1
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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.
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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.
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2
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Goovaerts S, Hoskens H, Eller RJ, Herrick N, Musolf AM, Justice CM, Yuan M, Naqvi S, Lee MK, Vandermeulen D, Szabo-Rogers HL, Romitti PA, Boyadjiev SA, Marazita ML, Shaffer JR, Shriver MD, Wysocka J, Walsh S, Weinberg SM, Claes P. Joint multi-ancestry and admixed GWAS reveals the complex genetics behind human cranial vault shape. Nat Commun 2023; 14:7436. [PMID: 37973980 PMCID: PMC10654897 DOI: 10.1038/s41467-023-43237-8] [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: 12/07/2022] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
The cranial vault in humans is highly variable, clinically relevant, and heritable, yet its genetic architecture remains poorly understood. Here, we conduct a joint multi-ancestry and admixed multivariate genome-wide association study on 3D cranial vault shape extracted from magnetic resonance images of 6772 children from the ABCD study cohort yielding 30 genome-wide significant loci. Follow-up analyses indicate that these loci overlap with genomic risk loci for sagittal craniosynostosis, show elevated activity cranial neural crest cells, are enriched for processes related to skeletal development, and are shared with the face and brain. We present supporting evidence of regional localization for several of the identified genes based on expression patterns in the cranial vault bones of E15.5 mice. Overall, our study provides a comprehensive overview of the genetics underlying normal-range cranial vault shape and its relevance for understanding modern human craniofacial diversity and the etiology of congenital malformations.
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Affiliation(s)
- Seppe Goovaerts
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium.
| | - Hanne Hoskens
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Ryan J Eller
- Department of Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Noah Herrick
- Department of Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Anthony M Musolf
- Statistical Genetics Section, Computational and Statistical Genomics Branch, NHGRI, NIH, MD, Baltimore, USA
| | - Cristina M Justice
- Genometrics Section, Computational and Statistical Genomics Branch, Division of Intramural Research, NHGRI, NIH, Baltimore, MD, USA
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Meng Yuan
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Genetics and Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Myoung Keun Lee
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dirk Vandermeulen
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Heather L Szabo-Rogers
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatchewan, Canada
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, IA, USA
| | - Simeon A Boyadjiev
- Department of Pediatrics, University of California Davis, Sacramento, CA, USA
| | - Mary L Marazita
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - John R Shaffer
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, State College, PA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Susan Walsh
- Department of Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Seth M Weinberg
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium.
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.
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3
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Shriner D, Bentley AR, Gouveia MH, Heuston EF, Doumatey AP, Chen G, Zhou J, Adeyemo A, Rotimi CN. Universal genome-wide association studies: Powerful joint ancestry and association testing. HGG ADVANCES 2023; 4:100235. [PMID: 37653728 PMCID: PMC10507155 DOI: 10.1016/j.xhgg.2023.100235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023] Open
Abstract
The vast majority of human populations and individuals have mixed ancestry. Consequently, adjustment for locus-specific ancestry is essential for genetic association studies. To empower association studies for all populations, it is necessary to integrate effects of locus-specific ancestry and genotype. We developed a joint test of ancestry and association that can be performed with summary statistics, is independent of study design, can take advantage of locus-specific ancestry effects to boost power in association testing, and can utilize association effects to fine map admixture peaks. We illustrate the test using the association between serum triglycerides and LPL. By combining data from African Americans, European Americans, and West Africans, we identify three conditionally independent variants with varying amounts of ancestrally differentiated allele frequencies. Using out-of-sample data, we demonstrate improved prediction achievable by accounting for multiple causal variants and locus-specific ancestry effects at a single locus.
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Affiliation(s)
- Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Mateus H Gouveia
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Elisabeth F Heuston
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA.
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4
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Singh S, Choudhury A, Hazelhurst S, Crowther N, Boua P, Sorgho H, Agongo G, Nonterah E, Micklesfield L, Norris S, Kisiangani I, Mohamed S, Gomez-Olive F, Tollman S, 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. RESEARCH SQUARE 2023:rs.3.rs-2532794. [PMID: 36824767 PMCID: PMC9949264 DOI: 10.21203/rs.3.rs-2532794/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Most hypertension-related genome-wide association studies (GWAS) 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-related traits (systolic and diastolic blood pressure, pulse pressure, mean-arterial pressure and hypertension) from three sub-Saharan African geographic regions (N=10,775), identified two genome-wide significant signals (p<5E-08): systolic blood pressure near P2RY1 (rs77846204; intergenic variant, p=4.25E-08) and pulse pressure near Linc01256 (rs80141533; intergenic variant, p=4.25E-08). No genome-wide signals were detected for the AWI-Gen GWAS meta-analysis with previous African-ancestry GWASs (UK Biobank (African), Uganda Genome Resource). Suggestive signals (p<5E-06) were observed for all traits, with 29 displaying pleiotropic effects and several replicating known associations. Polygenic risk scores developed from studies on different ancestries had limited transferability, with multi-ancestry models providing better prediction. This study provides insights into the genetics and physiology of blood pressure variation in African populations.
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Affiliation(s)
- Surina Singh
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand
| | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences & School of Electrical & Information Engineering, University of the Witwatersrand
| | - Nigel Crowther
- 11Department of Chemical Pathology, National Health Laboratory Service
| | - Palwende Boua
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé
| | | | | | | | - Shane Norris
- SAMRC Developmental Pathways For Health Research Unit, Department of Paediatrics & Child Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Francesc Gomez-Olive
- 8MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand
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5
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Kurniansyah N, Goodman MO, Kelly TN, Elfassy T, Wiggins KL, Bis JC, Guo X, Palmas W, Taylor KD, Lin HJ, Haessler J, Gao Y, Shimbo D, Smith JA, Yu B, Feofanova EV, Smit RAJ, Wang Z, Hwang SJ, Liu S, Wassertheil-Smoller S, Manson JE, Lloyd-Jones DM, Rich SS, Loos RJF, Redline S, Correa A, Kooperberg C, Fornage M, Kaplan RC, Psaty BM, Rotter JI, Arnett DK, Morrison AC, Franceschini N, Levy D, Sofer T. A multi-ethnic polygenic risk score is associated with hypertension prevalence and progression throughout adulthood. Nat Commun 2022; 13:3549. [PMID: 35729114 PMCID: PMC9213527 DOI: 10.1038/s41467-022-31080-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/31/2022] [Indexed: 12/12/2022] Open
Abstract
In a multi-stage analysis of 52,436 individuals aged 17-90 across diverse cohorts and biobanks, we train, test, and evaluate a polygenic risk score (PRS) for hypertension risk and progression. The PRS is trained using genome-wide association studies (GWAS) for systolic, diastolic blood pressure, and hypertension, respectively. For each trait, PRS is selected by optimizing the coefficient of variation (CV) across estimated effect sizes from multiple potential PRS using the same GWAS, after which the 3 trait-specific PRSs are combined via an unweighted sum called "PRSsum", forming the HTN-PRS. The HTN-PRS is associated with both prevalent and incident hypertension at 4-6 years of follow up. This association is further confirmed in age-stratified analysis. In an independent biobank of 40,201 individuals, the HTN-PRS is confirmed to be predictive of increased risk for coronary artery disease, ischemic stroke, type 2 diabetes, and chronic kidney disease.
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Affiliation(s)
- Nuzulul Kurniansyah
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew O Goodman
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Tali Elfassy
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Walter Palmas
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Henry J Lin
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yan Gao
- The Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Daichi Shimbo
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Bing Yu
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Elena V Feofanova
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Roelof A J Smit
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shih-Jen Hwang
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - Simin Liu
- Center for Global Cardiometabolic Health and Departments of Epidemiology, Medicine, and Surgery, Brown University, Providence, RI, USA
| | - Sylvia Wassertheil-Smoller
- Department of Epidemiology & Population Health, Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - JoAnn E Manson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Adolfo Correa
- Departments of Medicine and Pediatrics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Robert C Kaplan
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Daniel Levy
- The Population Sciences Branch of the National Heart, Lung and Blood Institute, Bethesda, MD, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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6
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Kizil C, Sariya S, Kim YA, Rajabli F, Martin E, Reyes-Dumeyer D, Vardarajan B, Maldonado A, Haines JL, Mayeux R, Jiménez-Velázquez IZ, Santa-Maria I, Tosto G. Admixture Mapping of Alzheimer's disease in Caribbean Hispanics identifies a new locus on 22q13.1. Mol Psychiatry 2022; 27:2813-2820. [PMID: 35365809 PMCID: PMC9167722 DOI: 10.1038/s41380-022-01526-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/28/2022] [Accepted: 03/14/2022] [Indexed: 11/09/2022]
Abstract
Late-onset Alzheimer's disease (LOAD) is significantly more frequent in Hispanics than in non-Hispanic Whites. Ancestry may explain these differences across ethnic groups. To this end, we studied a large cohort of Caribbean Hispanics (CH, N = 8813) and tested the association between Local Ancestry (LA) and LOAD ("admixture mapping") to identify LOAD-associated ancestral blocks, separately for ancestral components (European [EUR], African [AFR], Native American[NA]) and jointly (AFR + NA). Ancestral blocks significant after permutation were fine-mapped employing multi-ethnic whole-exome sequencing (WES) to identify rare variants associated with LOAD (SKAT-O) and replicated in the UK Biobank WES dataset. Candidate genes were validated studying (A) protein expression in human LOAD and control brains; (B) two animal AD models, Drosophila and Zebrafish. In the joint AFR + NA model, we identified four significant ancestral blocks located on chromosomes 1 (p value = 8.94E-05), 6 (p value = 8.63E-05), 21 (p value = 4.64E-05) and 22 (p value = 1.77E-05). Fine-mapping prioritized the GCAT gene on chromosome 22 (SKAT-O p value = 3.45E-05) and replicated in the UK Biobank (SKAT-O p value = 0.05). In LOAD brains, a decrease of 28% in GCAT protein expression was observed (p value = 0.038), and GCAT knockdown in Amyloid-β42 Drosophila exacerbated rough eye phenotype (68% increase, p value = 4.84E-09). In zebrafish, gcat expression increased after acute amyloidosis (34%, p value = 0.0049), and decreased upon anti-inflammatory Interleukin-4 (39%, p value = 2.3E-05). Admixture mapping uncovered genomic regions harboring new LOAD-associated loci that might explain the observed different frequency of LOAD across ethnic groups. Our results suggest that the inflammation-related activity of GCAT is a response to amyloid toxicity, and reduced GCAT expression exacerbates AD pathology.
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Affiliation(s)
- Caghan Kizil
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
- German Center for Neurodegenerative Diseases (DZNE), Helmholtz Association, Tatzberg 41, 01307, Dresden, Germany
| | - Sanjeev Sariya
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
| | - Yoon A Kim
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Eden Martin
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
| | - Badri Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
| | - Aleyda Maldonado
- Department of Medicine, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, 00936, USA
| | - Jonathan L Haines
- Department of Population & Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Medicine, College of Physicians and Surgeons, Columbia University, and the New York Presbyterian Hospital, 630 West 168th Street, New York, NY, 10032, USA
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, 1051 Riverside Drive, New York, NY, 10032, USA
| | - Ivonne Z Jiménez-Velázquez
- Department of Medicine, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, 00936, USA
| | - Ismael Santa-Maria
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA.
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA.
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA.
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7
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Bentley AR, Chen G, Doumatey AP, Shriner D, Meeks KAC, Gouveia MH, Ekoru K, Zhou J, Adeyemo A, Rotimi CN. GWAS in Africans identifies novel lipids loci and demonstrates heterogenous association within Africa. Hum Mol Genet 2021; 30:2205-2214. [PMID: 34196372 PMCID: PMC8561421 DOI: 10.1093/hmg/ddab174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 01/11/2023] Open
Abstract
Serum lipids are biomarkers of cardiometabolic disease risk, and understanding genomic factors contributing to their distribution is of interest. Studies of lipids in Africans are rare, though it is expected that such studies could identify novel loci. We conducted a GWAS of 4317 Africans enrolled from Nigeria, Ghana and Kenya. We evaluated linear mixed models of high-density lipoprotein cholesterol (HDLC), low-density lipoprotein cholesterol (LDLC), total cholesterol (CHOL), triglycerides (TG) and TG/HDLC. Replication was attempted in 9542 African Americans (AA). In our main analysis, we identified 28 novel associations in Africans. Of the 18 of these that could be tested in AA, three associations replicated (GPNMB-TG, ENPP1-TG and SMARCA4-LDLC). Five additional novel loci were discovered upon meta-analysis with AA (rs138282551-TG, PGBD5-HDLC, CD80-TG/HDLC, SLC44A1-CHOL and TLL2-CHOL). Analyses considering only those with predominantly West African ancestry (Nigeria, Ghana and AA) yielded new insights: ORC5-LDLC and chr20:60973327-CHOL. Among our novel findings are some loci with known connections to lipids pathways. For instance, rs147706369 (TLL2) alters a regulatory motif for sterol regulatory element-binding proteins, a family of transcription factors that control the expression of a range of enzymes involved in cholesterol, fatty acid and TG synthesis, and rs115749422 (SMARCA4), an independent association near the known LDLR locus that is rare or absent in populations without African ancestry. These findings demonstrate the utility of conducting genomic analyses in Africans for discovering novel loci and provide some preliminary evidence for caution against treating 'African ancestry' as a monolithic category.
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Affiliation(s)
- Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Karlijn A C Meeks
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Mateus H Gouveia
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Kenneth Ekoru
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
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8
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Genetic Ancestry Inference and Its Application for the Genetic Mapping of Human Diseases. Int J Mol Sci 2021; 22:ijms22136962. [PMID: 34203440 PMCID: PMC8269095 DOI: 10.3390/ijms22136962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
Admixed populations arise when two or more ancestral populations interbreed. As a result of this admixture, the genome of admixed populations is defined by tracts of variable size inherited from these parental groups and has particular genetic features that provide valuable information about their demographic history. Diverse methods can be used to derive the ancestry apportionment of admixed individuals, and such inferences can be leveraged for the discovery of genetic loci associated with diseases and traits, therefore having important biomedical implications. In this review article, we summarize the most common methods of global and local genetic ancestry estimation and discuss the use of admixture mapping studies in human diseases.
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9
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Chen G, Adeyemo A, Zhou J, Doumatey AP, Bentley AR, Ekoru K, Shriner D, Rotimi CN. A UGT1A1 variant is associated with serum total bilirubin levels, which are causal for hypertension in African-ancestry individuals. NPJ Genom Med 2021; 6:44. [PMID: 34117260 PMCID: PMC8196001 DOI: 10.1038/s41525-021-00208-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/15/2021] [Indexed: 02/05/2023] Open
Abstract
Serum bilirubin is associated with several clinical outcomes, including hypertension, type 2 diabetes (T2D), and drug metabolism. Here, we describe findings from our genome-wide association studies (GWAS) of serum (TBIL) using a generalized linear mixed model in West Africans (n = 1127), with adjustment for age, sex, body mass index, T2D, significant principal components of population structure, and cryptic relatedness. Genome-wide conditional analysis and CAVIARBF were used to fine map significant loci. The causal effect of TBIL on hypertension was assessed by Mendelian randomization (MR) using the GWAS findings as instrumental variables (IVs) in African Americans (n = 3,067). The SNP rs887829 (UGT1A1) was significantly associated with TBIL levels (effect allele (T) frequency = 0.49, β (SE) = 0.59 (0.04), p = 9.13 × 10-54). Genome-wide conditional analysis and regional fine mapping pointed to rs887829 as a possible causal variant with a posterior inclusion probability of 0.99. The T allele of rs887829 is associated with lower hepatic expression of UGT1A1. Using rs887829 as an IV, two-stage least-squares MR showed a causal effect of bilirubin on hypertension (β = -0.76, 95% CI [-1.52, -0.01], p = 0.0459). Our finding confirms that UGT1A1 influences bilirubin levels. Notably, lower TBIL is causally associated with the increased risk of hypertension.
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Affiliation(s)
- Guanjie Chen
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Adebowale Adeyemo
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Jie Zhou
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Ayo P. Doumatey
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Amy R. Bentley
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Kenneth Ekoru
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Daniel Shriner
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Charles N. Rotimi
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
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