Browsing by Subject "Human Genetics"
Now showing 1 - 20 of 53
Results Per Page
Sort Options
- ItemOpen AccessA Genome-wide Association Study of Schizophrenia in the South African Xhosa and Generalizability of Polygenic Risk Score across African populations(2021) Majara, Lerato Charlotte; Ramesar, Raj; Chimusa, EmileAfrican populations are vastly underrepresented in genetic studies despite having the most genetic variation globally and facing wide-ranging environmental exposures. Most of these studies have been conducted in populations of European (EUR) ancestry using GWAS arrays that represent the genetic variation in these populations. Thus, the prediction accuracy of polygenic risk scores (PRS) derived from EUR ancestry populations is less accurate in populations of non-European ancestry, and least accurate in African (AFR) ancestry populations. The extent to which PRS prediction accuracy varies within AFR ancestry populations has not, however, been previously investigated. This study had two aims: the first was to investigate the contribution of common variants to the risk of schizophrenia in the South African Xhosa (SAX) population through genome-wide association study (GWAS) analysis, and to determine if PRS derived from EUR and East Asian (EAS) ancestry populations from the Psychiatric Genomics Consortium (PGC) Schizophrenia Working Group were generalizable to SAX. The second aim was to assess the generalizability of PRS for non-psychiatric phenotypes that were derived from EUR ancestry individuals from the UK Biobank (UKB, n = ~350,000) in the Uganda General Population Cohort (GPC, n = 4,778) and the South African Drakenstein Child Health Study (DHCS, n = 638). To address the first aim, a GWAS was conducted in 2,086 Xhosa individuals from South Africa with and without schizophrenia (ncases = 1,038; ncontrols = 1,048) using a custom-designed Affymetrix GWAS array designed to capture variation in the Xhosa population. The schizophrenia GWAS in SAX yielded one SNP (rs35172303 ; P = 4.74e-08, OR = 0.6004, 95%CI:[0.499,0.721]) in ZFP3 that met genome-wide significance. The association of variants in ZFP3 from the schizophrenia GWAS is consistent with those from an earlier exomesequence study in SAX undertaken by colleagues, but this gene has not previously been associated with schizophrenia in large-scale schizophrenia GWAS of predominantly EUR ancestry. After characterizing the genetic architecture of schizophrenia in SAX, it was found that the heritability was enriched across functional categories involved in the regulation of gene expression. Then, the accuracy of PRS derived from PGC Schizophrenia Working Group from both EUR and EAS ancestries in predicting schizophrenia in SAX was quantified. There was low PRS prediction accuracy using PGC-derived summary statistics in SAX (PGC-EUR: max R2 = 0.0057, P = 0.008; PGC-EAS: max R2 = 0.0059, P = 0.007). These findings are consistent with previous findings that showed that PRS predication accuracy is low when discovery and target cohorts come from different ancestral backgrounds. For the second aim, PRS prediction accuracy was quantified in simulations using data from the African Genome Variation project (AGVP) to represent continental AFR diversity. Samples were categorised by geographical region into West, East and South Africa cohorts. Each cohort was divided into a discovery and target datasets. The West and East African discovery data was used to predict the simulated phenotype in the three target cohorts. Using UKB EUR ancestry individuals, PRS prediction accuracy was assessed for 34 anthropometric and blood panel traits in the Uganda GPC, and then meta-analysed UKB with PAGE (Population Architecture using Genomics and Epidemiology, comprising about 50,000 Latino/Hispanic and African-American individuals) and BBJ (Biobank Japan, n = ~162,000) to assess how the inclusion of diverse sample impacts PRS prediction accuracy. Simulations were limited by sample size but showed that PRS prediction accuracy was highest when the discovery and target cohorts were matched by African region, and for phenotypes with the sparsest genetic architecture. Using empirical data from UKB and the Uganda GPC, a low prediction accuracy was observed across all 34 quantitative traits in GPC when using GWAS data from UKB. There was differential prediction accuracy across AFR ancestry groups within UKB, i.e. the prediction accuracy was highest for the Ethiopian and admixed populations, and lowest for southern African populations. When comparing PRS prediction accuracy of East African individuals from the UKB to that of individuals from GPC, the prediction accuracy was lowest in the Ugandan GPC population, indicating that the difference in environments between the two groups may be contributing to the difference in PRS accuracy. Moreover, the cross-ancestry meta-analyses showed that the inclusion of diverse samples in large scale studies improves PRS prediction accuracy, most especially for phenotypes with population-enriched variants. It was demonstrated for the first time in this thesis that EUR ancestry-derived PRS prediction accuracy varied within continental AFR ancestry groups, and tracks with population history and the evolution of humans. The higher prediction accuracy observed in Ethiopians can be explained by their genetic proximity to Europeans as a result of the back to Africa migration, whereas the southern African populations (including SAX) are more proximal to the ancestral populations that never left the continent. It is therefore imperative to not only include more African samples in future large-scale studies, but to have samples that adequately represent the genetic and environmental diversity on the African continent.
- ItemOpen AccessAPOE, PCSK9, and CETP genetic variants as potential biomarkers of dyslipidaemia in black South Africans with Type 2 Diabetes Mellitus(2018) Evans, Jonathan; Dandara, ColletDyslipidaemia is a commonly encountered clinical condition and is a major risk factor for cardiovascular diseases. Although there are many factors associated with dyslipidaemia, a strong genetic component is evident. Apolipoprotein E (APOE), proprotein convertase subtilisin/kexin type 9 (PCSK9), and cholesteryl ester transfer protein (CETP) are key regulators of plasma cholesterol levels. Thus, genetic variation in the genes coding for these proteins contributes to dyslipidaemia. In this study, a cohort of black South African Type 2 Diabetes Mellitus (T2DM) patients was characterized for mutations in genes coding for APOE, PCSK9, and CETP, and the possible effects of these variants on their lipid profiles was evaluated. Participants (n=417) were recruited from the Chris Hani Baragwaneth Hospital Diabetes Clinic, Johannesburg from whom blood samples were obtained for DNA extraction. The cohort was further stratified into two groups; individuals on statin treatment (Sim+, n=291), and the second that was not on treatment (Sim-, n=87). Lipid profiles were determined by enzymatic methods. DNA was genotyped for APOE, PCSK9, and CETP variants using PCRRFLP and Sanger sequencing. Analysis of the effects of the genetic variants was carried out in two ways. Firstly, for all the participants combined, and then by separating those on statin treatment from those without (Sim+ vs. Sim-). Genotype and allele frequencies were calculated followed by genotype-phenotype correlations with lipid profiles. Univariate analysis showed a significant association between the APOE4 isoform and lower HDL-c levels in the combined cohort (p=0.034). The effects were more pronounced in the Sim- group (p=0.004) but were absent in the Sim+ group. Contrary to above, APOE2 was significantly associated with lower total cholesterol (TC) (p< 0.001) and lower LDL-c (p< 0.001) when compared to APOE3 in the combined cohort. Upon analysing treatment groups, the correlations were observed in the Sim+ group (p=0.027 and p=0.003, respectively), while there were no observed correlations in the Sim- group. The CETP rs34065661C/G and G/G genotypes were significantly associated with increased HDL-c levels (p=0.017; when applying a dominant genetic model) in the combined cohort, as well as in the Sim+ group (p=0.026). Multivariate analysis, using a generalized linear model, confirmed associations between APOE rs429358C and lower HDL-c (OR=0.881, p=1.64e04), and APOE rs7412T and decreased LDL-c (OR=0.759, p=0.012). No significant associations were observed for PCSK9 polymorphisms. We report significant associations between APOE and CETP genetic variations and altered lipid levels in this black South African T2DM population. These genetic variants could be biomarkers for dyslipidaemia among Africans. However, it is imperative that the APOE, PCSK9, and CETP genes are fully characterized for additional polymorphisms in order to come up with a better genetic profile that explains the variance in lipid levels observed in the black South African population. The impact of these genetic variants could be relevant to other black African populations as well.
- ItemOpen AccessAssociation of variants in APOL1, MYH9 and HMOX1 WITH micro-Albuminuria among Sickle Cell disease patients from Cameroon(2016) Geard, Amy; Wonkam, Ambroise; Chimusa, Emile RIntroduction: Sickle Cell Disease (SCD) is a monogenic, multi-organ hemoglobinopathy disorder that is highly prevalent in Africa, with nearly 300 000 newborn cases per year. The underlying pathophysiological mechanism of the disease involves alteration of the normal soft and biconcave disc shape of erythrocytes, to that of a rigid crescent. These abnormal red blood cells cause vaso-occlusion and intravascular hemolysis, resulting in a variety of clinical manifestations, including acute pain crises, anemia, and damage to various organs. Kidney disease is a clinical proxy of severity, developing only in a subset of patients, and is subject to modification by genetic variations. Indeed, reports have shown significant association between proteinuria and specific genetic variants in MYH9 and APOL1, and between estimated Glomerular Filtration Rate (eGFR) and End Stage Kidney Disease (ESKD) with HMOX1 variants among adult African Americans affected by SCD. However, the association between these variants and micro-albuminuria, a primary indicator of renal dysfunction, has not been investigated, nor has any study of these variants been performed among SCD patients in Africa. Aim: The aim of this study was to investigate the association of targeted single nucleotide polymorphisms (SNPs) in APOL1, MYH9 and HMOX1, as well as a 5' promoter dinucleotide repeat in HMOX1, with micro-albuminuria among SCD patients from Cameroon; and to compare the results to that from a cohort of non-SCD Cameroonian individuals affected by ESKD.
- ItemOpen AccessA candidate gene analysis of arrhythmogenic right ventricular cardiomyopathy (ARVC)(2006) Du Preez, Janine; Mayosi, Bongani MHeart failure is a major public health problem throughout the world. In South Africa 17% of mortality is attributed to cardiovascular disease (CVD). Heart failure may be either ischemic or non-ischemic in origin. A significant proportion of non-ischemic heart failur is due to cardiomyopathy. There are currently five types of cardiomyopathy recognised, of which arrhythmogenic right ventricular cardiomyopathy (ARVC) is one. ARVC is familial in 30 to 50% of cases and it is inherited in an autosomal dominant or an autosomal recessive manner. Twelve chromosomal loci have been linked to ARVC and six genes have been identified. In 2004 Asano and colleagues reported a mouse model of ARVC that established LAMRI and CBX5 as candidate genes for the human form of ARVC.
- ItemOpen AccessComputational selection and prioritization of candidate genes for Fetal Alcohol Syndrome(BioMed Central Ltd, 2007) Lombard, Zane; Tiffin, Nicki; Hofmann, Oliver; Bajic, Vladimir; Hide, Winston; Ramsay, MicheleBACKGROUND:Fetal alcohol syndrome (FAS) is a serious global health problem and is observed at high frequencies in certain South African communities. Although in utero alcohol exposure is the primary trigger, there is evidence for genetic- and other susceptibility factors in FAS development. No genome-wide association or linkage studies have been performed for FAS, making computational selection and -prioritization of candidate disease genes an attractive approach. RESULTS: 10174 Candidate genes were initially selected from the whole genome using a previously described method, which selects candidate genes according to their expression in disease-affected tissues. Hereafter candidates were prioritized for experimental investigation by investigating criteria pertinent to FAS and binary filtering. 29 Criteria were assessed by mining various database sources to populate criteria-specific gene lists. Candidate genes were then prioritized for experimental investigation using a binary system that assessed the criteria gene lists against the candidate list, and candidate genes were scored accordingly. A group of 87 genes was prioritized as candidates and for future experimental validation. The validity of the binary prioritization method was assessed by investigating the protein-protein interactions, functional enrichment and common promoter element binding sites of the top-ranked genes. CONCLUSION: This analysis highlighted a list of strong candidate genes from the TGF-beta, MAPK and Hedgehog signalling pathways, which are all integral to fetal development and potential targets for alcohol's teratogenic effect. We conclude that this novel bioinformatics approach effectively prioritizes credible candidate genes for further experimental analysis.
- ItemOpen AccessDevelopment of a SCA7 patient-derived lymphoblast cell model for testing RNAi knock-down of the disease-causing gene(2011) Berkowitz, Danielle Claire; Greenberg, Jacquie; Scholefield, Janine; Weinberg, MarcoSpinocerebellar ataxia type 7 (SCA7) is an inherited neurodegenerative disease caused by the expansion of a CAG repeat within the ataxin-7 gene. The South African SCA7 population has been shown to have arisen due to a founder effect, and a single nucleotide polymorphism (SNP) within ataxin-7 has been linked to the SCA7 mutation in all South African patients genotyped to date. Recently, this SNP has been exploited in a potential allele-specific RNA interference (RNAi) based therapy, in order to knock down the expression of the mutant transcript in heterozygous patients. Although this approach has been tested in an artificial cellbased model of SCA7, focus has shifted towards testing the therapy in SCA7 patient-derived transformed lymphoblast cell lines
- ItemOpen AccessFunctional analysis of A 5' untranslated variant in rhodopsin : implications for the retinitis pigmentosa phenotype(2011) Akinyi, Maureen Veronica; Ramesar, RajRetinitis Pigmentosa (RP) is a group of heterogeneous retinal degenerative diseases that predominantly affect rod photoreceptor cells. Symptoms include night blindness and gradual peripheral vision loss, which progresses to a complete loss of vision. Clinical, phenotypic and genetic heterogeneity are frequently observed in RP. Mutations in Rhodopsin (RHO) have been identified as a major cause of RP. A sequence variant identified in the 5' untranslated region of RHO, g.269A>G, also known as c.-26A>G, was proposed to increase the risk of developing RP. In this study, the functional effect of this variant, individually and in cis with known pathogenic variants, was investigated using mammalian cell lines in order to determine whether the variant is a modifier of disease phenotype.
- ItemOpen AccessFunctional Genome Wide Association Study in Susceptibility and Resistance of Malaria(2021) Kabongo, Etienne Ntumba; Chimusa, Emile RBackground: More than century, malaria is qualified as a mortal infectious disease, worldwide causing high morbidity and mortality. The World Health Organization (WHO) has shown that, Distribution of Malaria in Africa takes a major part, it's accounting for 95% (about 229 million) and 67% (about 274000) of reported cases and death respectively. One of solutions for reducing this threat is to find drugs or to develop vaccines which can resist and adapt to populations. Unfortunately, despite several efforts, malaria parasites are still developing resistance to the frontline antimalarials. Objectives: Our aim in this project is to conduct a systematic Meta-analysis and various functional analysis across three study populations in Africa ( Kenya, Malawi and Gambia ). Method and Materials: Our first analysis is directed to the Genome Wide Association Study (GWAS) of three study populations (Kenya, Malawi and Gambia) using the Emmax tool to identify the genetic variants associated with severe malaria. We then conducted GWAS based meta-analysis on the summary statistics from the three studies using Metasoft and Metal. Further, we implemented Functional GWAS (FGWAS) to re-weight the GWAS meta-analysis using functional genomic information software (fgwas-tool). Using results from fgwas-tool, we performed biological interpretation using Functional Mapping (FUMA) tool. We mapped the significant SNPs to the genes, and elucidated their functions and their associated cell types. We then performed pathway analysis and enrichment analysis of the genes using Genemania and Enrichr. Additionally, we performed a polygenic risk score for individuals in each study population using PRSice, and evaluated the level of risk exposure for each individual based on the best predictive threshold. Finally, we filtered the rare variants from each study, and performed SKAT analysis to aggregate the effect of the rare variants Results: We identified 29 significant SNPs (14 replicates and 15 novels) reweighted from FGWAS based on GWAS Meta-Analysis. The SNPs mapped to 15 genes (HBB, HBD, ATP2B4, ABO, CBLB, EYA2, HERPUDI, IQCJ, MPP7, NAVI, NUP210, SAMD5 , TCERG1L ,TMEM229B, C4orf19) at gene level. Five of these genes (HBB, HBD, ATP2B4, ABO, CBLB) had been reported by different studies to be associated with malaria. In the PRS analysis we have shown the best prediction based on the best threshold estimated of each population. We found best-fit prediction best-fit PRS for Gambia is 0.00443458 at PT = 0.00165005, for Kenya is 8.4666e-158 at PT= 1 and for Malawi is 1.5151e-55 at PT = 1 predict the risk of an infectious disease like severe malaria. However, the prediction rate is very low and may fail to distinguish the cases from the controls. Conclusion: The functional analysis based on fgwas result have shown that 5 genes (ATP2B4, ABO, HBD, HBB, CBLB) are highly associated to malaria across these 3 studies populations (Gambia, Malawi and Kenya) and 10 candidate novel genes, including high number of mutations in the gene C4orf19 which will constitute one of the future major studies. Also, we have shown the best prediction based on the best threshold estimated of each population. The results have shown that the prediction rate is very low and may fail to distinguish the cases from the controls.
- ItemOpen AccessFunctional Genome-wide Association Studies (fGWAS) and genomics landscape of signatures of polygenic adaptation in Botswana populations with HIV-1 C infection(2022) Choga, Wonderful Tatenda; Chimusa, Emile Rugamika; Dandara, Collet; Thami, Prisca KThe burden of the human immunodeficiency virus subtype (HIV) is catastrophic, especially in Botswana, a nation in Southern Africa, where 20.7% of persons aged 15 to 49 years are living with HIV (PWH). Although HIV exposure rates are extremely high, individual differences in clinical outcomes point to the importance of host genetic variables. Genome-wide association studies (GWAS) are methods widely used for identifying single nucleotide polymorphisms (SNPs) linked to different phenotypes such as HIV-1 subtype C (HIV-1C) susceptibility or resistance. Even though, conventional GWAS techniques alone cannot illuminate the associated functional pathways beyond detecting association SNPs. Alternatively, functional genome-wide association studies (fGWAS), which are post-GWAS analyses, can be utilized to put GWAS summary results into functional context. We hereby, first describe the fGWAS employing whole genome sequences (WGS) of Batswana exposed to HIV-1C. Although autosomal SNPs are widely utilized for functional-GWAS research, recent studies have also linked mitochondria DNA (mtDNA) haplotypes to various HIV outcomes. We explored the possibility of using both autosomal and mtDNA SNPs to enrich fGWAS analysis. On another hand, people from Botswana (collectively called Batswana) exhibits a homogenous genetic structure and has also been identified as the closest population to the most recent common ancestor (MRCA) of human species. Concomitantly the population has extremely high HIV1C burden. It remains unclear if increased susceptibility to HIV-1C infection may be associated with its closeness to the ancestral genomes. We investigated the genomics landscape of signatures of polygenic adaptation to the HIV-1C in Botswana using genomewide scans for selection (GWSS). For the first goal, we looked at several HIV-related studies that had been done in Botswana from 1995 to 2020. We saw significant advancements in the fight against the pandemic, including the early introduction of second generation antiretrovirals like dolutegravir (DTG), the first African nation to reach the 2030 UNIAIDS targets (95-95-95), and a 0.3% decrease in mother-to-child transmission rates. However, the main limitations include the spread of HIV 1C that is resistant to treatment and the evolution of medication resistance mutations have presented a serious danger to ending the epidemic. We demonstrated that research on host genetic variables that affect HIV-1C clinical outcomes among Batswana are still understudied. Overall, Botswana has significant advancements in the widespread deployment of antiretroviral treatment (ART) and high viral load suppression rates. For the second goal, we employed WGS to carry out GWAS using autosomal SNPs (chromosomes 1-22). fGWAS was conducted using the ensuing results. There were 394 WGS of the Batswana that were analysed. The research subjects came from the earlier Botswana based Mashi and Tshedimoso studies. A total of 11,364,691 million autosomal, biallelic SNPs were collected and utilised for further studies after variant calling, strict variant filtering, quality checking; and phasing using the tools PLINK V2.00A2LM and EAGLE v2.1, respectively. A total of 226 PWH (all female) and 112 controls (those without HIV infection30 men and 82 females-) were included in the 338 samples that passed quality control. Despite the fact that the data come from a population of Botswana that speaks 25 different languages and that there are well-known linguistic and cultural differences, principal component analysis (PCA) based on autosomal SNPs failed to identify any substructures. Interestingly, we identified 12.2% of the genetic variants that were reported among Batswana but not found in publicly available. Softwares EMMAX and PLINK V2.00A2LM were used concurrently for association analysis, and 137 significant SNPs located on chromosomes 1, 3, 6, and 7 were identified. Nine of the closest genes including –LINC01266, LINC00578, SLC26A8, DNAH11, PLCB1, CRYBB2P1, AL512484.1, SMYD3, LOC105373269–, were effectively mapped to six of the seven lead SNPs at -log10Pvalue≤6. For gene set enrichment analysis, the Gene MANIA online tool was employed, and 20 additional genes with physical co-expression of 81% were identified: – CFTR, RACGAP1, PCF11, DGKQ, HAP1, PRKCA, GNA11, SLC26A10, SLC26A7, SLC26A11, SLC26A9, DCTN1, SPTBN1, DNAH2, SLC26A5, SLC26A1, SLC26A6, SLC26A3, SLC26A4, CDC20–. Both the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases had several terms related to these genes. Enriched biological pathways include enhanced antiporter activity, gastric and pancreatic secretion, solute carrier (SLC)-mediated transmembrane transport, and neurodegenerative processes. Such terms have also been linked to various clinical phenotypes including HIV-1 infection, human cytomegalovirus (CMV), and cancers suggesting possible cross phenotype associations. For the third goal, we used PRSice to calculate polygenic risk scores for individuals; Botswana population was set as target data while summary statistics of Uganda population exposed to HIV was base dataset. We then used the results to determine everyone's risk exposure level based on the best predictive threshold (PT). PT and HIV susceptibility were substantially associated. The best-fit prediction for Botswana was PT =0.129 (β=-120.02, standard error=61.14, pvalue=5.0x10-2) and 1.3% of the variance in HIV-1 susceptibility at the population level could be explained by the scores. In order to evaluate the population recombination history, we also evaluated the linkage disequilibrium (LD) degradation. According to LD decay statistics of r 2, LD decays more quickly in PWH than in those without HIV, suggesting the potential influence of selection pressure acting on HIV infection response. In addition, we evaluated the minor allele frequency (MAF) and generated allele frequency distributions. When comparing cases and controls, derived allele frequency (DAF) revealed a significant difference in the derived allele at low MAF (bin-width = 0-0.05), suggesting that uncommon variations may be involved in HIV-1 susceptibility. Consequently, the postGWAS studies also included the rare-variant analyses that were available. Thirdly, we looked at mtDNA to identify variations linked to HIV-1 susceptibility and their functional pathways. Analyses of phylogenetic relatedness and haplogroups were also conducted. The mtDNA sequences' median coverage was (1060; Q1:738.5 – Q3:1397). The total genotyping rate for mtDNA QC was 0.99, with 560 variations being eliminated because of minor allele criteria of 0.01. We then discovered a total of 351 variation sites and 64 highresolution haplogroups among the 338 people who passed QC. One mtDNA variation, m.2072A>G, was identified by association analysis using a logistic regression model with 10 PCs and gender as covariates. Based on functional predictions, it was assigned to a non-coding transcript exon of the MT-RNR2 gene's 16S ribosomal RNA (rRNA), and it was regarded as having potential pathogenicity. We were able to identify 67 high-resolution haplogroups. L0a1b1a1 was the most prevalent haplogroup (n = 39), but 27 uncommon haplotypes, such as H, R, L0f1, and L0g, were also discovered. Other common haplotypes included L0a1b1a1, L2a1b1a, and L0d1b2b1b, which had prevalence rates of 10%, 8%, and 7%, respectively, while L0d3b1 and L3e1b2 each had a 6%. L3e1b2 and L0a1bla1 (pvalue=0.02), L3d1a1a1 (pvalue=0.03), L3e1a3a, L0d2a1a3, L0d2a1, and L0d1d (pvalue <0.01), totaling 7 (11%) haplogroups, were statistically higher among PWH than HIV-negative persons. When a post-analysis was conducted to see if any of the 7 significant haplogroups were related to vulnerability to HIV infection, no significant connection was discovered. Finally, we investigated the genetic basis of HIV-1 infection susceptibility in Batswana. Integrated Haplotype Scores (iHS) revealed strong selection signals on 32 out of 332 genes putatively under strong selection, including BX664718.2, EMB, ERICH1, GGNBP1, GOSR2, KSR1P1, LINC01016, LINC01667, LINC01691, LINC02798, MAP3K14, MIR1268 2. The most enriched clusters were associated with immune pathways, including cytokine signaling pathways, cytokine regulatory pathways, and phosphorylation, when substantially overrepresented GO terms and KEGG pathways were searched for among the candidate genes. Notably, the majority of the genes were involved in the regulation and activation of NF-kappaB and I-kappaB kinase. In addition to HIV-1 infections, IKBKB has also been linked to CMV, hepatitis virus infections, and tuberculosis (TB). In conclusion, this project presented new insights into the multifaceted demographic history that shaped the existing genetic landscape of the population of Botswana. Although utilizing autosomal chromosomes failed to reveal any population sub-structuring, mtDNA diversity confirms variety and substantial sub-structure in the population of Botswana. Additionally, we identified new potential genes, pathways, and targets that are involved in the regulation of HIV-1 susceptibility Batswana, which predisposes the population to high acquisition than resistance rates seen. The gene sets identified here were also enriched for other features, including as TB, HBV, and CMV, which have been found to be very prevalent in Botswana and among PWH.
- ItemOpen AccessGaucer Disease in the Ashkenazi-Jewish Community of South Africa(1980) Goldblatt, Jack; Beighton, PeterGaucher disease is a biochemical genetic disorder of the lipid storage group. It is characterised by an accumulation of a glycosphingolipid, glycosyl ceramide in the reticulo-endothelial system. The condition presents clinically with hepatosplenomegaly, haematologic and orthopaedic problems. Affected individuals suffer from chronic ill-health and debility, with a clinical course of acute exacerbations, remissions and relapses. The basic defect has been shown to be a genetically determined abnormality in the enzyme beta-glucosidase, (Brady et aZ, 1965; Patrick, 1965). The diagnosis can now be accurately confirmed by laboratory procedures, which also enable determination of carrier status. Of particular interest is the high prevalence of the condition in the Ashkenazi-Jews. Fried, (1958), in a survey of cases in Jerusalem, estimated the minimal carrier or heterozygote rate to be 1 in 25. Other studies of Ashkenazi-Jews have revealed carrier frequencies ranging from 1 in 25 to about 1 in 40. This stimulated the investigation which was initially undertaken under the supervision of Professor Beighton in the Department of Human Genetics, University of Cape Town Medical School in 1975 and 1976. Further data has been accumulated by the author as a medical registrar at Groote Schuur Hospital in the ensuing period until 1979.
- ItemOpen AccessGenetic aetiology of autosomal recessive non-syndromic hearing loss in sub-Saharan African patients: evaluation using targeted and whole exome sequencing(2019) Lebeko, Kamogelo; Wonkam, Ambroise; Dandara, Collet; Mowla, ShaheenHearing Loss (HL) is one of the highest contributors to disability worldwide. The highest incidence of the disease is seen in developing countries, such as those in subSaharan Africa (SSA). Patients affected with disabling HL are reported to be more than 466 million worldwide. The causes of HL can either be environmental or genetic with each contributing about 50% towards all cases, in many settings. In developing countries, the environment might contribute more due to poor health services and infrastructure available to the population. In the absence of environmental causes, there is a genetic component at play, that is largely unknown in African populations. Up to 70% of HL of genetic origin are non-syndromic (NS). The mode of inheritance is recessive in nearly 77% of non-syndromic HL. Up to date, more than 100 genes have been associated with HL harbouring more than 1000 causative variants. In many populations of European and Asian descent, pathogenic variants in GJB2 (connexin gene 26) and GJB6 (connexin gene 30) are a major contributor to autosomal recessive non-syndromic hearing loss (ARNSHL). Comprehensive hearing health care programs should cover genetic causes by providing molecular testing, and genetic counselling, specifically SSA where genes and mutations causing HL remain largely unknown. The aim of this project was thus to uncover the genetic causes of HL among patients’ cohorts from Cameroon and South Africa. This was addressed by 1) sequencing common variants in the most relevant genes in other populations (GJB2 and GJB6), 2) using a targeted gene panel to resolve HL in 10 multiplex families from Cameroon presenting with ARNSHL and negative for GJB2 and GJB6 mutations screening, 3) screening novel variants found in known genes in a cohort of 82 singleplex HL cases from Cameroon and South Africa, and lastly, 4) using Whole Exome sequencing to explore the two unresolved multiplex cases with and subsequent findings confirmed by functional studies, and also screened in 80 singleplex HL cases. The following findings are reported: GJB6, GJA1 mutations screening and literature review No GJA1 or GJB6 mutation was not found in multiplex and simplex cases of HL in both Cameroonians and South Africans. The review of the literature confirms that the prevalence of GJB2- or GJB6-related NSHL is approximating to zero in most subSaharan African populations. Targeted Exome Sequencing (OtoSCOPE) The targeted genes, panel that included 116 genes, was able to resolve 7 of 9 families (77.8%) which were successfully sequenced, with one family failing to be sequenced. The causative variants identified in the 7 resolved families were : 1) compound heterozygous c.5806_5808delCTC and c.5880_5882delCTT in MYO7A; 2) compound heterozygous c.646T>A (p.Phe216Ile) and c.38G>A (p.Arg13His) in LOXHD1; 3) homozygous c.766-2A>G in OTOF; 4) a deletion and a complex copy number variation in STRC; 5) compound heterozygous c.1678G>A (p.Asp560Asn) and c.2007C>A(p.Asp669Glu) in SLC26A4; 6) Homozygous c.1996C>T(p.Arg666Stop) in MYO7A; 7) compound heterozygous c.6399C>A(p.Asp2133Glu) and c.2000T>C (p.Met667Thr) in CDH23. Five out of 12 variants were novel. Screening of these causative variants in known genes, in 82 singleplex HL cases from Cameroon and South Africa was unable to resolve any of the cases: the variants were in either heterozygous in low frequency or absent. Bioinformatic pathways exploration of SNP data of known HL genes revealed an extensive network within the HL genes, with 10 identified as important nodes, including MYO7A. Most HL genes were found to be involved in two biological processes which were sensory perception of mechanical stimulus (GO: 0050954, p= 1.430e-8) and sound (GO: 0007605, p = 1.246e-8). The molecular functions of variants found within these genes were found to mostly fall within the binding (GO: 0005488) and/or structural molecule activity (GO: 0005198). Whole Exome sequencing Whole exome sequencing was performed on four of the nine multiplex families: the two families that were unresolved by targeted panel sequencing, and two previously resolved families that were used as positive controls for the variant annotation and filtering pipeline. The results were the resolution of 3/4 families, including the two- positive control. The previously unresolved “family 8” was found to harbour a novel variant within the GRXCR2 gene, a gene only associated with HL once before. The c.251delC variant was revealed through in silico studies to cause a premature stop codon at position 116 due to its frameshift effect. The screening of this variant in our cohort of 80 singleplex cases revealed one other unrelated HL patient harbouring this causative variant. Due to the limited literature on the gene and its protein, in silico studies were used to show the predicted secondary structure folding of the protein as well as potential protein binding regions. Analysis showed that the predicted loss of a stable region of the protein as well as that of a putative binding domain could explain the pathogenic nature of the variant. In vitro studies showed that the variant hindered the detection of the protein by way of a DDK tag downstream in the plasmid. Additionally, GFP-Tagged GRXCR2 showed altered expression pattern in the variant when compared to the wildtype. In summary, our data has revealed the efficacy of using next generation sequencing tools in resolving HL among sub-Saharan African patients as opposed to the single candidate gene approach. In our quest, we have employed two widely used strategies, targeted panel and whole exome sequencing (WES), both of which have had great successes in various populations. The targeted approach was able to resolve 77.8% of our families but did not detect variants for two of the families revealing the presence of other variants harboured in rarely associated gene not captured or included on the panel. This prompted for the use of a more comprehensive approach such as WES. These results corroborated with those of two families previously resolved by targeted exome sequencing. Additionally, one of the previously unresolved family was now resolved. This showed that WES was sensitive enough to detect variants in known HL genes but comprehensive enough to detect variants in other regions of the exome which have not been associated with HL or rarely associated with HL. The benefit of WES also extends to the contribution of exomic data from patients of African descent as there is an underrepresentation of this group in exome repositories as well as genomic or SNP databases. To the best of our knowledge, this is the first study to use WES to resolve HL in patients of African descent. The other benefit of such a venture is the use of this data not only for patients in SSA but also those in the diaspora. In conclusion, we have successfully demonstrated the feasibility of using NGS tools in identifying causative variants in HL patients in SSA. Additionally, we have shown that WES is a more suitable approach to trying to resolve HL in Africa. Therefore, the data strongly support that genetic studies on families segregating HL in SSA could be the next frontier of HL genetic research, of global importance through discovering novel variants in known genes, and potentially novel genes. These studies will improve HL genetic diagnosis, retrospective counselling and testing, prevention and care including future prediction of treatment outcomes in sub-Saharan Africans, and in people of African descent.
- ItemOpen AccessGenetic analysis of bipolar disorder and alcohol use disorder(2015) Dalvie, Shareefa; Ramesar, Rajkumar; Stein, Dan JBackground: Mental health disorders represent a major public health problem in most countries around the world. In South Africa, the lifetime prevalence of psychiatric disorders is 30.3%, with substance-use disorders and mood disorders being the second and third most prevalent classes of lifetime disorders, respectively. Bipolar disorder (BD) has a lifetime prevalence of 1.4% and alcohol use disorder (AUD) a lifetime prevalence of 30.3%, and they are frequently comorbid. Both of these disorders have a relatively high heritability, yet the exact genetic basis of each remains unknown. Genetic variants within the hypothalamic-pituitary-adrenal (HPA)-axis and glutamatergic pathways have previously been implicated in both phenotypes. The aim of this project was to investigate the aetiology of BD and AUD, using high-throughput genomic technologies, bioinformatics, brain-imaging and environmental measures. An additional aim was to assess the genetic aetiology of BD-AUD comorbidity. Methods: For the genetic analysis underlying BD, a South African 'Afrikaner' family was investigated. Whole-genome sequencing (WGS) and whole-genome linkage analysis was performed for individuals with BD Type I (BDI) and unaffected family members using the Illumina HiSeq2000 and Affymetrix Axiom TM Genome-wide CEU 1 Array, respectively. For the AUD analysis, two groups were investigated; a South African adolescent group comprising 80 individuals with AUD and 80 controls, and a group of 8123 individuals from the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort. The South African group of adolescents were genotyped using the Illumina Infinium iSelect custom 6000 BeadChip, childhood trauma data was obtained and brain magnetic resonance images were collected for a subset of this group. Genotype data on HPA-axis genes were obtained from a previous study for the ALSPAC cohort. The fourth group of individuals investigated in this thesis comprised 233 individuals with BD-AUD comorbidity from the Systemic Treatment Enhancement Program for BD (STEP-BD). Genotype data for genes from the glutamatergic and HPA-axis pathways were obtained from a previous study conducted on these individuals. Results: The chromosomal regions 6p25, 10p14-10p15.1, 11q23-11q25, and 13q21-22 scored the highest LOD scores for BD and the most over-represented pathway in the affected family members was the T-cell receptor signalling pathway. In the South African adolescent group, circadian rhythm genes were associated with AUD and childhood trauma predicted alcohol use in adolescence. The gene-imaging analysis identified a SNP in the glutamate receptor, ionotropic, N-methyl D-aspartate 2B (GRIN2B) gene as being associated with brain volume in the left orbitofrontal cortex and posterior cingulate. HPA-axis genes did not show an association with AUD and no significant gene x environment interactions were detected for AUD in the ALSPAC cohort. Single variants in the glutamatergic genes and HPA-axis were not associated with BD-AUD comorbidity. However, from the gene-based analysis, the glutamatergic gene PRKCI was associated with BD-AUD comorbidity. Conclusions: It appears that disruption in immune-related genes may contribute to the development of BD in an Afrikaner family. No significant gene x environment interactions were detected for adolescent AUD. The circadian pathway and childhood trauma may play a role in the development of adolescent AUD. Differential brain volume and BD-AUD comorbidity may be characterised by variation in the glutamatergic pathway. These pathways and the interactions between them should be further investigated in BD and AUD.
- ItemOpen AccessGenetic analysis of inherited retinal diseases in indigenous Southern African populations(2017) Roberts, Lisa Jane; Ramesar, Rajkumar; Swaroop, AnandBackground: 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.
- ItemOpen AccessGenetics of age-related macular degeneration and Stargardt disease in South African populations(2016) Baard, Johannes; Ramesar, Rajkumar; Roberts, LisaBackground: 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.
- ItemOpen AccessThe genetics of anthracycline-induced cardiotoxicity in cancer patients(2018) Naidoo, Horacia; Ramesar, Rajkumar; Simonds, Hannah MINTRODUCTION: Breast cancer makes up 25% of all cancers diagnosed worldwide. Despite an increasing yearly incidence, there has been a significant decrease in mortality owing to early diagnosis and advances in treatment. Anthracycline-based chemotherapy is a relatively low cost yet highly effective anti-cancer treatment, increasing survival from 30% to >80%, presently. However, treatment efficacy is marred by the increased risk of anthracycline-induced cardiotoxicity (ACT) - estimated at 10-26%. Internationally, there has been evidence of ACT having a genetic basis. Currently in South Africa, there is little information on ACT in cancer patients and survivors, and no information on the genetic basis of this phenomenon. Our recruitment sites in Cape Town - Groote Schuur Hospital (GSH) and Tygerberg Hospital (TBH), routinely treat hundreds of patients, notably with breast cancer, with anthracycline-based therapy every year, and provided the environment to assess ACT, as well as genetic factors which may influence this adverse drug reaction. Left ventricular ejection fraction (LVEF) acts as a surrogate measure of cardiac function in the public health-care setting. OBJECTIVES: To provide insight into the clinical management of breast cancer patients on anthracycline-based treatment with a focus on the prevalence of ACT. To provide an index of genetic susceptibility to ACT and potentially contribute to a personalized medicine approach for a genetically diverse population. METHODOLOGY: In the retrospective part of the study, the clinical records of cancer patients treated with anthracyclines from 2011- 2016 at the Oncology Clinic at GSH were analysed. Clinical co-morbidities such as hypertension, diabetes, pre-existing cardiac disease and smoking as well as type and dose of anthracyclines, cardiac function and patient status were assessed. In the prospective study, breast cancer patients treated with anthracyclines, with a pre and post-treatment LVEF measure were recruited at GSH and TBH from 2013 to 2016. Patients were consented for access to both clinical information and biological material. Demographics, clinical risk factors and chemotherapeutic regimen data were analysed. LVEF, biomarkers and clinical status were also assessed in terms of reflecting ACT. In some instances certain clinical information was not available (i.e. LVEF) and out of necessity, a statistical correlation model or classifier was created in order to use available clinical data to derive missing clinical measures. Patients' DNA were analysed for seven genetic variants in the following six genes ABCC1 (rs246221); ABCC2 (rs17222723; rs8187710); HNMT (rs17583889); NCF4 (rs1883112): RAC2 (rs13058338) and RARG (rs2229774), and tested for correlation with clinical status and cardiac injury. Finally, a corollary study was conducted on a subset of patients in an attempt to determine whether cardiac biomarkers may be more sensitive measures of cardiotoxicity. RESULTS & DISCUSSION: In the retrospective cohort (n=402) 19.7% of patients showed diminished cardiac function. Logistic regression showed that the following predictors: type of first line chemotherapy, and total dose significantly contributed to the ACT phenotype as measured by change in LVEF. In the prospective patients (n=272), 14% were affected with ACT, with an increased likelihood of cardiotoxicity in the Indigenous African population. Logistic regression showed that both total anthracycline dose and change in LVEF were predictive of ACT. In the association study of prospective patients, only the RARG rs2229774 variant was significantly associated with patient ACT status (p=0.049, Chi-Square Test). Forty-two patients were assessed for the β-Natriuretic Peptide (BNP) biomarker and showed limited utility in correlating clinical status and/or LVEF decrease in all patients except Indigenous Africans indicating potential increased susceptibility of population group to ACT. LVEF was found to be unreliable as significant LVEF decreases did not always correlate with cardiac impairment and vice-versa. Changes in routine clinical patient management and overburdening of the nuclear medicine department also translated to only one LVEF measure being obtained in some instances. The statistically derived classifier for missing indicators of heart function was useful, but will require refinement. CONCLUSIONS AND RECOMMENDATIONS: Despite the inability of genotype as a predictor of ACT in this study, the increased susceptibility in the Indigenous African population to ACT as well as increased BNP levels after chemotherapy requires a closer look. The interrogation of lndigenous African patient genomes for novel variants of susceptibility to ACT are recommended; this requires building up of a substantial cohort from this population group, which would likely require collaboration with health care institutions in one of the other provinces of South Africa e.g. Eastern Cape, KwaZulu-Natal and/or Gauteng. Both this study and literature recommend the need for clinical trials for new and existing drugs on local African populations for both safety and efficacy. Furthermore, the BNP biomarker may be better suited to the prediction of irreversible cardiac damage rather than early cardiotoxicity. Troponin, released in response to cardiomyocyte death, may be a more sensitive biomarker in predicting ACT. Similarly, the inherent variability and lack of sensitivity of LVEF as a measure of cardiac function warrants the consideration of alternatives such as echocardiography or tissue-doppler imaging. Findings derived from this study indicate the need for refined patient management of ACT in a South African population to potentially allow for treatment with minimised risk and event-free breast cancer survival.
- ItemOpen AccessGenetics of hearing impairment and peripheral neuropathy in Mali(2023) Yalcouye, Abdoulaye; Wonkam, Ambroise; Chimusa EmileBackground Hearing impairment (HI), the most common sensory disturbance, affects about 1 in 1000 living newborns globally. Its incidence is reported higher in sub-Saharan African (SSA) populations. HI is caused by environmental and genetics factors. In many developing countries, environmental factors are reported to be the most prevalent aetiologies while genetic causes are predominant in the developed countries. Over 50% of congenital HI has a genetic origin with more than 120 genes identified to date. Despite this large number of known genes, only GJB2 (OMIM: 121011) and GJB6 (OMIM: 604418) are systematically studied in SSA populations for which the prevalence of HI-causal variants is insignificant. Charcot-Marie-Tooth disease (CMT), is the most common inherited peripheral neuropathy (IPN) with a high clinical and genetic heterogeneity and over 100 genes are related to CMT, mostly in populations of Caucasian ancestry. Yet, despite being described more than 130 years ago, there remains a paucity of information on its global prevalence and genetic epidemiology due largely to challenges in diagnosis, especially in countries with limited resources. Over 90% of CMT are caused by mutations in PMP22 (OMIM: 601097), GJB1 (OMIM: 304040), MFN2 (OMIM: 608507), MPZ (OMIM: 159440) genes. HI is the common audiological symptom associated with CMT and is caused by several genes including PMP22 and GJB1. HI and IPN are inherited in autosomal (dominant and recessive), X-linked, and mitochondrial transmission. However, the genetic epidemiology of these diseases are largely unknown in Africa, and have not been investigated in Mali where consanguineous marriage is a common practice that may increase recessive conditions.
- ItemOpen AccessGenomics of Lynch syndrome and Constitutional mismatch repair deficiency syndrome(2018) Lamola, Lindiwe; Ramesar, RajkumarIntroduction: 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).
- ItemOpen AccessHuntington’s chorea in South Africa(1979) Hayden, Michael Reuben; Beighton, PeterSouth Africa offers unique opportunities for the investigation of genetically determined illnesses in view of the excellent facilities available and the different origins of the various population groups. Huntington's chorea is generally considered to be a very rare disease in South Africa. Evidence in support of this, is the dearth of publications concerning the disorder in this country. By 1977 there had been only two such articles, in marked contrast to the plethora of reports from around the world. This investigation was concerned with the study of many different aspects of Huntington's chorea in South Africa. The primary aims were to determine the history, frequency, clinical presentation and course of Huntington's chorea in the Republic. In the wake of the genealogical and clinical findings, interesting new observations and exploration of the established concepts of the genetics of Huntington's chorea have been undertaken. A major attempt has been made to investigate the hypothesis that dopamine excess is important in the pathophysiology of this condition. Since dopamine has an important regulatory function on anterior pituitary hormone secretion, affected individuals might be expected to have abnormal patterns of hormonal regulation. The disturbances in prolactin, thyrotropin and growth hormone secretion reported in this thesis, support the concept of dopamine predominance. The demonstration of similar neuroendocrine abnormalities in twelve of 23 clinically normal first-generation relatives may have importance for presymptomatic diagnosis. Although not a primary focus of the investigation, it soon became apparent that the social implications of this disorder were extremely important and largely unexplored. The attention of all health professionals is drawn to the tremendous cost of the disorder, and recommendations for improved care are proposed. Huntington's chorea is a far more serious problem in South Africa than was initially suspected. The gene was probably introduced by the first Dutch settlers over 300 years ago, and is found today in all population groups. The South African population of mixed ancestry has amongst the highest frequency of juvenile Huntington's chorea in the world. Even though the present study deals with only one relatively uncommon illness, the concepts presented are pertinent to numerous other unrelated chronic diseases, with which Huntington's chorea has shared concerns and needs.
- ItemOpen AccessIdentification of a suitable SNP for allele-specific silencing of the disease-causing gene in SCA1 patients in South Africa(2010) Baine, Fiona Kebirungi; Greenberg, L J ; Bryer, Alan ; Wood, M ; Scholefield, JanineSpinocerebellar ataxia 1 (SCA1) is part of a broader group of dominant neurodegenerative disorders caused by an unstable CAG trinucleotide repeat. There is no known cure for this disease and symptoms worsen progressively culminating in death. The disease-causing mutation in SCA1 occurs in the ATXN1 gene. The function of the gene product (the ataxin-1 protein) is unknown, however; the protein has been linked to RNA processing in the cell. The first part of this study followed on a 1997 report of two founder haplotypes in the Mixed Ancestry SCA1 families in the Western Cape of South Africa, using microsatellites. The aim was to narrow the region investigated in the previous study, and confirm the existence of founder haplotypes using a SNP-based haplotype. The SNPbased haplotype was constructed using 4 SNPs in individuals from 5 different families of Mixed Ancestry origin from the Western Cape and the two founder events were confirmed. The SNP-based haplotype also shows the existence of a minimum common interval and indicates regions of possible break-points which may be useful in determining the extent and origins of the two haplotypes. The second aim of the study was to preferentially silence the mutant transcript of the ATXN1 gene by targeting a single nucleotide difference. Two of the SNPs genotyped for the SNP-based haplotype were found to be heterozygous in over half of the patient cohort. Eight shRNA effector molecules were screened against short target sequences incorporating one of these SNPs. Results are promising, with significant discrimination achieved between the wild-type and mutant alleles by targeting this SNP. This study has shown that RNAi may be developed as a beneficial therapeutic technique for a subset of SCA1 patients in South Africa.
- ItemOpen AccessIdentifying Genes and Novel Variants Involved in Nonsyndromic Hearing Impairment, and Assessment of the Psychosocial Burden of Hearing Impairment in Cameroon(2021) Wonkam, Tingang Edmond; Chimusa, Emile R; Wonkam, AmbroiseBackground Hearing impairment (HI) is the most common sensory disability and occurs in about 1 per 1000 live births in high-income countries, with a much higher incidence of up to 6 per 1000 live births in sub-Saharan Africa (SSA). HI can be due to environmental or genetic causes, and in many cases, it is not possible to establish a definite aetiology. Hereditary HI contributes to 30% to 50% of HI cases in SSA. Hereditary HI can be syndromic or non-syndromic, depending on whether it is associated with additional abnormalities in other organs or not. Non-syndromic HI (NSHI) accounts for 70% of hereditary hearing loss, and is genetically highly heterogeneous, with approximately 170 loci and 121 genes identified to date. Studies in European and Asian populations have identified pathogenic variants in GJB2 (MIM: 121011), and GJB6 (MIM: 604418) genes as the major contributors to autosomal recessive NSHI (ARNSHI). The genetic aetiology of HI in Cameroon is unclear, as previous studies have found no contribution of GJB2 and GJB6 genes to NSHI in Cameroon. However, patients included in those studies consisted of both familial and isolated cases, therefore, underlying environmental/multifactorial causes in some cases cannot be excluded (especially for the isolated cases). Six loci for X-linked HI have been described to date, including DFNX3 (Xp21.2), where DMD is located. Variants in DMD in humans are known to be responsible for Duchenne muscular dystrophy (DMD; MIM: 310200), and Becker muscular dystrophy (BMD; MIM: 300376), an Xlinked recessive disorder. Previous studies have demonstrated that mdx mice, (an animal knockout model for DMD), have an increased threshold for hearing when compared to wildtype mice. However, the contribution of DMD to HI in humans has not been extensively studied. Besides, most of the previous studies on DMD were conducted in Caucasians, Asians, and Arabs; therefore, little is known about the features of this condition in Africans. Parents of children with HI tend to face challenges of parenting especially in terms of communication and social interaction. In Africa, parent's perceived causes of deafness vary from environmental factors to mysterious (“evil forces”) or superstitious beliefs. Also, the attitude of the society towards people with HI does not encourage their participation and involvement in the community, as they face overt discrimination. Aim and methods The aim of this project was to examine the genetic aetiologies of HI in the Cameroonian population, and undercover the challenges faced by persons with HI in Cameroon and their understanding of the causes of HI. This was addressed by 1) Establishing the current status of knowledge on HI in Africa (in terms of prevalence, aetiologies, and genetics aspects) with a particular focus on Cameroon, and assessing the contribution of connexin genes to HI in humans at a global level, through systematic literature reviews; 2) Revisiting the contribution of GJB2 and GJB6 genes to NSHI in 29 multiplex Cameroonian families with NSHI and with strong evidence of non-environmental causes, through targeted gene sequencing and specific multiplex polymerase chain reaction (PCR); 3) Using multiplex ligand-dependent probe amplification (MLPA) technique to investigate the most common variants associated with DMD in Cameroon and assess their possible implication in HI in humans; 4) Performing whole exome sequencing (WES) on 2 Cameroonian multiplex families with NSHI and who tested negative for pathogenic variants in GJB2 and GJB6, to identify the underlying causative genes; 5) Performing in-depth interviews to gain an understanding of the challenges faced by people with HI in Cameroon, their understanding of the causes of hearing impairment (HI), and how challenges could be remedied to improve the quality of life of persons with HI. Results Literature reviews Our first systematic review showed that HI is a public health issue in Cameroon, especially in the elder population where the prevalence of HI is 14.8% in people aged 50 years and more. Environmental factors, including meningitis, impacted wax, and age-related disorders are the leading aetiologies of HI in Cameroon as in many other SSA countries, contributing 52.6% to 62.2% of HI cases. Hereditary HI comprises 0.8% to 14.8% of all cases in Cameroon, and in 32.6% to 37% of HI cases, the origin remains unknown. This contrasts with findings from highincome countries where hereditary HI constitutes the main aetiology of HI, contributing to approximately 50% of cases. NSHI is the most frequent clinical entity and accounts for 86.1% to 92.5% of cases of hereditary HI in the Cameroonian population. No pathogenic variant was described in GJB6 gene, and the prevalence of pathogenic variants in GJB2 ranged from 0% to 0.5%. The prevalence of pathogenic variants in other known NSHI genes was with type 2 Waardenburg syndrome, and three cases of type 2 Usher syndrome were identified in one family. By direct gene sequencing of the coding region of GJB2, no variants were found in any of the 29 families with NSHI. Additionally, through a specific multiplex PCR, the GJB6- D3S1830 deletion which contributes to 9.7% of NSHI cases in Europeans was not identified in any of the patients with HI. Subsequently, a total of 17 males with DMD from 14 families were recruited, aged 14 ± 5.1 (8–23) years. The mean age at onset of symptoms was 4.6 ± 1.5 years, and the mean age at diagnosis was 12.1 ± 5.2 years. Proximal muscle weakness was noted in all patients and calf hypertrophy in the large majority of them (88.2%; 15/17). Flexion contractures were particularly frequent on the ankle (85.7%; 12/14). Wasting of the shoulder girdle and thigh muscles was present in 50% (6/12) and 46.2% (6/13) of patients, respectively. No patient presented with HI. The MLPA found that deletions of at least one exon in DMD occurred in 45.5% of patients (5/11), while duplications were observed in 27.3% (3/11). Both variant types were clustered between exons 45 and 50, and the proportion of de novo variant was estimated at 18.2% (2/11). Whole exome sequencing We submitted DNA samples from five members of a multiplex non-consanguineous Cameroonian family segregating prelingual and progressive ARNSHI for WES. We identified novel bi-allelic compound heterozygous pathogenic variants in CLIC5 (MIM: 607293). The variants identified, i.e. the missense [NM_016929.5:c.224T>C; p.(Leu75Pro)] and the splicing (NM_016929.5:c.63+1G>A), were validated using Sanger sequencing in all seven available family members and co-segregated with HI in the three family members with HI. The three affected individuals were compound heterozygous for both variants, and all unaffected individuals were heterozygous for one of the two variants. Both variants classify as pathogenic by the American College of Medical Genetics (ACMG) guidelines for classification of variants and are absent from the genome aggregation database (gnomAD), UK10K, Greater Middle East (GME) database, and the Single Nucleotide Polymorphism Database (dbSNP), as well in 122 healthy controls from Cameroon. We also did not identify these pathogenic variants in 118 unrelated sporadic cases of NSHI from Cameroon. A second multiplex family was also screened through the use of WES, followed by direct Sanger sequencing in additional patients and control participants. We identified a heterozygous novel missense variant [NM_001174116.2:c.918G>T; p.(Gln306His)] in DMXL2 (MIM:612186) which was transmitted in an autosomal dominant manner, and co-segregates with congenital/prelingual profound to total non-syndromic sensorineural HI in a family from Cameroon. The described family showed a variable expressivity of the HI phenotype. The p.(Gln306His) variant which substitutes a highly conserved glutamine residue is predicted deleterious by various bioinformatics tools and is absent from several genome databases including genome aggregation database (gnomAD), and trans-omics for precision medicine (TOPMed) database. This variant was neither found in 121 healthy controls without personal or family history of HI, nor 112 sporadic cases of NSHI from Cameroon. Our study identified novel variants in CLIC5 and DMXL2 in two Cameroonian families, and provided only the second report of variants in these genes worldwide; thus, strengthening the case for these two genes as candidate genes for NSHI in humans. The psychosocial burden of HI We performed in-depth interviews with 10 HI professionals (healthcare workers, and educationists), and 10 persons affected by HI (persons with HI, and caregivers). The results show that in this study population, the cause of HI is attributed to a variety of causes, including genetics, environmental factors, and a spiritual curse. There were reported cases of stigma and discrimination with persons with HI in the Cameroonian population sometimes seen as having a “mental disorder”. Our participants also highlighted the difficulty that persons with HI have in accessing the necessary education and healthcare services, and suggested the need for policymakers and researchers to develop strategies to improve the social integration of persons with HI and their access to basic social services. This includes 1) Increased awareness amongst the general population, 2) the establishment of more special schools, and 3) building and equipping facilities for proper management of HI. Conclusions Our project confirms that variants in GJB2 and GJB6 genes do not contribute significantly to NSHI in the Cameroonian population. Also, variants in DMD that were shown to be associated with an increased hearing threshold in mice, do not seem to be implicated in HI in Cameroon, neither in previous human studies (although they did not objectively assess hearing using standardized testing methods). Despite the first symptoms of DMD occurring in infancy, the diagnosis is frequently made later in adolescence, indicating an underestimation of the number of cases of DMD in Cameroon. Future screening of deletions and duplications in patients from Cameroon should focus on the distal part of the DMD gene. Subsequently, this study successfully identified the candidate genes in two Cameroonian multiplex families with NSHI through the use of WES, and thus highlights the efficacy of next-generation sequencing techniques in resolving HI cases in Cameroonians and in cases where no pathogenic variants are found in common HI-genes. Additionally, our project which confirms that CLIC5 and DMXL2 genes are associated with HI in humans advocate for the inclusion of these two genes in diagnostic gene panels for NSHI in clinical settings. Last, this study shows the difficult social interaction and access to proper management faced by persons with HI in Cameroon, and highlights the need to educate populations on the causes of HI for a better acceptance of persons with HI in the Cameroonian society.
- «
- 1 (current)
- 2
- 3
- »