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Croock D, Swart Y, Schurz H, Petersen DC, Möller M, Uren C. Data Harmonization Guidelines to Combine Multi-platform Genomic Data from Admixed Populations and Boost Power in Genome-Wide Association Studies. Curr Protoc 2024; 4:e1055. [PMID: 38837690 DOI: 10.1002/cpz1.1055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Data harmonization involves combining data from multiple independent sources and processing the data to produce one uniform dataset. Merging separate genotypes or whole-genome sequencing datasets has been proposed as a strategy to increase the statistical power of association tests by increasing the effective sample size. However, data harmonization is not a widely adopted strategy due to the difficulties with merging data (including confounding produced by batch effects and population stratification). Detailed data harmonization protocols are scarce and are often conflicting. Moreover, data harmonization protocols that accommodate samples of admixed ancestry are practically non-existent. Existing data harmonization procedures must be modified to ensure the heterogeneous ancestry of admixed individuals is incorporated into additional downstream analyses without confounding results. Here, we propose a set of guidelines for merging multi-platform genetic data from admixed samples that can be adopted by any investigator with elementary bioinformatics experience. We have applied these guidelines to aggregate 1544 tuberculosis (TB) case-control samples from six separate in-house datasets and conducted a genome-wide association study (GWAS) of TB susceptibility. The GWAS performed on the merged dataset had improved power over analyzing the datasets individually and produced summary statistics free from bias introduced by batch effects and population stratification. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Processing separate datasets comprising array genotype data Alternate Protocol 1: Processing separate datasets comprising array genotype and whole-genome sequencing data Alternate Protocol 2: Performing imputation using a local reference panel Basic Protocol 2: Merging separate datasets Basic Protocol 3: Ancestry inference using ADMIXTURE and RFMix Basic Protocol 4: Batch effect correction using pseudo-case-control comparisons.
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Affiliation(s)
- Dayna Croock
- 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, Stellenbosch, South Africa
| | - 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, Stellenbosch, South Africa
| | - Haiko Schurz
- 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, Stellenbosch, South Africa
| | - 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, 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, Stellenbosch, 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, Stellenbosch, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
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Bothma NP, L'abbé EN, Liebenberg L. Evaluating postcranial macromorphoscopic traits to estimate population variation among modern South Africans. Forensic Sci Int 2024; 356:111954. [PMID: 38382241 DOI: 10.1016/j.forsciint.2024.111954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/20/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024]
Abstract
Population overlap and the variation within and among populations have been globally observed but is often difficult to quantify. To achieve this, numerous different methods need to be explored and validated to assist with the creation of an accurate biological profile. The current lack of databases for postcranial macromorphoscopic traits indicates the need to further investigate if the method can be employed repeatably in a forensic context. The current study aimed to assess the prevalence of eleven postcranial macromorphoscopic traits in a South African sample. A total of 271 postcrania of adult black, coloured, and white South Africans were assessed. The intra- and inter-observer agreement ranged from fair to almost perfect except for the accessory transverse foramen of C1, which had poor agreement between observers. Only seven traits differed significantly between at least two of the groups. Univariate and multivariate random forest models were created to test the positive predictive performance of the traits to classify population affinity. The classification accuracies for the univariate models ranged from 33.3% to 53.0% and ranged from 54.6% to 62.1% for the multivariate models. Based on the variable importance, the traits assessing spinous process bifurcation were the most discriminatory variables. The results indicate that the postcranial MMS approach does not outperform current methods employed to estimate population affinity. Further research needs to be done for the method to have practical applicability for medicolegal casework in South Africa.
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Affiliation(s)
- N P Bothma
- University of Pretoria, Department of Anatomy, Pretoria, South Africa, Private Bag x323, Gezina 0031, South Africa.
| | - E N L'abbé
- University of Pretoria, Department of Anatomy, Pretoria, South Africa, Private Bag x323, Gezina 0031, South Africa
| | - L Liebenberg
- University of Pretoria, Department of Anatomy, Pretoria, South Africa, Private Bag x323, Gezina 0031, South Africa
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Daniels RJ, D'Amato ME, Lesaoana M, Kasu M, Ehlers K, Chauke PA, Lecheko P, Challis S, Rockett K, Montinaro F, González-Santos M, Capelli C. Genetic heritage of the Baphuthi highlights an over-ethnicized notion of "Bushman" in the Maloti-Drakensberg, southern Africa. Am J Hum Genet 2023; 110:880-894. [PMID: 37105174 PMCID: PMC10183465 DOI: 10.1016/j.ajhg.2023.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Using contemporary people as proxies for ancient communities is a contentious but necessary practice in anthropology. In southern Africa, the distinction between the Cape KhoeSan and eastern KhoeSan remains unclear, as ethnicity labels have been changed through time and most communities were decimated if not extirpated. The eastern KhoeSan may have had genetic distinctions from neighboring communities who speak Bantu languages and KhoeSan further away; alternatively, the identity may not have been tied to any notion of biology, instead denoting communities with a nomadic "lifeway" distinct from African agro-pastoralism. The Baphuthi of the 1800s in the Maloti-Drakensberg, southern Africa had a substantial KhoeSan constituency and a lifeway of nomadism, cattle raiding, and horticulture. Baphuthi heritage could provide insights into the history of the eastern KhoeSan. We examine genetic affinities of 23 Baphuthi to discern whether the narrative of KhoeSan descent reflects distinct genetic ancestry. Genome-wide SNP data (Illumina GSA) were merged with 52 global populations, for 160,000 SNPs. Genetic analyses show no support for a unique eastern KhoeSan ancestry distinct from other KhoeSan or southern Bantu speakers. The Baphuthi have strong affinities with early-arriving southern Bantu-speaking (Nguni) communities, as the later-arriving non-Nguni show strong evidence of recent African admixture possibly related to late-Iron Age migrations. The references to communities as "San" and "Bushman" in historic literature has often been misconstrued as notions of ethnic/biological distinctions. The terms may have reflected ambiguous references to non-sedentary polities instead, as seems to be the case for the eastern "Bushman" heritage of the Baphuthi.
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Affiliation(s)
- Ryan Joseph Daniels
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ Oxfordshire, UK; Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Cape Town 7535, South Africa.
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Cape Town 7535, South Africa
| | - Mpasi Lesaoana
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Cape Town 7535, South Africa; Lesotho Mounted Police Service, Technical Support Services, Maseru 100, Lesotho
| | - Mohaimin Kasu
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Cape Town 7535, South Africa
| | - Karen Ehlers
- Department of Genetics, University of the Free State, Bloemfontein 9300, South Africa
| | - Paballo Abel Chauke
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Puseletso Lecheko
- Rock Art Research Institute, School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Sam Challis
- Rock Art Research Institute, School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Kirk Rockett
- Wellcome Centre for Human Genomics, Oxford, OX3 7BN Oxfordshire, UK
| | - Francesco Montinaro
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ Oxfordshire, UK; Department of Biology-Genetics, University of Bari, Via E. Orabona, 4, 70124 Bari, Italy
| | | | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ Oxfordshire, UK; Dipartimento delle Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, 43121 Parma, Italy.
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4
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Elhaik E. Principal Component Analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated. Sci Rep 2022; 12:14683. [PMID: 36038559 PMCID: PMC9424212 DOI: 10.1038/s41598-022-14395-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/06/2022] [Indexed: 12/29/2022] Open
Abstract
Principal Component Analysis (PCA) is a multivariate analysis that reduces the complexity of datasets while preserving data covariance. The outcome can be visualized on colorful scatterplots, ideally with only a minimal loss of information. PCA applications, implemented in well-cited packages like EIGENSOFT and PLINK, are extensively used as the foremost analyses in population genetics and related fields (e.g., animal and plant or medical genetics). PCA outcomes are used to shape study design, identify, and characterize individuals and populations, and draw historical and ethnobiological conclusions on origins, evolution, dispersion, and relatedness. The replicability crisis in science has prompted us to evaluate whether PCA results are reliable, robust, and replicable. We analyzed twelve common test cases using an intuitive color-based model alongside human population data. We demonstrate that PCA results can be artifacts of the data and can be easily manipulated to generate desired outcomes. PCA adjustment also yielded unfavorable outcomes in association studies. PCA results may not be reliable, robust, or replicable as the field assumes. Our findings raise concerns about the validity of results reported in the population genetics literature and related fields that place a disproportionate reliance upon PCA outcomes and the insights derived from them. We conclude that PCA may have a biasing role in genetic investigations and that 32,000-216,000 genetic studies should be reevaluated. An alternative mixed-admixture population genetic model is discussed.
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Affiliation(s)
- Eran Elhaik
- Department of Biology, Lund University, 22362, Lund, Sweden.
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5
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Evaluation of the obturator foramen as a sex assessment trait. Forensic Sci Med Pathol 2022:10.1007/s12024-022-00514-0. [PMID: 35960449 DOI: 10.1007/s12024-022-00514-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2022] [Indexed: 10/15/2022]
Abstract
Correctly assessing sex from skeletal remains is one of the main elements of creating a biological profile. Many traits allow for this, the obturator foramen being one. However, research on its accuracy has provided mixed results. This study examines the obturator foramen using a 5-point grading scale to assess the degree of sexual dimorphism in four known age and sex skeletal collections from the UK and South Africa. Overall, sexual dimorphism was found in the obturator foramen when using the new scoring system; however, accuracies for correct sex classification ranged from ~ 46 to ~ 75%. Considering its wide range in accuracy rates across the four samples and difficulty in identifying the subtle changes in morphology, the obturator foramen should only be used as part of a multifactorial assessment of sex.
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Baliso A, Heathfield LJ, Gibbon VE. Forensic human identification: retrospective investigation of anthropological assessments in the Western Cape, South Africa. Int J Legal Med 2022; 137:793-807. [PMID: 35908103 DOI: 10.1007/s00414-022-02870-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/14/2022] [Indexed: 11/24/2022]
Abstract
The identification of unknown persons, particularly those who are decomposed or burnt, is a global challenge. Forensic Anthropology Cape Town (FACT) is a service provider that assists the South African state with the identification of human remains. However, empirical data pertaining to anthropologically analysed forensic cases in the Western Cape Province of South Africa are lacking. Therefore, anthropological data pertaining to the forensic cases submitted to FACT between 2006 and 2018 from Forensic Pathology Services were retrospectively reviewed (n = 172). This study also sought to assess demographic, traumatic and pathological factors that impacted successful identification. Most decedents were male (67%) and older than 35 years (54%). While ante-mortem trauma was observed in 41% of decedents, the lack of medical records on ante-mortem injuries hindered the use of this information for identification. Positive identifications were reached for 37% of decedents, and of these, anthropological estimations were correct in 98% of cases for sex, 84% of cases for age at death and 100% of cases for stature. Considering globally accepted accuracies of 70-80%, these estimations were considered highly accurate, suggesting the anthropological methods used are suited to the population. However, 63% of cases remained unidentified, and this study showed that skeletal completeness and pathological conditions were the main factors that hindered demographic estimations. Lastly, not all unidentified bodies in the province were referred to FACT; given the highly accurate estimations, these data advocate for the routine, if not mandatory, use of forensic anthropology services for skeletonised remains in South Africa, with the overall purpose of positively impacting human identification. To improve identification rates globally, these data highlight the value of retrospective and region-specific studies to identify strengths and weaknesses in the system.
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Affiliation(s)
- Athi Baliso
- Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Laura Jane Heathfield
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
| | - Victoria Elaine Gibbon
- Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, 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] [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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Ribbans WJ, September AV, Collins M. Tendon and Ligament Genetics: How Do They Contribute to Disease and Injury? A Narrative Review. Life (Basel) 2022; 12:life12050663. [PMID: 35629331 PMCID: PMC9147569 DOI: 10.3390/life12050663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 12/15/2022] Open
Abstract
A significant proportion of patients requiring musculoskeletal management present with tendon and ligament pathology. Our understanding of the intrinsic and extrinsic mechanisms that lead to such disabilities is increasing. However, the complexity underpinning these interactive multifactorial elements is still not fully characterised. Evidence highlighting the genetic components, either reducing or increasing susceptibility to injury, is increasing. This review examines the present understanding of the role genetic variations contribute to tendon and ligament injury risk. It examines the different elements of tendon and ligament structure and considers our knowledge of genetic influence on form, function, ability to withstand load, and undertake repair or regeneration. The role of epigenetic factors in modifying gene expression in these structures is also explored. It considers the challenges to interpreting present knowledge, the requirements, and likely pathways for future research, and whether such information has reached the point of clinical utility.
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Affiliation(s)
- William J. Ribbans
- School of Health, The University of Northampton, Northampton NN1 5PH, UK
- The County Clinic, Northampton NN1 5DB, UK
- Correspondence: ; Tel.: +44-1604-795414
| | - Alison V. September
- Division of Physiological Sciences, Department of Human Biology, Health Sciences Faculty, University of Cape Town, Cape Town 7700, South Africa; (A.V.S.); (M.C.)
- Health Through Physical Activity, Lifestyle and Sport Research Centre (HPALS), Department of Human Biology, Health Sciences Faculty, University of Cape Town, Cape Town 7700, South Africa
- International Federation of Sports Medicine (FIMS), Collaborative Centre of Sports Medicine, Department of Human Biology, University of Cape Town, Cape Town 7700, South Africa
| | - Malcolm Collins
- Division of Physiological Sciences, Department of Human Biology, Health Sciences Faculty, University of Cape Town, Cape Town 7700, South Africa; (A.V.S.); (M.C.)
- Health Through Physical Activity, Lifestyle and Sport Research Centre (HPALS), Department of Human Biology, Health Sciences Faculty, University of Cape Town, Cape Town 7700, South Africa
- International Federation of Sports Medicine (FIMS), Collaborative Centre of Sports Medicine, Department of Human Biology, University of Cape Town, Cape Town 7700, South Africa
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Keith MH, Flinn MV, Durbin HJ, Rowan TN, Blomquist GE, Taylor KH, Taylor JF, Decker JE. Genetic ancestry, admixture, and population structure in rural Dominica. PLoS One 2021; 16:e0258735. [PMID: 34731205 PMCID: PMC8565749 DOI: 10.1371/journal.pone.0258735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/04/2021] [Indexed: 12/23/2022] Open
Abstract
The Caribbean is a genetically diverse region with heterogeneous admixture compositions influenced by local island ecologies, migrations, colonial conflicts, and demographic histories. The Commonwealth of Dominica is a mountainous island in the Lesser Antilles historically known to harbor communities with unique patterns of migration, mixture, and isolation. This community-based population genetic study adds biological evidence to inform post-colonial narrative histories in a Dominican horticultural village. High density single nucleotide polymorphism data paired with a previously compiled genealogy provide the first genome-wide insights on genetic ancestry and population structure in Dominica. We assessed family-based clustering, inferred global ancestry, and dated recent admixture by implementing the fastSTRUCTURE clustering algorithm, modeling graph-based migration with TreeMix, assessing patterns of linkage disequilibrium decay with ALDER, and visualizing data from Dominica with Human Genome Diversity Panel references. These analyses distinguish family-based genetic structure from variation in African, European, and indigenous Amerindian admixture proportions, and analyses of linkage disequilibrium decay estimate admixture dates 5–6 generations (~160 years) ago. African ancestry accounts for the largest mixture components, followed by European and then indigenous components; however, our global ancestry inferences are consistent with previous mitochondrial, Y chromosome, and ancestry marker data from Dominica that show uniquely higher proportions of indigenous ancestry and lower proportions of African ancestry relative to known admixture in other French- and English-speaking Caribbean islands. Our genetic results support local narratives about the community’s history and founding, which indicate that newly emancipated people settled in the steep, dense vegetation along Dominica’s eastern coast in the mid-19th century. Strong genetic signals of post-colonial admixture and family-based structure highlight the localized impacts of colonial forces and island ecologies in this region, and more data from other groups are needed to more broadly inform on Dominica’s complex history and present diversity.
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Affiliation(s)
- Monica H. Keith
- Department of Anthropology, University of Missouri, Columbia, Missouri, United States of America
- * E-mail: (MHK); (JED)
| | - Mark V. Flinn
- Department of Anthropology, University of Missouri, Columbia, Missouri, United States of America
| | - Harly J. Durbin
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Troy N. Rowan
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
- Genomics Center for the Advancement of Agriculture, University of Tennessee Institute for Agriculture, Knoxville, Tennessee, United States of America
| | - Gregory E. Blomquist
- Department of Anthropology, University of Missouri, Columbia, Missouri, United States of America
| | - Kristen H. Taylor
- Department of Anatomy and Pathological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Jared E. Decker
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
- * E-mail: (MHK); (JED)
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10
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Cacciatore S, Wium M, Licari C, Ajayi-Smith A, Masieri L, Anderson C, Salukazana AS, Kaestner L, Carini M, Carbone GM, Catapano CV, Loda M, Libermann TA, Zerbini LF. Inflammatory metabolic profile of South African patients with prostate cancer. Cancer Metab 2021; 9:29. [PMID: 34344464 PMCID: PMC8336341 DOI: 10.1186/s40170-021-00265-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/21/2021] [Indexed: 12/24/2022] Open
Abstract
Background Men with African ancestry are more likely to develop aggressive prostate cancer (PCa) and to die from this disease. The study of PCa in the South African population represents an opportunity for biomedical research due to the high prevalence of aggressive PCa. While inflammation is known to play a significant role in PCa progression, its association with tumor stage in populations of African descent has not been explored in detail. Identification of new metabolic biomarkers of inflammation may improve diagnosis of patients with aggressive PCa. Methods Plasma samples were profiled from 41 South African men with PCa using nuclear magnetic resonance (NMR) spectroscopy. A total of 41 features, including metabolites, lipid classes, total protein, and the inflammatory NMR markers, GlycA, and GlycB, were quantified from each NMR spectrum. The Bruker’s B.I.-LISA protocols were used to characterize 114 parameters related to the lipoproteins. The unsupervised KODAMA method was used to stratify the patients of our cohort based on their metabolic profile. Results We found that the plasma of patients with very high risk, aggressive PCa and high level of C-reactive protein have a peculiar metabolic phenotype (metabotype) characterized by extremely high levels of GlycA and GlycB. The inflammatory processes linked to the higher level of GlycA and GlycB are characterized by a deep change of the plasma metabolome that may be used to improve the stratification of patients with PCa. We also identified a not previously known relationship between high values of VLDL and low level of GlycB in a different metabotype of patients characterized by lower-risk PCa. Conclusions For the first time, a portrait of the metabolic changes in African men with PCa has been delineated indicating a strong association between inflammation and metabolic profiles. Our findings indicate how the metabolic profile could be used to identify those patients with high level of inflammation, characterized by aggressive PCa and short life expectancy. Integrating a metabolomic analysis as a tool for patient stratification could be important for opening the door to the development of new therapies. Further investigations are needed to understand the prevalence of an inflammatory metabotype in patients with aggressive PCa. Supplementary Information The online version contains supplementary material available at 10.1186/s40170-021-00265-6.
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Affiliation(s)
- Stefano Cacciatore
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Institute for Reproductive and Developmental Biology, Imperial College, London, UK
| | - Martha Wium
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Cristina Licari
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy
| | - Aderonke Ajayi-Smith
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Lorenzo Masieri
- Department of Urology, Clinica Urologica I, Azienda Ospedaliera Careggi, University of Florence, Florence, Italy.,Pediatric Urology Unit, Meyer Children Hospital, University of Florence, Florence, Italy
| | - Chanelle Anderson
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | | | - Lisa Kaestner
- Division of Urology, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Marco Carini
- Department of Urology, Clinica Urologica I, Azienda Ospedaliera Careggi, University of Florence, Florence, Italy
| | - Giuseppina M Carbone
- Institute of Oncology Research (IOR), Università della Svizzera italiana, Bellinzona, Switzerland
| | - Carlo V Catapano
- Institute of Oncology Research (IOR), Università della Svizzera italiana, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,Department of Oncology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Massimo Loda
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.,Harvard Medical School, MA, Boston, USA
| | - Towia A Libermann
- Harvard Medical School, MA, Boston, USA.,BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, MA, Boston, USA
| | - Luiz F Zerbini
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.
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11
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Swart C, Meldau S, Centner CM, Marais AD, Omar F. Validation of PHASE for deriving N-acetyltransferase 2 haplotypes in the Western Cape mixed ancestry population. Afr J Lab Med 2020; 9:988. [PMID: 33392048 PMCID: PMC7756977 DOI: 10.4102/ajlm.v9i1.988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 09/14/2020] [Indexed: 11/17/2022] Open
Abstract
Background There is a shortage of data on the accuracy of statistical methods for the prediction of N-acetyltransferase 2 (NAT2) haplotypes in the mixed ancestry population of the Western Cape. Objective This study aimed to identify the NAT2 haplotypes and assess the accuracy of PHASE version 2.1.1 in assigning NAT2 haplotypes to a mixed ancestry population from the Western Cape. Methods This study was conducted between 2013 and 2016. The NAT2 gene was amplified and sequenced from the DNA of 100 self-identified mixed ancestry participants. Haplotyping was performed by molecular and computational techniques. Agreement was assessed between the two techniques. Results Haplotypes were assigned to 93 samples, of which 67 (72%) were ambiguous. Haplotype prediction by PHASE demonstrated 94.6% agreement (kappa 0.94, p < 0.001) with those assigned using molecular techniques. Five haplotype combinations (from 10 chromosomes) were incorrectly predicted, four of which were flagged as uncertain by the PHASE software. Only one resulted in the assignment of an incorrect acetylation phenotype (intermediate to slow), although the software flagged this for further analysis. The most common haplotypes were NAT2*4 (28%) followed by NAT2*5B (27.4%), NAT2*6A (21.5%) and NAT2*12A (7.5%). Four rare single nucleotide variants (c.589C>T, c.622T>C, c.809T>C and c.387C>T) were detected. Conclusion PHASE accurately predicted the phenotype in 92 of 93 samples (99%) from genotypic data in our mixed ancestry sample population, and is therefore a suitable alternative to molecular methods to individualise isoniazid therapy in this high burden tuberculosis setting.
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Affiliation(s)
- Celeste Swart
- Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,National Health Laboratory Service (NHLS), Groote Schuur Hospital, Cape Town, South Africa
| | - Surita Meldau
- National Health Laboratory Service (NHLS), Groote Schuur Hospital, Cape Town, South Africa.,Division of Chemical Pathology, University of Cape Town, Cape Town, South Africa
| | - Chad M Centner
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa.,National Health Laboratory Service (NHLS), Medical Microbiology, Groote Schuur Hospital, Cape Town, South Africa
| | - Adrian D Marais
- Division of Chemical Pathology, University of Cape Town, Cape Town, South Africa
| | - Fierdoz Omar
- Division of Chemical Pathology, University of Cape Town, Cape Town, South Africa
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12
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du Plessis S, Bekker M, Buckle C, Vink M, Seedat S, Bardien S, Carr J, Abrahams S. Association Between a Variable Number Tandem Repeat Polymorphism Within the DAT1 Gene and the Mesolimbic Pathway in Parkinson's Disease. Front Neurol 2020; 11:982. [PMID: 32982958 PMCID: PMC7493621 DOI: 10.3389/fneur.2020.00982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/28/2020] [Indexed: 01/23/2023] Open
Abstract
The loss of ventral striatal dopaminergic neurons in Parkinson's disease (PD) predicts an impact on the reward system. The ventrostriatal system is involved in motivational processing and its dysfunction may be related to non-motor symptoms such as depression and apathy. We previously documented that patients with PD had blunted Blood Oxygen Level Dependent functional magnetic resonance imaging (BOLD fMRI) reward task related activity during both reward anticipation (i.e., in the ventral striatum) and reward outcome (i.e., in the orbitofrontal cortex). Evidence for the modulation of brain function by dopaminergic genes in PD is limited. Genes implicated in dopamine transmission, such as the dopamine transporter gene (DAT1) may influence the clinical heterogeneity seen in PD, including reward processing. This study therefore sought to determine whether genetic differences in the DAT gene are associated with brain activity associated with response to reward in PD patients and controls. A sample of PD cases on treatment (n = 15) and non-PD controls (n = 30) from an ethnic group unique to South Africa were genotyped. We found a three-way interaction between GENOTYPE × BOLD fMRI REWARD × DIAGNOSIS [F(1, 40) = 4.666, p = 0.037, partial η2 = 0.104]. PD patients with the DAT1 homozygous 10/10 repeat genotype showed a relative decrease in orbitofrontal cortex reward outcome related activity compared to the patient group who did not have this repeat. PD patients with other genotypes showed an expected increase in orbitofrontal cortex reward outcome related activity compared to controls. Given the small sample size of the PD group with the 10/10 repeat, these results should be considered preliminary. Nevertheless, these preliminary findings highlight the potential modulation of dopamine transporter polymorphisms on orbitofrontal reward system activity in PD and highlight the need for further studies.
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Affiliation(s)
- Stefan du Plessis
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Stellenbosch University Genomics of Brain Disorders Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Minke Bekker
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Chanelle Buckle
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Matthijs Vink
- Departments of Developmental and Experimental Psychology, Utrecht University, Utrecht, Netherlands
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Stellenbosch University Genomics of Brain Disorders Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Soraya Bardien
- Stellenbosch University Genomics of Brain Disorders Research Unit, South African Medical Research Council, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jonathan Carr
- Stellenbosch University Genomics of Brain Disorders Research Unit, South African Medical Research Council, Cape Town, South Africa.,Division of Neurology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Shameemah Abrahams
- Stellenbosch University Genomics of Brain Disorders Research Unit, South African Medical Research Council, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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13
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Henning F, Heckmann JM, Naidu K, Vlok L, Cross HM, Marin B. Incidence of motor neuron disease/amyotrophic lateral sclerosis in South Africa: a 4-year prospective study. Eur J Neurol 2020; 28:81-89. [PMID: 32888367 DOI: 10.1111/ene.14499] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND PURPOSE Little is known about the epidemiological features of amyotrophic lateral sclerosis (ALS) in sub-Saharan Africa, and data from the region are limited to clinical series or case reports. The aim of the study was to investigate the incidence rate and presentation of ALS in an ethnically diverse region of South Africa. METHODS We performed a 4-year prospective incidence study in the Western Cape Province of South Africa between 1 July 2014 and 30 June 2018, and used a two-source capture-recapture method for case ascertainment. Age- and sex-adjusted incidence rates (ASAIRs) were calculated using the 2010 US population as the reference. RESULTS A total of 203 incident cases were identified over the study period, resulting in a crude incidence rate (IR) of 1.09 [95% confidence interval (CI) 0.94-1.24] per 100 000 person-years in the at-risk population (aged >15 years). Capture-recapture analysis resulted in an estimated IR of 1.11 (95% CI 1.01-1.22) per 100 000 person-years. The ASAIR was 1.67 (95% CI 1.09-2.26) overall; 1.99 (95% CI 1.60-2.39) for men and 1.37 (95% CI 1.06-1.68) for women. When analysed separately, there was a substantial difference in ASAIRs between the different population groups, with the highest in the European ancestry group (2.62; 95% CI 2.49-2.75), the lowest in the African ancestry group (0.56, 95% CI 0.0-1.23), and an ASAIR in between these two in the mixed ancestry group (1.09, 95% CI 0.80-1.37). CONCLUSION The overall incidence of ALS in the Western Cape Province of South Africa appears to be lower than in North African and Western countries, but higher than in Asian countries. As suggested by previous epidemiological studies, ALS may be less frequent in people of African ancestry.
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Affiliation(s)
- F Henning
- Division of Neurology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - J M Heckmann
- Division of Neurology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - K Naidu
- Division of Neurology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - L Vlok
- Division of Neurology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - H M Cross
- Division of Neurology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - B Marin
- Ministere de la Sante et des Solidarites, Cellule Interministérielle Recherche MSS/MESRI, Paris, France
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14
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Hollfelder N, Erasmus JC, Hammaren R, Vicente M, Jakobsson M, Greeff JM, Schlebusch CM. Patterns of African and Asian admixture in the Afrikaner population of South Africa. BMC Biol 2020; 18:16. [PMID: 32089133 PMCID: PMC7038537 DOI: 10.1186/s12915-020-0746-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/31/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct and characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5 and 7.2%. RESULTS To investigate the genetic ancestry of the Afrikaner population today (11-13 generations after initial colonization), we genotyped approximately five million genome-wide markers in 77 Afrikaner individuals and compared their genotypes to populations across the world to determine parental source populations and admixture proportions. We found that the majority of Afrikaner ancestry (average 95.3%) came from European populations (specifically northwestern European populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European admixture originated mostly from people who were brought to South Africa as slaves and, to a lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding population, there is no sign of a recent bottleneck in the Afrikaner compared to other European populations. Admixture amongst diverse groups from Europe and elsewhere during early colonial times might have counterbalanced the effects of a small founding population. CONCLUSIONS While Afrikaners have an ancestry predominantly from northwestern Europe, non-European admixture signals are ubiquitous in the Afrikaner population. Interesting patterns and similarities could be observed between genealogical predictions and our genetic inferences. Afrikaners today have comparable inbreeding levels to current-day European populations.
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Affiliation(s)
- N Hollfelder
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
| | - J C Erasmus
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - R Hammaren
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
| | - M Vicente
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
| | - M Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa
| | - J M Greeff
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa.
| | - C M Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden.
- Science for Life Laboratory, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden.
- Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
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15
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Tawha T, Dinkele E, Mole C, Gibbon VE. Assessing zygomatic shape and size for estimating sex and ancestry in a South African sample. Sci Justice 2020; 60:284-292. [PMID: 32381245 DOI: 10.1016/j.scijus.2020.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/14/2020] [Accepted: 01/26/2020] [Indexed: 11/26/2022]
Abstract
Unidentified, decomposed and skeletonised human remains are frequently found in South Africa, therefore, standardised, reliable and relevant sex and ancestry estimation methods are required for forensic identification. This study assessed sex and ancestral variation in zygomatic size and shape in a South African population using geometric morphometric analyses. The zygoma of 158 South African individuals were sampled. Eight zygomatic landmarks were captured in 3-dimensions using a Microscribe G2 digitiser and assessed using procrustean geometric morphometrics. Shape and size differences were analysed using multivariate linear regression, discriminant function and canonical variate analyses. Males had significantly larger zygomas than females. Significant shape variation was found between ancestral groups. Bantu-speaking and Mixed ancestry individuals had narrower, shorter and more anteriorly projecting orbital margins, whilst Europeans had vertically elongated and receded orbital margins. European ancestral groups were most discernible from Bantu-speakers and Mixed ancestral groups. Ancestry estimation accuracies improved when ancestry was aggregated with sex. Pairwise ancestry-linked comparisons in females were as follows; Bantu-speakers (76%) from Europeans (72%), Bantu-speakers (71%) from Mixed ancestry (59%) and European (72%) from Mixed ancestry (63%). Similarly, ancestry-linked comparisons in males were as follows; Bantu-speakers (77%) from Europeans (81%), Bantu-speakers (53%) from Mixed ancestry (59%) and European (72%) from Mixed ancestry (82%). Size differences are putatively linked to variations in hormone-regulated growth and muscular robusticity between males and females. Shape variations between ancestral groups are likely attributable to the heterogenous genetic and ancestral origins of the South African population. It is challenging to distinguish between South Africa Bantu speakers and Mixed ancestry people due to Mixed ancestry individuals having variable genetic contributions from Khoesan, Bantu-speakers, Europeans and Asians. Bantu-speaking and Mixed ancestry people had zygomatic morphologies consistent with historical thermoregulatory adaptations to sub-Saharan climates, reported in African-descendants. Zygomatic morphology in European descendants suggests ancestral origins from colder climatic regions. This study demonstrated the utility of the zygoma in distinguishing between ancestral groups in South Africa, but further research is required to develop population-specific standards to distinguish between South African populations with shared African ancestry. The zygoma shows a promising ability to estimate sex and ancestry in South Africans, suggesting population specific standards for this bone may be of forensic interest.
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Affiliation(s)
- Tafadzwa Tawha
- Department of Human Biology, University of Cape Town, Observatory, Cape Town, South Africa; Department of Pathology, University of Cape Town, Observatory, Cape Town, South Africa
| | - Elizabeth Dinkele
- Department of Human Biology, University of Cape Town, Observatory, Cape Town, South Africa
| | - Calvin Mole
- Department of Pathology, University of Cape Town, Observatory, Cape Town, South Africa
| | - Victoria E Gibbon
- Department of Human Biology, University of Cape Town, Observatory, Cape Town, South Africa.
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16
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Mokoena P, Billings BK, Gibbon V, Bidmos MA, Mazengenya P. Development of discriminant functions to estimate sex in upper limb bones for mixed ancestry South Africans. Sci Justice 2019; 59:660-666. [DOI: 10.1016/j.scijus.2019.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/16/2019] [Accepted: 06/02/2019] [Indexed: 11/25/2022]
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17
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Chan EKF, Timmermann A, Baldi BF, Moore AE, Lyons RJ, Lee SS, Kalsbeek AMF, Petersen DC, Rautenbach H, Förtsch HEA, Bornman MSR, Hayes VM. Human origins in a southern African palaeo-wetland and first migrations. Nature 2019; 575:185-189. [PMID: 31659339 DOI: 10.1038/s41586-019-1714-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 09/24/2019] [Indexed: 01/17/2023]
Abstract
Anatomically modern humans originated in Africa around 200 thousand years ago (ka)1-4. Although some of the oldest skeletal remains suggest an eastern African origin2, southern Africa is home to contemporary populations that represent the earliest branch of human genetic phylogeny5,6. Here we generate, to our knowledge, the largest resource for the poorly represented and deepest-rooting maternal L0 mitochondrial DNA branch (198 new mitogenomes for a total of 1,217 mitogenomes) from contemporary southern Africans and show the geographical isolation of L0d1'2, L0k and L0g KhoeSan descendants south of the Zambezi river in Africa. By establishing mitogenomic timelines, frequencies and dispersals, we show that the L0 lineage emerged within the residual Makgadikgadi-Okavango palaeo-wetland of southern Africa7, approximately 200 ka (95% confidence interval, 240-165 ka). Genetic divergence points to a sustained 70,000-year-long existence of the L0 lineage before an out-of-homeland northeast-southwest dispersal between 130 and 110 ka. Palaeo-climate proxy and model data suggest that increased humidity opened green corridors, first to the northeast then to the southwest. Subsequent drying of the homeland corresponds to a sustained effective population size (L0k), whereas wet-dry cycles and probable adaptation to marine foraging allowed the southwestern migrants to achieve population growth (L0d1'2), as supported by extensive south-coastal archaeological evidence8-10. Taken together, we propose a southern African origin of anatomically modern humans with sustained homeland occupation before the first migrations of people that appear to have been driven by regional climate changes.
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Affiliation(s)
- Eva K F Chan
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Axel Timmermann
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea. .,Pusan National University, Busan, South Korea.
| | - Benedetta F Baldi
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Andy E Moore
- Department of Geology, Rhodes University, Grahamstown, South Africa
| | - Ruth J Lyons
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Sun-Seon Lee
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea.,Pusan National University, Busan, South Korea
| | - Anton M F Kalsbeek
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Desiree C Petersen
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,The Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | - Hannes Rautenbach
- Climate Change and Variability, South African Weather Service, Pretoria, South Africa.,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.,Akademia, Johannesburg, South Africa
| | | | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia. .,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia. .,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa. .,Faculty of Health Sciences, University of Limpopo, Sovenga, South Africa. .,Central Clinical School, University of Sydney, Sydney, New South Wales, Australia.
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18
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Frequency of the LRRK2 G2019S mutation in South African patients with Parkinson’s disease. Neurogenetics 2019; 20:215-218. [DOI: 10.1007/s10048-019-00588-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/27/2019] [Indexed: 12/14/2022]
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19
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Petersen DC, Jaratlerdsiri W, van Wyk A, Chan EKF, Fernandez P, Lyons RJ, Mutambirw SBA, van der Merwe A, Venter PA, Bates W, Bornman MSR, Hayes VM. African KhoeSan ancestry linked to high-risk prostate cancer. BMC Med Genomics 2019; 12:82. [PMID: 31164124 PMCID: PMC6549381 DOI: 10.1186/s12920-019-0537-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 05/21/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUNDS Genetic diversity is greatest within Africa, in particular the KhoeSan click-speaking peoples of southern Africa. South African populations represent admixture fractions including differing degrees of African, African-KhoeSan and non-African genetic ancestries. Within the United States, African ancestry has been linked to prostate cancer presentation and mortality. Together with environmental contributions, genetics is a significant risk factor for high-risk prostate cancer, defined by a pathological Gleason score ≥ 8. METHODS Using genotype array data merged with ancestry informative reference data, we investigate the contribution of African ancestral fractions to high-risk prostate cancer. Our study includes 152 South African men of African (Black) or African-admixed (Coloured) ancestries, in which 40% showed high-risk prostate cancer. RESULTS Genetic fractions were determined for averaging an equal African to non-African genetic ancestral contribution in the Coloured; we found African ancestry to be linked to high-risk prostate cancer (P-value = 0.0477). Adjusting for age, the associated African ancestral fraction was driven by a significant KhoeSan over Bantu contribution, defined by Gleason score ≥ 8 (P-value = 0.02329) or prostate specific antigen levels ≥20 ng/ml (P-value = 0.03713). Additionally, we observed the mean overall KhoeSan contribution to be increased in Black patients with high-risk (11.8%) over low-risk (10.9%) disease. Linking for the first time KhoeSan ancestry to a common modern disease, namely high-risk prostate cancer, we tested in this small study the validity of using KhoeSan ancestry as a surrogate for identifying potential high-risk prostate cancer risk loci. As such, we identified four loci within chromosomal regions 2p11.2, 3p14, 8q23 and 22q13.2 (P-value = all age-adjusted < 0.01), two of which have previously been associated with high-risk prostate cancer. CONCLUSIONS Our study suggests that ancient KhoeSan ancestry may be linked to common modern diseases, specifically those of late onset and therefore unlikely to have undergone exclusive selective pressure. As such we show within a uniquely admixed South African population a link between KhoeSan ancestry and high-risk prostate cancer, which may explain the 2-fold increase in presentation in Black South Africans compared with African Americans.
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Affiliation(s)
- Desiree C Petersen
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, NSW, 2010, Australia
- Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia
- Centre for Proteomic and Genomic Research (CPGR), 1st Floor, St. Peters Mall, Cnr. Anzio and Main Road, Observatory, Cape Town, 7925, South Africa
| | - Weerachai Jaratlerdsiri
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, NSW, 2010, Australia
| | - Abraham van Wyk
- Division of Anatomical Pathology, NHLS Tygerberg and Stellenbosch University, Tygerberg, South Africa
| | - Eva K F Chan
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, NSW, 2010, Australia
- Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia
| | - Pedro Fernandez
- Division of Urology, Department of Surgical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ruth J Lyons
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, NSW, 2010, Australia
| | - Shingai B A Mutambirw
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa, South Africa
| | - Andre van der Merwe
- Division of Urology, Department of Surgical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Philip A Venter
- Faculty of Health Sciences, University of Limpopo, Mankweng, South Africa
| | - William Bates
- Division of Anatomical Pathology, NHLS Tygerberg and Stellenbosch University, Tygerberg, South Africa
| | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Vanessa M Hayes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, NSW, 2010, Australia.
- Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia.
- Faculty of Health Sciences, University of Limpopo, Mankweng, South Africa.
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.
- Central Clinical School, University of Sydney, Camperdown, NSW, Australia.
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Roberts L, Rebello G, Greenberg J, Ramesar R. Update on Inherited Retinal Disease in South Africa: Encouraging Diversity in Molecular Genetics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1185:257-261. [PMID: 31884621 DOI: 10.1007/978-3-030-27378-1_42] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
There is a glaring disparity in the populations included in genetic research; the majority of work involves European-derived cohorts, while other global populations - including Africans - are underrepresented. This is also true for the study of inherited retinal diseases. Being the most ancient of extant populations, African samples carry more variation than others, making them valuable for novel gene and variant discovery. The inclusion of diverse populations in research is essential to gain a more comprehensive understanding of genetic variation and molecular mechanisms of disease.
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Affiliation(s)
- Lisa Roberts
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - George Rebello
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jacquie Greenberg
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Raj Ramesar
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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21
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Montinaro F, Capelli C. The evolutionary history of Southern Africa. Curr Opin Genet Dev 2018; 53:157-164. [PMID: 30522870 DOI: 10.1016/j.gde.2018.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 10/12/2018] [Accepted: 11/06/2018] [Indexed: 01/15/2023]
Abstract
The genomic variability of Southern African groups is characterized by an exceptional degree of diversity, which is the result of long-term local evolutionary history, migrations and gene-flow. Over the last few years several investigations have identified and described signatures related to these processes, revealing how ancient and more recent events have shaped the structure and ancestry composition of local populations. Here we discuss recent insights into the genetic history of the Southernmost part of the African continent provided by the analysis of modern and ancient genomes. Future work is expected to clarify the population dynamics associated with the emergence of Homo sapiens across Africa and the details of the process of dispersion and admixture associated with the arrival of Bantu-speaking groups in the region.
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Affiliation(s)
- Francesco Montinaro
- Department of Zoology, University of Oxford, UK; Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
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22
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Thorstenson YR, Creary LE, Huang H, Rozot V, Nguyen TT, Babrzadeh F, Kancharla S, Fukushima M, Kuehn R, Wang C, Li M, Krishnakumar S, Mindrinos M, Fernandez Viña MA, Scriba TJ, Davis MM. Allelic resolution NGS HLA typing of Class I and Class II loci and haplotypes in Cape Town, South Africa. Hum Immunol 2018; 79:839-847. [PMID: 30240896 DOI: 10.1016/j.humimm.2018.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/23/2018] [Accepted: 09/17/2018] [Indexed: 11/18/2022]
Abstract
The development of next-generation sequencing (NGS) methods for HLA genotyping has already had an impact on the scope and precision of HLA research. In this study, allelic resolution HLA typing was obtained for 402 individuals from Cape Town, South Africa. The data were produced by high-throughput NGS sequencing as part of a study of T-cell responses to Mycobacterium tuberculosis in collaboration with the University of Cape Town and Stanford University. All samples were genotyped for 11 HLA loci, namely HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4, and -DRB5. NGS HLA typing of samples from Cape Town inhabitants revealed a unique cohort, including unusual haplotypes, and 22 novel alleles not previously reported in the IPD-IMGT/HLA Database. Eight novel alleles were in Class I loci and 14 were in Class II. There were 62 different alleles of HLA-A, 72 of HLA-B, and 47 of HLA-C. Alleles A∗23:17, A∗43:01, A∗29:11, A∗68:27:01, A∗01:23, B∗14:01:01, B∗15:10:01, B∗39:10:01, B∗45:07, B∗82:02:01 and C∗08:04:01 were notably more frequent in Cape Town compared to other populations reported in the literature. Class II loci had 21 different alleles of DPA1, 46 of DPB1, 27 of DQA1, 26 of DQB1, 41 of DRB1, 5 of DRB3, 4 of DRB4 and 6 of DRB5. The Cape Town cohort exhibited high degrees of HLA diversity and relatively high heterozygosity at most loci. Genetic distances between Cape Town and five other sub-Saharan African populations were also calculated and compared to European Americans.
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Affiliation(s)
| | - Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Huang Huang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Virginie Rozot
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | | | | | | | | | - Raquel Kuehn
- Immucor, Sirona Genomics, Mountain View, CA, USA
| | - Chunlin Wang
- Immucor, Sirona Genomics, Mountain View, CA, USA
| | - Ming Li
- Immucor, Sirona Genomics, Mountain View, CA, USA
| | | | | | | | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mark M Davis
- Stanford University and Howard Hughes Medical Institute, Stanford, CA
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23
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Postcraniometric sex and ancestry estimation in South Africa: a validation study. Int J Legal Med 2018; 133:289-296. [DOI: 10.1007/s00414-018-1865-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 05/15/2018] [Indexed: 10/16/2022]
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24
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Womersley JS, Martin LI, van der Merwe L, Seedat S, Hemmings SMJ. Hypothalamic-pituitary-adrenal axis variants and childhood trauma influence anxiety sensitivity in South African adolescents. Metab Brain Dis 2018; 33:601-613. [PMID: 29101603 DOI: 10.1007/s11011-017-0138-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/20/2017] [Indexed: 10/18/2022]
Abstract
Anxiety sensitivity (AS) is characterised by the fear of anxiety-related symptoms and is a risk factor for the development of anxiety-related disorders. We examined whether genetic variation in three stress response genes, CRHR1, NR3C1, and FKBP5, interact with childhood trauma (CT) to predict AS in South African adolescents. Xhosa (n = 634) and Coloured (n = 317) students completed self-report measures of AS and CT, and a total of eighteen polymorphisms within CRHR1, NR3C1, and FKBP5 were genotyped. Differences in AS based on genetic variation and CT were analysed within population and gender groups using multiple linear regression. Associations were found between AS and FKBP5 rs9296158 (p = 0.025) and rs737054 (p = 0.045) in Coloured males. Analysis of gene x CT interactions indicated that NR3C1 rs190488 CC-genotype, NR3C1 rs10482605 G-allele addition, and FKBP5 rs3800373 C-allele addition protect against AS with increasing CT in Xhosa females (p = 0.009), Xhosa males (p = 0.036) and Coloured males (p = 0.049), respectively. We identified two different protective single nucleotide polymorphism (SNP) combinations in a four-SNP CRHR1 haplotype in Coloured males. An analysis of the interaction between CT and a six-SNP FKBP5 haplotype in Coloured males revealed both protective and risk allelic combinations. Our results provide evidence for the influence of both genetic variation in CRHR1, NR3C1 and FKBP5, as well as CT x SNP interactions, on AS in South African adolescents. This study reinforces the importance of examining the influence of gene-environment (G X E) interactions within gender and population groups.
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Affiliation(s)
- Jacqueline S Womersley
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Lindi I Martin
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Lize van der Merwe
- Department of Human Genetics, Faculty of Agriculture, Stellenbosch University, Stellenbosch, South Africa
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Sian M J Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
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Yew CW, Hoque MZ, Pugh-Kitingan J, Minsong A, Voo CLY, Ransangan J, Lau STY, Wang X, Saw WY, Ong RTH, Teo YY, Xu S, Hoh BP, Phipps ME, Kumar SV. Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome-wide SNP data. Ann Hum Genet 2018. [PMID: 29521412 DOI: 10.1111/ahg.12246] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the "North Borneo"-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non-Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (FST ) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non-Austro-Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent strong genetic differentiation. This report contributes to addressing the paucity of genetic data on representatives from this strategic region of ancient human migration event(s).
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Affiliation(s)
- Chee Wei Yew
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | - Mohd Zahirul Hoque
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | | | - Alexander Minsong
- Faculty of Humanities, Arts & Heritage, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | | | - Julian Ransangan
- Borneo Marine Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | - Sophia Tiek Ying Lau
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | - Xu Wang
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore
| | - Woei Yuh Saw
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore
| | - Rick Twee-Hee Ong
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Yik-Ying Teo
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology (PICB), Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTec University, Shanghai, China.,Collaborative Innovation Centre of Genetics and Development, Shanghai, China
| | - Boon-Peng Hoh
- Institute for Molecular Medical Biotechnology, Universiti Teknologi MARA, Selangor, Malaysia.,Faculty of Medicine and Health Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor, Malaysia
| | - S Vijay Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
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26
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Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans. Nat Commun 2017; 8:2062. [PMID: 29233967 PMCID: PMC5727231 DOI: 10.1038/s41467-017-00663-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 07/17/2017] [Indexed: 11/08/2022] Open
Abstract
The Southern African Human Genome Programme is a national initiative that aspires to unlock the unique genetic character of southern African populations for a better understanding of human genetic diversity. In this pilot study the Southern African Human Genome Programme characterizes the genomes of 24 individuals (8 Coloured and 16 black southeastern Bantu-speakers) using deep whole-genome sequencing. A total of ~16 million unique variants are identified. Despite the shallow time depth since divergence between the two main southeastern Bantu-speaking groups (Nguni and Sotho-Tswana), principal component analysis and structure analysis reveal significant (p < 10−6) differentiation, and FST analysis identifies regions with high divergence. The Coloured individuals show evidence of varying proportions of admixture with Khoesan, Bantu-speakers, Europeans, and populations from the Indian sub-continent. Whole-genome sequencing data reveal extensive genomic diversity, increasing our understanding of the complex and region-specific history of African populations and highlighting its potential impact on biomedical research and genetic susceptibility to disease. African populations show a high level of genetic diversity and extensive regional admixture. Here, the authors sequence the whole genomes of 24 South African individuals of different ethnolinguistic origin and find substantive genomic divergence between two southeastern Bantu-speaking groups.
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27
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Galaverni M, Caniglia R, Pagani L, Fabbri E, Boattini A, Randi E. Disentangling Timing of Admixture, Patterns of Introgression, and Phenotypic Indicators in a Hybridizing Wolf Population. Mol Biol Evol 2017; 34:2324-2339. [PMID: 28549194 PMCID: PMC5850710 DOI: 10.1093/molbev/msx169] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hybridization is a natural or anthropogenic process that can deeply affect the genetic make-up of populations, possibly decreasing individual fitness but sometimes favoring local adaptations. The population of Italian wolves (Canis lupus), after protracted demographic declines and isolation, is currently expanding in anthropic areas, with documented cases of hybridization with stray domestic dogs. However, identifying admixture patterns in deeply introgressed populations is far from trivial. In this study, we used a panel of 170,000 SNPs analyzed with multivariate, Bayesian and local ancestry reconstruction methods to identify hybrids, estimate their ancestry proportions and timing since admixture. Moreover, we carried out preliminary genotype-phenotype association analyses to identify the genetic bases of three phenotypic traits (black coat, white claws, and spur on the hind legs) putative indicators of hybridization. Results showed no sharp subdivisions between nonadmixed wolves and hybrids, indicating that recurrent hybridization and deep introgression might have started mostly at the beginning of the population reexpansion. In hybrids, we identified a number of genomic regions with excess of ancestry in one of the parental populations, and regions with excess or resistance to introgression compared with neutral expectations. The three morphological traits showed significant genotype-phenotype associations, with a single genomic region for black coats and white claws, and with multiple genomic regions for the spur. In all cases the associated haplotypes were likely derived from dogs. In conclusion, we show that the use of multiple genome-wide ancestry reconstructions allows clarifying the admixture dynamics even in highly introgressed populations, and supports their conservation management.
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Affiliation(s)
- Marco Galaverni
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
- Area Conservazione, WWF Italia, Rome, Italy
| | - Romolo Caniglia
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
| | - Luca Pagani
- Dipartimento di Biologia, Universita degli Studi di Padova, Padua, Italy
- Estonian Biocentre, Tartu, Estonia
| | - Elena Fabbri
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Ettore Randi
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
- Department 18/Section of Environmental Engineering, Aalborg Universitet, Aalborg, Denmark
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28
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Botha D, Steyn M, Scholtz Y, Ribot I. Revisiting historical Khoe-San skeletal remains in European collections: A search for identity through craniometric analysis. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2017; 68:243-255. [PMID: 28733025 DOI: 10.1016/j.jchb.2017.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/27/2017] [Indexed: 11/16/2022]
Abstract
As the identity of a large number of Khoe-San skeletal material in European collections recently came into question during its documentation, a re-evaluation of the remains by employing a non-invasive method such as craniometrics was done to investigate the biological affinity. For this purpose, gene flow and population diversity present within the group, as well as between the study sample (N=63) and other modern and historic population groups from southern, central and east Africa were explored. Available comparative groups included the historic Khoe-San from Riet River (N=31), the Sotho-Tswana from southern Africa (N=61), the Basuku from central Africa (N=66) and the Bahutu (N=53) and Teita (N=24) from east Africa. Ten craniometric variables were selected and used to perform population structure analysis based on model bound quantitative genetics and multiple discriminant function analysis (MDA). Quantitative genetic distances revealed that the Khoe-San sample was closest to the Riet River group. Residual variance analysis performed on two-sample subsets of the Khoe-San group (Cape KS and Various KS) showed a higher level of heterogeneity in the Cape KS than seen in the Khoe-San from various other areas in southern Africa. MDA revealed that Khoe-San intra-sample variance is relatively high, with 44% of the sample (sexes pooled) classified into the Riet River group. The remaining individuals were classified (in decreasing order) into Bahutu (24%), Basuku (24%) and Sotho-Tswana (8%). Although the Khoe-San specimens are closest to the Riet River group, they are clearly not homogenous. Their high level of phenotypic diversity most likely originated from a complex population history involving many group interactions driven by social and political marginalization.
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Affiliation(s)
- D Botha
- Forensic Anthropology Research Centre, Department of Anatomy, University of Pretoria, Private Bag X323, Arcadia 0007, Pretoria, South Africa.
| | - M Steyn
- Human Variation and Identification Research Unit, School of Anatomical Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg, South Africa
| | - Y Scholtz
- Forensic Anthropology Research Centre, Department of Anatomy, University of Pretoria, Private Bag X323, Arcadia 0007, Pretoria, South Africa
| | - I Ribot
- Department of Anthropology, University of Montréal, C.P. 6128 Succursale, Centre-ville, Montréal, QC H3C 3J7, Canada
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29
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Human leukocyte antigen class I (A, B and C) allele and haplotype variation in a South African Mixed ancestry population. Hum Immunol 2017; 78:399-400. [PMID: 28438553 PMCID: PMC5451074 DOI: 10.1016/j.humimm.2017.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/13/2017] [Accepted: 04/19/2017] [Indexed: 11/20/2022]
Abstract
South Africa has a large (∼53million), ethnically diverse population (black African, Caucasian, Indian/Asian and Mixed ancestry) and a high disease burden (particularly HIV-1 and Mycobacterium tuberculosis). The Mixed ancestry population constitutes ∼9% of the total population and was established ∼365years ago in the Western Cape region through interracial mixing of black Africans, Europeans and Asians. Admixed populations present unique opportunities to identify genetic factors involved in disease susceptibility. Since HLA genes are important mediators of host immunity, we investigated HLA-A, -B and -C allele and haplotype diversity in 50 healthy, unrelated individuals recruited from the Mixed ancestry population.
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30
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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] [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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31
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Krüger GC, L’Abbé EN, Stull KE. Sex estimation from the long bones of modern South Africans. Int J Legal Med 2016; 131:275-285. [DOI: 10.1007/s00414-016-1488-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/21/2016] [Indexed: 11/24/2022]
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32
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McCrow JP, Petersen DC, Louw M, Chan EKF, Harmeyer K, Vecchiarelli S, Lyons RJ, Bornman MSR, Hayes VM. Spectrum of mitochondrial genomic variation and associated clinical presentation of prostate cancer in South African men. Prostate 2016; 76:349-58. [PMID: 26660354 PMCID: PMC4832339 DOI: 10.1002/pros.23126] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/05/2015] [Indexed: 01/09/2023]
Abstract
BACKGROUND Prostate cancer incidence and mortality rates are significantly increased in African-American men, but limited studies have been performed within Sub-Saharan African populations. As mitochondria control energy metabolism and apoptosis we speculate that somatic mutations within mitochondrial genomes are candidate drivers of aggressive prostate carcinogenesis. METHODS We used matched blood and prostate tissue samples from 87 South African men (77 with African ancestry) to perform deep sequencing of complete mitochondrial genomes. Clinical presentation was biased toward aggressive disease (Gleason score >7, 64%), and compared with men without prostate cancer either with or without benign prostatic hyperplasia. RESULTS We identified 144 somatic mtDNA single nucleotide variants (SNVs), of which 80 were observed in 39 men presenting with aggressive disease. Both the number and frequency of somatic mtDNA SNVs were associated with higher pathological stage. CONCLUSIONS Besides doubling the total number of somatic PCa-associated mitochondrial genome mutations identified to date, we associate mutational load with aggressive prostate cancer status in men of African ancestry.
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Affiliation(s)
| | - Desiree C. Petersen
- J. Craig Venter InstituteLa JollaCalifornia
- Laboratory for Human Comparative and Prostate Cancer GenomicsGarvan Institute of Medical ResearchDarlinghurst, SydneyNSWAustralia
- Faculty of MedicineUniversity of New SouthWales Australia, RandwickNSWAustralia
| | - Melanie Louw
- Department of PathologyUniversity of PretoriaSouth Africa
| | - Eva K. F. Chan
- Laboratory for Human Comparative and Prostate Cancer GenomicsGarvan Institute of Medical ResearchDarlinghurst, SydneyNSWAustralia
- Faculty of MedicineUniversity of New SouthWales Australia, RandwickNSWAustralia
| | - Katherine Harmeyer
- J. Craig Venter InstituteLa JollaCalifornia
- Laboratory for Human Comparative and Prostate Cancer GenomicsGarvan Institute of Medical ResearchDarlinghurst, SydneyNSWAustralia
| | - Stefano Vecchiarelli
- Laboratory for Human Comparative and Prostate Cancer GenomicsGarvan Institute of Medical ResearchDarlinghurst, SydneyNSWAustralia
| | - Ruth J. Lyons
- Laboratory for Human Comparative and Prostate Cancer GenomicsGarvan Institute of Medical ResearchDarlinghurst, SydneyNSWAustralia
| | - M. S. Riana Bornman
- School of Health Systems and Public HealthUniversity of PretoriaSouth Africa
| | - Vanessa M. Hayes
- J. Craig Venter InstituteLa JollaCalifornia
- Laboratory for Human Comparative and Prostate Cancer GenomicsGarvan Institute of Medical ResearchDarlinghurst, SydneyNSWAustralia
- Faculty of MedicineUniversity of New SouthWales Australia, RandwickNSWAustralia
- School of Health Systems and Public HealthUniversity of PretoriaSouth Africa
- Central Clinical SchoolUniversity of SydneyCamperdown, SydneyNSWAustralia
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33
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Wei FF, Drummen NE, Schutte AE, Thijs L, Jacobs L, Petit T, Yang WY, Smith W, Zhang ZY, Gu YM, Kuznetsova T, Verhamme P, Allegaert K, Schutte R, Lerut E, Evenepoel P, Vermeer C, Staessen JA. Vitamin K Dependent Protection of Renal Function in Multi-ethnic Population Studies. EBioMedicine 2016; 4:162-9. [PMID: 26981580 PMCID: PMC4776057 DOI: 10.1016/j.ebiom.2016.01.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Following activation by vitamin K (VK), matrix Gla protein (MGP) inhibits arterial calcification, but its role in preserving renal function remains unknown. METHODS In 1166 white Flemish (mean age, 38.2 years) and 714 South Africans (49.2% black; 40.6 years), we correlated estimated glomerular filtration (eGFR [CKD-EPI formula]) and stage of chronic kidney disease (CKD [KDOQI stages 2-3]) with inactive desphospho-uncarboxylated MGP (dp-ucMGP), using multivariable linear and logistic regression. RESULTS Among Flemish and white and black Africans, between-group differences in eGFR (90, 100 and 122 mL/min/1.73 m(2)), dp-ucMGP (3.7, 6.5 and 3.2 μg/L), and CKD prevalence (53.5, 28.7 and 10.5%) were significant, but associations of eGFR with dp-ucMGP did not differ among ethnicities (P ≥ 0.075). For a doubling of dp-ucMGP, eGFR decreased by 1.5 (P = 0.023), 1.0 (P = 0.56), 2.8 (P = 0.0012) and 2.1 (P < 0.0001) mL/min/1.73 m(2) in Flemish, white Africans, black Africans and all participants combined; the odds ratios for moving up one CKD stage were 1.17 (P = 0.033), 1.03 (P = 0.87), 1.29 (P = 0.12) and 1.17 (P = 0.011), respectively. INTERPRETATION In the general population, eGFR decreases and CKD risk increases with higher dp-ucMGP, a marker of VK deficiency. These findings highlight the possibility that VK supplementation might promote renal health.
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Affiliation(s)
- Fang-Fei Wei
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
| | | | - Aletta E. Schutte
- Hypertension in Africa Research Team, North-West University, Potchefstroom, South Africa
- MRC Research Unit on Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
| | - Lutgarde Thijs
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
| | - Lotte Jacobs
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
| | - Thibaut Petit
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
| | - Wen-Yi Yang
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
| | - Wayne Smith
- Hypertension in Africa Research Team, North-West University, Potchefstroom, South Africa
| | - Zhen-Yu Zhang
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
| | - Yu-Mei Gu
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
| | - Tatiana Kuznetsova
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
| | - Peter Verhamme
- Centre for Molecular and Vascular Biology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
| | - Karel Allegaert
- Research Unit Organ Systems, KU Leuven Department of Development and Regeneration, University of Leuven, Leuven, Belgium
| | - Rudolph Schutte
- Hypertension in Africa Research Team, North-West University, Potchefstroom, South Africa
- MRC Research Unit on Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
| | - Evelyne Lerut
- Department of Morphology and Molecular Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Pieter Evenepoel
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Cees Vermeer
- R & D Group VitaK, Maastricht University, Maastricht, The Netherlands
| | - Jan A. Staessen
- Studies Coordinating Centre, Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Belgium
- R & D Group VitaK, Maastricht University, Maastricht, The Netherlands
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Matsha TE, Pheiffer C, Humphries SE, Gamieldien J, Erasmus RT, Kengne AP. Genome-Wide DNA Methylation in Mixed Ancestry Individuals with Diabetes and Prediabetes from South Africa. Int J Endocrinol 2016; 2016:3172093. [PMID: 27555869 PMCID: PMC4983374 DOI: 10.1155/2016/3172093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 06/06/2016] [Accepted: 06/28/2016] [Indexed: 01/09/2023] Open
Abstract
Aims. To conduct a genome-wide DNA methylation in individuals with type 2 diabetes, individuals with prediabetes, and control mixed ancestry individuals from South Africa. Methods. We used peripheral blood to perform genome-wide DNA methylation analysis in 3 individuals with screen detected diabetes, 3 individuals with prediabetes, and 3 individuals with normoglycaemia from the Bellville South Community, Cape Town, South Africa, who were age-, gender-, body mass index-, and duration of residency-matched. Methylated DNA immunoprecipitation (MeDIP) was performed by Arraystar Inc. (Rockville, MD, USA). Results. Hypermethylated DMRs were 1160 (81.97%) and 124 (43.20%), respectively, in individuals with diabetes and prediabetes when both were compared to subjects with normoglycaemia. Our data shows that genes related to the immune system, signal transduction, glucose transport, and pancreas development have altered DNA methylation in subjects with prediabetes and diabetes. Pathway analysis based on the functional analysis mapping of genes to KEGG pathways suggested that the linoleic acid metabolism and arachidonic acid metabolism pathways are hypomethylated in prediabetes and diabetes. Conclusions. Our study suggests that epigenetic changes are likely to be an early process that occurs before the onset of overt diabetes. Detailed analysis of DMRs that shows gradual methylation differences from control versus prediabetes to prediabetes versus diabetes in a larger sample size is required to confirm these findings.
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Affiliation(s)
- Tandi E. Matsha
- Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Cape Town 7535, South Africa
- *Tandi E. Matsha:
| | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town 7505, South Africa
| | - Stephen E. Humphries
- Centre for Cardiovascular Genetics, British Heart Foundation Laboratories, Institute of Cardiovascular Science, The Rayne Building, University College London, London WC1E 6JF, UK
| | - Junaid Gamieldien
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town 7535, South Africa
| | - Rajiv T. Erasmus
- Division of Chemical Pathology and National Health Laboratory Service (NHLS), Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town 7505, South Africa
| | - Andre P. Kengne
- Non-Communicable Diseases Research Unit, South African Medical Research Council, Cape Town 7505, South Africa
- Department of Medicine, University of Cape Town, Cape Town 8000, South Africa
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Liebenberg L, L'Abbé EN, Stull KE. Population differences in the postcrania of modern South Africans and the implications for ancestry estimation. Forensic Sci Int 2015; 257:522-529. [PMID: 26584515 DOI: 10.1016/j.forsciint.2015.10.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/07/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
Abstract
The cranium is widely recognized as the most important skeletal element to use when evaluating population differences and estimating ancestry. However, the cranium is not always intact or available for analysis, which emphasizes the need for postcranial alternatives. The purpose of this study was to quantify postcraniometric differences among South Africans that can be used to estimate ancestry. Thirty-nine standard measurements from 11 postcranial bones were collected from 360 modern black, white and coloured South Africans; the sex and ancestry distribution were equal. Group differences were explored with analysis of variance (ANOVA) and Tukey's honestly significant difference (HSD) test. Linear and flexible discriminant analysis (LDA and FDA, respectively) were conducted with bone models as well as numerous multivariate subsets to identify the model and method that yielded the highest correct classifications. Leave-one-out (LDA) and k-fold (k=10; FDA) cross-validation with equal priors were used for all models. ANOVA and Tukey's HSD results reveal statistically significant differences between at least two of the three groups for the majority of the variables, with varying degrees of group overlap. Bone models, which consisted of all measurements per bone, resulted in low accuracies that ranged from 46% to 63% (LDA) and 41% to 66% (FDA). In contrast, the multivariate subsets, which consisted of different variable combinations from all elements, achieved accuracies as high as 85% (LDA) and 87% (FDA). Thus, when using a multivariate approach, the postcranial skeleton can distinguish among three modern South African groups with high accuracy.
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Affiliation(s)
- Leandi Liebenberg
- Department of Anatomy, University of Pretoria, Arcadia, South Africa; Department of Basic Medical Sciences, University of the Free State, Bloemfontein, South Africa.
| | - Ericka N L'Abbé
- Department of Anatomy, University of Pretoria, Arcadia, South Africa
| | - Kyra E Stull
- Department of Anthropology, Idaho State University, Pocatello, ID, USA
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Pharmacogenetic comparison of CYP2D6 predictive and measured phenotypes in a South African cohort. THE PHARMACOGENOMICS JOURNAL 2015; 16:566-572. [PMID: 26503815 DOI: 10.1038/tpj.2015.76] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 08/20/2015] [Accepted: 09/08/2015] [Indexed: 11/08/2022]
Abstract
The relationship between genetic variation in CYP2D6 and variable drug response represents a potentially powerful pharmacogenetic tool. However, little is known regarding this relationship in the genetically diverse South African population. The aim was therefore to evaluate the relationship between predicted and measured CYP2D6 phenotype. An XL-PCR+Sequencing approach was used to determine CYP2D6 genotype in 100 healthy volunteers and phenotype was predicted using activity scores. With dextromethorphan as the probe drug, metabolic ratios served as a surrogate measure of in vivo CYP2D6 activity. Three-hour plasma metabolic ratios of dextrorphan/dextromethorphan were measured simultaneously using semi-automated online solid phase extraction coupled with tandem mass spectrometry. Partial adaptation of the activity score system demonstrated a strong association between genotype and phenotype, as illustrated by a kappa value of 0.792, inter-rater discrepancy of 0.051 and sensitivity of 72.7%. Predicted phenotype frequencies using the modified activity score were 1.3% for poor metabolisers (PM), 7.6% for intermediate metabolisers (IM) and 87.3% for extensive metabolisers (EM). Measured phenotype frequencies were 1.3% for PM, 13.9% for IM and 84.8% for EM. Comprehensive CYP2D6 genotyping reliably predicts CYP2D6 activity in this South African cohort and can be utilised as a valuable pharmacogenetic tool.
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Vitamin D Status in South Africa and Tuberculosis. Lung 2015; 193:975-84. [DOI: 10.1007/s00408-015-9789-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/19/2015] [Indexed: 12/11/2022]
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Dodgen TM, Drögemöller BI, Wright GEB, Warnich L, Steffens FE, Cromarty AD, Alessandrini M, Pepper MS. Evaluation of predictive CYP2C19 genotyping assays relative to measured phenotype in a South African cohort. Pharmacogenomics 2015; 16:1343-54. [PMID: 26244421 DOI: 10.2217/pgs.15.80] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
AIM To align predicted and measured CYP2C19 phenotype in a South African cohort. MATERIALS & METHODS Genotyping of CYP2C19*2, *3, *9, *15, *17, *27 and *28 was performed using PCR-RFLP, and an activity score (AS) system was used to predict phenotype. True phenotype was measured using plasma concentrations of omeprazole and its metabolite 5'-hydroxyomperazole. RESULTS Partial genotype-phenotype discrepancies were reported, and an adapted AS system was developed, which showed a marked improvement in phenotype prediction. Results highlight the need for a more comprehensive CYP2C19 genotyping approach to improve prediction of omeprazole metabolism. CONCLUSION Evidence for the utility of a CYP2C19 AS system is provided, for which the accuracy can be further improved by means of comprehensive genotyping and substrate-specific modification.
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Affiliation(s)
- Tyren M Dodgen
- Department of Pharmacology, University of Pretoria, Pretoria, South Africa.,Department of Immunology, Faculty of Health Sciences, University of Pretoria, PO Box 2034, Pretoria 0001, South Africa.,Institute for Cellular & Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Britt I Drögemöller
- Department of Genetics, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | - Galen E B Wright
- Department of Genetics, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | - Louise Warnich
- Department of Genetics, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | - Francois E Steffens
- Department of Statistics, Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - A Duncan Cromarty
- Department of Pharmacology, University of Pretoria, Pretoria, South Africa
| | - Marco Alessandrini
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, PO Box 2034, Pretoria 0001, South Africa.,Institute for Cellular & Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Michael S Pepper
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, PO Box 2034, Pretoria 0001, South Africa.,Institute for Cellular & Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.,Department of Genetic Medicine & Development, Faculty of Medicine, University of Geneva, Switzerland
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Campbell MC, Hirbo JB, Townsend JP, Tishkoff SA. The peopling of the African continent and the diaspora into the new world. Curr Opin Genet Dev 2015; 29:120-32. [PMID: 25461616 DOI: 10.1016/j.gde.2014.09.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/03/2014] [Accepted: 09/05/2014] [Indexed: 12/22/2022]
Abstract
Africa is the birthplace of anatomically modern humans, and is the geographic origin of human migration across the globe within the last 100,000 years. The history of African populations has consisted of a number of demographic events that have influenced patterns of genetic and phenotypic variation across the continent. With the increasing amount of genomic data and corresponding developments in computational methods, researchers are able to explore long-standing evolutionary questions, expanding our understanding of human history within and outside of Africa. This review will summarize some of the recent findings regarding African demographic history, including the African Diaspora, and will briefly explore their implications for disease susceptibility in populations of African descent.
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Coussens AK, Naude CE, Goliath R, Chaplin G, Wilkinson RJ, Jablonski NG. High-dose vitamin D3 reduces deficiency caused by low UVB exposure and limits HIV-1 replication in urban Southern Africans. Proc Natl Acad Sci U S A 2015; 112:8052-7. [PMID: 26080414 PMCID: PMC4491791 DOI: 10.1073/pnas.1500909112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cape Town, South Africa, has a seasonal pattern of UVB radiation and a predominantly dark-skinned urban population who suffer high HIV-1 prevalence. This coexistent environmental and phenotypic scenario puts residents at risk for vitamin D deficiency, which may potentiate HIV-1 disease progression. We conducted a longitudinal study in two ethnically distinct groups of healthy young adults in Cape Town, supplemented with vitamin D3 in winter, to determine whether vitamin D status modifies the response to HIV-1 infection and to identify the major determinants of vitamin D status (UVB exposure, diet, pigmentation, and genetics). Vitamin D deficiency was observed in the majority of subjects in winter and in a proportion of individuals in summer, was highly correlated with UVB exposure, and was associated with greater HIV-1 replication in peripheral blood cells. High-dosage oral vitamin D3 supplementation attenuated HIV-1 replication, increased circulating leukocytes, and reversed winter-associated anemia. Vitamin D3 therefore presents as a low-cost supplementation to improve HIV-associated immunity.
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Affiliation(s)
- Anna K Coussens
- Clinical Infectious Diseases Research Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Celeste E Naude
- Centre for Evidence-based Health Care, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Rene Goliath
- Clinical Infectious Diseases Research Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa
| | - George Chaplin
- Department of Geography, The Pennsylvania State University, University Park, PA 16802; Department of Anthropology, The Pennsylvania State University, University Park, PA 16802; Stellenbosch Institute for Advanced Studies, Stellenbosch 7600, South Africa
| | - Robert J Wilkinson
- Clinical Infectious Diseases Research Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa; The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, United Kingdom; Department of Medicine, Imperial College London, London W2 1PG, United Kingdom
| | - Nina G Jablonski
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802; Stellenbosch Institute for Advanced Studies, Stellenbosch 7600, South Africa;
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Matsha TE, Kengne AP, Masconi KL, Yako YY, Erasmus RT. APOL1 genetic variants, chronic kidney diseases and hypertension in mixed ancestry South Africans. BMC Genet 2015; 16:69. [PMID: 26112018 PMCID: PMC4482162 DOI: 10.1186/s12863-015-0228-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 06/10/2015] [Indexed: 01/07/2023] Open
Abstract
Background The frequencies of apolipoprotein L1 (APOL1) variants and their associations with chronic kidney disease (CKD) vary substantially in populations from Africa. Moreover, available studies have used very small sample sizes to provide reliable estimates of the frequencies of these variants in the general population. We determined the frequency of the two APOL1 risk alleles (G1 and G2) and investigated their association with renal traits in a relatively large sample of mixed-ancestry South Africans. APOL1 risk variants (G1: rs60910145 and rs73885319; G2: rs71785313) were genotyped in 859 African mixed ancestry individuals using allele-specific TaqMan technology. Glomerular filtration rate (eGFR) was estimated using the Modification of Diet in Renal Disease (MDRD) and Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equations. Results The frequencies of rs73885319, rs60910145 and rs71785313 risk alleles were respectively, 3.6 %, 3.4 %, and 5.8 %, resulting in a 1.01 % frequency of the APOL1 two-risk allele (G1:G1 or G1:G2 or G2:G2). The presence of the two-risk allele increased serum creatinine with a corresponding reduction in eGFR (either MDRD or CKD-EPI based). In dominant and log-additive genetic models, significant associations were found between rs71785313 and systolic blood pressure (both p ≤ 0.025), with a significant statistical interaction by diabetes status, p = 0.022, reflecting a negative non-significant effect in nondiabetics and a positive effect in diabetics. Conclusions Although the APOL1 variants are not common in the mixed ancestry population of South Africa, the study does provide an indication that APOL1 variants may play a role in conferring an increased risk for renal and cardiovascular risk in this population.
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Affiliation(s)
- Tandi E Matsha
- Department of Biomedical Sciences, Faculty of Health and Wellness Science, Cape Peninsula University of Technology, PO Box 1906, Bellville, Cape Town, 7530, South Africa.
| | - Andre P Kengne
- Non-Communicable Diseases Research Unit, South African Medical Research Council & University of Cape Town, Cape Town, South Africa.
| | - Katya L Masconi
- Department of Surgery, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.
| | - Yandiswa Y Yako
- Department of Surgery, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.
| | - Rajiv T Erasmus
- Division of Chemical Pathology, Faculty of Health Sciences, National Health Laboratory Service (NHLS) and University of Stellenbosch, Cape Town, South Africa.
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Daya M, van der Merwe L, van Helden PD, Möller M, Hoal EG. Investigating the Role of Gene-Gene Interactions in TB Susceptibility. PLoS One 2015; 10:e0123970. [PMID: 25919455 PMCID: PMC4412713 DOI: 10.1371/journal.pone.0123970] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 02/24/2015] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis (TB) is the second leading cause of mortality from infectious disease worldwide. One of the factors involved in developing disease is the genetics of the host, yet the field of TB susceptibility genetics has not yielded the answers that were expected. A commonly posited explanation for the missing heritability of complex disease is gene-gene interactions, also referred to as epistasis. In this study we investigate the role of gene-gene interactions in genetic susceptibility to TB using a cohort recruited from a high TB incidence community from Cape Town, South Africa. Our discovery data set incorporates genotypes from a large a number of candidate gene studies as well as genome-wide data. After limiting our search space to pairs of putative TB susceptibility genes, as well as pairs of genes that have been curated in online databases as potential interactors, we use statistical modelling to identify pairs of interacting SNPs. We attempt to validate the top models identified in our discovery data set using an independent genome-wide TB case-control data set from The Gambia. A number of models were successfully validated, indicating that interplay between the NRG1 - NRG3, GRIK1 - GRIK3 and IL23R - ATG4C gene pairs may modify susceptibility to TB. Gene pairs involved in the NF-κB pathway were also identified in the discovery data set (SFTPD - NOD2, ISG15 - TLR8 and NLRC5 - IL12RB1), but could not be tested in the Gambian study group due to lack of overlapping data.
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Affiliation(s)
- Michelle Daya
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Lize van der Merwe
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, 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 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 Tuberculosis 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 Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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McDowell JL, Kenyhercz MW, L'Abbé EN. An evaluation of nasal bone and aperture shape among three South African populations. Forensic Sci Int 2015; 252:189.e1-7. [PMID: 25963274 DOI: 10.1016/j.forsciint.2015.04.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 03/02/2015] [Accepted: 04/15/2015] [Indexed: 11/16/2022]
Abstract
Reliable and valid population specific standards are necessary to accurately develop a biological profile, which includes an estimation of peer-reported social identification (Hefner, 2009). During the last 300 years, colonialism, slavery and apartheid created geographic, physical and social divisions of population groups in South Africa. The purpose of this study was to evaluate variation in nasal bone and aperture shape in a modern population of black, white, and coloured South Africans using standard craniometric variables and geometric morphometrics, namely general Procrustes and elliptical Fourier analyses. Fourteen standard landmarks were digitally recorded or computationally derived from 310 crania using a 3D coordinate digitizer for discriminant function, principal components and generalized Procrustes analyses. For elliptical Fourier analysis, outlines of the nasal aperture were generated from standardized photographs. All classification accuracies were better than chance; the lowest accuracies were for coloured and the highest accuracies were for white South Africans. Most difficulties arose in distinguishing coloured and black South African groups from each other. Generally, misclassifications were noted between the sexes within each group rather than among groups, which suggests that sex has less influence on nasal bone and aperture shape than ancestry. Quantifiable variation in shape of the nasal aperture region between white and non-white South African groups was observed.
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Affiliation(s)
- Jennifer L McDowell
- Department of Anatomy, University of Pretoria, Private Bag x 323, Arcadia 0007, South Africa
| | - Michael W Kenyhercz
- Department of Anthropology, University of Alaska, Fairbanks, AK 99775, United States; Department of Anatomy, University of Tennessee, Knoxville, TN 37996, United States
| | - Ericka N L'Abbé
- Department of Anatomy, University of Pretoria, Private Bag x 323, Arcadia 0007, South Africa.
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Common mutation causes cystinosis in the majority of black South African patients. Pediatr Nephrol 2015; 30:595-601. [PMID: 25326109 DOI: 10.1007/s00467-014-2980-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 09/03/2014] [Accepted: 09/29/2014] [Indexed: 01/01/2023]
Abstract
BACKGROUND The mutations responsible for cystinosis in South African patients are currently unknown. A pertinent question is whether they are similar to those described elsewhere in the world. METHODS Children who were being managed for cystinosis in the Western Cape Province of South Africa between 2002 and 2013 were studied. All underwent molecular analysis to detect sequence variations in the cystinosis gene. RESULTS This cohort study included 20 patients, 13 of whom were Xhosa-speaking black South Africans and seven were Cape Coloureds (mixed race); none were Caucasian. All had nephropathic infantile-type cystinosis with evidence of proximal tubulopathy, with glycosuria and renal phosphate wasting. Diagnosis was confirmed in 19 cases by demonstrating an elevated cystine concentration in leukocytes. Molecular analysis of the cystinosin gene revealed that 19 patients had a G > A mutation in intron 11 (CTNS-c.971-12G > A p.D324AfsX44) which caused an out-of-frame 10-bp insertion. Of these 19 patients, 16 were homozygous for this mutation, which was the most frequent mutation identified in the alleles of the black South African and Cape Coloured patients (96 and 71 %, respectively). CONCLUSION We recommend that black South African and Cape Coloured patients presenting with cystinosis be tested for CTNS-c.971-12G > A in the first instance, with the possibility of prenatal testing being offered to at-risk families.
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Daya M, van der Merwe L, Gignoux CR, van Helden PD, Möller M, Hoal EG. Using multi-way admixture mapping to elucidate TB susceptibility in the South African Coloured population. BMC Genomics 2014; 15:1021. [PMID: 25422094 PMCID: PMC4256931 DOI: 10.1186/1471-2164-15-1021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 11/19/2014] [Indexed: 01/07/2023] Open
Abstract
Background The admixed South African Coloured population is ideally suited to the discovery of tuberculosis susceptibility genetic variants and their probable ethnic origins, but previous attempts at finding such variants using genome-wide admixture mapping were hampered by the inaccuracy of local ancestry inference. In this study, we infer local ancestry using the novel algorithm implemented in RFMix, with the emphasis on identifying regions of excess San or Bantu ancestry, which we hypothesize may harbour TB susceptibility genes. Results Using simulated data, we demonstrate reasonable accuracy of local ancestry inference by RFMix, with a tendency towards miss-calling San ancestry as Bantu. Regions with either excess San ancestry or excess African (San or Bantu) ancestry are less likely to be affected by this bias, and we therefore proceeded to identify such regions, found in cases but not in controls (642 cases and 91 controls). A number of promising regions were found (overall p-values of 7.19×10-5 for San ancestry and <2.00×10-16 for African ancestry), including chromosomes 15q15 and 17q22, which are close to genomic regions previously implicated in TB. Promising immune-related susceptibility genes such as the GADD45A, OSM and B7-H5 genes are also harboured in the identified regions. Conclusion Admixture mapping is feasible in the South African Coloured population and a number of novel TB susceptibility genomic regions were uncovered. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1021) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Eileen G Hoal
- Molecular Biology and Human Genetics, MRC Centre for TB Research and the DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
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Paraoxonase1 genetic polymorphisms in a mixed ancestry African population. Mediators Inflamm 2014; 2014:217019. [PMID: 25477710 PMCID: PMC4248356 DOI: 10.1155/2014/217019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 02/03/2023] Open
Abstract
Paraoxonase 1 (PON1) activity is markedly influenced by coding polymorphisms, Q/R at position 192 and M/L at position 55 of the PON1 gene. We investigated the frequencies of these polymorphisms and their effects on PON1 and antioxidant activities in 844 South African mixed ancestry individuals. Genotyping was done using allele-specific TaqMan technology, PON1 activities were measured using paraoxon and phenylacetate, oxidative status was determined by measuring the antioxidant activities of ferric reducing antioxidant power and trolox equivalent antioxidant capacity, and lipid peroxidation markers included malondialdehyde and oxidized LDL. The frequencies of Q192R and L55M were 47.6% and 28.8%, respectively, and the most common corresponding alleles were 192R (60.4%) and 55M (82.6%). The Q192 was significantly associated with 5.8 units' increase in PON1 concentration and 15.4 units' decrease in PONase activity after adjustment for age, sex, BMI, and diabetes, with suggestion of differential effects by diabetes status. The PON1 L55 variant was associated with none of the measured indices. In conclusion, we have shown that the Q192R polymorphism is a determinant of both PON1 concentration and activity and this association appeared to be enhanced in subjects with diabetes.
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Hatin WI, Nur-Shafawati AR, Etemad A, Jin W, Qin P, Xu S, Jin L, Tan SG, Limprasert P, Feisal MA, Rizman-Idid M, Zilfalil BA. A genome wide pattern of population structure and admixture in peninsular Malaysia Malays. THE HUGO JOURNAL 2014; 8:5. [PMID: 27090253 PMCID: PMC7735395 DOI: 10.1186/s11568-014-0005-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 05/19/2014] [Indexed: 12/23/2022]
Abstract
Background The Malays consist of various sub-ethnic groups which are believed to have different ancestral origins based on their migrations centuries ago. The sub-ethnic groups can be divided based on the region they inhabit; the northern (Melayu Kedah and Melayu Kelantan), western (Melayu Minang) and southern parts (Melayu Bugis and Melayu Jawa) of Peninsular Malaysia. We analyzed 54,794 autosomal single nucleotide polymorphisms (SNPs) which were shared by 472 unrelated individuals from 17 populations to determine the genetic structure and distributions of the ancestral genetic components in five Malay sub-ethnic groups namely Melayu Bugis, Melayu Jawa, Melayu Minang, Melayu Kedah, and Melayu Kelantan. We also have included in the analysis 12 other study populations from Thailand, Indonesia, China, India, Africa and Orang Asli sub-groups in Malay Peninsula, obtained from the Pan Asian SNP Initiative (PASNPI) Consortium and International HapMap project database. Results We found evidence of genetic influx from Indians to Malays, more in Melayu Kedah and Melayu Kelantan which are genetically different from the other Malay sub-ethnic groups, but similar to Thai Pattani. More than 98% of these northern Malays haplotypes could be found in either Indians or Chinese populations, indicating a highly admixture pattern among populations. Nevertheless, the ancestry lines of Malays, Indonesians and Thais were traced back to have shared a common ancestor with the Proto-Malays and Chinese. Conclusions These results support genetic admixtures in the Peninsular Malaysia Malay populations and provided valuable information on the enigmatic demographical history as well as shed some insights into the origins of the Malays in the Malay Peninsula.
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Affiliation(s)
- Wan Isa Hatin
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia
| | - Ab Rajab Nur-Shafawati
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia
| | - Ali Etemad
- Department of Pediatrics, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia
| | - Wenfei Jin
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Pengfei Qin
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Shuhua Xu
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Li Jin
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Soon-Guan Tan
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Selangor, Malaysia
| | - Pornprot Limprasert
- Human Genetics Unit, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Merican Amir Feisal
- Institute of Biological Sciences, 50603, Kuala Lumpur, Malaysia.,Centre of Research for Computational Sciences and Informatics in Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL),Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | | | - Bin Alwi Zilfalil
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia. .,Department of Pediatrics, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia.
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Stull KE, Kenyhercz MW, L'Abbé EN. Ancestry estimation in South Africa using craniometrics and geometric morphometrics. Forensic Sci Int 2014; 245:206.e1-7. [PMID: 25459274 DOI: 10.1016/j.forsciint.2014.10.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 08/04/2014] [Accepted: 10/05/2014] [Indexed: 11/30/2022]
Abstract
Population history and positive assortative mating directs gene flow in such a way that biological differences are recognized among groups. In turn, forensic anthropologists quantify biological differences to estimate ancestry. Some anthropologists argue that highly admixed population groups, such as South African coloureds, cannot achieve acceptable accuracies because within group variance is too large. Whereas ancestry estimation in South Africa has been limited to craniometric data from South African blacks and whites, the current study integrates craniometric and geometric morphometric data from the three largest South African groups. Crania from 377 South African individuals (black=158, white=112, and coloured=107) comprised the sample. Standard measurements were collected and the coordinate data were subjected to Generalized Procrustes Analysis (GPA), which resulted in size-free shape variables (ProCoords). A principal component analysis was used to combine the shape variation captured in the ProCoords (ProCoords PC). Linear discriminant analysis (LDA), using equal priors, stepwise variable selection and leave-one-out cross-validation, was conducted on the ProCoords, the ProCoords PCs, and the traditional craniometric data. The LDA using 18 stepwise selected ProCoords resulted in the highest cross-validated accuracy (89%). Utilization of geometric morphometric data emphasized that the relative location of cranial landmarks was more discriminating than simple linear distances. Regardless of high levels of genetic admixture, South African coloureds are a homogeneous group and morphologically distinct from other contemporaneous South African populations. Furthermore, the present study demonstrated a correspondence between peer-reported race and morphological differences in the crania of black, white, and coloured South Africans.
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Affiliation(s)
- Kyra E Stull
- Department of Anthropology, Idaho State University, 921 South 8th Avenue, Stop 8005, Pocatello, ID 83209, USA.
| | - Michael W Kenyhercz
- Department of Anthropology, University of Tennessee, Knoxville, 250 South Stadium Hall, Knoxville, TN 37996, USA.
| | - Ericka N L'Abbé
- Department of Anatomy, Faculty of Health Sciences, University of Pretoria, Private Bag x323, Arcadia 0007, South Africa.
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Loubser S, Paximadis M, Gentle N, Puren A, Gray CM, Tiemessen CT. Frequencies of immune hypersensitivity reaction-associated HLA class I alleles in healthy South African Indian and mixed ancestry populations determined by a novel real-time PCR assay. ACTA ACUST UNITED AC 2014; 84:389-97. [PMID: 25154892 DOI: 10.1111/tan.12414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 06/12/2014] [Accepted: 07/09/2014] [Indexed: 11/28/2022]
Abstract
We have determined the frequencies of human leucocyte antigen (HLA)-B*57:01, HLA-B*35:05, HLA-C*04 and HLA-C*08 in healthy individuals of South African Indian (SAI) ethnicity (n = 50) and South African mixed (SAM) ancestry (n = 50) using real-time allele-specific polymerase chain reaction (AS-PCR) assay. HLA-B*57:01 associates with immune hypersensitivity reaction (IHR) in individuals exposed to abacavir (ABC), while nevirapine (NVP) IHR associates with HLA-B*35:05, HLA-C*04 and HLA-C*08. Real-time AS-PCR assays typically use less DNA, are more cost-effective and rapid compared with conventional genotyping methods, such as sequence-based typing (SBT). The assay was developed using samples of known HLA class I genotype and subsequently applied to the SAI and SAM samples. HLA-B*57:01 was detected in SAM and SAI populations at frequencies of 8.0% and 12.0%, respectively, while HLA-B*35:05 was not found in SAI individuals, but was present in 6.0% of SAM individuals. HLA-C*04 was detected in 22.0% and 24.0% of SAM and SAI individuals, respectively, while 10.0% and 8.0% of SAM and SAI individuals, respectively, were HLA-C*08 positive. This study reports the development of a novel real-time AS-PCR assay to identify HLA class I alleles associated with ABC and NVP IHR and has established the frequencies of these alleles present in healthy SAI and SAM populations. Using South African demographic data, our hypothetical analysis suggests that a substantial number of individuals would benefit from the assay.
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Affiliation(s)
- S Loubser
- Centre for HIV and STIs, National Institute for Communicable Diseases, the National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Basson A, Swart R, Jordaan E, Mazinu M, Watermeyer G. The association between race and Crohn's disease phenotype in the Western Cape population of South Africa, defined by the Montreal Classification System. PLoS One 2014; 9:e104859. [PMID: 25118187 PMCID: PMC4130615 DOI: 10.1371/journal.pone.0104859] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/18/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Inter-racial differences in disease characteristics and in the management of Crohn's disease (CD) have been described in African American and Asian subjects, however for the racial groups in South Africa, no such recent literature exists. METHODS A cross sectional study of all consecutive CD patients seen at 2 large inflammatory bowel disease (IBD) referral centers in the Western Cape, South Africa between September 2011 and January 2013 was performed. Numerous demographic and clinical variables at diagnosis and date of study enrolment were identified using an investigator administered questionnaire as well as clinical examination and patient case notes. Using predefined definitions, disease behavior was stratified as 'complicated' or 'uncomplicated'. RESULTS One hundred and ninety four CD subjects were identified; 35 (18%) were white, 152 (78%) were Cape Coloured and 7(4%) were black. On multiple logistic regression analysis Cape Coloureds were significantly more likely to develop 'complicated' CD (60% vs. 9%, p = 0.023) during the disease course when compared to white subjects. In addition, significantly more white subjects had successfully discontinued cigarette smoking at study enrolment (31% vs. 7% reduction, p = 0.02). No additional inter-racial differences were found. A low proportion of IBD family history was observed among the non-white subjects. CONCLUSIONS Cape Coloured patients were significantly more likely to develop 'complicated' CD over time when compared to whites.
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Affiliation(s)
- Abigail Basson
- Dietetics Department, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Rina Swart
- Dietetics Department, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Esme Jordaan
- Biostatistics Unit, Medical Research Council of South Africa, Parow, Western Cape, South Africa
- Statistics and Population Studies Department, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Mikateko Mazinu
- Biostatistics Unit, Medical Research Council of South Africa, Parow, Western Cape, South Africa
| | - Gillian Watermeyer
- Department of Gastroenterology, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
- Department of Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
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