1
|
Mugo JW, Day C, Choudhury A, Deetlefs M, Freercks R, Geraty S, Panieri A, Cotchbos C, Ribeiro M, Engelbrecht A, Lisa K Micklesfield, Ramsay M, Sarah P, Peter J. A GWAS of ACE Inhibitor-Induced Angioedema in a South African Population. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.13.24313664. [PMID: 39314982 PMCID: PMC11419215 DOI: 10.1101/2024.09.13.24313664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Background Angiotensin-converting enzyme inhibitor-induced angioedema (AE-ACEI) is a life-threatening adverse event and, globally, the commonest cause of emergency presentations with angioedema. Several large genome-wide association studies (GWAS) have found genomic associations with AE-ACEI. However, despite African Americans having a 5-fold increased risk of AE-ACEI, there are no published GWAS from Africa. The aim of this study was to conduct a case-control GWAS of AE-ACEI in a South African population and perform a meta-analysis with an African American and European American population. Methods The GWAS included 202 South African adults with a history of AE-ACEI and 513 controls without angioedema following angiotensin-converting enzyme inhibitor (ACEI) treatment for at least 2 years. A meta-analysis was conducted with GWAS summary statistics from an African American and European American cohort (from Vanderbilt/Marshfield with 174 cases and 489 controls). Results No SNPs attained genome-wide significance. However, 26 SNPs in the post-imputation standard GWAS of the South African cohort and 37 SNPs in the meta-analysis were associated to AE-ACEI with suggestive threshold(p-value<5.0×10-06). Some of these SNPs were found to be located close to the genes PRKCQ and RIMS1, previously linked with drug-induced angioedema, and also close to the CSMD1 gene linked to ACEI cough, providing replication at the gene level, but with novel lead SNPs. Conclusions Our results highlight the importance of African populations to detect novel variants in replication studies. Further increased sampling across the continent and matched functional work are needed to confirm the importance of genetic variation in understanding the biology of AE-ACEI.
Collapse
Affiliation(s)
- Jacquiline W Mugo
- Division of Allergy and Clinical Immunology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7625, Western Cape, South Africa
| | - Cascia Day
- Division of Allergy and Clinical Immunology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7625, Western Cape, South Africa
- Allergy and Immunology Unit, University of Cape Town Lung Institute (Pty) Ltd, George Street, Mowbray, Cape Town, 7700, Western Cape, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Braamfontein, Johannesburg, 2000, South Africa
| | - Maria Deetlefs
- Division of Allergy and Clinical Immunology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7625, Western Cape, South Africa
| | - Robert Freercks
- Faculty of Health Sciences, Department of Medicine, Nelson Mandela University, Gqeberha, South Africa
| | - Sian Geraty
- Faculty of Health Sciences, Department of Medicine, Nelson Mandela University, Gqeberha, South Africa
| | - Angelica Panieri
- Faculty of Health Sciences, Department of Medicine, Nelson Mandela University, Gqeberha, South Africa
| | - Christian Cotchbos
- Faculty of Health Sciences, Department of Medicine, Nelson Mandela University, Gqeberha, South Africa
| | - Melissa Ribeiro
- Allergy and Immunology Unit, University of Cape Town Lung Institute (Pty) Ltd, George Street, Mowbray, Cape Town, 7700, Western Cape, South Africa
| | - Adelein Engelbrecht
- Western Cape Department of Health, District 6 Day Hospital, 50 Caledon Street, Zonnebloem, Cape Town, Western Cape, South Africa
| | - Lisa K Micklesfield
- South African Medical Research Council/Wits Developmental Pathways for Health Research Unit (DPHRU), Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Braamfontein, Johannesburg, 2000, South Africa
| | - Pedretti Sarah
- Allergy and Immunology Unit, University of Cape Town Lung Institute (Pty) Ltd, George Street, Mowbray, Cape Town, 7700, Western Cape, South Africa
| | - Jonny Peter
- Division of Allergy and Clinical Immunology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7625, Western Cape, South Africa
- Allergy and Immunology Unit, University of Cape Town Lung Institute (Pty) Ltd, George Street, Mowbray, Cape Town, 7700, Western Cape, South Africa
| |
Collapse
|
2
|
Osler TS, Brandenburg JT, Schoeman M, Chen WC, Urban MF, Mathew CG. Prevalence and Reclassification of Genetic Variants in South African Populations with Breast Cancer. Genes Chromosomes Cancer 2024; 63:e23275. [PMID: 39324485 DOI: 10.1002/gcc.23275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 09/06/2024] [Indexed: 09/27/2024] Open
Abstract
Concurrent testing of numerous genes for hereditary breast cancer (BC) is available but can result in management difficulties. We evaluated use of an expanded BC gene panel in women of diverse South African ancestries and assessed use of African genomic data to reclassify variants of uncertain significance (VUS). A total of 331 women of White, Black African, or Mixed Ancestry with BC had a 9-gene panel test, with an additional 75 genes tested in those without a pathogenic/likely pathogenic (P/LP) variant. The proportion of VUS reclassified using ClinGen gene-specific allele frequency (AF) thresholds or an AF > 0.001 in nonguidelines genes in African genomic data was determined. The 9-gene panel identified 58 P/LP variants, but only two of the P/LP variants detected using the 75-gene panel were in confirmed BC genes, resulting in a total of 60 (18.1%) in all participants. P/LP variant prevalence was similar across ancestry groups, but VUS prevalence was higher in Black African and Mixed Ancestry than in White participants. In total, 611 VUS were detected, representing 324 distinct variants. 10.8% (9/83) of VUS met ClinGen AF thresholds in genomic data while 10.8% (26/240) in nonguideline genes had an AF > 0.001. Overall, 27.0% of VUS occurrences could potentially be reclassified using African genomic data. Thus, expanding the gene panel yielded few clinically actionable variants but many VUS, particularly in participants of Black African and Mixed Ancestry. However, use of African genomic data has the potential to reclassify a significant proportion of VUS.
Collapse
Affiliation(s)
- Tabitha S Osler
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mardelle Schoeman
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, University of Stellenbosch and Tygerberg Hospital, Cape Town, Parow, South Africa
| | - Wenlong Carl Chen
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Cancer Registry, National Institute for Communicable Diseases a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Michael F Urban
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Sciences, University of Stellenbosch and Tygerberg Hospital, Cape Town, Parow, South Africa
| | - Christopher G Mathew
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, UK
| |
Collapse
|
3
|
Kullo IJ. Promoting equity in polygenic risk assessment through global collaboration. Nat Genet 2024; 56:1780-1787. [PMID: 39103647 DOI: 10.1038/s41588-024-01843-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 06/24/2024] [Indexed: 08/07/2024]
Abstract
The long delay before genomic technologies become available in low- and middle-income countries is a concern from both scientific and ethical standpoints. Polygenic risk scores (PRSs), a relatively recent advance in genomics, could have a substantial impact on promoting health by improving disease risk prediction and guiding preventive strategies. However, clinical use of PRSs in their current forms might widen global health disparities, as their portability to diverse groups is limited. This Perspective highlights the need for global collaboration to develop and implement PRSs that perform equitably across the world. Such collaboration requires capacity building and the generation of new data in low-resource settings, the sharing of harmonized genotype and phenotype data securely across borders, novel population genetics and statistical methods to improve PRS performance, and thoughtful clinical implementation in diverse settings. All this needs to occur while considering the ethical, legal and social implications, with support from regulatory and funding agencies and policymakers.
Collapse
Affiliation(s)
- Iftikhar J Kullo
- Department of Cardiovascular Medicine and the Gonda Vascular Center, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
4
|
Kamp M, Pain O, Lewis CM, Ramsay M. Ancestry-aligned polygenic scores combined with conventional risk factors improve prediction of cardiometabolic outcomes in African populations. Genome Med 2024; 16:106. [PMID: 39187845 PMCID: PMC11346299 DOI: 10.1186/s13073-024-01377-6] [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: 12/19/2023] [Accepted: 08/12/2024] [Indexed: 08/28/2024] Open
Abstract
BACKGROUND Cardiovascular diseases (CVD) are a major health concern in Africa. Improved identification and treatment of high-risk individuals can reduce adverse health outcomes. Current CVD risk calculators are largely unvalidated in African populations and overlook genetic factors. Polygenic scores (PGS) can enhance risk prediction by measuring genetic susceptibility to CVD, but their effectiveness in genetically diverse populations is limited by a European-ancestry bias. To address this, we developed models integrating genetic data and conventional risk factors to assess the risk of developing cardiometabolic outcomes in African populations. METHODS We used summary statistics from a genome-wide association meta-analysis (n = 14,126) in African populations to derive novel genome-wide PGS for 14 cardiometabolic traits in an independent African target sample (Africa Wits-INDEPTH Partnership for Genomic Research (AWI-Gen), n = 10,603). Regression analyses assessed relationships between each PGS and corresponding cardiometabolic trait, and seven CVD outcomes (CVD, heart attack, stroke, diabetes mellitus, dyslipidaemia, hypertension, and obesity). The predictive utility of the genetic data was evaluated using elastic net models containing multiple PGS (MultiPGS) and reference-projected principal components of ancestry (PPCs). An integrated risk prediction model incorporating genetic and conventional risk factors was developed. Nested cross-validation was used when deriving elastic net models to enhance generalisability. RESULTS Our African-specific PGS displayed significant but variable within- and cross- trait prediction (max.R2 = 6.8%, p = 1.86 × 10-173). Significantly associated PGS with dyslipidaemia included the PGS for total cholesterol (logOR = 0.210, SE = 0.022, p = 2.18 × 10-21) and low-density lipoprotein (logOR = - 0.141, SE = 0.022, p = 1.30 × 10-20); with hypertension, the systolic blood pressure PGS (logOR = 0.150, SE = 0.045, p = 8.34 × 10-4); and multiple PGS associated with obesity: body mass index (max. logOR = 0.131, SE = 0.031, p = 2.22 × 10-5), hip circumference (logOR = 0.122, SE = 0.029, p = 2.28 × 10-5), waist circumference (logOR = 0.013, SE = 0.098, p = 8.13 × 10-4) and weight (logOR = 0.103, SE = 0.029, p = 4.89 × 10-5). Elastic net models incorporating MultiPGS and PPCs significantly improved prediction over MultiPGS alone. Models including genetic data and conventional risk factors were more predictive than conventional risk models alone (dyslipidaemia: R2 increase = 2.6%, p = 4.45 × 10-12; hypertension: R2 increase = 2.6%, p = 2.37 × 10-13; obesity: R2 increase = 5.5%, 1.33 × 10-34). CONCLUSIONS In African populations, CVD and associated cardiometabolic trait prediction models can be improved by incorporating ancestry-aligned PGS and accounting for ancestry. Combining PGS with conventional risk factors further enhances prediction over traditional models based on conventional factors. Incorporating data from target populations can improve the generalisability of international predictive models for CVD and associated traits in African populations.
Collapse
Affiliation(s)
- Michelle Kamp
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, The University of the Witwatersrand, Johannesburg, South Africa.
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, Psychology & Neuroscience, London, UK.
| | - Oliver Pain
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, Psychology & Neuroscience, London, UK
- Department of Medical & Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Michèle Ramsay
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, The University of the Witwatersrand, Johannesburg, South Africa.
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| |
Collapse
|
5
|
Breton G, Barham L, Mudenda G, Soodyall H, Schlebusch CM, Jakobsson M. BaTwa populations from Zambia retain ancestry of past hunter-gatherer groups. Nat Commun 2024; 15:7307. [PMID: 39181874 PMCID: PMC11344834 DOI: 10.1038/s41467-024-50733-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/19/2024] [Indexed: 08/27/2024] Open
Abstract
Sub-equatorial Africa is today inhabited predominantly by Bantu-speaking groups of Western African descent who brought agriculture to the Luangwa valley in eastern Zambia ~2000 years ago. Before their arrival the area was inhabited by hunter-gatherers, who in many cases were subsequently replaced, displaced or assimilated. In Zambia, we know little about the genetic affinities of these hunter-gatherers. We examine ancestry of two isolated communities in Zambia, known as BaTwa and possible descendants of recent hunter-gatherers. We genotype over two million genome-wide SNPs from two BaTwa populations (total of 80 individuals) and from three comparative farming populations to: (i) determine if the BaTwa carry genetic links to past hunter-gatherer-groups, and (ii) characterise the genetic affinities of past Zambian hunter-gatherer-groups. The BaTwa populations do harbour a hunter-gatherer-like genetic ancestry and Western African ancestry. The hunter-gatherer component is a unique local signature, intermediate between current-day Khoe-San ancestry from southern Africa and central African rainforest hunter-gatherer ancestry.
Collapse
Affiliation(s)
- Gwenna Breton
- Department of Organismal Biology, Human Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
- Department of Clinical Genetics and Genomics, Centre for Medical Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden.
| | - Lawrence Barham
- Department of Archaeology, Classics & Egyptology, University of Liverpool, Liverpool, UK
| | - George Mudenda
- Livingstone Museum, Livingstone, Zambia
- National Museums Board, Lusaka, Zambia
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
- Academy of Science of South Africa, Pretoria, South Africa
| | - Carina M Schlebusch
- Department of Organismal Biology, Human Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
- SciLifeLab, Uppsala, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.
- SciLifeLab, Uppsala, Sweden.
| |
Collapse
|
6
|
Hazelhurst S, Boua P, Choudhury A, Madala S, Sengupta D, Tluway F, Ramsay M. Computation of Socio-Economic Status in the AWI-Gen Project. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.22.24312411. [PMID: 39228720 PMCID: PMC11370514 DOI: 10.1101/2024.08.22.24312411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Socio-economic status of participants in many public health, epidemiological, and genome-wide association studies is an important trait of interest. It is often used in these studies as a measure of direct interest or as a covariate. The Africa Wits INDEPTH Partnership for Genomic and Environmental Research (AWI-Gen) explores genomic and environmental factors in non-communicable diseases, particularly cardio-metabolic disease. In Phase I of AWI-Gen, approximately 12,000 participants were recruited at six sites in four African countries. Participants were asked questions about asset ownership. This technical note describes how AWI-Gen computed socio-economic status from the asset register.
Collapse
Affiliation(s)
- Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Palwendé Boua
- Clinical Research Unit of Nanoro
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Siyanda Madala
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Furahini Tluway
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| |
Collapse
|
7
|
Ramsay M, Crampin AC, Bawah AA, Gitau E, Herbst K. The Value Proposition of Coordinated Population Cohorts Across Africa. Annu Rev Biomed Data Sci 2024; 7:277-294. [PMID: 39178423 DOI: 10.1146/annurev-biodatasci-020722-015026] [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: 08/25/2024]
Abstract
Building longitudinal population cohorts in Africa for coordinated research and surveillance can influence the setting of national health priorities, lead to the introduction of appropriate interventions, and provide evidence for targeted treatment, leading to better health across the continent. However, compared to cohorts from the global north, longitudinal continental African population cohorts remain scarce, are relatively small in size, and lack data complexity. As infections and noncommunicable diseases disproportionately affect Africa's approximately 1.4 billion inhabitants, African cohorts present a unique opportunity for research and surveillance. High genetic diversity in African populations and multiomic research studies, together with detailed phenotyping and clinical profiling, will be a treasure trove for discovery. The outcomes, including novel drug targets, biological pathways for disease, and gene-environment interactions, will boost precision medicine approaches, not only in Africa but across the globe.
Collapse
Affiliation(s)
- Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa;
| | - Amelia C Crampin
- Malawi Epidemiology and Intervention Research Unit, Lilongwe, Malawi
| | - Ayaga A Bawah
- Regional Institute for Population Studies, University of Ghana, Accra, Ghana
| | - Evelyn Gitau
- African Population and Health Research Center, Nairobi, Kenya
| | - Kobus Herbst
- Africa Health Research Institute, Durban, South Africa
- South African Population Research Infrastructure Network, Department of Science and Innovation and South African Medical Research Council, Durban, South Africa
| |
Collapse
|
8
|
Bahmani A, Cha K, Alavi A, Dixit A, Ross A, Park R, Goncalves F, Ma S, Saxman P, Nair R, Akhavan-Sarraf R, Zhou X, Wang M, Contrepois K, Than JLP, Monte E, Rodriguez DJF, Lai J, Babu M, Tondar A, Rose SMSF, Akbari I, Zhang X, Yegnashankaran K, Yracheta J, Dale K, Miller AD, Edmiston S, McGhee EM, Nebeker C, Wu JC, Kundaje A, Snyder M. Achieving Inclusive Healthcare through Integrating Education and Research with AI and Personalized Curricula. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.31.24311182. [PMID: 39211867 PMCID: PMC11361244 DOI: 10.1101/2024.07.31.24311182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Precision medicine promises significant health benefits but faces challenges such as the need for complex data management and analytics, interdisciplinary collaboration, and education of researchers, healthcare professionals, and participants. Addressing these needs requires the integration of computational experts, engineers, designers, and healthcare professionals to develop user-friendly systems and shared terminologies. The widespread adoption of large language models (LLMs) like GPT-4 and Claude 3 highlights the importance of making complex data accessible to non-specialists. The Stanford Data Ocean (SDO) strives to mitigate these challenges through a scalable, cloud-based platform that supports data management for various data types, advanced research, and personalized learning in precision medicine. SDO provides AI tutors and AI-powered data visualization tools to enhance educational and research outcomes and make data analysis accessible for users from diverse educational backgrounds. By extending engagement and cutting-edge research capabilities globally, SDO particularly benefits economically disadvantaged and historically marginalized communities, fostering interdisciplinary biomedical research and bridging the gap between education and practical application in the biomedical field.
Collapse
|
9
|
Wiener E, Cottino L, Botha G, Nyangiri O, Noyes H, McLeod A, Jakubosky D, Adebamowo C, Awadalla P, Landouré G, Matshaba M, Matovu E, Ramsay M, Simo G, Simuunza M, Tiemessen C, Wonkam A, Sahibdeen V, Krause A, Lombard Z, Hazelhurst S. An assessment of the genomic structural variation landscape in Sub-Saharan African populations. RESEARCH SQUARE 2024:rs.3.rs-4485126. [PMID: 39041024 PMCID: PMC11261963 DOI: 10.21203/rs.3.rs-4485126/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Structural variants are responsible for a large part of genomic variation between individuals and play a role in both common and rare diseases. Databases cataloguing structural variants notably do not represent the full spectrum of global diversity, particularly missing information from most African populations. To address this representation gap, we analysed 1,091 high-coverage African genomes, 545 of which are public data sets, and 546 which have been analysed for structural variants for the first time. Variants were called using five different tools and datasets merged and jointly called using SURVIVOR. We identified 67,795 structural variants throughout the genome, with 10,421 genes having at least one variant. Using a conservative overlap in merged data, 6,414 of the structural variants (9.5%) are novel compared to the Database of Genomic Variants. This study contributes to knowledge of the landscape of structural variant diversity in Africa and presents a reliable dataset for potential applications in population genetics and health-related research.
Collapse
Affiliation(s)
- Emma Wiener
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Laura Cottino
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gerrit Botha
- Computational Biology Unit, University of Cape Town, Cape Town, South Africa
| | - Oscar Nyangiri
- College of Veterinary Medicine, Animal Resources and Biosecurity Makerere University, Kampala, Uganda
| | - Harry Noyes
- Centre for Genomic Research, University of Liverpool, Liverpool, United Kingdom
| | - Annette McLeod
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - David Jakubosky
- Department of Biomedical Informatics, University of California, San Diego, United States of America
- Institute of Genomic Medicine, University of California, San Diego, United States of America
| | - Clement Adebamowo
- Department of Epidemiology and Public Health and Greenebaum Comprehensive Cancer Center University of Maryland School of Medicine, Baltimore, United States of America
| | - Phillip Awadalla
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Guida Landouré
- Faculty of Medicine and Odontostomatology University of Sciences, Techniques and Technology of Bamako, Bamako Mali
- Neurology Department Point ”G” University Hospital, Bamako, Mali
| | - Mogomotsi Matshaba
- Botswana-Baylor Children’s Clinical Center of Excellence, Gaborone, Botswana
- Baylor College of Medicine, Houston, United States
| | - Enock Matovu
- College of Veterinary Medicine, Animal Resources and Biosecurity Makerere University, Kampala, Uganda
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Gustave Simo
- Molecular Parasitology and Entomology Unit, Department of Biochemistry University of Dschang, Dschang, Cameroon
| | - Martin Simuunza
- Department of Disease Control, School of Veterinary Medicine University of Zambia, Lusaka, Zambia
| | - Caroline Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health Sciences University of the Witwatersrand, Johannesburg, South Africa
| | - Ambroise Wonkam
- McKusick-Nathans Institute and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States of America
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Venesa Sahibdeen
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | | |
Collapse
|
10
|
Chikowore T, Läll K, Micklesfield LK, Lombard Z, Goedecke JH, Fatumo S, Norris SA, Magi R, Ramsay M, Franks PW, Pare G, Morris AP. Variability of polygenic prediction for body mass index in Africa. Genome Med 2024; 16:74. [PMID: 38816834 PMCID: PMC11140909 DOI: 10.1186/s13073-024-01348-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 05/21/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Polygenic prediction studies in continental Africans are scarce. Africa's genetic and environmental diversity pose a challenge that limits the generalizability of polygenic risk scores (PRS) for body mass index (BMI) within the continent. Studies to understand the factors that affect PRS variability within Africa are required. METHODS Using the first multi-ancestry genome-wide association study (GWAS) meta-analysis for BMI involving continental Africans, we derived a multi-ancestry PRS and compared its performance to a European ancestry-specific PRS in continental Africans (AWI-Gen study) and a European cohort (Estonian Biobank). We then evaluated the factors affecting the performance of the PRS in Africans which included fine-mapping resolution, allele frequencies, linkage disequilibrium patterns, and PRS-environment interactions. RESULTS Polygenic prediction of BMI in continental Africans is poor compared to that in European ancestry individuals. However, we show that the multi-ancestry PRS is more predictive than the European ancestry-specific PRS due to its improved fine-mapping resolution. We noted regional variation in polygenic prediction across Africa's East, South, and West regions, which was driven by a complex interplay of the PRS with environmental factors, such as physical activity, smoking, alcohol intake, and socioeconomic status. CONCLUSIONS Our findings highlight the role of gene-environment interactions in PRS prediction variability in Africa. PRS methods that correct for these interactions, coupled with the increased representation of Africans in GWAS, may improve PRS prediction in Africa.
Collapse
Affiliation(s)
- Tinashe Chikowore
- SAMRC/Wits Developmental Pathways for Health Research Unit, Department of Pediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Harvard Medical School, Boston, MA, USA.
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
| | - Kristi Läll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Lisa K Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit, Department of Pediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zane Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Julia H Goedecke
- SAMRC/Wits Developmental Pathways for Health Research Unit, Department of Pediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa
| | - Segun Fatumo
- NCD Genomics, MRC/UVRI LSHTM Uganda Research Unit, Entebbe, Uganda
- Precision Healthcare University Research Institute (PHURI), Queen Mary University of London, London, UK
| | - Shane A Norris
- SAMRC/Wits Developmental Pathways for Health Research Unit, Department of Pediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Human Development and Health, University of Southampton, Southampton, UK
| | - Reedik Magi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Paul W Franks
- Department of Clinical Sciences, Lund University, Helsingborg, Sweden
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Guillaume Pare
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK.
| |
Collapse
|
11
|
Brandenburg JT, Chen WC, Boua PR, Govender MA, Agongo G, Micklesfield LK, Sorgho H, Tollman S, Asiki G, Mashinya F, Hazelhurst S, Morris AP, Fabian J, Ramsay M. Genetic association and transferability for urinary albumin-creatinine ratio as a marker of kidney disease in four Sub-Saharan African populations and non-continental individuals of African ancestry. Front Genet 2024; 15:1372042. [PMID: 38812969 PMCID: PMC11134365 DOI: 10.3389/fgene.2024.1372042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/12/2024] [Indexed: 05/31/2024] Open
Abstract
Background Genome-wide association studies (GWAS) have predominantly focused on populations of European and Asian ancestry, limiting our understanding of genetic factors influencing kidney disease in Sub-Saharan African (SSA) populations. This study presents the largest GWAS for urinary albumin-to-creatinine ratio (UACR) in SSA individuals, including 8,970 participants living in different African regions and an additional 9,705 non-resident individuals of African ancestry from the UK Biobank and African American cohorts. Methods Urine biomarkers and genotype data were obtained from two SSA cohorts (AWI-Gen and ARK), and two non-resident African-ancestry studies (UK Biobank and CKD-Gen Consortium). Association testing and meta-analyses were conducted, with subsequent fine-mapping, conditional analyses, and replication studies. Polygenic scores (PGS) were assessed for transferability across populations. Results Two genome-wide significant (P < 5 × 10-8) UACR-associated loci were identified, one in the BMP6 region on chromosome 6, in the meta-analysis of resident African individuals, and another in the HBB region on chromosome 11 in the meta-analysis of non-resident SSA individuals, as well as the combined meta-analysis of all studies. Replication of previous significant results confirmed associations in known UACR-associated regions, including THB53, GATM, and ARL15. PGS estimated using previous studies from European ancestry, African ancestry, and multi-ancestry cohorts exhibited limited transferability of PGS across populations, with less than 1% of observed variance explained. Conclusion This study contributes novel insights into the genetic architecture of kidney disease in SSA populations, emphasizing the need for conducting genetic research in diverse cohorts. The identified loci provide a foundation for future investigations into the genetic susceptibility to chronic kidney disease in underrepresented African populations Additionally, there is a need to develop integrated scores using multi-omics data and risk factors specific to the African context to improve the accuracy of predicting disease outcomes.
Collapse
Affiliation(s)
- Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Wenlong Carl Chen
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
| | - Palwende Romuald Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso
| | | | - Godfred Agongo
- Navrongo Health Research Centre, Navrongo, Ghana
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C. K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Lisa K. Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso
| | - Stephen Tollman
- Medical Research Council/Wits University Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gershim Asiki
- African Population and Health Research Center, Nairobi, Kenya
- Department of Women’s and Children’s Health, Karolinska Institute, Stockholm, Sweden
| | - Felistas Mashinya
- Department of Pathology and Medical Sciences, School of Healthcare Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrew P. Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, United Kingdom
| | - June Fabian
- Medical Research Council/Wits University Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Wits Donald Gordon Medical Centre, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
12
|
Brandenburg JT, Chen WC, Boua PR, Govender MA, Agongo G, Micklesfield LK, Sorgho H, Tollman S, Asiki G, Mashinya F, Hazelhurst S, Morris AP, Fabian J, Ramsay M. Genetic Association and Transferability for Urinary Albumin-Creatinine Ratio as a Marker of Kidney Disease in four Sub-Saharan African Populations and non-continental Individuals of African Ancestry. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.17.24301398. [PMID: 38293229 PMCID: PMC10827237 DOI: 10.1101/2024.01.17.24301398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
BACKGROUND Genome-wide association studies (GWAS) have predominantly focused on populations of European and Asian ancestry, limiting our understanding of genetic factors influencing kidney disease in Sub-Saharan African (SSA) populations. This study presents the largest GWAS for urinary albumin-to-creatinine ratio (UACR) in SSA individuals, including 8,970 participants living in different African regions and an additional 9,705 non-resident individuals of African ancestry from the UK Biobank and African American cohorts. METHODS Urine biomarkers and genotype data were obtained from two SSA cohorts (AWI-Gen and ARK), and two non-resident African-ancestry studies (UK Biobank and CKD-Gen Consortium). Association testing and meta-analyses were conducted, with subsequent fine-mapping, conditional analyses, and replication studies. Polygenic scores (PGS) were assessed for transferability across populations. RESULTS Two genome-wide significant (P<5x10-8) UACR-associated loci were identified, one in the BMP6 region on chromosome 6, in the meta-analysis of resident African individuals, and another in the HBB region on chromosome 11 in the meta-analysis of non-resident SSA individuals, as well as the combined meta-analysis of all studies. Replication of previous significant results confirmed associations in known UACR-associated regions, including THB53, GATM, and ARL15. PGS estimated using previous studies from European ancestry, African ancestry, and multi-ancestry cohorts exhibited limited transferability of PGS across populations, with less than 1% of observed variance explained. CONCLUSION This study contributes novel insights into the genetic architecture of kidney disease in SSA populations, emphasizing the need for conducting genetic research in diverse cohorts. The identified loci provide a foundation for future investigations into the genetic susceptibility to chronic kidney disease in underrepresented African populations Additionally, there is a need to develop integrated scores using multi-omics data and risk factors specific to the African context to improve the accuracy of predicting disease outcomes. METHODS Urine biomarkers and genotype data were obtained from two SSA cohorts (AWI-Gen and ARK), and two non-resident African-ancestry studies (UK Biobank and CKD-Gen Consortium). Association testing and meta-analyses were conducted, with subsequent fine-mapping, conditional analyses, and replication studies. Polygenic scores (PGS) were assessed for transferability across populations. RESULTS Two genome-wide significant (P<5x10-8) UACR-associated loci were identified, one in the BMP6 region on chromosome 6, in the meta-analysis of resident African individuals, and another in the HBB region on chromosome 11 in the meta-analysis of non-resident SSA individuals, as well as the combined meta-analysis of all studies. Replication of previous significant results confirmed associations in known UACR-associated regions, including THB53, GATM, and ARL15. PGS estimated using previous studies from European ancestry, African ancestry, and multi-ancestry cohorts exhibited limited transferability of PGS across populations, with less than 1% of observed variance explained. CONCLUSION This study contributes novel insights into the genetic architecture of kidney function in SSA populations, emphasizing the need for conducting genetic research in diverse cohorts. The identified loci provide a foundation for future investigations into the genetic susceptibility to chronic kidney disease in underrepresented African populations.
Collapse
|
13
|
Maghini DG, Oduaran OH, Wirbel J, Olubayo LAI, Smyth N, Mathema T, Belger CW, Agongo G, Boua PR, Choma SSR, Gómez-Olivé FX, Kisiangani I, Mashaba GR, Micklesfield L, Mohamed SF, Nonterah EA, Norris S, Sorgho H, Tollman S, Wafawanaka F, Tluway F, Ramsay M, Bhatt AS, Hazelhurst S. Expanding the human gut microbiome atlas of Africa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584859. [PMID: 38559015 PMCID: PMC10980044 DOI: 10.1101/2024.03.13.584859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world's population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.
Collapse
Affiliation(s)
- Dylan G Maghini
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Jakob Wirbel
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Luicer A Ingasia Olubayo
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Natalie Smyth
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Theophilous Mathema
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Carl W Belger
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, C. K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Palwendé R Boua
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Solomon SR Choma
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Given R Mashaba
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - Lisa Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Shane Norris
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Human Development and Health, University of Southampton, Southampton, United Kingdom
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Furahini Tluway
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Ami S Bhatt
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
14
|
Masango B, Goedecke JH, Ramsay M, Storbeck KH, Micklesfield LK, Chikowore T. Postprandial glucose variability and clusters of sex hormones, liver enzymes, and cardiometabolic factors in a South African cohort of African ancestry. BMJ Open Diabetes Res Care 2024; 12:e003927. [PMID: 38453238 PMCID: PMC10921533 DOI: 10.1136/bmjdrc-2023-003927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024] Open
Abstract
INTRODUCTION This study aimed to, first, determine the clusters of sex hormones, liver enzymes, and cardiometabolic factors associated with postprandial glucose (PPG) and, second to evaluate the variation these clusters account for jointly and independently with polygenic risk scores (PRSs) in South Africans of African ancestry men and women. RESEARCH DESIGN AND METHODS PPG was calculated as the integrated area under the curve for glucose during the oral glucose tolerance test (OGTT) using the trapezoidal rule in 794 participants from the Middle-aged Soweto Cohort. Principal component analysis was used to cluster sex hormones, liver enzymes, and cardiometabolic factors, stratified by sex. Multivariable linear regression was used to assess the proportion of variance in PPG accounted for by principal components (PCs) and type 2 diabetes (T2D) PRS while adjusting for selected covariates in men and women. RESULTS The T2D PRS did not contribute to the PPG variability in both men and women. In men, the PCs' cluster of sex hormones, liver enzymes, and cardiometabolic explained 10.6% of the variance in PPG, with PC1 (peripheral fat), PC2 (liver enzymes and steroid hormones), and PC3 (lipids and peripheral fat) contributing significantly to PPG. In women, PC factors of sex hormones, cardiometabolic factors, and liver enzymes explained a similar amount of the variance in PPG (10.8%), with PC1 (central fat) and PC2 (lipids and liver enzymes) contributing significantly to PPG. CONCLUSIONS We demonstrated that inter-individual differences in PPG responses to an OGTT may be differentially explained by body fat distribution, serum lipids, liver enzymes, and steroid hormones in men and women.
Collapse
Affiliation(s)
- Bontle Masango
- Division of Human Genetics, National Health Laboratory Service (NHLS), School of Pathology, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa
- South African Medical Research Council/University of the Witwatersrand, Developmental Pathways for Health Research Unit (DPHRU), University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa
| | - Julia H Goedecke
- South African Medical Research Council/University of the Witwatersrand, Developmental Pathways for Health Research Unit (DPHRU), University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa
| | - Karl-Heinz Storbeck
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Lisa K Micklesfield
- South African Medical Research Council/University of the Witwatersrand, Developmental Pathways for Health Research Unit (DPHRU), University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa
| | - Tinashe Chikowore
- South African Medical Research Council/University of the Witwatersrand, Developmental Pathways for Health Research Unit (DPHRU), University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa
- Harvard Medical School, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| |
Collapse
|
15
|
Twesigomwe D, Drögemöller BI, Wright GEB, Adebamowo C, Agongo G, Boua PR, Matshaba M, Paximadis M, Ramsay M, Simo G, Simuunza MC, Tiemessen CT, Lombard Z, Hazelhurst S. Characterization of CYP2B6 and CYP2A6 Pharmacogenetic Variation in Sub-Saharan African Populations. Clin Pharmacol Ther 2024; 115:576-594. [PMID: 38049200 DOI: 10.1002/cpt.3124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/16/2023] [Indexed: 12/06/2023]
Abstract
Genetic variation in CYP2B6 and CYP2A6 is known to impact interindividual response to antiretrovirals, nicotine, and bupropion, among other drugs. However, the full catalogue of clinically relevant pharmacogenetic variants in these genes is yet to be established, especially across African populations. This study therefore aimed to characterize the star allele (haplotype) distribution in CYP2B6 and CYP2A6 across diverse and understudied sub-Saharan African (SSA) populations. We called star alleles from 961 high-depth full genomes using StellarPGx, Aldy, and PyPGx. In addition, we performed CYP2B6 and CYP2A6 star allele frequency comparisons between SSA and other global biogeographical groups represented in the new 1000 Genomes Project high-coverage dataset (n = 2,000). This study presents frequency information for star alleles in CYP2B6 (e.g., *6 and *18; frequency of 21-47% and 2-19%, respectively) and CYP2A6 (e.g., *4, *9, and *17; frequency of 0-6%, 3-10%, and 6-20%, respectively), and predicted phenotypes (for CYP2B6), across various African populations. In addition, 50 potentially novel African-ancestry star alleles were computationally predicted by StellarPGx in CYP2B6 and CYP2A6 combined. For each of these genes, over 4% of the study participants had predicted novel star alleles. Three novel star alleles in CYP2A6 (*54, *55, and *56) and CYP2B6 apiece, and several suballeles were further validated via targeted Single-Molecule Real-Time resequencing. Our findings are important for informing the design of comprehensive pharmacogenetic testing platforms, and are highly relevant for personalized medicine strategies, especially relating to antiretroviral medication and smoking cessation treatment in Africa and the African diaspora. More broadly, this study highlights the importance of sampling diverse African ethnolinguistic groups for accurate characterization of the pharmacogene variation landscape across the continent.
Collapse
Affiliation(s)
- David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Britt I Drögemöller
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Galen E B Wright
- Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Winnipeg Health Sciences Centre and Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Clement Adebamowo
- Institute for Human Virology, Abuja, Nigeria
- Division of Cancer Epidemiology, Department of Epidemiology and Public Health, and the Marlene and Stewart Greenebaum Comprehensive Cancer Centre, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Godfred Agongo
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C.K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Palwendé R Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso
| | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
- Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gustave Simo
- Molecular Parasitology and Entomology Unit, Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Martin C Simuunza
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
16
|
Okekunle AP, Asowata OJ, Akpa OM, Fakunle AG, Chikowore T, Mohamed SF, Obiako R, Komolafe M, Osaigbovo GO, Ogbole G, Arulogun O, Sarfo FS, Wahab K, Owolabi L, Akinyemi J, Akpalu A, Uvere E, Akinyemi R, Jenkins C, Arnett DK, Lackland D, Ovbiagele B, Ramsay M, Owolabi M. Factors associated with frequency of fruit and vegetable consumption among selected sub-Saharan African populations: evidence from the Cardiovascular H3Africa Innovation Resource Project. Int J Epidemiol 2024; 53:dyad171. [PMID: 38199785 PMCID: PMC10859155 DOI: 10.1093/ije/dyad171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Frequent fruit and vegetable consumption is considered a promising dietary behaviour that protects health. However, most existing studies about the factors associated with this phenomenon among Africans are based on single-country reports, apart from one meta-regression combining smaller studies. This study harmonized large datasets and assessed factors associated with the frequency of fruit and vegetable consumption in this population. METHODS Individual-level data on sociodemographics, lifestyle and diet from 20 443 participants across five African countries (Burkina Faso, Ghana, Kenya, South Africa and Nigeria), from the Stroke Investigative Research and Educational Network (SIREN) and Africa Wits-INDEPTH partnership for Genomic Research (AWI-Gen) studies, were harmonized. Total frequency of fruit and vegetable consumption (in portions/week) was classified as 'low' (≤6), 'moderate' (7-14) and 'high' (≥15). Adjusted odds ratios (aORs) and 95% confidence intervals (CIs) of factors associated with the total frequency of fruit and vegetable consumption (using 'low' consumption as the reference) were estimated using multinomial regression models. RESULTS Mean age of participants was 54.3 ± 11.8 years, 10 641 (52.1%) were female, and the median (interquartile range) frequency of total fruit and vegetable consumption was 10.0 (4.0, 21.0) portions/week. Participants with a family history of cardiovascular disease [moderate (aOR, 0.92; 95% CI, 0.85, 1.00) and high (aOR, 0.85; 95% CI, 0.78, 0.92)], current smokers [moderate (aOR, 0.83; 95% CI, 0.74, 0.94) and high (aOR, 0.78; 95% CI, 0.69, 0.88)], current alcohol users [moderate (aOR, 0.92; 95% CI, 0.85, 1.00) and high (aOR, 0.82; 95% CI, 0.76, 0.89)] and physically inactive participants [moderate (aOR, 0.85; 95% CI, 0.75, 0.96) and high (aOR, 0.80; 95% CI, 0.70, 0.90)] were less likely to consume fruits and vegetables frequently. CONCLUSION Africans with lifestyle risk factors for cardiovascular disease were less likely to consume fruit and vegetables frequently.
Collapse
Affiliation(s)
- Akinkunmi Paul Okekunle
- Department of Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Food and Nutrition, Seoul National University, Seoul, Korea
| | - Osahon Jeffery Asowata
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Onoja Matthew Akpa
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Institute of Cardiovascular Diseases, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Adekunle Gregory Fakunle
- Department of Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Public Health, College of Health Sciences, Osun State University, Osogbo, Nigeria
| | - Tinashe Chikowore
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular, Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shukri F Mohamed
- Health and Well-Being Program, African Population and Health Research Center, Nairobi, Kenya
| | - Reginald Obiako
- Department of Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Morenikeji Komolafe
- Department of Medicine, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | | | - Godwin Ogbole
- Department of Radiology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oyedunni Arulogun
- Department of Health Promotion and Education, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Fred Stephen Sarfo
- Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Kolawole Wahab
- Department of Medicine, University of Ilorin Teaching Hospital, Ilorin, Nigeria
| | - Lukman Owolabi
- Department of Medicine, Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Joshua Akinyemi
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Albert Akpalu
- Department of Medicine, University of Ghana Medical School, Accra, Ghana
| | - Ezinne Uvere
- Department of Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Rufus Akinyemi
- Neuroscience and Ageing Research Unit, Institute for Advanced Medical Research and Training College of Medicine, University of Ibadan, Ibadan, Nigeria
- Center for Genomic and Precision Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Carolyn Jenkins
- Department of Nursing, Medical University of South Carolina, Charleston, SC, USA
| | - Donna K Arnett
- Office of the Provost, University of South Carolina, Charleston, SC, USA
| | - Daniel Lackland
- Department of Neurology, Medical University of South Carolina, Charleston, SC, USA
| | - Bruce Ovbiagele
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular, Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Mayowa Owolabi
- Department of Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Center for Genomic and Precision Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
- School of Medicine, Lebanese American University, Beirut, Lebanon
- Department of Medicine, University College Hospital, Ibadan, Nigeria
| |
Collapse
|
17
|
Singh S, Choudhury A, Hazelhurst S, Crowther NJ, Boua PR, Sorgho H, Agongo G, Nonterah EA, Micklesfield LK, Norris SA, Kisiangani I, Mohamed S, Gómez-Olivé FX, Tollman SM, Choma S, Brandenburg JT, Ramsay M. Genome-wide association study meta-analysis of blood pressure traits and hypertension in sub-Saharan African populations: an AWI-Gen study. Nat Commun 2023; 14:8376. [PMID: 38104120 PMCID: PMC10725455 DOI: 10.1038/s41467-023-44079-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
Most hypertension-related genome-wide association studies (GWASs) focus on non-African populations, despite hypertension (a major risk factor for cardiovascular disease) being highly prevalent in Africa. The AWI-Gen study GWAS meta-analysis for blood pressure (BP)-related traits (systolic and diastolic BP, pulse pressure, mean-arterial pressure and hypertension) from three sub-Saharan African geographic regions (N = 10,775), identifies two novel genome-wide significant signals (p < 5E-08): systolic BP near P2RY1 (rs77846204; intergenic variant, p = 4.95E-08) and pulse pressure near LINC01256 (rs80141533; intergenic variant, p = 1.76E-08). No genome-wide signals are detected for the AWI-Gen GWAS meta-analysis with previous African-ancestry GWASs (UK Biobank (African), Uganda Genome Resource). Suggestive signals (p < 5E-06) are observed for all traits, with 29 SNPs associating with more than one trait and several replicating known associations. Polygenic risk scores (PRSs) developed from studies on different ancestries have limited transferability, with multi-ancestry PRS providing better prediction. This study provides insights into the genetics of BP variation in African populations.
Collapse
Affiliation(s)
- Surina Singh
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Nigel J Crowther
- Department of Chemical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Palwendé R Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Sante, Ouagadougou, Burkina Faso
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Sante, Ouagadougou, Burkina Faso
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C.K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Engelbert A Nonterah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Julius Global Health, Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Lisa K Micklesfield
- SAMRC Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shane A Norris
- SAMRC Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Health and Human Development, University of Southampton, Southampton, UK
| | | | - Shukri Mohamed
- African Population and Health Research Center, Nairobi, Kenya
| | - Francesc X Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen M Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Solomon Choma
- Department of Medical Science, Public Health and Health Promotion, School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - J-T Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Strengthening Oncology Services, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| |
Collapse
|
18
|
Sleiman PM, Qu HQ, Connolly JJ, Mentch F, Pereira A, Lotufo PA, Tollman S, Choudhury A, Ramsay M, Kato N, Ozaki K, Mitsumori R, Jeon JP, Hong CH, Son SJ, Roh HW, Lee DG, Mukadam N, Foote IF, Marshall CR, Butterworth A, Prins BP, Glessner JT, Hakonarson H. Trans-ethnic genomic informed risk assessment for Alzheimer's disease: An International Hundred K+ Cohorts Consortium study. Alzheimers Dement 2023; 19:5765-5772. [PMID: 37450379 PMCID: PMC10854406 DOI: 10.1002/alz.13378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/26/2023] [Accepted: 05/05/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND As a collaboration model between the International HundredK+ Cohorts Consortium (IHCC) and the Davos Alzheimer's Collaborative (DAC), our aim was to develop a trans-ethnic genomic informed risk assessment (GIRA) algorithm for Alzheimer's disease (AD). METHODS The GIRA model was created to include polygenic risk score calculated from the AD genome-wide association study loci, the apolipoprotein E haplotypes, and non-genetic covariates including age, sex, and the first three principal components of population substructure. RESULTS We validated the performance of the GIRA model in different populations. The proteomic study in the participant sites identified proteins related to female infertility and autoimmune thyroiditis and associated with the risk scores of AD. CONCLUSIONS As the initial effort by the IHCC to leverage existing large-scale datasets in a collaborative setting with DAC, we developed a trans-ethnic GIRA for AD with the potential of identifying individuals at high risk of developing AD for future clinical applications.
Collapse
Affiliation(s)
- Patrick M. Sleiman
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Hui-Qi Qu
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - John J Connolly
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Frank Mentch
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Alexandre Pereira
- Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Centro de Pesquisas Clínicas e Epidemiológicas, Hospital Universitário, Universidade de São Paulo, São Paulo, Brazil
| | - Paulo A Lotufo
- Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Centro de Pesquisas Clínicas e Epidemiológicas, Hospital Universitário, Universidade de São Paulo, São Paulo, Brazil
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Norihiro Kato
- National Center for Global Health and Medicine, Tokyo, 1628655, Japan
| | - Kouichi Ozaki
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology (NCGG), Obu City, Aichi Prefecture, Japan
| | - Risa Mitsumori
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology (NCGG), Obu City, Aichi Prefecture, Japan
| | - Jae-Pil Jeon
- Korea Biobank Project, Korea National Institute of Health, Osong, Korea
| | - Chang Hyung Hong
- Department of Psychiatry, Ajou University School of Medicine, Suwon, Korea
| | - Sang Joon Son
- Department of Psychiatry, Ajou University School of Medicine, Suwon, Korea
| | - Hyun Woong Roh
- Department of Psychiatry, Ajou University School of Medicine, Suwon, Korea
| | - Dong-gi Lee
- Department of Psychiatry, Ajou University School of Medicine, Suwon, Korea
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Naaheed Mukadam
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, UK
| | - Isabelle F Foote
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, UK
- Genes & Health, Blizard Institute, Queen Mary University of London, UK
| | - Charles R Marshall
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, UK
- Genes & Health, Blizard Institute, Queen Mary University of London, UK
| | - Adam Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Bram P Prins
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joseph T Glessner
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Division of Pulmonary Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| |
Collapse
|
19
|
Fatumo S, Sathan D, Samtal C, Isewon I, Tamuhla T, Soremekun C, Jafali J, Panji S, Tiffin N, Fakim YJ. Polygenic risk scores for disease risk prediction in Africa: current challenges and future directions. Genome Med 2023; 15:87. [PMID: 37904243 PMCID: PMC10614359 DOI: 10.1186/s13073-023-01245-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 10/12/2023] [Indexed: 11/01/2023] Open
Abstract
Early identification of genetic risk factors for complex diseases can enable timely interventions and prevent serious outcomes, including mortality. While the genetics underlying many Mendelian diseases have been elucidated, it is harder to predict risk for complex diseases arising from the combined effects of many genetic variants with smaller individual effects on disease aetiology. Polygenic risk scores (PRS), which combine multiple contributing variants to predict disease risk, have the potential to influence the implementation for precision medicine. However, the majority of existing PRS were developed from European data with limited transferability to African populations. Notably, African populations have diverse genetic backgrounds, and a genomic architecture with smaller haplotype blocks compared to European genomes. Subsequently, growing evidence shows that using large-scale African ancestry cohorts as discovery for PRS development may generate more generalizable findings. Here, we (1) discuss the factors contributing to the poor transferability of PRS in African populations, (2) showcase the novel Africa genomic datasets for PRS development, (3) explore the potential clinical utility of PRS in African populations, and (4) provide insight into the future of PRS in Africa.
Collapse
Affiliation(s)
- Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda.
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria.
- Department of Non-Communicable Disease Epidemiology (NCDE), London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
| | - Dassen Sathan
- H3Africa Bioinformatics Network (H3ABioNet) Node, University of Mauritius, Reduit, Mauritius
| | - Chaimae Samtal
- Laboratory of Biotechnology, Environment, Agri-Food and Health, Faculty of Sciences Dhar El Mahraz-Sidi Mohammed Ben Abdellah University, 30000, Fez, Morocco
| | - Itunuoluwa Isewon
- Department of Computer and Information Sciences, Covenant University, P. M. B. 1023, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Km 10 Idiroko Road, P.M.B. 1023, Ota, Ogun State, Nigeria
- Covenant Applied Informatics and Communication African Centre of Excellence (CApIC-ACE), Covenant University, P.M.B. 1023, Ota, Ogun State, Nigeria
| | - Tsaone Tamuhla
- Division of Computational Biology, Integrative Biomedical Sciences Department, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Chisom Soremekun
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
- Department of Immunology and Molecular Biology, College of Health Science, Makerere University, Kampala, Uganda
| | - James Jafali
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Clinical Infection, Microbiology & Immunology, The University of Liverpool, Liverpool, UK
| | - Sumir Panji
- Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Nicki Tiffin
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | | |
Collapse
|
20
|
Gao S, Rohr JK, de Vivo I, Ramsay M, Krieger N, Kabudula CW, Farrell MT, Bassil DT, Harriman NW, Corona-Perez D, Pesic K, Berkman LF. Telomere Length, Health, and Mortality in a Cohort of Older Black South African Adults. J Gerontol A Biol Sci Med Sci 2023; 78:1983-1990. [PMID: 37352164 PMCID: PMC10613001 DOI: 10.1093/gerona/glad153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Indexed: 06/25/2023] Open
Abstract
Telomere length (TL) may be a biomarker of aging processes as well as age-related diseases. However, most studies of TL and aging are conducted in high-income countries. Less is known in low- and middle-income countries (LMICs) such as South Africa, where life expectancy remains lower despite population aging. We conducted a descriptive analysis of TL in a cohort of older adults in rural South Africa. TL was assayed from venous blood draws using quantitative polymerase chain reaction (T/S ratio). We examined the correlation between TL and biomarkers, demographic characteristics, mental/cognitive health measures, and physical performance measures in a subsample of the Wave 1 2014-2015 "Health and Aging in Africa: A Longitudinal Study of an INDEPTH Community in South Africa" (HAALSI) cohort (n = 510). We used logistic regression to measure the association between TL and mortality through Wave 3 (2021-2022). In bivariate analyses, TL was significantly correlated with age (r = -0.29, p < .0001), self-reported female sex (r = 0.13, p = .002), mortality (r = -0.1297, p = .003), diastolic blood pressure (r = 0.09, p = .037), pulse pressure (r = -0.09, p = .045), and being a grandparent (r = -0.17, p = .0001). TL was significantly associated with age (β = -0.003; 95% confidence interval [CI] = -0.005, -0.003). TL was significantly associated in unadjusted multivariate analyses with mortality, but the relationship between TL and mortality was attenuated after adjusting for age (odds ratio [OR] = 0.19; 95% CI = 0.03, 1.27) and other covariates (OR = 0.17; 95% CI = 0.02, 1.19). Our study is the first analysis of TL in an older adult South African population. Our results corroborate existing relationships between TL and age, sex, cardiometabolic disease, and mortality found in higher-income countries.
Collapse
Affiliation(s)
- Sarah Gao
- Harvard Center for Population and Development Studies, Harvard University, Cambridge, Massachusetts, USA
| | - Julia K Rohr
- Harvard Center for Population and Development Studies, Harvard University, Cambridge, Massachusetts, USA
| | - Immaculata de Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Nancy Krieger
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Meagan T Farrell
- Harvard Center for Population and Development Studies, Harvard University, Cambridge, Massachusetts, USA
| | - Darina T Bassil
- Harvard Center for Population and Development Studies, Harvard University, Cambridge, Massachusetts, USA
| | - Nigel W Harriman
- Harvard Center for Population and Development Studies, Harvard University, Cambridge, Massachusetts, USA
| | - Diana Corona-Perez
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Katarina Pesic
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Lisa F Berkman
- Harvard Center for Population and Development Studies, Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
21
|
Zass L, Johnston K, Benkahla A, Chaouch M, Kumuthini J, Radouani F, Mwita LA, Alsayed N, Allie T, Sathan D, Masamu U, Seuneu Tchamga MS, Tamuhla T, Samtal C, Nembaware V, Gill Z, Ahmed S, Hamdi Y, Fadlelmola F, Tiffin N, Mulder N. Developing Clinical Phenotype Data Collection Standards for Research in Africa. Glob Health Epidemiol Genom 2023; 2023:6693323. [PMID: 37766808 PMCID: PMC10522421 DOI: 10.1155/2023/6693323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 06/30/2023] [Accepted: 07/21/2023] [Indexed: 09/29/2023] Open
Abstract
Modern biomedical research is characterised by its high-throughput and interdisciplinary nature. Multiproject and consortium-based collaborations requiring meaningful analysis of multiple heterogeneous phenotypic datasets have become the norm; however, such analysis remains a challenge in many regions across the world. An increasing number of data harmonisation efforts are being undertaken by multistudy collaborations through either prospective standardised phenotype data collection or retrospective phenotype harmonisation. In this regard, the Phenotype Harmonisation Working Group (PHWG) of the Human Heredity and Health in Africa (H3Africa) consortium aimed to facilitate phenotype standardisation by both promoting the use of existing data collection standards (hosted by PhenX), adapting existing data collection standards for appropriate use in low- and middle-income regions such as Africa, and developing novel data collection standards where relevant gaps were identified. Ultimately, the PHWG produced 11 data collection kits, consisting of 82 protocols, 38 of which were existing protocols, 17 were adapted, and 27 were novel protocols. The data collection kits will facilitate phenotype standardisation and harmonisation not only in Africa but also across the larger research community. In addition, the PHWG aims to feed back adapted and novel protocols to existing reference platforms such as PhenX.
Collapse
Affiliation(s)
- Lyndon Zass
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Katherine Johnston
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Alia Benkahla
- Laboratory of BioInformatics, BioMathematics and BioStatistics LR16IPT09, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Melek Chaouch
- Laboratory of BioInformatics, BioMathematics and BioStatistics LR16IPT09, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Judit Kumuthini
- South African National Bioinformatics Institute (SANBI), Life Sciences Building, University of Western Cape, Bellville, Cape Town, South Africa
| | - Fouzia Radouani
- Chlamydiae & Mycoplasmas Laboratory Research Department, Institut Pasteur du Maroc, 20360 Casablanca, Morocco
| | - Liberata Alexander Mwita
- Muhimbili Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
| | - Nihad Alsayed
- Kush Centre for Genomics & Biomedical Informatics, Biotechnology Perspectives Organization, Khartoum 11111, Sudan
| | - Taryn Allie
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Dassen Sathan
- Software Information Systems Department, FOICDT, University of Mauritius, Reduit, Mauritius
| | - Upendo Masamu
- Muhimbili Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
| | | | - Tsaone Tamuhla
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Chaimae Samtal
- Laboratory of Biotechnology, Environment, Agri-Food and Health, Faculty of Sciences Dhar El Mahraz-Sidi Mohammed Ben Abdellah University, Fez 30000, Morocco
| | - Victoria Nembaware
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Zoe Gill
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
- Department of Molecular Biology, Johannes Gutenberg University, Mainz, Germany
| | - Samah Ahmed
- Kush Centre for Genomics & Biomedical Informatics, Biotechnology Perspectives Organization, Khartoum 11111, Sudan
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Faisal Fadlelmola
- Kush Centre for Genomics & Biomedical Informatics, Biotechnology Perspectives Organization, Khartoum 11111, Sudan
| | - Nicki Tiffin
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
- South African National Bioinformatics Institute (SANBI), Life Sciences Building, University of Western Cape, Bellville, Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Diseases and Molecular Medicine, Faculty of Cape Town, University of Cape Town, Cape Town, South Africa
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Diseases and Molecular Medicine, Faculty of Cape Town, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
22
|
Kamiza AB, Touré SM, Zhou F, Soremekun O, Cissé C, Wélé M, Touré AM, Nashiru O, Corpas M, Nyirenda M, Crampin A, Shaffer J, Doumbia S, Zeggini E, Morris AP, Asimit JL, Chikowore T, Fatumo S. Multi-trait discovery and fine-mapping of lipid loci in 125,000 individuals of African ancestry. Nat Commun 2023; 14:5403. [PMID: 37669986 PMCID: PMC10480211 DOI: 10.1038/s41467-023-41271-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
Most genome-wide association studies (GWAS) for lipid traits focus on the separate analysis of lipid traits. Moreover, there are limited GWASs evaluating the genetic variants associated with multiple lipid traits in African ancestry. To further identify and localize loci with pleiotropic effects on lipid traits, we conducted a genome-wide meta-analysis, multi-trait analysis of GWAS (MTAG), and multi-trait fine-mapping (flashfm) in 125,000 individuals of African ancestry. Our meta-analysis and MTAG identified four and 14 novel loci associated with lipid traits, respectively. flashfm yielded an 18% mean reduction in the 99% credible set size compared to single-trait fine-mapping with JAM. Moreover, we identified more genetic variants with a posterior probability of causality >0.9 with flashfm than with JAM. In conclusion, we identified additional novel loci associated with lipid traits, and flashfm reduced the 99% credible set size to identify causal genetic variants associated with multiple lipid traits in African ancestry.
Collapse
Affiliation(s)
- Abram Bunya Kamiza
- The African Computational Genomic (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda
- Malawi Epidemiology and Intervention Research Unit, Lilongwe, Malawi
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sounkou M Touré
- The African Computational Genomic (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda
- African Center of Excellence in Bioinformatics, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Feng Zhou
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Opeyemi Soremekun
- The African Computational Genomic (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda
| | - Cheickna Cissé
- African Center of Excellence in Bioinformatics, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- Faculty of Sciences and Techniques, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mamadou Wélé
- Malawi Epidemiology and Intervention Research Unit, Lilongwe, Malawi
- Faculty of Sciences and Techniques, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Aboubacrine M Touré
- Faculty of Sciences and Techniques, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Oyekanmi Nashiru
- H3Africa Bioinformatics Network (H3ABioNet) Node, Center for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Manuel Corpas
- School of Life sciences, University of Westminster, London, UK
| | - Moffat Nyirenda
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Amelia Crampin
- Malawi Epidemiology and Intervention Research Unit, Lilongwe, Malawi
| | - Jeffrey Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Seydou Doumbia
- African Center of Excellence in Bioinformatics, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- Faculty of Medicine and Odonto-stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- TUM School of Medicine, Translational Genomics, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK
| | | | - Tinashe Chikowore
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Pediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Segun Fatumo
- The African Computational Genomic (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda.
- H3Africa Bioinformatics Network (H3ABioNet) Node, Center for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria.
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
| |
Collapse
|
23
|
Littlejohn PT, Glover JS. Ethical gut microbiota research in Africa. Nat Microbiol 2023; 8:1376-1377. [PMID: 37460625 DOI: 10.1038/s41564-023-01436-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Affiliation(s)
- Paula T Littlejohn
- Department of Medical Genetics, Center for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia School of Medicine, Vancouver, British Columbia, Canada.
- Department of Pediatrics, Division of Gastroenterology, BC Children's Hospital Research Institute, University of British Columbia School of Medicine, Vancouver, British Columbia, Canada.
| | - Janiece S Glover
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA.
| |
Collapse
|
24
|
Sengupta D, Botha G, Meintjes A, Mbiyavanga M, Hazelhurst S, Mulder N, Ramsay M, Choudhury A. Performance and accuracy evaluation of reference panels for genotype imputation in sub-Saharan African populations. CELL GENOMICS 2023; 3:100332. [PMID: 37388906 PMCID: PMC10300601 DOI: 10.1016/j.xgen.2023.100332] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 02/11/2023] [Accepted: 05/02/2023] [Indexed: 07/01/2023]
Abstract
Based on evaluations of imputation performed on a genotype dataset consisting of about 11,000 sub-Saharan African (SSA) participants, we show Trans-Omics for Precision Medicine (TOPMed) and the African Genome Resource (AGR) to be currently the best panels for imputing SSA datasets. We report notable differences in the number of single-nucleotide polymorphisms (SNPs) that are imputed by different panels in datasets from East, West, and South Africa. Comparisons with a subset of 95 SSA high-coverage whole-genome sequences (WGSs) show that despite being about 20-fold smaller, the AGR imputed dataset has higher concordance with the WGSs. Moreover, the level of concordance between imputed and WGS datasets was strongly influenced by the extent of Khoe-San ancestry in a genome, highlighting the need for integration of not only geographically but also ancestrally diverse WGS data in reference panels for further improvement in imputation of SSA datasets. Approaches that integrate imputed data from different panels could also lead to better imputation.
Collapse
Affiliation(s)
- Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gerrit Botha
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ayton Meintjes
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Mamana Mbiyavanga
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
25
|
Madanhire T, Goedecke JH, Ward KA, Jaff N, Crowther NJ, Norris S, Ferrand RA, Rehman AM, Micklesfield LK, Gregson CL. The Impact of Human Immunodeficiency Virus and Menopause on Bone Mineral Density: A Longitudinal Study of Urban-Dwelling South African Women. J Bone Miner Res 2023; 38:619-630. [PMID: 36726211 PMCID: PMC10946789 DOI: 10.1002/jbmr.4765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 12/01/2022] [Accepted: 12/29/2022] [Indexed: 02/03/2023]
Abstract
An estimated 25% of South African women live with human immunodeficiency virus (HIV). Antiretroviral therapy roll-out has improved life expectancy, so many more women now reach menopause. We aimed to quantify changes in bone mineral density (BMD) during the menopausal transition in urban-dwelling South African women with and without HIV and determine whether HIV infection modified the effect of menopause on BMD changes. A 5-year population-based longitudinal study recruited women aged 40-60 years residing in Soweto and collected demographic and clinical data, including HIV status, anthropometry, and BMD, at baseline and at 5-year follow-up. All women were staged as pre-, peri-, or postmenopausal at both time points. Multivariable linear regression assessed relationships and interactions between HIV infection, menopause, and change in BMD. At baseline, 450 women had mean age 49.5 (SD 5.7) years, 65 (14.4%) had HIV, and 140 (31.1%), 119 (26.4%), and 191 (42.4%) were pre-, peri-, and postmenopausal, respectively; 34/205 (13.6%) women ≥50 years had a total hip (TH) or lumbar spine (LS) T-score ≤ -2.5. At follow-up 38 (8.4%), 84 (18.7%), and 328 (72.9%) were pre-, peri-, and postmenopausal. Those with HIV at baseline lost more total body (TB) BMD (mean difference -0.013 [95% confidence interval -0.026, -0.001] g/cm2 , p = 0.040) and gained more weight 1.96 [0.32, 3.60] kg; p = 0.019 than HIV-uninfected women. After adjusting for age, baseline weight, weight change, and follow-up time, the transition from pre- to postmenopause was associated with greater TB BMD losses in women with HIV (-0.092 [-0.042, -0.142] g/cm2 ; p = 0.001) than without HIV (-0.038 [-0.016, -0.060] g/cm2 , p = 0.001; interaction p = 0.034). Similarly, in women who were postmenopausal at both time points, those with HIV lost more TB BMD (-0.070 [-0.031, -0.108], p = 0.001) than women without HIV (-0.036 [-0.015, -0.057], p = 0.001, interaction p = 0.049). Findings were consistent but weaker at the LS and TH. Menopause-related bone loss is greater in women with HIV, suggesting women with HIV may be at greater risk of osteoporotic fractures. HIV services should consider routine bone health assessment in midlife women as part of long-term HIV care delivery. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
Collapse
Affiliation(s)
- Tafadzwa Madanhire
- SAMRC/Wits Developmental Pathways for Health Research Unit, School of Clinical Medicine, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Biomedical Research and Training InstituteHarareZimbabwe
- MRC International Statistics and Epidemiology Group, Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population HealthLondon School of Hygiene and Tropical MedicineLondonUK
| | - Julia H. Goedecke
- SAMRC/Wits Developmental Pathways for Health Research Unit, School of Clinical Medicine, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Non‐Communicable Diseases Research UnitSouth African Medical Research CouncilCape TownSouth Africa
| | - Kate A. Ward
- SAMRC/Wits Developmental Pathways for Health Research Unit, School of Clinical Medicine, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- MRC Lifecourse Epidemiology Centre, School of Human Development and HealthUniversity of SouthamptonSouthamptonUK
| | - Nicole Jaff
- Department of Chemical Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Nigel J. Crowther
- Department of Chemical Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Department of Chemical PathologyNational Health Laboratory ServiceJohannesburgSouth Africa
| | - Shane Norris
- SAMRC/Wits Developmental Pathways for Health Research Unit, School of Clinical Medicine, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Global Health Research Institute, School of Human Development and HealthUniversity of SouthamptonSouthamptonUK
| | - Rashida A. Ferrand
- Biomedical Research and Training InstituteHarareZimbabwe
- Clinical Research Department, Faculty of Infectious and Tropical DiseasesLondon School of Hygiene and Tropical MedicineLondonUK
| | - Andrea M. Rehman
- MRC International Statistics and Epidemiology Group, Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population HealthLondon School of Hygiene and Tropical MedicineLondonUK
| | - Lisa K. Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit, School of Clinical Medicine, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Celia L. Gregson
- SAMRC/Wits Developmental Pathways for Health Research Unit, School of Clinical Medicine, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| |
Collapse
|
26
|
Wade AN, Maposa I, Agongo G, Asiki G, Boua P, Choma SSR, Gómez-Olivé FX, Maimela E, Micklesfield LK, Mohamed SF, Nonterah EA, Norris SA, Sorgho H, Ramsay M, Crowther NJ. Diabetes care cascade and associated factors in 10 700 middle-aged adults in four sub-Saharan African countries: a cross-sectional study. BMJ Open 2023; 13:e069193. [PMID: 37105688 PMCID: PMC10151877 DOI: 10.1136/bmjopen-2022-069193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
OBJECTIVES We investigated progression through the care cascade and associated factors for people with diabetes in sub-Saharan Africa to identify attrition stages that may be most appropriate for targeted intervention. DESIGN Cross-sectional study. SETTING Community-based study in four sub-Saharan African countries. PARTICIPANTS 10 700 individuals, aged 40-60 years. PRIMARY AND SECONDARY OUTCOME MEASURES The primary outcome measure was the diabetes cascade of care defined as the age-adjusted diabetes prevalence (self-report of diabetes, fasting plasma glucose (FPG) ≥7 mmol/L or random plasma glucose ≥11.1 mmol/L) and proportions of those who reported awareness of having diabetes, ever having received treatment for diabetes and those who achieved glycaemic control (FPG <7.2 mmol/L). Secondary outcome measures were factors associated with having diabetes and being aware of the diagnosis. RESULTS Diabetes prevalence was 5.5% (95% CI 4.4% to 6.5%). Approximately half of those with diabetes were aware (54%; 95% CI 50% to 58%); 73% (95% CI 67% to 79%) of aware individuals reported ever having received treatment. However, only 38% (95% CI 30% to 46%) of those ever having received treatment were adequately controlled. Increasing age (OR 1.1; 95% CI 1.0 to 1.1), urban residence (OR 2.3; 95% CI 1.6 to 3.5), hypertension (OR 1.9; 95% CI 1.5 to 2.4), family history of diabetes (OR 3.9; 95% CI 3.0 to 5.1) and measures of central adiposity were associated with higher odds of having diabetes. Increasing age (OR 1.1; 95% CI 1.0 to 1.1), semi-rural residence (OR 2.5; 95% CI 1.1 to 5.7), secondary education (OR 2.4; 95% CI 1.2 to 4.9), hypertension (OR 1.6; 95% CI 1.0 to 2.4) and known HIV positivity (OR 2.3; 95% CI 1.2 to 4.4) were associated with greater likelihood of awareness of having diabetes. CONCLUSIONS There is attrition at each stage of the diabetes care cascade in sub-Saharan Africa. Public health strategies should target improving diagnosis in high-risk individuals and intensifying therapy in individuals treated for diabetes.
Collapse
Affiliation(s)
- Alisha N Wade
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, University of the Witwatersrand Johannesburg Faculty of Health Sciences, Johannesburg, South Africa
| | - Innocent Maposa
- Division of Epidemiology and Biostatistics, University of the Witwatersrand Johannesburg Faculty of Health Sciences, Johannesburg, South Africa
| | - Godfred Agongo
- Navrongo Health Research Centre, Navrongo, Ghana
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C. K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Gershim Asiki
- Health and Systems for Health Unit, African Population and Health Research Center, Nairobi, Kenya
| | - Palwende Boua
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Sante, Ouagadougou, Burkina Faso
| | - Solomon S R Choma
- Department of Pathology and Medical Sciences, DIMAMO Population Health Research Centre, University of Limpopo, Sovenga, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, University of the Witwatersrand Johannesburg Faculty of Health Sciences, Johannesburg, South Africa
| | - Eric Maimela
- Department of Public Health, University of Limpopo, Sovenga, South Africa
| | - Lisa K Micklesfield
- South African Medical Research Council/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shukri F Mohamed
- Health and Systems for Health Unit, African Population and Health Research Center, Nairobi, Kenya
| | | | - Shane A Norris
- South African Medical Research Council/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Global Health Research Institute, School of Health and Human Development, University of Southampton, Southampton, UK
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Sante, Ouagadougou, Burkina Faso
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand Johannesburg Faculty of Health Sciences, Johannesburg, South Africa
| | - Nigel J Crowther
- Department of Chemical Pathology, National Health Laboratory Service, University of the Witwatersrand Johannesburg Faculty of Health Sciences, Johannesburg, South Africa
| |
Collapse
|
27
|
Majara L, Kalungi A, Koen N, Tsuo K, Wang Y, Gupta R, Nkambule LL, Zar H, Stein DJ, Kinyanda E, Atkinson EG, Martin AR. Low and differential polygenic score generalizability among African populations due largely to genetic diversity. HGG ADVANCES 2023; 4:100184. [PMID: 36873096 PMCID: PMC9982687 DOI: 10.1016/j.xhgg.2023.100184] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/04/2023] [Indexed: 02/15/2023] Open
Abstract
African populations are vastly underrepresented in genetic studies but have the most genetic variation and face wide-ranging environmental exposures globally. Because systematic evaluations of genetic prediction had not yet been conducted in ancestries that span African diversity, we calculated polygenic risk scores (PRSs) in simulations across Africa and in empirical data from South Africa, Uganda, and the United Kingdom to better understand the generalizability of genetic studies. PRS accuracy improves with ancestry-matched discovery cohorts more than from ancestry-mismatched studies. Within ancestrally and ethnically diverse South African individuals, we find that PRS accuracy is low for all traits but varies across groups. Differences in African ancestries contribute more to variability in PRS accuracy than other large cohort differences considered between individuals in the United Kingdom versus Uganda. We computed PRS in African ancestry populations using existing European-only versus ancestrally diverse genetic studies; the increased diversity produced the largest accuracy gains for hemoglobin concentration and white blood cell count, reflecting large-effect ancestry-enriched variants in genes known to influence sickle cell anemia and the allergic response, respectively. Differences in PRS accuracy across African ancestries originating from diverse regions are as large as across out-of-Africa continental ancestries, requiring commensurate nuance.
Collapse
Affiliation(s)
- Lerato Majara
- Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER), Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Allan Kalungi
- Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER), Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Department of Psychiatry, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Mental Health Project, Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) & London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Nastassja Koen
- Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER), Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Cape Town, South Africa
| | - Kristin Tsuo
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Ying Wang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rahul Gupta
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Lethukuthula L. Nkambule
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heather Zar
- Department of Paediatrics and Child Health, Red Cross Children’s Hospital and Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Dan J. Stein
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Cape Town, South Africa
| | - Eugene Kinyanda
- Mental Health Project, Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) & London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Elizabeth G. Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alicia R. Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| |
Collapse
|
28
|
Soo CC, Brandenburg JT, Nebel A, Tollman S, Berkman L, Ramsay M, Choudhury A. Genome-wide association study of population-standardised cognitive performance phenotypes in a rural South African community. Commun Biol 2023; 6:328. [PMID: 36973338 PMCID: PMC10043003 DOI: 10.1038/s42003-023-04636-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
Cognitive function is an indicator for global physical and mental health, and cognitive impairment has been associated with poorer life outcomes and earlier mortality. A standard cognition test, adapted to a rural-dwelling African community, and the Oxford Cognition Screen-Plus were used to capture cognitive performance as five continuous traits (total cognition score, verbal episodic memory, executive function, language, and visuospatial ability) for 2,246 adults in this population of South Africans. A novel common variant, rs73485231, reached genome-wide significance for association with episodic memory using data for ~14 million markers imputed from the H3Africa genotyping array data. Window-based replication of previously implicated variants and regions of interest support the discovery of African-specific associated variants despite the small population size and low allele frequency. This African genome-wide association study identifies suggestive associations with general cognition and domain-specific cognitive pathways and lays the groundwork for further genomic studies on cognition in Africa.
Collapse
Affiliation(s)
- Cassandra C Soo
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Almut Nebel
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lisa Berkman
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Center for Population and Development Studies, Harvard University, Cambridge, MA, USA
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| |
Collapse
|
29
|
Micklesfield LK, Munthali R, Agongo G, Asiki G, Boua P, Choma SS, Crowther NJ, Fabian J, Gómez-Olivé FX, Kabudula C, Maimela E, Mohamed SF, Nonterah EA, Raal FJ, Sorgho H, Tluway FD, Wade AN, Norris SA, Ramsay M. Identifying the prevalence and correlates of multimorbidity in middle-aged men and women: a cross-sectional population-based study in four African countries. BMJ Open 2023; 13:e067788. [PMID: 36918238 PMCID: PMC10016250 DOI: 10.1136/bmjopen-2022-067788] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 02/15/2023] [Indexed: 03/16/2023] Open
Abstract
OBJECTIVES To determine the prevalence of multimorbidity, to identify which chronic conditions cluster together and to identify factors associated with a greater risk for multimorbidity in sub-Saharan Africa (SSA). DESIGN Cross-sectional, multicentre, population-based study. SETTING Six urban and rural communities in four sub-Saharan African countries. PARTICIPANTS Men (n=4808) and women (n=5892) between the ages of 40 and 60 years from the AWI-Gen study. MEASURES Sociodemographic and anthropometric data, and multimorbidity as defined by the presence of two or more of the following conditions: HIV infection, cardiovascular disease, chronic kidney disease, asthma, diabetes, dyslipidaemia, hypertension. RESULTS Multimorbidity prevalence was higher in women compared with men (47.2% vs 35%), and higher in South African men and women compared with their East and West African counterparts. The most common disease combination at all sites was dyslipidaemia and hypertension, with this combination being more prevalent in South African women than any single disease (25% vs 21.6%). Age and body mass index were associated with a higher risk of multimorbidity in men and women; however, lifestyle correlates such as smoking and physical activity were different between the sexes. CONCLUSIONS The high prevalence of multimorbidity in middle-aged adults in SSA is of concern, with women currently at higher risk. This prevalence is expected to increase in men, as well as in the East and West African region with the ongoing epidemiological transition. Identifying common disease clusters and correlates of multimorbidity is critical to providing effective interventions.
Collapse
Affiliation(s)
- Lisa K Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard Munthali
- SAMRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C.K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
- Navrongo Health Research Centre, Ghana Health Service, Accra, Ghana
| | - Gershim Asiki
- African Population and Health Research Center, Nairobi, Kenya
| | - Palwende Boua
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Ouagadougou, Burkina Faso
- Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Solomon Sr Choma
- Department of Public Health, University of Limpopo, Sovenga, South Africa
| | - Nigel J Crowther
- Department of Chemical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - June Fabian
- Wits Donald Gordon Medical Centre, University of the Witwatersrand, Johannesburg, South Africa
| | - Francesc Xavier Gómez-Olivé
- South African Medical Research Council/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Chodziwadziwa Kabudula
- South African Medical Research Council/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Eric Maimela
- Department of Public Health, University of Limpopo, Sovenga, South Africa
| | - Shukri F Mohamed
- Health and Systems for Health, African Population and Health Research Center, Nairobi, Kenya
| | - Engelbert A Nonterah
- Navrongo Health Research Centre, Ghana Health Service, Accra, Ghana
- Julius Global Health, Julius Centre for Health Sciences and Primary Care, Utrecht University, Utrecht, The Netherlands
| | - Frederick J Raal
- Department of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Hermann Sorgho
- Institut de Recherche en Sciences de la Santé, Ouagadougou, Burkina Faso
| | - Furahini D Tluway
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Alisha N Wade
- South African Medical Research Council/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shane A Norris
- SAMRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Human Development and Health, University of Southampton, Southampton, UK
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
30
|
Muti M, Ware LJ, Micklesfield LK, Ramsay M, Agongo G, Boua PR, Kisiangani I, Cook I, Gómez-Olivé FX, Crowther NJ, Kabudula C, Norris SA, Chikowore T. Physical Activity and Its Association With Body Mass Index: A Cross-Sectional Analysis in Middle-Aged Adults From 4 Sub-Saharan African Countries. J Phys Act Health 2023; 20:217-225. [PMID: 36746155 DOI: 10.1123/jpah.2022-0539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/24/2022] [Accepted: 12/03/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND This study aimed to explore association of self-reported physical activity domains of work, leisure, and transport-related physical activity and body mass index (BMI) in 9388 adult men and women from the Africa-Wits-INDEPTH partnership for Genomic (AWI-Gen) study in Africa. Africa-Wits-INDEPTH partnership for Genomic is a large, population-based cross-sectional cohort with participants from 6 sites from rural and urban areas in 4 sub-Saharan African countries. METHODS A sex-stratified meta-analysis of cross-sectional data from men and women aged 29-82 years was used to assess the association of physical activity with BMI. RESULTS Overall, meeting physical activity guidelines of at least 150 minutes per week was associated with 0.82 kg/m2 lower BMI in men (β = -0.80 kg/m2; 95% confidence interval [CI], -1.14 to -0.47) and 0.68 kg/m2 lower BMI in women (β = -0.68 kg/m2; 95% CI, -1.03 to -0.33). Sex and site-specific differences were observed in the associations between physical activity domains and BMI. Among those who met physical activity guidelines, there was an inverse association between transport-related physical activity and BMI in men from Nanoro (Burkina Faso) (β = -0.79 kg/m2; 95% CI, -1.25 to -0.33) as well as work-related physical activity and BMI in Navrongo men (Ghana) (β = -0.76 kg/m2; 95% CI, -1.25 to -0.27) and Nanoro women (β = -0.90 kg/m2; 95% CI, -1.44 to -0.36). CONCLUSIONS Physical activity may be an effective strategy to curb rising obesity in Africa. More studies are needed to assess the impact of sex and geographic location-specific physical activity interventions on obesity.
Collapse
Affiliation(s)
- Monica Muti
- SAMRC/Wits Developmental Pathways for Health Research Unit (DPHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg,South Africa
- Food and Nutrition Security Research Institute, Harare,Zimbabwe
| | - Lisa J Ware
- SAMRC/Wits Developmental Pathways for Health Research Unit (DPHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg,South Africa
- DSI-NRF Centre of Excellence in Human Development, University of the Witwatersrand, Johannesburg,South Africa
| | - Lisa K Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit (DPHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg,South Africa
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg,South Africa
| | - Godfred Agongo
- Navrongo Health Research Centre, Ghana Health Service, Navrongo,Ghana
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C. K. Tedam University of Technology and Applied Sciences, Navrongo,Ghana
| | - Palwende R Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg,South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro,Burkina Faso
| | | | - Ian Cook
- Physical Activity Epidemiology Laboratory (EDST), School of Education, Faculty of Humanities, University of Limpopo, Polokwane,South Africa
| | - Francesc Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg,South Africa
| | - Nigel J Crowther
- Department of Chemical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg,South Africa
| | - Chodziwadziwa Kabudula
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg,South Africa
| | - Shane A Norris
- SAMRC/Wits Developmental Pathways for Health Research Unit (DPHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg,South Africa
- School of Human Development and Health, University of Southampton, Southampton,United Kingdom
| | - Tinashe Chikowore
- SAMRC/Wits Developmental Pathways for Health Research Unit (DPHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg,South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg,South Africa
| |
Collapse
|
31
|
Carstens N, Goolam S, Hulley M, Brandenburg JT, Ramsay M, Williams SEI. Exome-based mutation screening in South African children with primary congenital glaucoma. Eye (Lond) 2023; 37:362-368. [PMID: 35094026 PMCID: PMC9873788 DOI: 10.1038/s41433-022-01941-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 01/03/2022] [Accepted: 01/14/2022] [Indexed: 01/29/2023] Open
Abstract
OBJECTIVES To identify pathogenic variants in a cohort of 23 black South African children with sporadic primary congenital glaucoma (PCG) using an exome-based approach. METHODS Children with PCG were recruited from two Paediatric Ophthalmology Clinics in Johannesburg, South Africa. Whole exome sequencing was performed on genomic DNA. Of the 23 children, 19 were male and 19 had bilateral PCG. A variant prioritization strategy was employed whereby variants in known PCG genes (CYP1B1, LTBP2 and TEK) were evaluated first, followed by the identification of putative disease-causing variants in other genes related to eye diseases and phenotypes. RESULTS Validated pathogenic variants in the CYP1B1 gene (c.1169 G>A; p.Arg390His) and TEK gene (c.922 G>A; p.Gly308Arg) were identified in one child each. No LTBP2 mutations were identified in this cohort. In silico predictions identified potentially damaging rare variants in genes previously associated with eye development phenotypes or glaucoma in a further 12 children. CONCLUSIONS This study demonstrates the value of whole exome sequencing in identifying disease-causing variants in African children with PCG. It is the first report of a TEK disease-causing variant in an African PCG patient. Potential causative variants detected in PCG candidate genes warrant further investigation.
Collapse
Affiliation(s)
- Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Saadiah Goolam
- Division of Ophthalmology, Department of Neurosciences, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michaella Hulley
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michele Ramsay
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan Eileen Isabella Williams
- Division of Ophthalmology, Department of Neurosciences, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| |
Collapse
|
32
|
Agongo G, Raal F, Nonterah EA, Debpuur C, Oduro AR, Ramsay M, Crowther NJ. Non-HDL-C and LDL-C/HDL-C are associated with self-reported cardiovascular disease in a rural West African population: Analysis of an array of lipid metrics in an AWI-Gen sub-study. PLoS One 2022; 17:e0278375. [PMID: 36477684 PMCID: PMC9728928 DOI: 10.1371/journal.pone.0278375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Few studies have compared the utility of serum levels of lipid fractions in cardiovascular disease (CVD) risk assessment in sub-Saharan Africa (SSA). The current study interrogated this question among men and women aged 40-60 years in rural northern Ghana. This was a cross-sectional study in which data was collected on socio-demography, behaviour, health history, anthropometry and lipid levels. Adjusted multivariable logistic regression models were used to assess the association of various lipid metrics with CVD. All tests were considered statistically significant at P<0.05. Data were available for 1839 participants. The prevalence of self-reported CVD was 1.6% (n = 29). Non-HDL-C (median (interquartile range): 2.4 (1.9-3.0) vs 2.0 (1.6-2.5) mmol/L; P = 0.009), LDL-C/HDL-C (1.8 (1.4-2.4) vs 1.5 (1.1-2.6); P = 0.019) and TC/HDL-C (3.3 (2.9-3.9) vs 2.9 (2.4-3.5); P = 0.003) were all significantly higher in participants with self-reported CVD compared to those without. However, after adjusting for socioeconomic status (SES) and meals from vendors in a logistic regression model, only non-HDL-C (odds ratio [95% CIs]): (1.58 [1.05, 2.39]), P = 0.029 and LDL-C/HDL-C levels (odds ratio [95% CIs]): (1.26 [1.00, 1.59]), P = 0.045 remained significantly associated with self-reported CVD. While our findings suggest non-HDL-C and LDL-C/HDL-C measures may be appropriate biomarkers for assessing CVD risk in this population, further studies using established clinical endpoints are required to validate these findings in sub-Saharan Africans.
Collapse
Affiliation(s)
- Godfred Agongo
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C.K Tedam University of Technology and Applied Sciences, Navrongo, Ghana
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- * E-mail:
| | - Frederick Raal
- Division of Endocrinology and Metabolism, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Engelbert A. Nonterah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Cornelius Debpuur
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Research and Development Division, Ghana Health Service, Accra, Ghana
| | - Abraham R. Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Research and Development Division, Ghana Health Service, Accra, Ghana
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nigel J. Crowther
- Department of Chemical Pathology, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
33
|
Ibe C, Otu AA, Mnyambwa NP. Advancing disease genomics beyond COVID-19 and reducing health disparities: what does the future hold for Africa? Brief Funct Genomics 2022; 22:241-249. [DOI: 10.1093/bfgp/elac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/03/2022] [Accepted: 10/14/2022] [Indexed: 11/27/2022] Open
Abstract
Abstract
The COVID-19 pandemic has ushered in high-throughput sequencing technology as an essential public health tool. Scaling up and operationalizing genomics in Africa is crucial as enhanced capacity for genome sequencing could address key health problems relevant to African populations. High-quality genomics research can be leveraged to improve diagnosis, understand the aetiology of unexplained illnesses, improve surveillance of infectious diseases and inform efficient control and therapeutic methods of known, rare and emerging infectious diseases. Achieving these within Africa requires strong commitment from stakeholders. A roadmap is needed to guide training of scientists, infrastructural development, research funding, international collaboration as well as promote public–private partnerships. Although the COVID-19 pandemic has significantly boosted genomics capacity in Africa, the continent still lags other regions. Here, we highlighted key initiatives in genomics research and efforts to address health challenges facing the diverse and fast-growing populations on the continent. We explore the scalability of genomic tools and techniques to tackle a broader range of infectious diseases in Africa, a continent that desperately requires a boost from genomic science.
Collapse
Affiliation(s)
- Chibuike Ibe
- Abia State University Department of Microbiology, Faculty of Biological Sciences, , Uturu, Nigeria
| | | | - Nicholaus P Mnyambwa
- National Institute for Medical Research , Muhimbili Research Centre, Dar es Salaam , Tanzania
- Alliance for Africa Health and Research (A4A), Dar es Salaam , Tanzania
| |
Collapse
|
34
|
Brandenburg JT, Clark L, Botha G, Panji S, Baichoo S, Fields C, Hazelhurst S. H3AGWAS: a portable workflow for genome wide association studies. BMC Bioinformatics 2022; 23:498. [PMID: 36402955 PMCID: PMC9675212 DOI: 10.1186/s12859-022-05034-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 11/02/2022] [Indexed: 11/21/2022] Open
Abstract
Background Genome-wide association studies (GWAS) are a powerful method to detect associations between variants and phenotypes. A GWAS requires several complex computations with large data sets, and many steps may need to be repeated with varying parameters. Manual running of these analyses can be tedious, error-prone and hard to reproduce. Results The H3AGWAS workflow from the Pan-African Bioinformatics Network for H3Africa is a powerful, scalable and portable workflow implementing pre-association analysis, implementation of various association testing methods and post-association analysis of results. Conclusions The workflow is scalable—laptop to cluster to cloud (e.g., SLURM, AWS Batch, Azure). All required software is containerised and can run under Docker or Singularity.
Collapse
Affiliation(s)
- Jean-Tristan Brandenburg
- grid.11951.3d0000 0004 1937 1135Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Lindsay Clark
- grid.35403.310000 0004 1936 9991HPCBio, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.240741.40000 0000 9026 4165Present Address: Research Scientific Computing, Seattle Children’s Research Institute, Seattle, WA 98101 USA
| | - Gerrit Botha
- grid.7836.a0000 0004 1937 1151Computational Biology Division, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Sumir Panji
- grid.7836.a0000 0004 1937 1151Computational Biology Division, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Shakuntala Baichoo
- grid.45199.300000 0001 2288 9451Department of Digital Technologies, Faculty of Information, Communication and Digital Technologies, University of Mauritius, Moka, Mauritius
| | - Christopher Fields
- grid.35403.310000 0004 1936 9991HPCBio, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Scott Hazelhurst
- grid.11951.3d0000 0004 1937 1135Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa ,grid.11951.3d0000 0004 1937 1135School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
35
|
Piga NN, Boua PR, Soremekun C, Shrine N, Coley K, Brandenburg JT, Tobin MD, Ramsay M, Fatumo S, Choudhury A, Batini C. Genetic insights into smoking behaviours in 10,558 men of African ancestry from continental Africa and the UK. Sci Rep 2022; 12:18828. [PMID: 36335192 PMCID: PMC9637114 DOI: 10.1038/s41598-022-22218-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 10/11/2022] [Indexed: 11/08/2022] Open
Abstract
Smoking is a leading risk factor for many of the top ten causes of death worldwide. Of the 1.3 billion smokers globally, 80% live in low- and middle-income countries, where the number of deaths due to tobacco use is expected to double in the next decade according to the World Health Organization. Genetic studies have helped to identify biological pathways for smoking behaviours, but have mostly focussed on individuals of European ancestry or living in either North America or Europe. We performed a genome-wide association study of two smoking behaviour traits in 10,558 men of African ancestry living in five African countries and the UK. Eight independent variants were associated with either smoking initiation or cessation at P-value < 5 × 10-6, four being monomorphic or rare in European populations. Gene prioritisation strategy highlighted five genes, including SEMA6D, previously described as associated with several smoking behaviour traits. These results confirm the importance of analysing underrepresented populations in genetic epidemiology, and the urgent need for larger genomic studies to boost discovery power to better understand smoking behaviours, as well as many other traits.
Collapse
Affiliation(s)
- Noemi-Nicole Piga
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Palwende Romuald Boua
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de La Santé, Nanoro, Burkina Faso
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Chisom Soremekun
- Department of Immunology and Molecular Biology, College of Health Science, Makerere University, Kampala, Uganda
- H3Africa Bioinformatics Network (H3ABioNet) Node, Center for Genomics Research and Innovation (CGRI), National Biotechnology Development Agency CGRI/NABDA, Abuja, Nigeria
- The African Computational Genomics (TACG) Research Group, MRC/UVRI LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Kayesha Coley
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Segun Fatumo
- H3Africa Bioinformatics Network (H3ABioNet) Node, Center for Genomics Research and Innovation (CGRI), National Biotechnology Development Agency CGRI/NABDA, Abuja, Nigeria
- The African Computational Genomics (TACG) Research Group, MRC/UVRI LSHTM Uganda Research Unit, Entebbe, Uganda
- Department of Non-Communicable Disease Epidemiology (NCDE), London School of Hygiene and Tropical Medicine, London, UK
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Chiara Batini
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK.
| |
Collapse
|
36
|
Equitable partnerships and the path to inclusive, innovative and impactful human microbiome research. Nat Rev Gastroenterol Hepatol 2022; 19:683-684. [PMID: 36171273 DOI: 10.1038/s41575-022-00689-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
|
37
|
Coronavirus Host Genomics Study: South Africa (COVIGen-SA). GLOBAL HEALTH 2022; 2022:7405349. [PMID: 36263375 PMCID: PMC9560830 DOI: 10.1155/2022/7405349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022]
Abstract
Host genetic factors are known to modify the susceptibility, severity, and outcomes of COVID-19 and vary across populations. However, continental Africans are yet to be adequately represented in such studies despite the importance of genetic factors in understanding Africa's response to the pandemic. We describe the development of a research resource for coronavirus host genomics studies in South Africa known as COVIGen-SA-a multicollaborator strategic partnership designed to provide harmonised demographic, clinical, and genetic information specific to Black South Africans with COVID-19. Over 2,000 participants have been recruited to date. Preliminary results on 1,354 SARS-CoV-2 positive participants from four participating studies showed that 64.7% were female, 333 had severe disease, and 329 were people living with HIV. Through this resource, we aim to provide insights into host genetic factors relevant to African-ancestry populations, using both genome-wide association testing and targeted sequencing of important genomic loci. This project will promote and enhance partnerships, build skills, and develop resources needed to address the COVID-19 burden and associated risk factors in South African communities.
Collapse
|
38
|
Dlamini SN, Norris SA, Mendham AE, Mtintsilana A, Ward KA, Olsson T, Goedecke JH, Micklesfield LK. Targeted proteomics of appendicular skeletal muscle mass and handgrip strength in black South Africans: a cross-sectional study. Sci Rep 2022; 12:9512. [PMID: 35680977 PMCID: PMC9178538 DOI: 10.1038/s41598-022-13548-9] [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: 02/13/2022] [Accepted: 05/25/2022] [Indexed: 11/20/2022] Open
Abstract
Although appendicular skeletal muscle mass (ASM) and handgrip strength (HGS) are key components of sarcopenia, their underlying biological mechanisms remain poorly understood. We aimed to investigate associations of circulating biomarkers with ASM and HGS in middle-aged black South Africans. This study consisted of 934 black South Africans (469 men and 465 women, aged 41-72 years) from the Middle-aged Soweto cohort. Linear regression models were used to examine relationships between 182 biomarkers (measured with proximity extension assay) and dual-energy X-ray absorptiometry-measured ASM and dynamometer-measured HGS. Age, height, sex, smoking, alcohol, food insecurity, physical activity, visceral adipose tissue, HIV and menopausal status were included as confounders. Regression models showing sex-interactions were stratified by sex. The Benjamini-Hochberg false discovery rate (FDR) was used to control for multiple testing, and FDR-adjusted P values were reported. In the total sample, 10 biomarkers were associated with higher ASM and 29 with lower ASM (P < 0.05). Out of these 39 biomarkers, 8 were also associated with lower HGS (P < 0.05). MMP-7 was associated with lower HGS only (P = 0.011) in the total sample. Sex-interactions (P < 0.05) were identified for 52 biomarkers for ASM, and 6 for HGS. For men, LEP, MEPE and SCF were associated with higher ASM (P < 0.001, = 0.004, = 0.006, respectively), and MEPE and SCF were also associated with higher HGS (P = 0.001, 0.012, respectively). Also in men, 37 biomarkers were associated with lower ASM (P < 0.05), with none of these being associated with lower HGS. Furthermore, DLK-1 and MYOGLOBIN were associated with higher HGS only (P = 0.004, 0.006, respectively), while GAL-9 was associated with lower HGS only (P = 0.005), among men. For women, LEP, CD163, IL6, TNF-R1 and TNF-R2 were associated with higher ASM (P < 0.001, = 0.014, = 0.027, = 0.014, = 0.048, respectively), while IGFBP-2, CTRC and RAGE were associated with lower ASM (P = 0.043, 0.001, 0.014, respectively). No biomarker was associated with HGS in women. In conclusion, most biomarkers were associated with ASM and not HGS, and the associations of biomarkers with ASM and HGS displayed sex-specificity in middle-aged black South Africans. Proteomic studies should examine ASM and HGS individually. Future research should also consider sexual dimorphism in the pathophysiology of sarcopenia for development of sex-specific treatment and diagnostic methods.
Collapse
Affiliation(s)
- Siphiwe N Dlamini
- SAMRC/Wits Developmental Pathways for Health Research Unit, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Shane A Norris
- SAMRC/Wits Developmental Pathways for Health Research Unit, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Global Health Research Institute, School of Health and Human Development, University of Southampton, Southampton, UK
| | - Amy E Mendham
- SAMRC/Wits Developmental Pathways for Health Research Unit, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Health Through Physical Activity, Lifestyle and Sport Research Centre, FIMS International Collaborating Centre of Sports Medicine, Division of Physiological Sciences, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Asanda Mtintsilana
- SAMRC/Wits Developmental Pathways for Health Research Unit, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kate A Ward
- SAMRC/Wits Developmental Pathways for Health Research Unit, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Medical Research Council Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - Tommy Olsson
- Department of Public Health and Clinical Medicine, Medicine, Umeå University, Umeå, Sweden
| | - Julia H Goedecke
- SAMRC/Wits Developmental Pathways for Health Research Unit, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Non-Communicable Diseases Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Lisa K Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
39
|
Brandenburg JT, Govender MA, Winkler CA, Boua PR, Agongo G, Fabian J, Ramsay M. Apolipoprotein L1 High-Risk Genotypes and Albuminuria in Sub-Saharan African Populations. Clin J Am Soc Nephrol 2022; 17:798-808. [PMID: 35577564 PMCID: PMC9269651 DOI: 10.2215/cjn.14321121] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/30/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND AND OBJECTIVES Recessive inheritance of African-specific APOL1 kidney risk variants is associated with higher risk of nondiabetic kidney disease, progression to kidney failure, and early-onset albuminuria that precedes eGFR decline. The effect of APOL1 risk variants on kidney disease in continental Africans is understudied. Objectives of this study were to determine APOL1 risk allele prevalence and associations between APOL1 genotypes and kidney disease in West, East, and South Africa. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS This cross-sectional population-based study in four African countries included 10,769 participants largely aged 40-60 years with sociodemographic and health information, anthropometry data, and blood and urine tests for biomarkers of kidney disease. APOL1 risk alleles were imputed from the H3Africa genotyping array, APOL1 risk allele and genotype frequencies were determined, and genetic associations were assessed for kidney disease. Kidney disease was defined as the presence of eGFR <60 ml/min per 1.73 m2, albuminuria, or a composite end point including eGFR <60 ml/min per 1.73 m2 and/or albuminuria. RESULTS High G1 allele frequencies occurred in South and West Africa (approximately 7%-13%). G2 allele frequencies were highest in South Africa (15%-24%), followed by West Africa (9%-12%). Associations between APOL1 risk variants and albuminuria were significant for recessive (odds ratio, 1.63; 95% confidence interval, 1.25 to 2.12) and additive (odds ratio, 1.39; 95% confidence interval, 1.09 to 1.76) models. Associations were stronger for APOL1 G1/G1 genotypes versus G0/G0 (odds ratio, 3.87; 95% confidence interval, 2.16 to 6.93) compared with either G2/G2 (odds ratio, 1.65; 95% confidence interval, 1.09 to 2.51) or G1/G2 (odds ratio, 1.24; 95% confidence interval, 0.83 to 1.87). No association between APOL1 risk variants and eGFR <60 ml/min per 1.73 m2 was observed. CONCLUSIONS APOL1 G1 and G2 alleles and high-risk genotype frequencies differed between and within West and South Africa and were almost absent from East Africa. APOL1 risk variants were associated with albuminuria but not eGFR <60 ml/min per 1.73 m2. There may be differential effects of homozygous G1 and G2 genotypes on albuminuria that require further investigation. PODCAST This article contains a podcast at https://www.asn-online.org/media/podcast/CJASN/2022_05_16_CJN14321121.mp3.
Collapse
Affiliation(s)
- Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Melanie A Govender
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl A Winkler
- Molecular Genetic Epidemiology Section, Basic Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Palwende Romuald Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé-DRCO, Nanoro, Burkina Faso
| | - Godfred Agongo
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana.,Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C.K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - June Fabian
- Wits Donald Gordon Medical Centre, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Medical Research Council/Wits University Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa .,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
40
|
Choudhury A, Brandenburg JT, Chikowore T, Sengupta D, Boua PR, Crowther NJ, Agongo G, Asiki G, Gómez-Olivé FX, Kisiangani I, Maimela E, Masemola-Maphutha M, Micklesfield LK, Nonterah EA, Norris SA, Sorgho H, Tinto H, Tollman S, Graham SE, Willer CJ, Hazelhurst S, Ramsay M. Meta-analysis of sub-Saharan African studies provides insights into genetic architecture of lipid traits. Nat Commun 2022; 13:2578. [PMID: 35546142 PMCID: PMC9095599 DOI: 10.1038/s41467-022-30098-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 04/18/2022] [Indexed: 12/30/2022] Open
Abstract
Genetic associations for lipid traits have identified hundreds of variants with clear differences across European, Asian and African studies. Based on a sub-Saharan-African GWAS for lipid traits in the population cross-sectional AWI-Gen cohort (N = 10,603) we report a novel LDL-C association in the GATB region (P-value=1.56 × 10−8). Meta-analysis with four other African cohorts (N = 23,718) provides supporting evidence for the LDL-C association with the GATB/FHIP1A region and identifies a novel triglyceride association signal close to the FHIT gene (P-value =2.66 × 10−8). Our data enable fine-mapping of several well-known lipid-trait loci including LDLR, PMFBP1 and LPA. The transferability of signals detected in two large global studies (GLGC and PAGE) consistently improves with an increase in the size of the African replication cohort. Polygenic risk score analysis shows increased predictive accuracy for LDL-C levels with the narrowing of genetic distance between the discovery dataset and our cohort. Novel discovery is enhanced with the inclusion of African data. Genetic associations and polygenic scores for lipid traits have low transferability to African individuals. Here, the authors perform a large sub-Sarahan African lipid GWAS and find that larger datasets and better global representation in discovery GWAS help to bridge this gap.
Collapse
Affiliation(s)
- Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tinashe Chikowore
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,South African Medical Research Council/University of the Witwatersrand Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Palwende Romuald Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santè, Nanoro, Burkina Faso
| | - Nigel J Crowther
- Department of Chemical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Godfred Agongo
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana.,C.K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Gershim Asiki
- African Population and Health Research Center, Nairobi, Kenya
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Eric Maimela
- Department of Public Health, School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - Matshane Masemola-Maphutha
- Department of Pathology and Medical Sciences, School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - Lisa K Micklesfield
- South African Medical Research Council/University of the Witwatersrand Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Shane A Norris
- South African Medical Research Council/University of the Witwatersrand Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santè, Nanoro, Burkina Faso
| | - Halidou Tinto
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santè, Nanoro, Burkina Faso
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sarah E Graham
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48019, USA
| | | | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. .,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| |
Collapse
|
41
|
Goedecke JH, Nguyen KA, Kufe C, Masemola M, Chikowore T, Mendham AE, Norris SA, Crowther NJ, Karpe F, Olsson T, Kengne AP, Micklesfield LK. Waist circumference thresholds predicting incident dysglycaemia and type 2 diabetes in Black African men and women. Diabetes Obes Metab 2022; 24:918-927. [PMID: 35088498 PMCID: PMC9305761 DOI: 10.1111/dom.14655] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/07/2022] [Accepted: 01/24/2022] [Indexed: 12/31/2022]
Abstract
AIMS To determine the waist circumference (WC) thresholds for the prediction of incident dysglycaemia and type 2 diabetes (T2D) in Black South African (SA) men and women and to compare these to the advocated International Diabetes Federation (IDF) Europid thresholds. MATERIALS AND METHODS In this prospective study, Black SA men (n = 502) and women (n = 527) from the Middle-aged Sowetan Cohort study who had normal or impaired fasting glucose at baseline (2011-2015) were followed up until 2017 to 2018. Baseline measurements included anthropometry, blood pressure and fasting glucose, HDL cholesterol and triglyceride concentrations. At follow-up, glucose tolerance was assessed using an oral glucose tolerance test. The Youden index was used to determine the optimal threshold of WC to predict incident dysglycaemia and T2D. RESULTS In men, the optimal WC threshold was 96.8 cm for both dysglycaemia and T2D (sensitivity: 56% and 70%; specificity: 74% and 70%, respectively), and had higher specificity (P < 0.001) than the IDF threshold of 94 cm. In women, the optimal WC threshold for incident dysglycaemia was 91.8 cm (sensitivity 86%, specificity 37%) and for T2D it was 95.8 cm (sensitivity 85%, specificity 45%), which had lower sensitivity, but higher specificity to predict incident dysglycaemia and T2D than the IDF threshold of 80 cm (sensitivity: 97% and 100%; specificity: 12% and 11%, respectively)). CONCLUSIONS We show for the first time using prospective cohort data from Africa that the IDF Europid WC thresholds are not appropriate for an African population, and show that African-specific WC thresholds perform better than the IDF Europid thresholds to predict incident dysglycaemia and T2D.
Collapse
Affiliation(s)
- Julia H. Goedecke
- Non‐Communicable Diseases Research UnitSouth African Medical Research CouncilCape TownSouth Africa
- South African Medical Research Council/WITS Developmental Pathways for Health Research Unit (DPHRU), Department of PaediatricsFaculty of Health Sciences, University of the WitwatersrandJohannesburgSouth Africa
| | - Kim A. Nguyen
- Non‐Communicable Diseases Research UnitSouth African Medical Research CouncilCape TownSouth Africa
| | - Clement Kufe
- South African Medical Research Council/WITS Developmental Pathways for Health Research Unit (DPHRU), Department of PaediatricsFaculty of Health Sciences, University of the WitwatersrandJohannesburgSouth Africa
| | - Maphoko Masemola
- South African Medical Research Council/WITS Developmental Pathways for Health Research Unit (DPHRU), Department of PaediatricsFaculty of Health Sciences, University of the WitwatersrandJohannesburgSouth Africa
| | - Tinashe Chikowore
- South African Medical Research Council/WITS Developmental Pathways for Health Research Unit (DPHRU), Department of PaediatricsFaculty of Health Sciences, University of the WitwatersrandJohannesburgSouth Africa
| | - Amy E. Mendham
- South African Medical Research Council/WITS Developmental Pathways for Health Research Unit (DPHRU), Department of PaediatricsFaculty of Health Sciences, University of the WitwatersrandJohannesburgSouth Africa
- Health through Physical Activity, Lifestyle and Sport Research Centre (HPALS), FIMS International Collaborating Centre of Sports Medicine, Division of Physiological Sciences, Department of Human BiologyFaculty of Health Sciences, University of Cape TownCape TownSouth Africa
| | - Shane A. Norris
- South African Medical Research Council/WITS Developmental Pathways for Health Research Unit (DPHRU), Department of PaediatricsFaculty of Health Sciences, University of the WitwatersrandJohannesburgSouth Africa
| | - Nigel J. Crowther
- Department of Chemical PathologyNational Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the WitwatersrandJohannesburgSouth Africa
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, OUH Foundation TrustUniversity of OxfordOxfordUK
| | - Tommy Olsson
- Department of Public Health and Clinical MedicineMedicine, Umeå UniversityUmeåSweden
| | - Andre Pascal Kengne
- Non‐Communicable Diseases Research UnitSouth African Medical Research CouncilCape TownSouth Africa
| | - Lisa K. Micklesfield
- South African Medical Research Council/WITS Developmental Pathways for Health Research Unit (DPHRU), Department of PaediatricsFaculty of Health Sciences, University of the WitwatersrandJohannesburgSouth Africa
| |
Collapse
|
42
|
Nonterah EA, Boateng D, Crowther NJ, Klipstein-Grobusch K, Oduro AR, Agongo G, Mohamed SF, Boua PR, Choma SSR, Norris SA, Tollman SM, Bots ML, Ramsay M, Grobbee D. Carotid Atherosclerosis, Microalbuminuria, and Estimated 10-Year Atherosclerotic Cardiovascular Disease Risk in Sub-Saharan Africa. JAMA Netw Open 2022; 5:e227559. [PMID: 35471573 PMCID: PMC9044117 DOI: 10.1001/jamanetworkopen.2022.7559] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE Carotid atherosclerosis and microalbuminuria are associated with atherosclerotic cardiovascular disease (ASCVD) but are understudied in sub-Saharan Africa. OBJECTIVE To evaluate the association of carotid atherosclerosis and microalbuminuria with 10-year ASCVD risk in middle-aged sub-Saharan African individuals. DESIGN, SETTING, AND PARTICIPANTS This cross-sectional study conducted analyses of baseline data from the African-Wits-INDEPTH (International Network for the Demographic Evaluation of Populations and Their Health in Low- and Middle-Income Countries) genomic study (AWI-Gen). Women and men aged 40 to 60 years without baseline CVD and drawn from Burkina Faso, Ghana, Kenya, and South Africa were included. MAIN OUTCOMES AND MEASURES Hypotheses for the analyses were formulated after data collection. The main exposures were carotid atherosclerosis, assessed using carotid intima-media thickness (CIMT) using B-mode ultrasonography, and microalbuminuria, measured using spot urine albumin (SUA) and urine albumin-creatinine ratio (uACR). The main outcome was high ASCVD risk, defined as a 2018 Pooled Cohort Equations score of 7.5% or greater. Associations were estimated using adjusted multivariable logistic regression analyses. FINDINGS A total of 9010 participants with a mean (SD) age of 50 (6) years and 4533 (50.3%) women were included. High CIMT, SUA, and uACR were each associated with older age (eg, mean [SD] age of participants with high vs reference range CIMT: 55 [5] years vs 50 [6] years; P < .001) and high prevalence of both diabetes and hypertension (eg, hypertension among those with high vs reference range SUA: 213 of 1117 [19.1%] vs 356 of 2549 [14.0%]; P < .001). Smokers were likely to have higher vs reference range SUA (210 [18.8%] vs 407 [16.0%]) and uACR (138 of 707 [19.5%] vs 456 of 2797 [16.3%]). Carotid atherosclerosis was common in Burkina Faso (82 of 262 [31.3%]) and Ghana (91 [34.7%]), while microalbuminuria, measured by SUA, was common in Kenya (272 [24.4%]) and South Africa (519 [46.5%]). SUA was associated with higher odds of carotid atherosclerosis (odds ratio [OR], 1.77; 95% CI, 1.04-3.01) compared with uACR (OR, 0.51; 95% CI, 0.27-0.95). Common CIMT, SUA, and uACR were associated with 10-year ASCVD risk, with CIMT having a stronger association with 10-year ASCVD risk in both women (OR, 1.95; 95% CI, 1.78-2.14) and men (OR, 1.73; 95% CI, 1.55-1.93) than SUA (women: OR, 1.29; 95% CI, 1.12-1.43; men: OR, 1.46; 95% CI, 1.26-1.55) and uACR (women: OR, 1.32; 95% CI, 1.10-1.54; men: OR, 1.35; 95% CI, 1.15-1.46). CONCLUSIONS AND RELEVANCE The presence of microalbuminuria measured by SUA may indicate risk of subclinical carotid atherosclerosis and high 10-year ASCVD risk in middle-aged residents of sub-Saharan Africa. These data should be confirmed in longitudinal studies of cardiovascular events.
Collapse
Affiliation(s)
- Engelbert A. Nonterah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Daniel Boateng
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Nigel J. Crowther
- Department of Chemical Pathology, National Laboratory Health Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kerstin Klipstein-Grobusch
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Abraham R. Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Godfred Agongo
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C.K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | | | - Palwendé R. Boua
- Institut de Recherché en Sciences de la Santé, Clinical Research Unit of Nanoro, Nanoro, Burkina Faso
| | - Solomon S. R. Choma
- DIMAMO Health Demographic Surveillance Site, Department of Pathology and Medical Sciences, School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - Shane A. Norris
- MRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen M. Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michiel L. Bots
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Michèle Ramsay
- Sydney Brenner Institute of Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Diederick Grobbee
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| |
Collapse
|
43
|
Kufe CN, Micklesfield LK, Masemola M, Chikowore T, Kengne AP, Karpe F, Norris SA, Crowther NJ, Olsson T, Goedecke JH. Increased risk for type 2 diabetes in relation to adiposity in middle-aged Black South African men compared to women. Eur J Endocrinol 2022; 186:523-533. [PMID: 35225824 PMCID: PMC9010812 DOI: 10.1530/eje-21-0527] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 02/28/2022] [Indexed: 11/08/2022]
Abstract
AIMS Despite a higher prevalence of overweight/obesity in Black South African women compared to men, the prevalence of type 2 diabetes (T2D) does not differ. We explored if this could be due to sex differences in insulin sensitivity, clearance and/or beta-cell function and also sex-specific associations with total and regional adiposity. METHODS This cross-sectional study included 804 Black South African men (n = 388) and women (n = 416). Dual-energy X-ray absorptiometry was used to measure total and regional adiposity. Insulin sensitivity (Matsuda index), secretion (C-peptide index) and clearance (C-peptide/insulin ratio) were estimated from an oral glucose tolerance test. RESULTS After adjusting for sex differences in the fat mass index, men were less insulin sensitive and had lower beta-cell function than women (P < 0.001), with the strength of the associations with measures of total and central adiposity being greater in men than women (P < 0.001 for interactions). Further, the association between total adiposity and T2D risk was also greater in men than women (relative risk ratio (95% CI): 2.05 (1.42-2.96), P < 0.001 vs 1.38 (1.03-1.85), P = 0.031). CONCLUSION With increasing adiposity, particularly increased centralisation of body fat linked to decreased insulin sensitivity and beta-cell function, Black African men are at greater risk for T2D than their female counterparts.
Collapse
Affiliation(s)
- Clement N Kufe
- Department of Paediatrics, South African Medical Research Council (SAMRC), WITS, Developmental Pathways for Health Research Unit (DPHRU), Faculty of Health Sciences, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa
- Correspondence should be addressed to C Kufe;
| | - Lisa K Micklesfield
- Department of Paediatrics, South African Medical Research Council (SAMRC), WITS, Developmental Pathways for Health Research Unit (DPHRU), Faculty of Health Sciences, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa
| | - Maphoko Masemola
- Department of Paediatrics, South African Medical Research Council (SAMRC), WITS, Developmental Pathways for Health Research Unit (DPHRU), Faculty of Health Sciences, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa
| | - Tinashe Chikowore
- Department of Paediatrics, South African Medical Research Council (SAMRC), WITS, Developmental Pathways for Health Research Unit (DPHRU), Faculty of Health Sciences, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa
| | - Andre P Kengne
- Non-Communicable Diseases Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- National Institute for Health Research, Oxford Biomedical Research Centre, Oxford Radcliffe Hospitals Trust, OCDEM, Churchill Hospital, Oxford, UK
| | - Shane A Norris
- Department of Paediatrics, South African Medical Research Council (SAMRC), WITS, Developmental Pathways for Health Research Unit (DPHRU), Faculty of Health Sciences, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa
- Global Health Research Institute, School of Human Development and Health, University of Southampton, Southampton, UK
| | - Nigel J Crowther
- Department of Chemical Pathology, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tommy Olsson
- Department of Public Health and Clinical Medicine, Medicine, Umeå University, Umeå, Sweden
| | - Julia H Goedecke
- Department of Paediatrics, South African Medical Research Council (SAMRC), WITS, Developmental Pathways for Health Research Unit (DPHRU), Faculty of Health Sciences, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa
- Non-Communicable Diseases Research Unit, South African Medical Research Council, Cape Town, South Africa
| |
Collapse
|
44
|
Improving Experiences of the Menopause for Women in Zimbabwe and South Africa: Co-Producing an Information Resource. SOCIAL SCIENCES-BASEL 2022. [DOI: 10.3390/socsci11040143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Women in sub-Saharan Africa report multiple impacts of menopause on daily life and have requested further information to support themselves. This study co-produced contextually relevant resources—booklets and poster—about menopause with women in Zimbabwe and South Africa. The study was conducted in four stages: interviews with women about the menopause; the development of prototype information resources; workshops with women to discuss country-specific resources; and the refinement of resources. During the interviews, women explained that they had not received or accessed much information about the menopause and thought the physical and psychological issues associated with the menopause had to be “endured”. Prototype information resources comprised booklets and a poster with contextually relevant images and information. Workshop participants suggested several changes, including the addition of more diverse images and further information about treatments. The resources were refined, translated into several African languages, and endorsed by the Ministry of Health in Zimbabwe and the South African Menopause Society in South Africa. Women will be able to access resources through healthcare clinics, community groups and churches. Working with women and other stakeholders enabled a development that was cognisant of experiences and needs. Work is now needed to improve access to treatments and support for menopause to reduce health inequities.
Collapse
|
45
|
Kisiangani I, Mohamed SF, Kyobutungi C, Tindana P, Ghansah A, Ramsay M, Asiki G. Perspectives on returning individual and aggregate genomic research results to study participants and communities in Kenya: a qualitative study. BMC Med Ethics 2022; 23:27. [PMID: 35300680 PMCID: PMC8932129 DOI: 10.1186/s12910-022-00767-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 03/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A fundamental ethical challenge in conducting genomics research is the question of what and how individual level genetic findings and aggregate genomic results should be conveyed to research participants and communities. This is within the context of minimal guidance, policies, and experiences, particularly in Africa. The aim of this study was to explore the perspectives of key stakeholders' on returning genomics research results to participants in Kenya. METHODS This qualitative study involved focus group discussions (FGDs) and in-depth interviews (IDIs) with 69 stakeholders. The purposively selected participants, included research ethics committee (REC) members (8), community members (44), community resource persons (8), and researchers (9). A semi-structured interview guide was used to facilitate discussions. Six FGDs and twenty-five (IDIs) were conducted among the different stakeholders. The issues explored in the interviews included: (1) views on returning results, (2) kind of results to be returned, (3) value of returning results to participants, and (4) challenges anticipated in returning results to participants and communities. The interviews were audio-recorded, transcribed verbatim, and coded in Nvivo 12 pro. Thematic and content analysis was conducted. RESULTS Participants agreed on the importance of returning genomic results either as individual or aggregate results. The most cited reasons for returning of genomic results included recognizing participants' contribution to research, encouraging participation in future research, and increasing the awareness of scientific progress. Other aspects on how genomic research results should be shared included sharing easy to understand results in the shortest time possible and maintaining confidentiality when sharing sensitive results. CONCLUSIONS This study identified key stakeholders' perspectives on returning genomic results at the individual and community levels in two urban informal settlements of Nairobi. The majority of the participants expect to receive feedback about their genomic results, and it is an obligation for researchers to see how to best fulfil it.
Collapse
Affiliation(s)
- Isaac Kisiangani
- African Population and Health Research Center (APHRC), P.O. Box 10787, Nairobi, 00100 Kenya
| | - Shukri F. Mohamed
- African Population and Health Research Center (APHRC), P.O. Box 10787, Nairobi, 00100 Kenya
| | - Catherine Kyobutungi
- African Population and Health Research Center (APHRC), P.O. Box 10787, Nairobi, 00100 Kenya
| | - Paulina Tindana
- School of Public Health, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, The University of Witwatersrand, The Mount, 9 Jubilee Rd, Parktown, Johannesburg, 2193 South Africa
| | - Gershim Asiki
- African Population and Health Research Center (APHRC), P.O. Box 10787, Nairobi, 00100 Kenya
| |
Collapse
|
46
|
Tamburini FB, Maghini D, Oduaran OH, Brewster R, Hulley MR, Sahibdeen V, Norris SA, Tollman S, Kahn K, Wagner RG, Wade AN, Wafawanaka F, Gómez-Olivé FX, Twine R, Lombard Z, Hazelhurst S, Bhatt AS. Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa. Nat Commun 2022; 13:926. [PMID: 35194028 PMCID: PMC8863827 DOI: 10.1038/s41467-021-27917-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/25/2021] [Indexed: 12/15/2022] Open
Abstract
Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world's population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n = 118) or urban Soweto (n = 51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple "western-nonwestern" axis and contains undescribed microbial diversity.
Collapse
Affiliation(s)
| | - Dylan Maghini
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Ryan Brewster
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Michaella R Hulley
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | - Venesa Sahibdeen
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | - Shane A Norris
- SAMRC Developmental Pathways for Health Research Unit, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa.,School of Human Development and Health, University of Southampton, Southampton, UK
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Ryan G Wagner
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Alisha N Wade
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Rhian Twine
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa. .,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA. .,School of Medicine, Stanford University, Stanford, CA, USA. .,Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA.
| |
Collapse
|
47
|
Boua PR, Brandenburg JT, Choudhury A, Sorgho H, Nonterah EA, Agongo G, Asiki G, Micklesfield L, Choma S, Gómez-Olivé FX, Hazelhurst S, Tinto H, Crowther NJ, Mathew CG, Ramsay M. Genetic associations with carotid intima-media thickness link to atherosclerosis with sex-specific effects in sub-Saharan Africans. Nat Commun 2022; 13:855. [PMID: 35165267 PMCID: PMC8844072 DOI: 10.1038/s41467-022-28276-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/13/2022] [Indexed: 12/15/2022] Open
Abstract
Atherosclerosis precedes the onset of clinical manifestations of cardiovascular diseases (CVDs). We used carotid intima-media thickness (cIMT) to investigate genetic susceptibility to atherosclerosis in 7894 unrelated adults (3963 women, 3931 men; 40 to 60 years) resident in four sub-Saharan African countries. cIMT was measured by ultrasound and genotyping was performed on the H3Africa SNP Array. Two new African-specific genome-wide significant loci for mean-max cIMT, SIRPA (p = 4.7E-08), and FBXL17 (p = 2.5E-08), were identified. Sex-stratified analysis revealed associations with one male-specific locus, SNX29 (p = 6.3E-09), and two female-specific loci, LARP6 (p = 2.4E-09) and PROK1 (p = 1.0E-08). We replicate previous cIMT associations with different lead SNPs in linkage disequilibrium with SNPs primarily identified in European populations. Our study find significant enrichment for genes involved in oestrogen response from female-specific signals. The genes identified show biological relevance to atherosclerosis and/or CVDs, sex-differences and transferability of signals from non-African studies.
Collapse
Affiliation(s)
- Palwende Romuald Boua
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Centre national de la Recherche scientifique et technologique (CNRST), Nanoro, Burkina Faso.
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Centre national de la Recherche scientifique et technologique (CNRST), Nanoro, Burkina Faso
| | - Engelbert A Nonterah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Julius Global Health, Julius Centre for Health Sciences and Primary Care, University Medical Centre, Utrecht University, Utrecht, The Netherlands
| | - Godfred Agongo
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- C.K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Gershim Asiki
- African Population and Health Research Center, Nairobi, Kenya
| | - Lisa Micklesfield
- MRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Solomon Choma
- Department of Pathology and Medical Sciences, University of Limpopo, Polokwane, South Africa
| | - Francesc Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Halidou Tinto
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Centre national de la Recherche scientifique et technologique (CNRST), Nanoro, Burkina Faso
| | - Nigel J Crowther
- Department of Chemical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Christopher G Mathew
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| |
Collapse
|
48
|
Sex Differences in the Associations of Nutrient Patterns with Total and Regional Adiposity: A Study of Middle-Aged Black South African Men and Women. Nutrients 2021; 13:nu13124558. [PMID: 34960108 PMCID: PMC8706560 DOI: 10.3390/nu13124558] [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: 10/18/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/20/2022] Open
Abstract
The study evaluated the association between nutrient patterns with body fat and regional adiposity in middle-aged black South African (SA) men and women and determined if this differed by sex. Body fat and regional adiposity (dual-energy x-ray absorptiometry), and dietary intake (7-day quantified food frequency questionnaire) were measured in black SA men (n = 414) and women (n = 346). Using principal component analysis, nutrient patterns were computed from 25 nutrients in the combined sample. Four nutrient patterns were extracted, explaining 67% of the variance in nutrient intake. Animal and fat, as well as the vitamin C, sugar, and potassium driven patterns, were positively associated with total adiposity. In contrast, the retinol and vitamin B12 pattern was associated with the centralisation of fat. Notably, the strength of the association between the animal-driven nutrient pattern and BMI was greater in men (1.14 kg/m2, 95% CI (0.63–1.66)) than in women (0.81 kg/m2, 95% CI (0.25–1.36)) (Pint = 0.017). In contrast, the plant-driven pattern was associated with higher abdominal subcutaneous adipose tissue (SAT) in women (44 cm2, 95% CI (22–67)) but not men (Pint = 1.54 × 10−4). These differences suggest that although men and women have similar nutrient patterns, their associations with the whole body and regional body fat are different.
Collapse
|
49
|
da Rocha JEB, Othman H, Tiemessen CT, Botha G, Ramsay M, Masimirembwa C, Adebamowo C, Choudhury A, Brandenburg JT, Matshaba M, Simo G, Gamo FJ, Hazelhurst S. G6PD distribution in sub-Saharan Africa and potential risks of using chloroquine/hydroxychloroquine based treatments for COVID-19. THE PHARMACOGENOMICS JOURNAL 2021; 21:649-656. [PMID: 34302047 PMCID: PMC8299738 DOI: 10.1038/s41397-021-00242-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 05/12/2021] [Indexed: 02/07/2023]
Abstract
Chloroquine/hydroxychloroquine have been proposed as potential treatments for COVID-19. These drugs have warning labels for use in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency. Analysis of whole genome sequence data of 458 individuals from sub-Saharan Africa showed significant G6PD variation across the continent. We identified nine variants, of which four are potentially deleterious to G6PD function, and one (rs1050828) that is known to cause G6PD deficiency. We supplemented data for the rs1050828 variant with genotype array data from over 11,000 Africans. Although this variant is common in Africans overall, large allele frequency differences exist between sub-populations. African sub-populations in the same country can show significant differences in allele frequency (e.g. 16.0% in Tsonga vs 0.8% in Xhosa, both in South Africa, p = 2.4 × 10-3). The high prevalence of variants in the G6PD gene found in this analysis suggests that it may be a significant interaction factor in clinical trials of chloroquine and hydroxychloroquine for treatment of COVID-19 in Africans.
Collapse
Affiliation(s)
- Jorge E B da Rocha
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gerrit Botha
- Computational Biology Division and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Collen Masimirembwa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Clement Adebamowo
- Institute for Human Virology Abuja, Abuja, Nigeria
- Institute of Human Virology and Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Center of Excellence, Gaborone, Botswana
- Baylor College of Medicine, Houston, TX, USA
| | - Gustave Simo
- Molecular Parasitology and Entomology Unit, Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.
| |
Collapse
|
50
|
Singh S, Brandenburg JT, Choudhury A, Gómez-Olivé FX, Ramsay M. Systematic Review of Genomic Associations with Blood Pressure and Hypertension in Populations with African-Ancestry. Front Genet 2021; 12:699445. [PMID: 34745203 PMCID: PMC8564494 DOI: 10.3389/fgene.2021.699445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/10/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Despite hypertension being highly prevalent in individuals with African-ancestry, they are under-represented in large genome-wide association studies. Inclusion of African participants is essential to better understand genetic associations with blood pressure-related traits in Africans. This systematic review critically evaluates existing studies with African-ancestry participants and identifies knowledge gaps. Methods: We followed the PRISMA protocol, HuGE Review handbook to identify literature on original research, in English, on genetic association studies for blood pressure-related traits (systolic and diastolic blood pressure, pulse and mean-arterial pressure, and hypertension) in populations with African-ancestry (January 2007 to April 2020). A narrative synthesis of the evidence was conducted. Results: Twelve studies with African-ancestry participants met the eligibility criteria, within which 10 studies met the additional genetic association data criteria (i.e., reporting only on African-ancestry participants). Across the five blood pressure-related traits, 26 genome-wide significantly associated SNPs were identified, with six SNPs linked to more than one trait, illustrating pleiotropic effects. Among the SNP associations, 12 had not previously been described in non-African studies. Discussion: The limited number of relevant studies highlights the dearth of genomic association studies on participants with African-ancestry, especially those located within Africa. Variations in study methodology, participant inclusion, adjustment for covariates (e.g., antihypertensive medication) and relatively small sample sizes make comparisons challenging, and have resulted in fewer significant associations, compared to large European studies. Regional variation in the prevalence and associated risk factors of hypertension across Africa makes a compelling argument to develop African cohorts to facilitate large genomic studies, using African-centric arrays. Data harmonisation and comparable study designs, such as described in the H3Africa CHAIR initiative, provide a good example toward achieving this goal. Other relevant information: SS and J-TB were funded by the South African National Research Foundation. MR is a South African Research Chair in Genomics and Bioinformatics of African populations hosted by the University of the Witwatersrand, funded by the Department of Science and Innovation, and administered by the NRF. This review was registered at PROSPERO (registration number: CRD42020179221) and OSF (registration DOI: 10.17605/OSF.IO/QT2HA).
Collapse
Affiliation(s)
- S Singh
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J-T Brandenburg
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A Choudhury
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - F X Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - M Ramsay
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|