saving colorectal cancer screening services to individuals with Lynch syndrome in the Western and Northern Cape provinces of South Africa. The risk of colorectal cancer is reduced by 50% and mortality is decreased by 65% with regular colonoscopic screening; however, the attendance rate at the clinic has been declining over several years. Concerns exist for those individuals undergoing screening at levels below the desired recommendations. It was thus opportune for a formal evaluation of both the surveillance and predictive testing programmes to be conducted to determine factors affecting the access, utilisation and satisfaction with the service, from the perspective of the service users
Genetics of age-related macular degeneration and Stargardt disease in South African populations
No full textBackground: The Retinal Degenerative Diseases (RDD) Research Group in the Division of Human Genetics at UCT has for the past 25 years been intensively investigating a range of RDD phenotypes. Two points of particular note have emerged regarding Macular Degenerations (MD) : (i) that more than 58% of juvenile MD, notably Stargardt Disease (STGD) , in Caucasian populations may have the underlying causative genetic defect identified , while only 1 1 % of the similar phenotype in indigenous African populations is resolved, and (ii) that the 'elderly' form of MD, i.e. age - related macular degeneration (AMD) has a remarkably lower incidence in the indigenous African population when compared to any other population group, and most notably the Caucasian (or European - derived) population /s . This study investigates the genetic factors underlying macular degeneration (MD) in our study cohort comprising various South African ethnolinguistic groups with particular focus on disease in juvenile and elderly indigenous Africans. Materials and Methods: For the STGD part of the study, sequencing of the entire ABCA4 coding and splice region (comprising 50 amplicons) was performed in three African STGD patients who were representative of three common haplotypes identified within the larger cohort of 36 patients . Pathogenicity predictive software, PON - P and Human Splice Finder (HSF), were used for in silico data analysis. For the AMD subset: Available local indigenous southern African population - based genome - wide S ingle Nucleotide Polymorphism (SNP) chip (Affymetrix SNP6) data was used to identify SNPs within known AMD candidate genes in which allele frequencies were significantly different (i.e. 10 fold) between Caucasians and indigenous southern Africans. Nine SNPs occurring at higher frequencies within Africans compared to Caucasian controls were genotyped by SNaPshot PCR within a multi - ethnic AMD SA cohort. Minor allele frequencies (MAF) were compared using SHEsis. Results: Sequencing of ABCA 4 in three African STGD patients produced 39 unique variants, out of which only one, (V643M), was deemed pathogenic. HSF predicted 22 of these non - exonic variants to be 'possibly pathogenic', confounding analysis. No variants segregated with the common haplotypes. Regarding the AMD cohort, eight SNPs in candidate AMD genes showed a decreased MAF in African AMD cases compared to controls, two of which (rs9621622 in TIMP3 and rs17110714 in ABCA4 ), were statistically significant ( p values of 9.95 x 10 - 4 and 1.04 x 10 - 2 , respectively). Discussion and Conclusion: Although a number of variants were identified in the coding region of three haplotype - representative STGD subjects, only one variant proved pathogenic but did not co - segregate with the haplotype in the rest of the samples. It is possible that variants in regulatory regions not captured by the exonic screening might be involved, or that another gene may be imp licated in the 'STGD - like' phenotype in the indigenous African subjects. In the second part of the study, the investigation of the African AMD cohort suggested that SNPs in TIMP3 and ABCA4 are associated with a decreased susceptibility, and may therefore plausibly be protective for AMD in indigenous Africans. Overall, however, this should be considered only a pilot study of macular degeneration in the indigenous African population, providing leads to larger scale studies of this group of disorders in this population group
Leveraging gene/subnetwork meta-analysis to recover signal and deconvolute the interactions between genes in the risk of genetic disorders
No full textGenome-wide association studies (GWAS) have identified numerous loci associated with diverse human traits. While these discoveries offer valuable insights into disease biology and inform patient care, key challenges remain. These include the disconnect between identified variants and biological mechanisms, the difficulty in detecting low-frequency or moderate-effect variants, and the inherent complexity of most human phenotypes. To address these limitations and enhance discovery power, large sample sizes are increasingly employed through individual study expansion or meta-analysis. However, the classical single-variant approach, analyzing individual genes or variants in isolation, may not fully capture the intricate genetic architecture of complex diseases. This can be due to genetic heterogeneity or limitations associated with gene-based analysis, where power is lost due to non-effect variants within a gene or low-frequency causal variants. Consequently, traditional GWAS often lack robust mechanistic insights into the functional underpinnings of complex traits. This thesis proposes a novel framework that integrates GWAS signals across multiple studies, leveraging summary statistics to improve association mapping and detect weak signals missed in single GWAS. The method aggregates SNP-level signals to the gene level and incorporates protein-protein interaction (PPI) networks for association mapping at gene and pathway/subnetwork levels. We applied this framework to GWAS summary statistics from seven European bipolar disorder cohorts. The analysis identified seven genes, including a highly significant effect at the gene level for AGT. Additionally, a significant subnetwork was identified with Estrogen Receptor 1 (ESR1) as the central hub. Furthermore, the method was employed to explore the genetic overlap between suicide and psychiatric disorders in the FinnGen database. This analysis revealed disease-specific traits sharing common risk factors with suicide. Notably, several genes with small effects were identified at both the gene and subnetwork levels, highlighting the involvement of overlapping genes, pathways, and subnetworks in the underlying molecular mechanisms. Functional enrichment analysis of hub genes based on annotations from Reactome and KEGG databases revealed significant pathways, with top significant involved in signaling, nervous system development, and the immune system. Finally, the framework was applied to investigate the genetic overlap between suicidality and subcortical brain volume. This analysis identified potentially significant genes, hub genes with small effects, along with a network of interacting genes. Enrichment analysis of the network genes revealed pathways with top significance associated with signaling, immune function, and nervous system development. In conclusion, the method presented in this thesis provides new insights into functional and molecular mechanisms issued from a gene/subnetwork-centric approach and exhibits candidate genes for drug targets and drug re-purposing. Altogether, these findings point to important pathways and possible regulatory mechanisms that may be involved in the emergence of disorders, as well as the multi- and co-morbidities associated with them. Clinical research and an integrated strategy of additional modalities will advance individualized mechanistic understandings of these complex illnesses
Elucidating the genetic aetiology of Bipolar Disorder
No full textIntroduction: Bipolar disorder (BD) is a debilitating mood disorder with substantial genetic contributions. However, while the existence of its heritability is well-established, the precise genetic components and mechanisms of BD remain unknown. This is a pilot study aimed at optimising the use of small-scale next generation sequencing (NGS) of family members affected with BD and extending the finding of variants to larger scale association studies, and an attempt at replicating associations from a large genome-wide association study. Methods and Materials: This thesis describes the pathway analysis of whole-genome sequencing (WGS) data from four Afrikaner individuals to identify candidate variants for genotyping in a Family-Based Association Test (FBAT) of 621 individuals of Caucasian and Mixed Ancestry families from South Africa. This was followed by whole-exome sequencing (WES) of eight members of an Afrikaner family to identify rare, coding variation. These two approaches were used to identify both common and rare variation which may be involved in BD. Results: FBAT indicated that variants in the genes ACTN2 (rs4659702) and ANK3 (rs10994318) are associated with BD in a combined group of both Mixed Ancestry and Caucasian individuals, p = 0.0339 and 0.0443, respectively. Furthermore, this study identified a variant in ACTN2 (rs11355106) which was associated with a broad psychiatric phenotype in Mixed Ancestry families (p = 0.0083). WES revealed 168 exomic variants that were shared by five affected members of the family, one of which was rs142375896, a rare and potentially damaging missense variant in SLC26A9. Conclusions: Pathway analysis of both WGS and WES data implicated that the burden of variation in affected individuals lies in regulatory networks, including the regulation of the actin cytoskeleton and circadian entrainment pathways. The association of ANK3 (rs10994318) with BD in a European ancestry cohort was replicated in a South African cohort comprising of Caucasian and Mixed Ancestry individuals, indicating that some risk variants for the disorder could be shared across populations. This thesis confirms the validity of relatively small-scale family-based studies for the study of complex disorders
Genetic analysis of inherited retinal diseases in indigenous Southern African populations
No full textBackground: 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
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