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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.
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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
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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.
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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.
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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
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Gao B, Zhou X. MESuSiE enables scalable and powerful multi-ancestry fine-mapping of causal variants in genome-wide association studies. Nat Genet 2024; 56:170-179. [PMID: 38168930 DOI: 10.1038/s41588-023-01604-7] [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: 11/21/2022] [Accepted: 10/30/2023] [Indexed: 01/05/2024]
Abstract
Fine-mapping in genome-wide association studies attempts to identify causal SNPs from a set of candidate SNPs in a local genomic region of interest and is commonly performed in one genetic ancestry at a time. Here, we present multi-ancestry sum of the single effects model (MESuSiE), a probabilistic multi-ancestry fine-mapping method, to improve the accuracy and resolution of fine-mapping by leveraging association information across ancestries. MESuSiE uses summary statistics as input, accounts for the diverse linkage disequilibrium pattern observed in different ancestries, explicitly models both shared and ancestry-specific causal SNPs, and relies on a variational inference algorithm for scalable computation. We evaluated the performance of MESuSiE through comprehensive simulations and multi-ancestry fine-mapping of four lipid traits with both European and African samples. In the real data, MESuSiE improves fine-mapping resolution by 19.0% to 72.0% compared to existing approaches, is an order of magnitude faster, and captures and categorizes shared and ancestry-specific causal signals with enhanced functional enrichment.
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Affiliation(s)
- Boran Gao
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA.
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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.
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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
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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.
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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.
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Drouet DE, Liu S, Crawford DC. Assessment of multi-population polygenic risk scores for lipid traits in African Americans. PeerJ 2023; 11:e14910. [PMID: 37214096 PMCID: PMC10198155 DOI: 10.7717/peerj.14910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/25/2023] [Indexed: 05/24/2023] Open
Abstract
Polygenic risk scores (PRS) based on genome-wide discoveries are promising predictors or classifiers of disease development, severity, and/or progression for common clinical outcomes. A major limitation of most risk scores is the paucity of genome-wide discoveries in diverse populations, prompting an emphasis to generate these needed data for trans-population and population-specific PRS construction. Given diverse genome-wide discoveries are just now being completed, there has been little opportunity for PRS to be evaluated in diverse populations independent from the discovery efforts. To fill this gap, we leverage here summary data from a recent genome-wide discovery study of lipid traits (HDL-C, LDL-C, triglycerides, and total cholesterol) conducted in diverse populations represented by African Americans, Hispanics, Asians, Native Hawaiians, Native Americans, and others by the Population Architecture using Genomics and Epidemiology (PAGE) Study. We constructed lipid trait PRS using PAGE Study published genetic variants and weights in an independent African American adult patient population linked to de-identified electronic health records and genotypes from the Illumina Metabochip (n = 3,254). Using multi-population lipid trait PRS, we assessed levels of association for their respective lipid traits, clinical outcomes (cardiovascular disease and type 2 diabetes), and common clinical labs. While none of the multi-population PRS were strongly associated with the tested trait or outcome, PRSLDL-Cwas nominally associated with cardiovascular disease. These data demonstrate the complexity in applying PRS to real-world clinical data even when data from multiple populations are available.
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Affiliation(s)
- Domenica E. Drouet
- Department of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
| | - Shiying Liu
- Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Dana C. Crawford
- Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, United States of America
- Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, United States of America
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Kintu C, Soremekun O, Kamiza AB, Kalungi A, Mayanja R, Kalyesubula R, Bagaya S B, Jjingo D, Fabian J, Gill D, Nyirenda M, Nitsch D, Chikowore T, Fatumo S. The causal effects of lipid traits on kidney function in Africans: bidirectional and multivariable Mendelian-randomization study. EBioMedicine 2023; 90:104537. [PMID: 37001235 PMCID: PMC10070509 DOI: 10.1016/j.ebiom.2023.104537] [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: 10/15/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Observational studies have investigated the effect of serum lipids on kidney function, but these findings are limited by confounding, reverse causation and have reported conflicting results. Mendelian randomization (MR) studies address this confounding problem. However, they have been conducted mostly in European ancestry individuals. We, therefore, set out to investigate the effect of lipid traits on the estimated glomerular filtration rate (eGFR) based on serum creatinine in individuals of African ancestry. METHODS We used the two-sample and multivariable Mendelian randomization (MVMR) approaches; in which instrument variables (IV's) for the predictor (lipid traits) were derived from summary-level data of a meta-analyzed African lipid GWAS (MALG, n = 24,215) from the African Partnership for Chronic Disease Research (APCDR) (n = 13,612) & the Africa Wits-IN-DEPTH partnership for Genomics studies (AWI-Gen) dataset (n = 10,603). The outcome IV's were computed from the eGFR summary-level data of African-ancestry individuals within the Million Veteran Program (n = 57,336). A random-effects inverse variance method was used in our primary analysis, and pleiotropy was adjusted for using robust and penalized sensitivity testing. The lipid predictors for the MVMR were high-density lipoprotein (HDL) cholesterol, low-density lipoprotein (LDL) cholesterol, and triglycerides (TG). FINDINGS We found a significant causal association between genetically predicted low-density lipoprotein (LDL) cholesterol and eGFR in African ancestry individuals β = 1.1 (95% CI [0.411-1.788]; p = 0.002). Similarly, total cholesterol (TC) showed a significant causal effect on eGFR β = 1.619 (95% CI [0.412-2.826]; p = 0.009). However, the IVW estimate showed that genetically predicted HDL-C β = -0.164, (95% CI = [-1.329 to 1.00]; p = 0.782), and TG β = -0.934 (CI = [-2.815 to 0.947]; p = 0.33) were not significantly causally associated with the risk of eGFR. In the multivariable analysis inverse-variance weighted (MVIVW) method, there was evidence for a causal association between LDL and eGFR β = 1.228 (CI = [0.477-1.979]; p = 0.001). A significant causal effect of Triglycerides (TG) on eGFR in the MVIVW analysis β = -1.3 ([-2.533 to -0.067]; p = 0.039) was observed as well. All the causal estimates reported reflect a unit change in the outcome per a 1 SD increase in the exposure. HDL showed no evidence of a significant causal association with eGFR in the MVIVW method (β = -0.117 (95% CI [-1.252 to 0.018]; p = 0.840)). We found no evidence of a reverse causal impact of eGFR on serum lipids. All our sensitivity analyses indicated no strong evidence of pleiotropy or heterogeneity between our instrumental variables for both the forward and reverse MR analysis. INTERPRETATION In this African ancestry population, genetically predicted higher LDL-C and TC are causally associated with higher eGFR levels, which may suggest that the relationship between LDL, TC and kidney function may be U-shaped. And as such, lowering LDL_C does not necessarily improve risk of kidney disease. This may also imply the reason why LDL_C is seen to be a poorer predictor of kidney function compared to HDL. In addition, this further supports that more work is warranted to confirm the potential association between lipid traits and risk of kidney disease in individuals of African Ancestry. FUNDING Wellcome (220740/Z/20/Z).
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Affiliation(s)
- Christopher Kintu
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda; Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda; MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Opeyemi Soremekun
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda; MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Abram B Kamiza
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Allan Kalungi
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda; MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Richard Mayanja
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda; MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Robert Kalyesubula
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda; MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Bernard Bagaya S
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Daudi Jjingo
- African Center of Excellence in Bioinformatics (ACE-B), Makerere University, Kampala 10101, Uganda
| | - 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
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK; Chief Scientific Advisor Office, Research and Early Development, Novo Nordisk, Copenhagen, Denmark
| | - Moffat Nyirenda
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda; Department of Non-Communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Dorothea Nitsch
- Department of Non-Communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Tinashe Chikowore
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda; MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda; Department of Non-Communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
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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.
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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
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Araújo DS, Wheeler HE. Genetic and environmental variation impact transferability of polygenic risk scores. Cell Rep Med 2022; 3:100687. [PMID: 35858592 PMCID: PMC9381406 DOI: 10.1016/j.xcrm.2022.100687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Even when polygenic risk scores (PRSs) are trained in African ancestral populations, Kamiza and colleagues showed that genetic and environmental variation within sub-Saharan African populations impacts prediction performance, highlighting the challenges of clinical implementation of PRSs for risk assessment.
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