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Oyageshio OP, Myrick JW, Saayman J, van der Westhuizen L, Al-Hindi D, Reynolds AW, Zaitlen N, Uren C, Möller M, Henn BM. Strong Effect of Demographic Changes on Tuberculosis Susceptibility in South Africa. medRxiv 2023:2023.11.02.23297990. [PMID: 37961495 PMCID: PMC10635255 DOI: 10.1101/2023.11.02.23297990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
South Africa is among the world's top eight TB burden countries, and despite a focus on HIV-TB co-infection, most of the population living with TB are not HIV co-infected. The disease is endemic across the country with 80-90% exposure by adulthood. We investigated epidemiological risk factors for tuberculosis (TB) in the Northern Cape Province, South Africa: an understudied TB endemic region with extreme TB incidence (645/100,000) and the lowest provincial population density. We leveraged the population's high TB incidence and community transmission to design a case-control study with population-based controls, reflecting similar mechanisms of exposure between the groups. We recruited 1,126 participants with suspected TB from 12 community health clinics, and generated a cohort of 878 individuals (cases =374, controls =504) after implementing our enrollment criteria. All participants were GeneXpert Ultra tested for active TB by a local clinic. We assessed important risk factors for active TB using logistic regression and random forest modeling. Additionally, a subset of individuals were genotyped to determine genome-wide ancestry components. Male gender had the strongest effect on TB risk (OR: 2.87 [95% CI: 2.1-3.8]); smoking and alcohol consumption did not significantly increase TB risk. We identified two interactions: age by socioeconomic status (SES) and birthplace by residence locality on TB risk (OR = 3.05, p = 0.016) - where rural birthplace but town residence was the highest risk category. Finally, participants had a majority Khoe-San ancestry, typically greater than 50%. Epidemiological risk factors for this cohort differ from other global populations. The significant interaction effects reflect rapid changes in SES and mobility over recent generations and strongly impact TB risk in the Northern Cape of South Africa. Our models show that such risk factors combined explain 16% of the variance (r2) in case/control status.
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Affiliation(s)
- Oshiomah P. Oyageshio
- Center for Population Biology, University of California, Davis, Davis, CA 95616, USA
| | - Justin W. Myrick
- UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Jamie Saayman
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Lena van der Westhuizen
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Dana Al-Hindi
- Department of Anthropology, University of California, Davis, Davis, CA 95616, USA
| | | | - Noah Zaitlen
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Brenna M. Henn
- Center for Population Biology, University of California, Davis, Davis, CA 95616, USA
- UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA
- Department of Anthropology, University of California, Davis, Davis, CA 95616, USA
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2
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Oelofse C, Ndong Sima CAA, Möller M, Uren C. Pharmacogenetics as part of recommended precision medicine for tuberculosis treatment in African populations: Could it be a reality? Clin Transl Sci 2023. [PMID: 37291686 DOI: 10.1111/cts.13520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 06/10/2023] Open
Abstract
Globally, tuberculosis (TB) is the second most lethal infectious disease. However, in sub-Saharan Africa, TB has the largest disease burden, with drug-resistant TB increasingly becoming a concern. The social and economic impact of TB should not be overlooked, especially in areas where healthcare systems are overburdened, and resources need to be allocated judiciously. The aim of pharmacogenetics (PGx) is to improve therapeutic response and to minimize adverse drug reactions by selecting the most optimal drug and dosage for the individual patient. Implementation of PGx into routine clinical care has been slow, especially in resource-limited settings, because of perceived high costs relative to uncertain benefit. Given the impact of TB on the disease and disability burden in these regions, a better understanding and optimization of TB treatment in understudied African populations is vital. The first weeks of treatment are the most crucial for treatment success, and a point-of-care pre-emptive PGx test could start patients on the most bactericidal and least toxic drug combination. This may potentially reduce the number of patients returning to clinical care and streamline the use of limited resources across the healthcare system. This review explores the status of TB PGx in Africa, the utility of existing TB PGx testing panels, and the economic feasibility in developing a clinically valuable, cost-effective, pre-emptive PGx test to guide optimized, new dosing regimens specifically for African population groups. TB is a disease of poverty, but investment in PGx research in African populations could ensure improved treatments and long-term cost savings.
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Affiliation(s)
- Carola Oelofse
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Carene Anne Alene Ndong Sima
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
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3
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Smith MH, Myrick JW, Oyageshio O, Uren C, Saayman J, Boolay S, van der Westhuizen L, Werely C, Möller M, Henn BM, Reynolds AW. Epidemiological correlates of overweight and obesity in the Northern Cape Province, South Africa. PeerJ 2023; 11:e14723. [PMID: 36788809 PMCID: PMC9922494 DOI: 10.7717/peerj.14723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/19/2022] [Indexed: 02/11/2023] Open
Abstract
Background In the past several decades, obesity has become a major public health issue worldwide, associated with increased rates of chronic disease and death. Like many developing nations, South Africa is experiencing rapid increases in BMI, and as a result, evidence-based preventive strategies are needed to reduce the increasing burden of overweight and obesity. This study aimed to determine the prevalence and predictors of overweight and obesity among a multi-ethnic cohort from the rural Northern Cape of South Africa. Methods These data were collected as part of a tuberculosis (TB) case-control study, with 395 healthy control participants included in the final analysis. Overweight and obesity were defined according to WHO classification. Multivariate linear models of BMI were generated using sex, age, education level, smoking, alcohol consumption, and diabetes as predictor variables. We also used multivariable logistic regression analysis to assess the relationship of these factors with overweight and obesity. Results The average BMI in our study cohort was 25.2. The prevalence of overweight was 18.0% and the prevalence of obesity was 25.0%. We find that female sex, being older, having more years of formal education, having diabetes, and being in a rural area are all positively associated with BMI in our dataset. Women (OR = 5.6, 95% CI [3.3-9.8]), rural individuals (OR = 3.3, 95% CI [1.9-6.0]), older individuals (OR = 1.02, 95% CI [1-1.04]), and those with more years of education (OR = 1.2, 95% CI [1.09-1.32]) were all more likely to be overweight or obese. Alternatively, being a smoker is negatively associated with BMI and decreases one's odds of being overweight or obese (OR = 0.28, 95% CI [0.16-0.46]). Conclusions We observed a high prevalence of overweight and obesity in this study. The odds of being overweight and obese were higher in women, those living in rural areas, and those with more education, and increases with age. Community-based interventions to control obesity in this region should pay special attention to these groups.
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Affiliation(s)
| | - Justin W Myrick
- Department of Anthropology and UC Davis Genome Center, University of California, Davis, Davis, United States
| | - Oshiomah Oyageshio
- Center for Population Biology, University of California, Davis, Davis, United States
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, University of Stellenbosch, Cape Town, South Africa
| | - Jamie Saayman
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, South Africa
| | - Sihaam Boolay
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, South Africa
| | - Lena van der Westhuizen
- Department of Anthropology and UC Davis Genome Center, University of California, Davis, Davis, United States
| | - Cedric Werely
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, University of Stellenbosch, Cape Town, South Africa
| | - Brenna M Henn
- Department of Anthropology and UC Davis Genome Center, University of California, Davis, Davis, United States
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4
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Ndong Sima CAA, Smith D, Petersen DC, Schurz H, Uren C, Möller M. The immunogenetics of tuberculosis (TB) susceptibility. Immunogenetics 2022; 75:215-230. [DOI: 10.1007/s00251-022-01290-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
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5
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Swart Y, van Eeden G, Uren C, van der Spuy G, Tromp G, Möller M. GWAS in the southern African context. PLoS One 2022; 17:e0264657. [PMID: 36170230 PMCID: PMC9518849 DOI: 10.1371/journal.pone.0264657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/06/2022] [Indexed: 11/18/2022] Open
Abstract
Researchers would generally adjust for the possible confounding effect of population structure by considering global ancestry proportions or top principle components. Alternatively, researchers would conduct admixture mapping to increase the power to detect variants with an ancestry effect. This is sufficient in simple admixture scenarios, however, populations from southern Africa can be complex multi-way admixed populations. Duan et al. (2018) first described local ancestry adjusted allelic (LAAA) analysis as a robust method for discovering association signals, while producing minimal false positive hits. Their simulation study, however, was limited to a two-way admixed population. Realizing that their findings might not translate to other admixture scenarios, we simulated a three- and five-way admixed population to compare the LAAA model to other models commonly used in genome-wide association studies (GWAS). We found that, given our admixture scenarios, the LAAA model identifies the most causal variants in most of the phenotypes we tested across both the three-way and five-way admixed populations. The LAAA model also produced a high number of false positive hits which was potentially caused by the ancestry effect size that we assumed. Considering the extent to which the various models tested differed in their results and considering that the source of a given association is unknown, we recommend that researchers use multiple GWAS models when analysing populations with complex ancestry.
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Affiliation(s)
- Yolandi Swart
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerald van Eeden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Gian van der Spuy
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, Cape Town, South Africa
| | - Gerard Tromp
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
- SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, Cape Town, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
- * E-mail:
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6
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van Eeden G, Uren C, Pless E, Mastoras M, van der Spuy GD, Tromp G, Henn BM, Möller M. The recombination landscape of the Khoe-San likely represents the upper limits of recombination divergence in humans. Genome Biol 2022; 23:172. [PMID: 35945619 PMCID: PMC9361568 DOI: 10.1186/s13059-022-02744-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 08/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background Recombination maps are important resources for epidemiological and evolutionary analyses; however, there are currently no recombination maps representing any African population outside of those with West African ancestry. We infer the demographic history for the Nama, an indigenous Khoe-San population of southern Africa, and derive a novel, population-specific recombination map from the whole genome sequencing of 54 Nama individuals. We hypothesise that there are no publicly available recombination maps representative of the Nama, considering the deep population divergence and subsequent isolation of the Khoe-San from other African groups. Results We show that the recombination landscape of the Nama does not cluster with any continental groups with publicly available representative recombination maps. Finally, we use selection scans as an example of how fine-scale differences between the Nama recombination map and the combined Phase II HapMap recombination map can impact the outcome of selection scans. Conclusions Fine-scale differences in recombination can meaningfully alter the results of a selection scan. The recombination map we infer likely represents an upper bound on the extent of divergence we expect to see for a recombination map in humans and would be of interest to any researcher that wants to test the sensitivity of population genetic or GWAS analysis to recombination map input. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02744-5.
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Affiliation(s)
- Gerald van Eeden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Evlyn Pless
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California (UC) Davis, Davis, CA, USA
| | - Mira Mastoras
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California (UC) Davis, Davis, CA, USA
| | - Gian D van der Spuy
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa.,SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, Cape Town, South Africa
| | - Gerard Tromp
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa.,SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, Cape Town, South Africa
| | - Brenna M Henn
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California (UC) Davis, Davis, CA, USA
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa. .,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa.
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7
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Petersen DC, Steyl C, Scholtz D, Baker B, Abdullah I, Uren C, Möller M. African Genetic Representation in the Context of SARS-CoV-2 Infection and COVID-19 Severity. Front Genet 2022; 13:909117. [PMID: 35620464 PMCID: PMC9127354 DOI: 10.3389/fgene.2022.909117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Desiree C Petersen
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Chrystal Steyl
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Denise Scholtz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Bienyameen Baker
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Ibtisam Abdullah
- Division of Haematological Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University and NHLS Tygerberg Hospital, Cape Town, South Africa
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
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8
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Swart Y, Uren C, van Helden PD, Hoal EG, Möller M. Local Ancestry Adjusted Allelic Association Analysis Robustly Captures Tuberculosis Susceptibility Loci. Front Genet 2021; 12:716558. [PMID: 34721521 PMCID: PMC8554120 DOI: 10.3389/fgene.2021.716558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
Pulmonary tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease. The risk of developing active TB is in part determined by host genetic factors. Most genetic studies investigating TB susceptibility fail to replicate association signals particularly across diverse populations. South African populations arose because of multi-wave genetic admixture from the indigenous KhoeSan, Bantu-speaking Africans, Europeans, Southeast Asian-and East Asian populations. This has led to complex genetic admixture with heterogenous patterns of linkage disequilibrium and associated traits. As a result, precise estimation of both global and local ancestry is required to prevent both false positive and false-negative associations. Here, 820 individuals from South Africa were genotyped on the SNP-dense Illumina Multi-Ethnic Genotyping Array (∼1.7M SNPs) followed by local and global ancestry inference using RFMix. Local ancestry adjusted allelic association (LAAA) models were utilized owing to the extensive genetic heterogeneity present in this population. Hence, an interaction term, comprising the identification of the minor allele that corresponds to the ancestry present at the specific locus under investigation, was included as a covariate. One SNP (rs28647531) located on chromosome 4q22 was significantly associated with TB susceptibility and displayed a SNP minor allelic effect (G allele, frequency = 0.204) whilst correcting for local ancestry for Bantu-speaking African ancestry (p-value = 5.518 × 10-7; OR = 3.065; SE = 0.224). Although no other variants passed the significant threshold, clear differences were observed between the lead variants identified for each ancestry. Furthermore, the LAAA model robustly captured the source of association signals in multi-way admixed individuals from South Africa and allowed the identification of ancestry-specific disease risk alleles associated with TB susceptibility that have previously been missed.
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Affiliation(s)
- Yolandi Swart
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Paul D van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eileen G Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
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9
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van Eeden G, Uren C, van der Spuy G, Tromp G, Möller M. Local ancestry inference in heterogeneous populations-Are recent recombination events more relevant? Brief Bioinform 2021; 22:6337894. [PMID: 34343255 DOI: 10.1093/bib/bbab300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/29/2021] [Accepted: 07/14/2021] [Indexed: 12/11/2022] Open
Abstract
To date, numerous software tools have been developed to infer recombination maps. Many of these software tools infer the recombination rate from linkage disequilibrium, and therefore they infer recombination many generations into the past. Other recently developed methods rely on the inference of recent recombination events to determine the recombination rate, such as identity by descent- and local ancestry inference (LAI)-based tools. Methods that mainly use recent recombination events to infer the recombination rate might be more relevant for certain analyses like LAI. We therefore describe a protocol for creating high-resolution, population-specific recombination maps using methods that mainly use recent recombination events and a method that uses recent and distant recombination events for recombination rate inference. Subsequently, we compared the effect of using maps inferred by these two paradigms on LAI accuracy.
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Affiliation(s)
| | | | - Gian van der Spuy
- Department of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
| | - Gerard Tromp
- South African Tuberculosis Bioinformatics Initiative (SATBBI), South Africa
| | - Marlo Möller
- Department of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
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10
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van Eeden G, Uren C, Möller M, Henn BM. Inferring recombination patterns in African populations. Hum Mol Genet 2021; 30:R11-R16. [PMID: 33445180 DOI: 10.1093/hmg/ddab020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
Although several high-resolution recombination maps exist for European-descent populations, the recombination landscape of African populations remains relatively understudied. Given that there is high genetic divergence among groups in Africa, it is possible that recombination hotspots also diverge significantly. Both limitations and opportunities exist for developing recombination maps for these populations. In this review, we discuss various recombination inference methods, and the strengths and weaknesses of these methods in analyzing recombination in African-descent populations. Furthermore, we provide a decision tree and recommendations for which inference method to use in various research contexts. Establishing an appropriate methodology for recombination rate inference in a particular study will improve the accuracy of various downstream analyses including but not limited to local ancestry inference, haplotype phasing, fine-mapping of GWAS loci and genome assemblies.
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Affiliation(s)
- Gerald van Eeden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Brenna M Henn
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California Davis, Davis, CA 95616, USA
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Uren C, Hoal EG, Möller M. Mycobacterium tuberculosis complex and human coadaptation: a two-way street complicating host susceptibility to TB. Hum Mol Genet 2020; 30:R146-R153. [PMID: 33258469 DOI: 10.1093/hmg/ddaa254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/09/2020] [Accepted: 11/26/2020] [Indexed: 11/14/2022] Open
Abstract
For centuries, the Mycobacterium tuberculosis complex (MTBC) has infected numerous populations, both human and non-human, causing symptomatic tuberculosis (TB) in some hosts. Research investigating the MTBC and how it has evolved with its host over time is sparse and has not resulted in many significant findings. There are even fewer studies investigating adaptation of the human host susceptibility to TB and these have largely focused on genome-wide association and candidate gene association studies. However, results emanating from these association studies are rarely replicated and appear to be population specific. It is, therefore, necessary to relook at the approach taken to investigate the relationship between the MTBC and the human host. Understanding that the evolution of the pathogen is coupled to the evolution of the host might be the missing link needed to effectively investigate their relationship. We hypothesize that this knowledge will bolster future efforts in combating the disease.
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Affiliation(s)
- Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, 8000 Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, 7602 Stellenbosch, South Africa
| | - Eileen G Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, 8000 Cape Town, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, 8000 Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, 7602 Stellenbosch, South Africa
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12
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Bezuidenhout H, Bayley S, Smit L, Kinnear C, Möller M, Uren C, Urban MF. Hyperphosphatasia with mental retardation syndrome type 4 in three unrelated South African patients. Am J Med Genet A 2020; 182:2230-2235. [PMID: 32845056 DOI: 10.1002/ajmg.a.61797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/16/2020] [Accepted: 06/25/2020] [Indexed: 01/03/2023]
Abstract
Hyperphosphatasia with mental retardation syndrome (HPMRS) is a rare autosomal recessive disorder caused by pathogenic variants in genes involved in glycosylphosphatidylinositol metabolism that result in a similar phenotype. We describe the first three patients with HPMRS from sub-Saharan Africa. Detection was assisted by Face2Gene phenotype matching and confirmed by the presence of elevated serum alkaline phosphatase. All three patients had severe intellectual disability, absent speech, hypotonia and palatal abnormality (cleft palate in two, very high-arched palate in one), no or minimal brachytelephalangy, and high serum alkaline phosphatase levels. Additional findings included seizures in two, and brain imaging abnormalities in two. In all three patients HPMRS was a top-20 gestalt match using Face2Gene. The overall phenotype is consistent with descriptions in the literature of HPMRS type 4, although not specific to it. Whole exome sequencing in the index patient and his mother detected a candidate variant in a homozygous state in the index patient (PGAP3:c.557G>C, p.Arg186Thr) and heterozygous in the mother. Further variant interpretation indicated pathogenicity. Sanger sequencing of another two patients identified the same homozygous, pathogenic variant, confirming a diagnosis of HPMRS type 4. The shared homozygous variant in apparently unrelated families, and in the absence of consanguinity, suggests the possibility of genetic drift due to a population bottleneck effect, and further research is recommended.
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Affiliation(s)
- Heidre Bezuidenhout
- Faculty of Medicine and Health Sciences, Division of Molecular Biology and Human Genetics, Clinical Unit of Medical Genetics and Genetic Counseling, Tygerberg Academic Hospital and Stellenbosch University, Cape Town, South Africa
| | - Samantha Bayley
- Faculty of Medicine and Health Sciences, Division of Molecular Biology and Human Genetics, DSI-NRF Center of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Center for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Liani Smit
- Faculty of Medicine and Health Sciences, Division of Molecular Biology and Human Genetics, Clinical Unit of Medical Genetics and Genetic Counseling, Tygerberg Academic Hospital and Stellenbosch University, Cape Town, South Africa
| | - Craig Kinnear
- Faculty of Medicine and Health Sciences, Division of Molecular Biology and Human Genetics, DSI-NRF Center of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Center for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- Faculty of Medicine and Health Sciences, Division of Molecular Biology and Human Genetics, DSI-NRF Center of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Center for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Caitlin Uren
- Faculty of Medicine and Health Sciences, Division of Molecular Biology and Human Genetics, DSI-NRF Center of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Center for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Michael F Urban
- Faculty of Medicine and Health Sciences, Division of Molecular Biology and Human Genetics, Clinical Unit of Medical Genetics and Genetic Counseling, Tygerberg Academic Hospital and Stellenbosch University, Cape Town, South Africa
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13
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Abstract
Background Global and local ancestry inference in admixed human populations can be performed using computational tools implementing distinct algorithms. The development and resulting accuracy of these tools has been tested largely on populations with relatively straightforward admixture histories but little is known about how well they perform in more complex admixture scenarios. Results Using simulations, we show that RFMix outperforms ADMIXTURE in determining global ancestry proportions even in a complex 5-way admixed population, in addition to assigning local ancestry with an accuracy of 89%. The ability of RFMix to determine global and local ancestry to a high degree of accuracy, particularly in admixed populations provides the opportunity for more accurate association analyses. Conclusion This study highlights the utility of the extension of computational tools to become more compatible to genetically structured populations, as well as the need to expand the sampling of diverse world-wide populations. This is particularly noteworthy as modern-day societies are becoming increasingly genetically complex and some genetic tools and commonly used ancestral populations are less appropriate. Based on these caveats and the results presented here, we suggest that RFMix be used for both global and local ancestry estimation in world-wide complex admixture scenarios particularly when including these estimates in association studies.
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Affiliation(s)
- Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Room 4036, 4th Floor Education Building, Francie van Zijl Drive, Cape Town, 8000, South Africa.
| | - Eileen G Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Room 4036, 4th Floor Education Building, Francie van Zijl Drive, Cape Town, 8000, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Room 4036, 4th Floor Education Building, Francie van Zijl Drive, Cape Town, 8000, South Africa
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14
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Uren C, Henn BM, Franke A, Wittig M, van Helden PD, Hoal EG, Möller M. A post-GWAS analysis of predicted regulatory variants and tuberculosis susceptibility. PLoS One 2017; 12:e0174738. [PMID: 28384278 PMCID: PMC5383035 DOI: 10.1371/journal.pone.0174738] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/14/2017] [Indexed: 01/19/2023] Open
Abstract
Utilizing data from published tuberculosis (TB) genome-wide association studies (GWAS), we use a bioinformatics pipeline to detect all polymorphisms in linkage disequilibrium (LD) with variants previously implicated in TB disease susceptibility. The probability that these variants had a predicted regulatory function was estimated using RegulomeDB and Ensembl's Variant Effect Predictor. Subsequent genotyping of these 133 predicted regulatory polymorphisms was performed in 400 admixed South African TB cases and 366 healthy controls in a population-based case-control association study to fine-map the causal variant. We detected associations between tuberculosis susceptibility and six intronic polymorphisms located in MARCO, IFNGR2, ASHAS2, ACACA, NISCH and TLR10. Our post-GWAS approach demonstrates the feasibility of combining multiple TB GWAS datasets with linkage information to identify regulatory variants associated with this infectious disease.
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Affiliation(s)
- Caitlin Uren
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Brenna M. Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Rosalind-Franklin-Strasse Kiel, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Rosalind-Franklin-Strasse Kiel, Germany
| | - Paul D. van Helden
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eileen G. Hoal
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Uren C, Möller M, van Helden PD, Henn BM, Hoal EG. Population structure and infectious disease risk in southern Africa. Mol Genet Genomics 2017; 292:499-509. [PMID: 28229227 DOI: 10.1007/s00438-017-1296-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 02/01/2017] [Indexed: 02/06/2023]
Abstract
The KhoeSan populations are the earliest known indigenous inhabitants of southern Africa. The relatively recent expansion of Bantu-speaking agropastoralists, as well as European colonial settlement along the south-west coast, dramatically changed patterns of genetic diversity in a region which had been largely isolated for thousands of years. Owing to this unique history, population structure in southern Africa reflects both the underlying KhoeSan genetic diversity as well as differential recent admixture. This population structure has a wide range of biomedical and sociocultural implications; such as changes in disease risk profiles. Here, we consolidate information from various population genetic studies that characterize admixture patterns in southern Africa with an aim to better understand differences in adverse disease phenotypes observed among groups. Our review confirms that ancestry has a direct impact on an individual's immune response to infectious diseases. In addition, we emphasize the importance of collaborative research, especially for populations in southern Africa that have a high incidence of potentially fatal infectious diseases such as HIV and tuberculosis.
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Affiliation(s)
- Caitlin Uren
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Tygerberg, Parow, 7500, South Africa
| | - Marlo Möller
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Tygerberg, Parow, 7500, South Africa
| | - Paul D van Helden
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Tygerberg, Parow, 7500, South Africa
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Eileen G Hoal
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Tygerberg, Parow, 7500, South Africa.
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Abstract
Islet amyloid may have a pathological role in the development of Type 2 (non-insulin-dependent) diabetes mellitus. The prevalence of islet amyloid has been investigated on post-mortem pancreatic tissue from both diabetic and non-diabetic Pima Indian subjects who had previously been assessed by oral glucose tolerance tests. Islets were examined for amyloid deposits and for cellular immunoreactivity to pancreatic hormones and islet amyloid polypeptide, the constituent peptide of islet amyloid. Twenty of 26 diabetic subjects (77%) had islet amyloid, compared with one of 14 non-diabetic subjects (7%). Twelve of the diabetic subjects (46%) had amyloid in more than 10% of their islets, whereas only 4% of islets were affected in a single non-diabetic subject. Positive immunoreactivity for islet amyloid peptide was present in the islet amyloid and in islet cells in 54% of the diabetic and 50% of the non-diabetic subjects. Islet amyloid in diabetic Pima Indians may indicate a primary Beta-cell defect which interacts with insulin resistance to produce diabetes, or may develop as a result of Beta-cell dysfunction induced by insulin resistance and hyperglycaemia.
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Affiliation(s)
- A Clark
- Diabetes Research Laboratories, Radcliffe Infirmary, Oxford, UK
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Longnecker NE, Uren C. Factors influencing variability in manganese content of seeds, with emphasis on barley (Hordeum vulgare) and white lupins (Lupinus albus). ACTA ACUST UNITED AC 1990. [DOI: 10.1071/ar9900029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Considerable variability can occur in the manganese (Mn) content and concentration of seeds. This variability can influence plant growth and development, crop yield and seed quality. In order to understand which factors affect seed Mn variability, the effects of site of growth, season and genotype on the Mn content of barley seed were examined. Plant-to-plant and within-plant variability of white lupin seed were also examined. Manganese concentrations of seeds of barley, wheat and faba bean grown at the same site were compared. For barley, site of growth was the most important determinant of Mn content of the seed. Cultivar differences were not statistically significant. There was a significant season by site interaction which indicated that season affected seed Mn content at a site with low Mn availability but not at a site with adequate Mn. Manganese concentrations in seeds of different species grown at the same site varied considerably. 'Tatiara' wheat had more than twice the Mn concentration of 'Schooner' barley (48 and 21 mg kg-1, respectively), while small-seeded faba bean had the lowest Mn concentration of the three (6 mg kg-1). In white lupin, there were significant differences in seed Mn content of plants growing side by side at the same site. Significant within-plant variation was also found for both white lupins and barley. The range of Mn concentration of seed from one plant was 1530 to 3750 mg kg-1for white lupins and 1 1 to 24 mg kg-1 for barley. In barley (and probably most plants), variability of seed Mn concentration can be minimized by selecting seed by weight from parents grown at the same site during the same season. Variability of Mn concentration and content of white lupin seeds is not as easily accounted for and thus is more difficult to minimize. For barley, there was a positive relationship between seed weight and Mn concentration (r2= 0.66), while in white lupins, no such relationship was apparent. For white lupins with high concentrations of Mn, seed Mn variability could not be accounted for by genotype or seed weight.
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Turner RC, Harris E, Bloom SR, Uren C. Relation of fasting plasma glucose concentration to plasma insulin and glucagon concentrations. Studies in latent diabetics and women who have produced large-for-dates babies. Diabetes 1977; 26:166-71. [PMID: 838169 DOI: 10.2337/diab.26.3.166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mothers who have had gestations diabetes (latent diabetics-LD), as well as those who have produced a large-for-dates baby (LFD) but who were not known to have been diabetic, have raised fasting plasma glucose levels, and these may induce fetal overnutrition. The increased birthweight of babies of obese mothers may also be due to their raised fasting plasma glucose levels. LD and LFD have normal or raised fasting plasma insulin levels even though they have both decreased insulin secretion to small changes in plasma glucose and normal or increased insulin sensitivity. The high fasting plasma glucose probably results from the decreased insulin-secretory response to glucose. Normal subjects have little day-to-day variation of their fasting plasma glucose, whereas subjects with a high fasting plasma glucose have less precise control. Although LD and LFD had abnormal insulin responses, they have normal plasma glucagon concentrations that do not correlate with glucose tolerance or insulin sensitivity. The reported abnormalities of glucagon in diabetes are probably a secondary, not a primary event.
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