Browsing by Author "Ramesar, Raj"

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    Open Access
    A 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, Emile
    African 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.
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    Association of variants at BCL11A and HBS1L-MYB with hemoglobin F and hospitalization rates among sickle cell patients in Cameroon
    (Public Library of Science, 2014) Wonkam, Ambroise; Bitoungui, Valentina J Ngo; Vorster, Anna A; Ramesar, Raj; Cooper, Richard S; Tayo, Bamidele; Lettre, Guillaume; Ngogang, Jeanne
    BACKGROUND: Genetic variation at loci influencing adult levels of HbF have been shown to modify the clinical course of sickle cell disease (SCD). Data on this important aspect of SCD have not yet been reported from West Africa. We investigated the relationship between HbF levels and the relevant genetic loci in 610 patients with SCD (98% HbSS homozygotes) from Cameroon, and compared the results to a well-characterized African-American cohort. Methods and FINDINGS: Socio-demographic and clinical features were collected and medical records reviewed. Only patients >5 years old, who had not received a blood transfusion or treatment with hydroxyurea were included. Hemoglobin electrophoresis and a full blood count were conducted upon arrival at the hospital. RFLP-PCR was used to describe the HBB gene haplotypes. SNaPshot PCR, Capillary electrophoresis and cycle sequencing were used for the genotyping of 10 selected SNPs. Genetic analysis was performed with PLINK software and statistical models in the statistical package R. Allele frequencies of relevant variants at BCL11A were similar to those detected in African Americans; although the relationships with Hb F were significant (p <.001), they explained substantially less of the variance in HbF than was observed among African Americans (∼ 2% vs 10%). SNPs in HBS1L-MYB region ( HMIP ) likewise had a significant impact on HbF, however, we did not find an association between HbF and the variations in HBB cluster and OR51B5/6 locus on chromosome 11p, due in part to the virtual absence of the Senegal and Indian Arab haplotypes. We also found evidence that selected SNPs in HBS1L-MYB region ( HMIP ) and BCL11A affect both other hematological indices and rates of hospitalization. CONCLUSIONS: This study has confirmed the associations of SNPs in BCL11A and HBS1L-MYB and fetal haemoglobin in Cameroonian SCA patients; hematological indices and hospitalization rates were also associated with specific allelic variants.
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    The BDNF p.Val66Met polymorphism, childhood trauma, and brain volumes in adolescents with alcohol abuse
    (BioMed Central, 2014-12-16) Dalvie, Shareefa; Stein, Dan J; Koenen, Karestan; Cardenas, Valerie; Cuzen, Natalie L; Ramesar, Raj; Fein, George; Brooks, Samantha J
    Background: Previous studies have indicated that early life adversity, genetic factors and alcohol dependence are associated with reduced brain volume in adolescents. However, data on the interactive effects of early life adversity, genetic factors (e.g. p.Met66 allele of BDNF), and alcohol dependence, on brain structure in adolescents is limited. We examined whether the BDNF p.Val66Met polymorphism interacts with childhood trauma to predict alterations in brain volume in adolescents with alcohol use disorders (AUDs). Methods: We examined 160 participants (80 adolescents with DSM-IV AUD and 80 age- and gender-matched controls) who were assessed for trauma using the Childhood Trauma Questionnaire (CTQ). Magnetic resonance images were acquired for a subset of the cohort (58 AUD and 58 controls) and volumes of global and regional structures were estimated using voxel-based morphometry (VBM). Samples were genotyped for the p.Val66Met polymorphism using the TaqMan® Assay. Analysis of covariance (ANCOVA) and post-hoc t-tests were conducted using SPM8 VBM. Results: No significant associations, corrected for multiple comparisons, were found between the BDNF p.Val66Met polymorphism, brain volumes and AUD in adolescents with childhood trauma. Conclusions: These preliminary findings suggest that the BDNF p.Met66 allele and childhood trauma may not be associated with reduced structural volumes in AUD. Other genetic contributors should be investigated in future studies.
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    The co-inheritance of alpha-thalassemia and sickle cell anemia is associated with better hematological indices and lower consultations rate in Cameroonian patients and could improve their survival
    (Public Library of Science, 2014) Rumaney, Maryam Bibi; Bitoungui, Valentina Josiane Ngo; Vorster, Anna Alvera; Ramesar, Raj; Kengne, Andre Pascal; Ngogang, Jeanne; Wonkam, Ambroise
    BACKGROUND: Co-inheritance of α-thalassemia was reported to be associated with a delayed age of disease onset among Cameroonian Sickle Cell Anemia (SCA) patients. The present study aimed to explore the correlation between α-thalassemia, hematological indices, and clinical events in these patients. Methods and FINDINGS: We studied 161 Cameroonian SCA patients and 103 controls (59.1% HbAA) with median ages of 17.5 and 23 years. RFLP-PCR was used to confirm SCA genotype and to describe haplotypes in the HBB-like genes cluster. Multiplex Gap-PCR was performed to investigate the 3.7 kb α-globin gene deletions. SNaPshot PCR, capillary electrophoresis and cycle sequencing were used for the genotyping of 10 SNPs in BCL11A , HMIP1/2 , OR51B5/6 and HBG loci, known to influence HbF levels. Generalised linear regression models adjusted for age, sex and SNPs genotypes was used to investigate effects of α-thalassemia on clinical and hematological indices. The median rate of vaso-occlusive painful crisis and hospitalisations was two and one per year, respectively. Stroke was reported in eight cases (7.4%). Benin haplotype was the most prevalent (66.3%; n = 208 chromosomes). Among patients, 37.3% ( n = 60) had at least one 3.7 kb deletion, compared to 10.9% ( n = 6) among HbAA controls (p<0.001). Among patients, the median RBC count increased with the number of 3.7 kb deletions [2.6, 3.0 and 3.4 million/dl, with no, one and two deletions (p = 0.01)]. The median MCV decreased with the number of 3.7 kb deletion [86, 80, and 68fl, with no, one and two deletions (p<0.0001)], as well as median WBC counts [13.2, 10.5 and 9.8×10 9 /L (p<0.0001. The co-inheritance of α-thalassemia was associated with lower consultations rate (p = 0.038). CONCLUSION: The co-inheritance of α-thalassemia and SCA is associated with improved hematological indices, and lower consultations rate in this group of patients. This could possibly improve their survival and explain the higher proportion of α-thalassemia among patients than controls.
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    Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method
    (Public Library of Science, 2013) Chimusa, Emile R; Daya, Michelle; Möller, Marlo; Ramesar, Raj; Henn, Brenna M; van Helden, Paul D; Mulder, Nicola J; Hoal, Eileen G
    Admixed populations can make an important contribution to the discovery of disease susceptibility genes if the parental populations exhibit substantial variation in susceptibility. Admixture mapping has been used successfully, but is not designed to cope with populations that have more than two or three ancestral populations. The inference of admixture proportions and local ancestry and the imputation of missing genotypes in admixed populations are crucial in both understanding variation in disease and identifying novel disease loci. These inferences make use of reference populations, and accuracy depends on the choice of ancestral populations. Using an insufficient or inaccurate ancestral panel can result in erroneously inferred ancestry and affect the detection power of GWAS and meta-analysis when using imputation. Current algorithms are inadequate for multi-way admixed populations. To address these challenges we developed PROXYANC, an approach to select the best proxy ancestral populations. From the simulation of a multi-way admixed population we demonstrate the capability and accuracy of PROXYANC and illustrate the importance of the choice of ancestry in both estimating admixture proportions and imputing missing genotypes.
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    Ethical considerations in forensic genetics research on tissue samples collected post-mortem in Cape Town, South Africa
    (BioMed Central, 2017-11-29) Heathfield, Laura J; Maistry, Sairita; Martin, Lorna J; Ramesar, Raj; de Vries, Jantina
    Background: The use of tissue collected at a forensic post-mortem for forensic genetics research purposes remains of ethical concern as the process involves obtaining informed consent from grieving family members. Two forensic genetics research studies using tissue collected from a forensic post-mortem were recently initiated at our institution and were the first of their kind to be conducted in Cape Town, South Africa. Main body: This article discusses some of the ethical challenges that were encountered in these research projects. Among these challenges was the adaptation of research workflows to fit in with an exceptionally busy service delivery that is operating with limited resources. Whilst seeking guidance from the literature regarding research on deceased populations, it was noted that next of kin of decedents are not formally recognised as a vulnerable group in the existing ethical and legal frameworks in South Africa. The authors recommend that research in the forensic mortuary setting is approached using guidance for vulnerable groups, and the benefit to risk standard needs to be strongly justified. Lastly, when planning forensic genetics research, consideration must be given to the potential of uncovering incidental findings, funding to validate these findings and the feedback of results to family members; the latter of which is recommended to occur through a genetic counsellor. Conclusion: It is hoped that these experiences will contribute towards a formal framework for conducting forensic genetic research in medico-legal mortuaries in South Africa.
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    A Founder Mutation in MYO7A Underlies a Significant Proportion of Usher Syndrome in Indigenous South Africans: Implications for the African Diaspora
    (Association for Research in Vision and Ophthalmology (ARVO), 2015-10) Roberts, Lisa; George, Siddiqah; Greenberg, Jacquie; Ramesar, Raj
    PURPOSE. Research over the past 25 years at the University of Cape Town has led to the identification of causative mutations in 17% of the 1416 families in the Retinal Degenerative Diseases (RDD) biorepository in South Africa. A low rate of mutation detection has been observed in patients of indigenous African origin, hinting at novel genes and mutations in this population. Recently, however, data from our translational research program showed two unrelated indigenous African families with Usher syndrome (USH), with the same homozygous MYO7A mutation. Therefore, the extent to which this mutation contributes toward the disease burden in South Africa was investigated. METHODS. Cohorts of unrelated indigenous South African probands with different RDD diagnoses were tested for the MYO7A c.6377delC mutation. Familial cosegregation analysis was performed for homozygous probands, clinical data were evaluated, and SNP haplotypes were analyzed. RESULTS. This homozygous MYO7A mutation underlies a remarkable 43% of indigenous African USH cases investigated in this study, the majority of which (60%) were diagnosed clinically with Type 2 USH. All homozygotes shared a common haplotype. This mutation does not appear to cause nonsyndromic vision loss. CONCLUSIONS. Of interest is the origin of this common mutation relevant to the Bantu population migration into southern Africa. Further investigation of the phenotype may elucidate the disease biology, and perhaps reveal a larger cohort with the same mutation, with which to assess the impact of environmental and genetic modifiers and evaluate therapeutic trials.
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    Functional analysis of A 5' untranslated variant in rhodopsin : implications for the retinitis pigmentosa phenotype
    (2011) Akinyi, Maureen Veronica; Ramesar, Raj
    Retinitis 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.
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    Genetic polymorphisms and organophosphate neurotoxicity amongst emerging farmers in the Western Cape
    (2016) Glass, Tracy; Dalvie, Mohamed Aqiel; Holtman, Zelda; Ramesar, Raj
    BACKGROUND: Long-term exposure to organophosphates (OPs) can cause chronic neurotoxic effects which may be modulated by genetic polymorphisms of xenobiotic metabolising enzymes (XMEs). No previous study investigated XME modulation of neurotoxicity outcomes. OBJECTIVES: To investigate whether XMEs polymorphisms modulate OP neurotoxicity among emerging farmers. METHODS: A cross-sectional study of 301 emerging farmers was conducted in the rural Western Cape of South Africa. Neurotoxicity testing included the World Health Organisation Core Test Battery (digit span forward and backward) and vibration sensitivity testing. Questionnaire items included demographic data, potential confounders and work history of pesticide exposures. Blood samples were analysed for genetic polymorphisms of the following XMEs; glutathione S-transferases (GST), N-acetyltransferases (NAT) and Paraoxonase (PON1). RESULTS: Median age was 39 (30-48) and most had 9 years of education or less (65.5%). 54% of the participants were OP pesticide applicators. There was a low prevalence of the GST null genotype (GSTT-1% and GSTM-16%) and the GA and GG genotype for NAT (10%). Modulation of OP exposure and neurotoxic outcome relationships by NAT, PON1 at position 192 and GST was indicated in multivariate analysis. The strongest evidence of modification was by NAT on the relationship between pesticide poisoning and impaired vibration sense. Poisoned individuals with the GG genotype were more likely to suffer from impaired vibration sense compared to GA and AA genotypes. CONCLUSION: Genetic polymorphisms of NAT, PON1 (at position 192) and GSTM may modify the relationship between OP exposure and neurotoxicity. Larger longitudinal studies are required to determine whether preventive strategies can be developed to improve health amongst the identified vulnerable groups.
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    The genetics of lithium-induced adverse drug reactions in bipolar disorder patients : a pilot study
    (2013) Weideman, Reinette; Ramesar, Raj; Horn, Neil
    Lithium is regarded as the first-line pharmacotherapy for the treatment of acute mood episodes, suicide prevention and prophylactic treatment in patients with bipolar disorder (BPD). Response to lithium has a strong genetic component and lithium-responders have an increased frequency of BPD among their family members. Lithium has a narrow therapeutic index and 75-90% of patients on long-term lithium treatment experience one or more side effects, such as weight gain, cognitive decline and skin problems, amongst at least 20 side effects. The research project is immersed in a larger project on the genetics of bipolar disorder, in which a large number of individuals in families have been investigated over several years. The present pilot study explored whether single nucleotide polymorphisms (SNPs) within GSK3B, AKT1, ARRB2, GRIA2 and PPPARGC1A could be associated with the incidence and severity of lithium-induced side effects.
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    Global Globin Network Consensus Paper: Classification and Stratified Roadmaps for Improved Thalassaemia Care and Prevention in 32 Countries
    (2022-03-31) Halim-Fikri, Bin Hashim; Lederer, Carsten W; Baig, Atif Amin; Mat-Ghani, Siti Nor Assyuhada; Syed-Hassan, Sharifah-Nany Rahayu-Karmilla; Yusof, Wardah; Abdul Rashid, Diana; Azman, Nurul Fatihah; Fucharoen, Suthat; Panigoro, Ramdan; Silao, Catherine Lynn T; Viprakasit, Vip; Jalil, Norunaluwar; Mohd Yasin, Norafiza; Bahar, Rosnah; Selvaratnam, Veena; Mohamad, Norsarwany; Nik Hassan, Nik Norliza; Esa, Ezalia; Krause, Amanda; Robinson, Helen; Hasler, Julia; Stephanou, Coralea; Raja-Sabudin, Raja-Zahratul-Azma; Elion, Jacques; El-Kamah, Ghada; Coviello, Domenico; Yusoff, Narazah; Abdul Latiff, Zarina; Arnold, Chris; Burn, John; Kountouris, Petros; Kleanthous, Marina; Ramesar, Raj; Zilfalil, Bin Alwi
    The Global Globin Network (GGN) is a project-wide initiative of the Human Variome/Global Variome Project (HVP) focusing on haemoglobinopathies to build the capacity for genomic diagnosis, clinical services, and research in low- and middle-income countries. At present, there is no framework to evaluate the improvement of care, treatment, and prevention of thalassaemia and other haemoglobinopathies globally, despite thalassaemia being one of the most common monogenic diseases worldwide. Here, we propose a universally applicable system for evaluating and grouping countries based on qualitative indicators according to the quality of care, treatment, and prevention of haemoglobinopathies. We also apply this system to GGN countries as proof of principle. To this end, qualitative indicators were extracted from the IthaMaps database of the ITHANET portal, which allowed four groups of countries (A, B, C, and D) to be defined based on major qualitative indicators, supported by minor qualitative indicators for countries with limited resource settings and by the overall haemoglobinopathy carrier frequency for the target countries of immigration. The proposed rubrics and accumulative scores will help analyse the performance and improvement of care, treatment, and prevention of haemoglobinopathies in the GGN and beyond. Our proposed criteria complement future data collection from GGN countries to help monitor the quality of services for haemoglobinopathies, provide ongoing estimates for services and epidemiology in GGN countries, and note the contribution of the GGN to a local and global reduction of disease burden.
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    Human Immunodeficiency Virus/Human Papillomavirus co-infection and host molecular genetics of cervical carcinoma
    (2019) Chambuso, Ramadhani Salum; Ramesar, Raj; Gray, Clive; Williamson, Anna-Lise
    A subgroup of women who are co-infected with human immunodeficiency virus type 1 (HIV1) and human papillomavirus (HPV) progress relatively rapidly to cervical disease regardless of the number of absolute CD4 count. During infection, viral peptides are recognized by the host immune system. It is reasonable to propose that the development of viral-associated cancers, like cervical cancer, requires interference with specific immune-response genes. This thesis investigates this proposition with consideration of host molecular genetic alterations and variations of the human leukocyte antigen class II (HLA II) genes as one of the groups of immune-response genes that are involved in directing CD4 T-cell responses during infection, in the instance of cervical cancer progression in HIV-1/HPV co-infected women. Study I, reviewed the available literature on host molecular genetics and HIV-1/HPV coinfection on cervical cancer progression. This study suggests that the dual pro-oncogenic effects of HPV oncoproteins E6/E7 and the HIV-1 oncoprotein Tat, may exacerbate and accelerate the rate of cervical disease progression in a subgroup of HIV-1-positive women. Additionally, HIV-1-positive cervical cancer has three important carcinogenesis steps: firstly, HPV integration into the host genome, secondly, dual pro-oncogenic effects of HPV oncoproteins E6/E7, and the HIV-1 Tat oncoprotein in the host genome and, thirdly, the accumulation of repeated, unrepaired genetic mutations and genetic alterations within the host chromosomal DNA. Genetic variations or mutations that affect the following host gene categories were suggested to be responsible for cervical cancer susceptibility and disease progression; (i) genes for the immune-response against oncogenic HPV infection, (ii) oncogenes, (iii) tumour-suppressor genes, (iv) apoptosis-related genes, (v) DNA damagerepair genes, and (vi) cell cycle-regulatory genes. However, studies II, III and IV are linked together and listed according to the specific objectives of this thesis. Study II, characterized the distribution of HPV genotypes within cervical tumour biopsies from a cohort of 181 HPV-unvaccinated South African women and studied the relationships with HIV-1 infection, age of patients, absolute CD4 count, CD4 percentage and the stage of cervical disease, and identified the predictive power of these variables for cervical disease stage. Distribution of HPV genotypes was related to the stage of cervical disease in HIV-1-positive women. Older age was a significant predictor for invasive cervical cancer (ICC) in both HIV-1-seronegative (p<0.0001) ) and HIV1-positive women (p=0.0003, q=0.0003). Sixty-eight percent (59/87) of HIV-1-positive women with different stages of cervical disease presented with CD4 percentage below or equal to 28 and a median absolute CD4 count of 400 cells/µl (IQR 300-500 cells/µl). Of the HIV-1-positive women, 75% (30/40) with ICC, possessed ≤28% CD4 cells versus 25% (10/40) who possessed >28% CD4 cells (both p< 0.001, q<0.001). Furthermore, 70% (28/40) of women with ICC possessed absolute CD4 count >350 cells/µl compared to 30% (12/40) who possessed absolute CD4 count ≤ 350 cells/µl (both p< 0.001, q< 0.001). Study III, was the first case-control study to investigate the association of HIV-1/HPV coinfection with specific host HLA II-DRB1 and -DQB1 alleles in cervical cancer. Two hundred and fifty-six (256) women of the same ethnicity were recruited, comprising 56 cases and 200 age-matched controls. A total of 624 HLA-DRB1 and -DQB1 class II genotypes were studied. HLA II-DQB1*03:01 and -DQB1*06:02 alleles were associated with cervical cancer in HIV-1/HPV co-infected women (p=0.001 and p< 0.0001, respectively) while HLA II-DRB1*13:01 and -DQB1*03:19 were rare or absent in women with cervical disease when compared to the control population (p=0.012 and 0.011, respectively). Study IV, aimed to investigate the host genetic alterations that may be involved in rapid tumour progression in HIV-1/HPV co-infected women. The frequency of loss of heterozygosity (LOH) and microsatellite instability (MSI) at the HLA II locus on chromosome 6p was analysed in cervical tumour biopsy DNA, with regard to HIV-1/HPV co-infection in 164 women. Seventy-four women were HIV-1-positive and ninety women were HIV-1-seronegative. Tumour DNA from HIV-1/HPV co-infected women demonstrated a higher frequency of LOH/MSI at the HLA II locus at 6p21.21 than tumour DNA from HIV1-seronegative women (D6S2447, 74.2% versus 42.6%; p=0.001, q=0.003), D6S2881 at 6p21.31 (78.3% versus 42.9%; p=0.002, q=0.004), D6S1666 at 6p21.32 (79% versus 57.1%; p=0.035, q=0.052), and D6S2746, at 6p21.33 (64.3% versus 29.4%; p< 0.001, q< 0.001), respectively. This thesis provides novel insights and adds to the existing knowledge on the relationships between HIV-1/HPV co-infection, CD4 immune status, host HLA II allele variations and genetic alterations at chromosome 6p in association or likely protection to cervical disease in the studied cohort of South African women. Identification of host molecular genetic susceptibility to disease with regard to viral infection is important for individualized molecular targeted prevention of cervical cancer.
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    An investigation of genome-wide promoter region cytosine-phosphate-guanine (CpG) Island methylation profiles in patients with chronic hepatitis B virus infection
    (2014) Kgatle, Mankgopo Magdeline; Hairwadzi, H N; Ramesar, Raj
    Hepatitis B virus (HBV) is oncogenic and a major cause of hepatocellular carcinoma (HCC) in the developing world. It integrates parts of its genome such as the HBx gene, core and surface antigens into the human genome. The integrated viral DNA disrupts gene function resulting in physiological changes that cause liver disease. The viral inserts are inactivated through methylation. This is a protective innate response driven by human DNA methyltransferases triggered by the presence of viral DNA inserts. This thesis investigates the hypothesis that during the innate response to methylate integrated HBV DNA, there is unintended methylation of genomic DNA around the intercalated viral DNA that could be adjacent host promoter Cytosine-phosphateGuanine (CpG) islands. This would activate or silence genes including tumour suppressors and result in the clinical disease phenotypes of hepatic inflammation, fibrosis and HCC that characterise chronic HBV infection. Genome-wide microarray analysis was used to investigate for the presence of promoter CpG island methylation in a cohort of patients with liver disease due to HBV infection, HCC, autoimmune hepatitis which is a non-viral liver disease and normal cases with no liver disease. The study identified hypermethylation in promoter regions, transcription start sites, gene exons and introns. Only sites in the promoter region and within 100bp upstream of a transcription start site were analysed for this thesis presentation. Using an extended cohort of patients with chronic HBV infection and normal controls, bisulfite DNA sequencing was used to validate and confirm the presence of DNA methylation in a selection of some of genes identified. HBV infected patients were shown to have hypermethylation in the promoter CpG island regions of several genes that regulate hepatic metabolism, tumour suppression, ribonucleic acid splicing, vitamin D receptor binding, protein ubiquitination and the cell cycle. Many of these genes have transcriptional binding factors that are known to be affected by the transcriptional transactivator HBx protein, suggesting that HBx protein is important in the pathogenesis of liver disease. Amongst the most hypermethylated core promoter regions identified were those for cyclin kinases genes such as Cyclin D3 (CCND3). CCND3 gene is important in liver regeneration and wound healing and its abnormal function has been linked to the development of liver fibrosis and HCC. Increased methylation of CCND3 gene was associated with HBV e antigen positive status and genotype D, supporting the hypothesis that increased methylation is associated with host and viral factors. Methylation induced alteration in the function of the identified gene promoters would affect cellular signalling with effects on cell growth, differentiation, proliferation and apoptosis. These changes would explain the development of hepatic inflammation, apoptosis, fibrosis and malignant transformation seen in chronic HBV infection. Further investigation of these genes will provide new insights on mechanisms of HBV induced liver disease and the development of new molecular diagnostic tools or therapeutic interventions.
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    Investigation of the Shared Genetic Influences on Bipolar Disorder, Borderline Personality Disorder and Regional Brain Structures
    (2021) Campbell, Megan; Dalvie, Shareefa; Stein, Dan; Ramesar, Raj; Rockiki, Jaroslav
    Background: The heritabilities of bipolar disorder (BD) and borderline personality disorder (BPD) are 80% and 65%, respectively, indicating substantial genetic contributions to both disorders. BD and BPD are often comorbid, and both disorders have a polygenic architecture. These variants are thought to subtly affect multiple pathways, associated with structural brain abnormalities commonly observed in patients with BD and BPD. Brain regions have been shown to be highly heritable and under distinct genetic influences. However, the overlap in genetic risk between BD and BPD and altered brain regions, respectively, has not yet been determined. Aims and Objectives: The aim of this project was to determine whether genetic risk for BD and BPD overlaps with genetic risk for altered brain regions. Methods: Genome-wide association study (GWAS) summary statistics for BD (Ncases=20,352; Ncontrols= 31,358), BPD (Ncase=998; Ncontrol=1,545), eight subcortical brain volumes (nucleus accumbens, amygdala, caudate nucleus, hippocampus, pallidum, putamen and thalamus) and intracranial volume (ICV) (N=27,087), and cortical surface area and thickness (N=37,479) were obtained. Pleiotropy and concordance were assessed using SNP-Effect Concordance Analysis. Conditional false discovery rate (cFDR) was used to condition BD and BPD GWAS results on genetic variants that influence brain regions. Linkage Disequilibrium Score Regression was used to examine genome-wide correlations between BD, BPD and brain regions. Mendelian randomization was used to test for causal associations between BD, BPD and each brain region, respectively. Results: There was evidence of significant pleiotropy and positive concordance between BD and BPD (ppleiotropy=5x10-4; pconcordance=1x10-6, OR=1.29). Significant pleiotropy was observed between BD and the thickness of several cortical regions and two gyri, namely the lateral occipital (p=2.25x10-5), pars triangularis (p=1.1x10-4), rostral anterior cingulate regions (p=2.18x10-4) and post central (p=7.9x10-6) and supramarginal gyri (p=1.45x10-7). Significant positive concordance was noted between BPD and thickness of the lateral occipital region (p=3x10-4; OR=1.02). After conditioning BD onto BPD and each regional brain GWAS, 171 additional variants were significantly associated with BD (FDR<0.05). Three additional SNPs were significantly associated with BPD when conditioned on thickness of the lateral orbitofrontal, lingual, precentral and supramarginal regions. Discussion: The findings here of genetic overlap between BD, BPD and altered brain structure, while novel, are consistent with previous work. The cFDR analyses, highlight synapse and neurotransmitter regulation as a key underlying mechanism between BD and altered brain regions. Further fine-grained delineation of the role of the environment in these relationships and the inclusion of non-European populations are critical next steps, as they may provide insight into risk factors, new areas of treatment and aid in early detection of at risk individuals.
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    The molecular genetics of bipolar affective disorder : South African populations, endophenotypes, and environmental influence
    (2006) Savitz, Jonathan; Ramesar, Raj; Solms, Mark
    The identification of the genetic variants underpinning bipolar disorder (BPD) has been impeded by a complex pattern of inheritance that may include by genetic heterogeneity, genetic epistasis, gene-environment interactions, incomplete penetrance and variable expressivity. In this thesis three strategies were employed to ameliorate these confounding factors. The first strategy was to focus on a theoretically genetically-homogeneous population with BPD. A unique South African sample including 190 individuals of the relativity reproductively-isolated Afrikaner population yielded promising evidence of linkage to chromosome 1 q31-32 and weaker peaks at lOq23 and 13q32, regions previously implicated in the disorder. A family-based analysis suggested that the 3' variable number tandem repeat (VNTR) variant of the dopamine transporter gene (DAT) is associated with bipolar-spectrum illness in the 132-strong sample of British ancestry. The second strategy was to carry out genetic linkage and association analyses using quantitative traits (elldophenotypes) that were closely associated with BPD. As part of this process a variety of personality traits were evaluated in the cohort, and anxiety related, novelty-seeking, hyperthymic, and cyclothymic personality traits were found to aggregate in participants with BPD and to a lesser extent repeated unipolar illness (MDE-R). These traits were therefore used as quantitative markers or endophenotypes of BPD. The quantitative linkage analysis indicated that a variant in the region of 13q32 may influence the development of novelty-seeking-related traits in the largest Afrikaner pedigree, while the personality trait, ""Stability"", was weakly linked to 4p16 in the total sample. The catechol-o-methytransferase (COM1) Va1l58Mct and the Brain Derived Neurotrophic Factor (BDNF) Va1l66Met polymorphisms were associated with mood-labile-cyclothymic and hyperthymic·-novelty-seeking traits, respectively. the DA T VNTR and the Notch4 exonic repeat variants were associated with a broad range of ""pathological"" personality traits in the sa11lples of British and Afrikaner origin, respectively. The sample was also evaluated with a battery of neuropsychological tasks and the BPD 1 and MDE-R groups displayed both verbal and visual memory recall deficits while the BPD 1 sample also suffered from recognition memory deficits. The neurocognitive trait, ""Memory"" was therefore used as a second endophenotype generating potential linkage signals on IOq23 and 22q 11. The exonic 48bp VNTR polymorphism in the dopamine 4 receptor (DRD4) gene was associated with '""Memory"" performance. As a third strategy, a potentially important aetiological factor, childhood trauma, was measured, and used to test for gene-environment interactions between the various candidate genes and bipolar-illness or BPD-related endophenotypes in the cohort. BPD and M DE-R individuals displayed significantly higher levels of emotional and physical abuse, and the former variable was also associated with the development of anxiety-related and unstable personality traits. A functional variant of the COM1 gene was found to interact with abuse to predispose to anxiety-related, unstable cyclothymic and novelty-seeking related personality traits. The combination of childhood abuse and possession of low-activity MAO-A gene variants was also associated the development of more anxious and unstable personality traits. All interaction between sexual abuse and the B])NF gene modulated performance on verbal and visual memory tasks. A similar interaction between the ApoE gene and sexual abuse was observed. Although a number of theoretical obstacles remain to be resolved, the analyses of isolated populations coupled with the use of endophenotypes and the testing or gene environment interactions, holds out great promise for the eventual elucidation of the genetic basis of hi polar affective disorder.
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    The molecular investigation of Stargardt disease in South Africa
    (2003) September, Alison; Greenberg, Jacquie; Ramesar, Raj; Callaghan, R; Kerr, Ian; Linton, K
    Hereditary macular degeneration describes a group of conditions causing macular pathology. Stargardt disease (STGD) is the most common inherited juvenile macular dystrophy characterised by severed reduction of central visual acuity and normal peripheral vision. The ABCA4 (adenosine triphosphate binding cassette transporter) gene is the only gene implicated in the autosomal recessive (ar) form of the STGD phenotype, while one genetic locus and one gene have been shown to be causative of the autosomal dominant form.
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    Mutation analysis of important retinal candidate genes: progression from research to diagnostic service
    (2006) Roberts, Lisa Jane; Greenberg, Jacquie; Ramesar, Raj
    Approximately one third of all human inherited disease includes defects of the eye. Retinal degenerative disorders (RDDs) are a group of diseases characterised by photoreceptor cell death in the retina and consequent vision loss. The Division of Human Genetics at the University of Cape Town (UCT) has samples archived in the RDD DNA database from over 1000 South African families. The research in this Division currently involves mutation screening of retinal candidate genes, with the goal of identifying the causative genetic mutation in each of the families registered in the database, in order to facilitate future therapeutic intervention. The purpose of this study was to determine the distribution and clinical utility of mutations in important candidate genes in a subset of South African RDD patients. To this end, three important retinal candidate genes were selected and screened in appropriate patient cohorts. The mutation analysis included screening for large deletions which is a novel approach in the study of RDDs. The screening of Rhodopsin (RHO) in 61 individuals, retinitis pigmentosa 1 (RP1) in 70 individuals and retinal pigment epithelium-specific protein 65kDa (RPE65) in 87 individuals led to the identification of 10 families for whom a molecular diagnostic service can now be provided. For most families the amount of useful information available without further research is minimal, however for four of the families, therapeutic interventions may be possible, now or in the near future. In addition to the pathogenic mutations found, 17 single nucleotide polymorphisms (SNPs) were identified during this study. Furthermore, a significant association between ethnicity and the frequency of the high and low risk alleles of two of these SNPs (that may modify the phenotype of RDDs) was shown. This information may be useful in providing diagnostic or prognostic indicators in the future. The utility of RDD research should not be trivialised as it identifies families who may benefit from current interventions or be eligible for possible therapeutic trials, eliminates gene candidates in families, and is necessary for understanding the disease (which in itself is a requirement for development of therapies).
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    A mutation in a splicing factor that causes retinitis pigmentosa has a transcriptome-wide effect on mRNA splicing
    (BioMed Central, 2014-06-27) Korir, Paul K; Roberts, Lisa; Ramesar, Raj; Seoighe, Cathal
    Background: Substantial progress has been made in the identification of sequence elements that control mRNA splicing and the genetic variants in these elements that alter mRNA splicing (referred to as splicing quantitative trait loci – sQTLs). Genetic variants that affect mRNA splicing in trans are harder to identify because their effects can be more subtle and diffuse, and the variants are not co-located with their targets. We carried out a transcriptome-wide analysis of the effects of a mutation in a ubiquitous splicing factor that causes retinitis pigmentosa (RP) on mRNA splicing, using exon microarrays. Results: Exon microarray data was generated from whole blood samples obtained from four individuals with a mutation in the splicing factor PRPF8 and four sibling controls. Although the mutation has no known phenotype in blood, there was evidence of widespread differences in splicing between cases and controls (affecting approximately 20% of exons). Most probesets with significantly different inclusion (defined as the expression intensity of the exon divided by the expression of the corresponding transcript) between cases and controls had higher inclusion in cases and corresponded to exons that were shorter than average, AT rich, located towards the 5’ end of the gene and flanked by long introns. Introns flanking affected probesets were particularly depleted for the shortest category of introns, associated with splicing via intron definition. Conclusions: Our results show that a mutation in a splicing factor, with a phenotype that is restricted to retinal tissue, acts as a trans-sQTL cluster in whole blood samples. Characteristics of the affected exons suggest that they are spliced co-transcriptionally and via exon definition. However, due to the small sample size available for this study, further studies are required to confirm the widespread impact of this PRPF8 mutation on mRNA splicing outside the retina.
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    Pharmacogenetics of African populations : variation in major drug metabolising enzyme genes and potential impact on personalised medicine.
    (2009) Matimba, Alice; Ramesar, Raj; Masimirembwa, Collen
    Includes bibliographical references (leaves 167-200)
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    Pharmacogenomic profiling and clarification of the role of the mismatch repair genes in response to the chemotherapeutic agent 5-Fluorouracil in a South African colorectal cancer cohort
    (2009) Meyer, Jacqueline; Ramesar, Raj
    To date, surgery is the mainstay treatment for HNPCC. Adjuvant chemotherapy and radiotherapy are often used to reduce systemic and locoregional recurrence, respectively, after curative surgical resection. The main chemotherapeutic agent is 5-Fluoroucacil (5-FU). Studies have attempted to elucidate whether the MMR status of a colorectal cancer (CRC) cohort will define a response to 5-FU therapy. However, no difference in long term response or survival after 5-FU treatment between patients with MMR-proficient and MMR-deficient tomours were detected.