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Hampton G, Kim J, Edwards TL, Hellwege JN, Velez Edwards DR. Uterine leiomyomata and keloids fibrosis origins: a mini-review of fibroproliferative diseases. Am J Physiol Cell Physiol 2023; 325:C817-C822. [PMID: 37642233 PMCID: PMC10635651 DOI: 10.1152/ajpcell.00181.2023] [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: 05/02/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
Diseases such as uterine leiomyomata (fibroids and benign tumors of the uterus) and keloids (raised scars) may share common etiology. Fibroids and keloids can co-occur in individuals, and both are highly heritable, suggesting they may share common genetic risk factors. Fibroproliferative diseases are common and characterized by scarring and overgrowth of connective tissue, impacting multiple organ systems. These conditions both have racial disparities in prevalence, with the highest prevalence observed among individuals of African ancestry. Several fibroproliferative diseases are more severe and common in populations of sub-Saharan Africa. This mini-review aims to provide a broad overview of the current knowledge of the evolutionary origins and causes of fibroproliferative diseases. We also discuss current hypotheses proposing that the increased prevalence of these diseases in African-derived populations is due to the selection for profibrotic alleles that are protective against helminth infections and provide examples from knowledge of uterine fibroid and keloid research.
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Affiliation(s)
- Gabrielle Hampton
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Jeewoo Kim
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Todd L Edwards
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Jacklyn N Hellwege
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Digna R Velez Edwards
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, United States
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2
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Pan Y, Zhang C, Lu Y, Ning Z, Lu D, Gao Y, Zhao X, Yang Y, Guan Y, Mamatyusupu D, Xu S. Genomic diversity and post-admixture adaptation in the Uyghurs. Natl Sci Rev 2022; 9:nwab124. [PMID: 35350227 PMCID: PMC8953455 DOI: 10.1093/nsr/nwab124] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/30/2021] [Accepted: 06/07/2021] [Indexed: 11/17/2022] Open
Abstract
Population admixture results in genome-wide combinations of genetic variants derived from different ancestral populations of distinct ancestry, thus providing a unique opportunity for understanding the genetic determinants of phenotypic variation in humans. Here, we used whole-genome sequencing of 92 individuals with high coverage (30–60×) to systematically investigate genomic diversity in the Uyghurs living in Xinjiang, China (XJU), an admixed population of both European-like and East-Asian-like ancestry. The XJU population shows greater genetic diversity, especially a higher proportion of rare variants, compared with their ancestral source populations, corresponding to greater phenotypic diversity of XJU. Admixture-induced functional variants in EDAR were associated with the diversity of facial morphology in XJU. Interestingly, the interaction of functional variants between SLC24A5 and OCA2 likely influences the diversity of skin pigmentation. Notably, selection has seemingly been relaxed or canceled in several genes with significantly biased ancestry, such as HERC2–OCA2. Moreover, signatures of post-admixture adaptation in XJU were identified, including genes related to metabolism (e.g. CYP2D6), digestion (e.g. COL11A1), olfactory perception (e.g. ANO2) and immunity (e.g. HLA). Our results demonstrated population admixture as a driving force, locally or globally, in shaping human genetic and phenotypic diversity as well as in adaptive evolution.
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Affiliation(s)
- Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
| | - Chao Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438, China
| | - Zhilin Ning
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
| | - Dongsheng Lu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
| | - Yang Gao
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University , Shanghai 201210, China
| | - Xiaohan Zhao
- Human Phenome Institute, Fudan University , Shanghai 201203, China
| | - Yajun Yang
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438, China
| | - Yaqun Guan
- Department of Biochemistry and Molecular Biology, Preclinical Medicine College, Xinjiang Medical University , Urumqi 830011, China
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University , Urumqi 830046, China
| | - Shuhua Xu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438, China
- School of Life Science and Technology, ShanghaiTech University , Shanghai 201210, China
- Human Phenome Institute, Fudan University , Shanghai 201203, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming 650223, China
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University , Zhengzhou 450052, China
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3
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Simonin-Wilmer I, Orozco-del-Pino P, Bishop DT, Iles MM, Robles-Espinoza CD. An Overview of Strategies for Detecting Genotype-Phenotype Associations Across Ancestrally Diverse Populations. Front Genet 2021; 12:703901. [PMID: 34804113 PMCID: PMC8602802 DOI: 10.3389/fgene.2021.703901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association studies (GWAS) have been very successful at identifying genetic variants influencing a large number of traits. Although the great majority of these studies have been performed in European-descent individuals, it has been recognised that including populations with differing ancestries enhances the potential for identifying causal SNPs due to their differing patterns of linkage disequilibrium. However, when individuals from distinct ethnicities are included in a GWAS, it is necessary to implement a number of control steps to ensure that the identified associations are real genotype-phenotype relationships. In this Review, we discuss the analyses that are required when performing multi-ethnic studies, including methods for determining ancestry at the global and local level for sample exclusion, controlling for ancestry in association testing, and post-GWAS interrogation methods such as genomic control and meta-analysis. We hope that this overview provides a primer for those researchers interested in including distinct populations in their studies.
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Affiliation(s)
- Irving Simonin-Wilmer
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Queretaro, Mexico
| | | | - D. Timothy Bishop
- Leeds Institute for Data Analytics and Leeds Institute of Medical Research at St. James’s, University of Leeds, Leeds, United Kingdom
| | - Mark M. Iles
- Leeds Institute for Data Analytics and Leeds Institute of Medical Research at St. James’s, University of Leeds, Leeds, United Kingdom
| | - Carla Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Queretaro, Mexico
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
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4
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Leal BSS, Chaves CJN, Graciano VA, Boury C, Huacre LAP, Heuertz M, Palma-Silva C. Evidence of local adaptation despite strong drift in a Neotropical patchily distributed bromeliad. Heredity (Edinb) 2021; 127:203-218. [PMID: 33953353 PMCID: PMC8322333 DOI: 10.1038/s41437-021-00442-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 02/03/2023] Open
Abstract
Both genetic drift and divergent selection are predicted to be drivers of population differentiation across patchy habitats, but the extent to which these forces act on natural populations to shape traits is strongly affected by species' ecological features. In this study, we infer the genomic structure of Pitcairnia lanuginosa, a widespread herbaceous perennial plant with a patchy distribution. We sampled populations in the Brazilian Cerrado and the Central Andean Yungas and discovered and genotyped SNP markers using double-digest restriction-site associated DNA sequencing. In addition, we analyzed ecophysiological traits obtained from a common garden experiment and compared patterns of phenotypic and genetic divergence (PST-FST comparisons) in a subset of populations from the Cerrado. Our results from molecular analyses pointed to extremely low genetic diversity and a remarkable population differentiation, supporting a major role of genetic drift. Approximately 0.3% of genotyped SNPs were flagged as differentiation outliers by at least two distinct methods, and Bayesian generalized linear mixed models revealed a signature of isolation by environment in addition to isolation by distance for high-differentiation outlier SNPs among the Cerrado populations. PST-FST comparisons suggested divergent selection on two ecophysiological traits linked to drought tolerance. We showed that these traits vary among populations, although without any particular macro-spatial pattern, suggesting local adaptation to differences in micro-habitats. Our study shows that selection might be a relevant force, particularly for traits involved in drought stress, even for populations experiencing strong drift, which improves our knowledge on eco-evolutionary processes acting on non-continuously distributed species.
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Affiliation(s)
- Bárbara Simões Santos Leal
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Cleber Juliano Neves Chaves
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Vanessa Araujo Graciano
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Christophe Boury
- grid.412041.20000 0001 2106 639XINRAE, Univ. Bordeaux, Biogeco, Cestas France
| | - Luis Alberto Pillaca Huacre
- grid.10800.390000 0001 2107 4576Departamento de Ecología, Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Myriam Heuertz
- grid.412041.20000 0001 2106 639XINRAE, Univ. Bordeaux, Biogeco, Cestas France
| | - Clarisse Palma-Silva
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil ,grid.411087.b0000 0001 0723 2494Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
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5
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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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Keaton JM, Hellwege JN, Giri A, Torstenson ES, Kovesdy CP, Sun YV, Wilson PW, O’Donnell CJ, Edwards TL, Hung AM, Velez Edwards DR. Associations of biogeographic ancestry with hypertension traits. J Hypertens 2021; 39:633-642. [PMID: 33534346 PMCID: PMC8362794 DOI: 10.1097/hjh.0000000000002701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Ethnic disparities in hypertension prevalence are well documented, though the influence of genetic ancestry is unclear. The aim of this study was to evaluate associations of geographic genetic ancestry with hypertension and underlying blood pressure traits. METHODS We tested genetically inferred ancestry proportions from five 1000 Genomes reference populations (GBR, PEL, YRI, CHB, and LWK) for association with four continuous blood pressure (BP) traits (SBP, DBP, PP, MAP) and the dichotomous outcomes hypertension and apparent treatment-resistant hypertension in 220 495 European American, 59 927 African American, and 21 273 Hispanic American individuals from the Million Veteran Program. Ethnicity stratified results were meta-analyzed to report effect estimates per 10% difference for a given ancestry proportion in all samples. RESULTS Percentage GBR was negatively associated with BP (P = 2.13 × 10-19, 7.92 × 10-8, 4.41 × 10-11, and 3.57 × 10-13 for SBP, DBP, PP, and MAP, respectively; coefficient range -0.10 to -0.21 mmHg per 10% increase in ancestry proportion) and was protective against hypertension [P = 2.59 × 10-5, odds ratio (OR) = 0.98] relative to other ancestries. YRI percentage was positively associated with BP (P = 1.63 × 10-23, 1.94 × 10-26, 0.012, and 3.26 × 10-29 for SBP, DBP, PP, and MAP, respectively; coefficient range 0.06-0.32 mmHg per 10% increase in ancestry proportion) and was positively associated with hypertension risk (P = 3.10 × 10-11, OR = 1.04) and apparent treatment-resistant hypertension risk (P = 1.86 × 10-4, OR = 1.04) compared with other ancestries. Percentage PEL was inversely associated with DBP (P = 2.84 × 10-5, beta = -0.11 mmHg per 10% increase in ancestry proportion). CONCLUSION These results demonstrate that risk for BP traits varies significantly by genetic ancestry. Our findings provide insight into the geographic origin of genetic factors underlying hypertension risk and establish that a portion of BP trait ethnic disparities are because of genetic differences between ancestries.
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Affiliation(s)
- Jacob M. Keaton
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center
- Van-Vanderbilt Genetics Institute, Vanderbilt University
- Institute for Medicine and Public Health, Vanderbilt University Medical Center
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University
| | - Jacklyn N. Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center
- Van-Vanderbilt Genetics Institute, Vanderbilt University
- Institute for Medicine and Public Health, Vanderbilt University Medical Center
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University
| | - Ayush Giri
- Van-Vanderbilt Genetics Institute, Vanderbilt University
- Institute for Medicine and Public Health, Vanderbilt University Medical Center
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University
- Di-Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center
| | - Eric S. Torstenson
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University
| | - Csaba P. Kovesdy
- Nephrology Section, Memphis VA Medical Center, Memphis, Nashville, Tennessee
| | - Yan V. Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Department of Biomedical Informatics, Emory University School of Medicine
| | - Peter W.F. Wilson
- Atlanta VAMC and Emory Clinical Cardiovascular Research Institute, Atlanta, Georgia
| | - Christopher J. O’Donnell
- VA Boston Healthcare, Section of Cardiology and Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Todd L. Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center
- Van-Vanderbilt Genetics Institute, Vanderbilt University
- Institute for Medicine and Public Health, Vanderbilt University Medical Center
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University
| | - Adriana M. Hung
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University
- Division of Nephrology and Hypertension, Department of Medicine
| | - Digna R. Velez Edwards
- Van-Vanderbilt Genetics Institute, Vanderbilt University
- Institute for Medicine and Public Health, Vanderbilt University Medical Center
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University
- Di-Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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7
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Ojji D, Ale BM, Shedul L, Umuerri E, Ejim E, Alikor C, Agunyenwa C, Njideofor U, Eze H, Ansa V. The Effect of Nebivolol on Office Blood Pressure of Blacks Residing in Sub-Saharan Africa (A Pilot Study). Front Cardiovasc Med 2021; 7:613917. [PMID: 33505995 PMCID: PMC7829216 DOI: 10.3389/fcvm.2020.613917] [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: 10/04/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Introduction: There is substantial clinical evidence that monotherapy with beta-blockers are less effective in reducing blood pressure among hypertensive Black patients compared to Whites. The highly selective beta-1 agents like nebivolol and bisoprolol have, however, been reported to be effective in reducing blood pressure in African Americans. However, results in African Americans cannot be extrapolated to native Africans because of genetic admixture and gene-environment interaction. There is, therefore, the need for us to generate data that are applicable to Africans residing in sub-Saharan Africa. We therefore decided to evaluate the efficacy and tolerability of highly selective beta-1 agent nebivolol in hypertensive Black patients residing in sub-Saharan Africa. Materials and Methods: The nebivolol study was a multicenter, prospective, observational program among hypertensive patients with 4- and 8-week follow up which was conducted in 5 cities in Nigeria of Abuja, Calabar, Enugu, Oghara, and Port Harcourt. Dosages of nebivolol used in keeping with local prescribing information were 5 and 10 mg once daily each. The effectiveness of treatment was assessed by change from baseline in mean office systolic and diastolic blood pressures, and the proportion of patients achieving the therapeutic goal of <140/90 mmHg. Safety and tolerability of this medication were also assessed. Results: We report the results of the 140 patients studied. The mean age and body mass index were 46.9 ± 7.3 years and 22.3 ± 5.8 kg/m2, respectively, and 57.1% were female. Nebivolol reduced SBP and DBP by 7.6 and 6.6 mmHg, respectively, in 4 weeks, and by 11.1 and 8.0 mm Hg, respectively, in 8 weeks. Blood pressure control was achieved in 54.8% of the patients in 4 weeks and increased to 60.4% in 8 weeks. There was no change in metabolic profile between randomization and at 8 weeks, and erectile dysfunction occurred in 1.3% of the study population. Conclusions: Nebivolol 5 and 10 mg appear efficacious in Nigerian Africans with no negative metabolic effect and minimal side effect profile. Clinical Trial Registration: www.ClinicalTrials.gov, Study Identification: NCT03598673.
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Affiliation(s)
- Dike Ojji
- Department of Internal Medicine, Faculty of Clinical Sciences, College of Health Sciences, University of Abuja and University of Abuja Teaching Hospital, Gwagwalada, Nigeria.,Cardiovacular Research Unit, Department of Internal Medicine, University of Abuja and University of Abuja Teaching Hospital, Gwagwalada, Nigeria
| | | | - Lamkur Shedul
- Department of Family Medicine, University of Abuja Teaching Hospital, Gwagwalada, Nigeria
| | - Ejiroghene Umuerri
- Department of Internal Medicine, Faculty of Clinical Medicine, College of Health Sciences, Delta State University, Abraka, Nigeria.,Delta State University Teaching Hospital, Oghara, Nigeria
| | - Emmanuel Ejim
- Department of Internal Medicine, University of Nigeria and University of Nigeria Teaching Hospital, Enugu, Nigeria
| | - Chizindu Alikor
- Department of Internal Medicine, University of Port Harcourt and University of Port Harcourt Teaching, Port Harcourt, Nigeria
| | - Charles Agunyenwa
- Department of Internal Medicine, University of Nigeria and University of Nigeria Teaching Hospital, Enugu, Nigeria
| | - Uche Njideofor
- Department of Internal Medicine, University of Calabar and University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Helen Eze
- Cardiovacular Research Unit, Department of Internal Medicine, University of Abuja and University of Abuja Teaching Hospital, Gwagwalada, Nigeria
| | - Victor Ansa
- Department of Internal Medicine, University of Calabar and University of Calabar Teaching Hospital, Calabar, Nigeria
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8
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Sharma V, Perry DJ, Eghtesady P. Role of coxsackie-adenovirus receptor in cardiac development and pathogenesis of congenital heart disease. Birth Defects Res 2020; 113:535-545. [PMID: 33369284 DOI: 10.1002/bdr2.1860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/30/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022]
Abstract
The coxsackie-adenovirus receptor (CAR) is a cell surface transmembrane protein originally recognized for its role as a binding site for coxsackie- and adeno-viruses. As such, it is believed to play an important role in pathogenesis of myocarditis. Other studies have suggested that CAR also plays an important role in embryonic development, which is not surprising given the strong expression of the receptor in heart, brain, liver, pancreas, kidney, small intestine, and various epithelia during development. A number of studies have looked at downregulation and upregulation of CAR and have confirmed the central role of CAR during critical periods of development. These studies all demonstrated embryonic lethality with variable phenotypes: electrophysiological abnormalities, cardiac structural deformations, and extracardiac abnormalities, such as lymphatic malformations. The purpose of this review is to summarize the existing literature about CAR and formulate some questions for future studies, with an emphasis on the role of CAR during embryonic heart development.
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Affiliation(s)
- Vipul Sharma
- Division of Pediatric Cardiothoracic Surgery, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Daniel J Perry
- Division of Pediatric Cardiothoracic Surgery, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Pirooz Eghtesady
- Division of Pediatric Cardiothoracic Surgery, Washington University School of Medicine, St. Louis, Missouri, USA
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9
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Chen TK, Katz R, Estrella MM, Post WS, Kramer H, Rotter JI, Tayo B, Mychaleckyj JC, Wassel CL, Peralta CA. Association of APOL1 Genotypes With Measures of Microvascular and Endothelial Function, and Blood Pressure in MESA. J Am Heart Assoc 2020; 9:e017039. [PMID: 32851884 PMCID: PMC7660790 DOI: 10.1161/jaha.120.017039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background APOL1 high‐risk genotypes are associated with increased risk for hypertension‐attributed kidney disease among Black adults in the United States. Biopsy studies show differences in kidney vasculature by APOL1 status; less is known about the variants' associations with systemic vascular and endothelial function. Whether APOL1 risk variants are associated with blood pressure (BP) is also uncertain. Methods and Results Using linear regression, we examined cross‐sectional associations of APOL1 risk genotypes (high=2 risk alleles, low=0 or 1 risk allele) with subclinical measures of vascular function (small arterial elasticity, n=1586; large arterial elasticity, n=1586; ascending aortic distensibility, n=985) and endothelial function (flow‐mediated dilation, n=777). Using linear mixed‐effects models, we studied longitudinal associations of APOL1 risk genotypes with BP (n=1619), adjusting for age, sex, and African ancestry. Among 1619 (12% APOL1 high‐risk) Black participants in MESA (Multi‐Ethnic Study of Atherosclerosis), mean age was 62 years old, 58% had hypertension, and mean systolic BP was 131 mm Hg at baseline. At examination 1 (2000–2002), there was no significant difference in small arterial elasticity, large arterial elasticity, ascending aortic distensibility, or flow‐mediated dilation in participants with APOL1 high‐ versus low‐risk genotypes (P>0.05 for all). Over a mean follow‐up of 7.8 years, relative annual changes in systolic and diastolic BP and pulse pressure did not differ significantly by APOL1 risk status (between‐group differences of −0.20, −0.14, and −0.25, respectively; P>0.05 for all). Conclusions Among Black participants in MESA, APOL1 high‐risk genotypes were not associated with subclinical vascular and endothelial function or BP trajectories. The relationship of APOL1 with kidney disease may be intrinsic to the kidney rather than through peripheral effects on systemic vasculature or BP.
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Affiliation(s)
- Teresa K Chen
- Division of Nephrology Department of Medicine Johns Hopkins University School of Medicine Baltimore MD.,Welch Center for Prevention, Epidemiology, and Clinical Research Johns Hopkins Medical Institutions Baltimore MD
| | - Ronit Katz
- Department of Medicine Kidney Research Institute University of Washington Seattle WA
| | - Michelle M Estrella
- Kidney Health Research Collaborative Department of Medicine University of California San Francisco CA.,San Francisco VA Health Care System San Francisco CA
| | - Wendy S Post
- Division of Cardiology Department of Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Holly Kramer
- Division of Nephrology Departments of Medicine and Public Health Sciences Loyola University Maywood IL
| | - Jerome I Rotter
- Department of Pediatrics The Institute for Translational Genomics and Population Sciences The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center Torrance CA
| | - Bamidele Tayo
- Department of Public Health Sciences Loyola University Maywood IL
| | - Josyf C Mychaleckyj
- Department of Public Health Sciences University of Virginia School of Medicine Charlottesville VA
| | | | - Carmen A Peralta
- Kidney Health Research Collaborative Department of Medicine University of California San Francisco CA.,San Francisco VA Health Care System San Francisco CA
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10
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Prospective avenues for human population genomics and disease mapping in southern Africa. Mol Genet Genomics 2020; 295:1079-1089. [PMID: 32440765 PMCID: PMC7240165 DOI: 10.1007/s00438-020-01684-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/06/2020] [Indexed: 12/22/2022]
Abstract
Population substructure within human populations is globally evident and a well-known confounding factor in many genetic studies. In contrast, admixture mapping exploits population stratification to detect genotype-phenotype correlations in admixed populations. Southern Africa has untapped potential for disease mapping of ancestry-specific disease risk alleles due to the distinct genetic diversity in its populations compared to other populations worldwide. This diversity contributes to a number of phenotypes, including ancestry-specific disease risk and response to pathogens. Although the 1000 Genomes Project significantly improved our understanding of genetic variation globally, southern African populations are still severely underrepresented in biomedical and human genetic studies due to insufficient large-scale publicly available data. In addition to a lack of genetic data in public repositories, existing software, algorithms and resources used for imputation and phasing of genotypic data (amongst others) are largely ineffective for populations with a complex genetic architecture such as that seen in southern Africa. This review article, therefore, aims to summarise the current limitations of conducting genetic studies on populations with a complex genetic architecture to identify potential areas for further research and development.
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11
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Liu Z, Shriner D, Hansen NF, Rotimi CN, Mullikin JC. Admixture mapping identifies genetic regions associated with blood pressure phenotypes in African Americans. PLoS One 2020; 15:e0232048. [PMID: 32315356 PMCID: PMC7173845 DOI: 10.1371/journal.pone.0232048] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/06/2020] [Indexed: 01/11/2023] Open
Abstract
Hypertension occurs at a higher rate in African Americans than in European Americans. Based on the assumption that causal variants are more frequently found on DNA segments inherited from the ancestral population with higher disease risk, we employed admixture mapping to identify genetic loci with excess local African ancestry associated with blood pressure. Chromosomal regions 1q21.2–21.3, 4p15.1, 19q12 and 20p13 were significantly associated with diastolic blood pressure (β = 5.28, -7.94, -6.82 and 5.89, P-value = 6.39E-04, 2.07E-04, 6.56E-05 and 5.04E-04, respectively); 1q21.2–21.3 and 19q12 were also significantly associated with mean arterial pressure (β = 5.86 and -6.40, P-value = 5.32E-04 and 6.37E-04, respectively). We further selected SNPs that had large allele frequency differences within these regions and tested their association with blood pressure. SNP rs4815428 was significantly associated with diastolic blood pressure after Bonferroni correction (β = -2.42, P-value = 9.57E-04), and it partially explained the admixture mapping signal at 20p13. SNPs rs771205 (β = -1.99, P-value = 3.37E-03), rs3126067, rs2184953 and rs58001094 (the latter three exhibit strong linkage disequilibrium, β = -2.3, P-value = 1.4E-03) were identified to be significantly associated with mean arterial pressure, and together they fully explained the admixture signal at 1q21.2–21.3. Although no SNP at 4p15.1 showed large ancestral allele frequency differences in our dataset, we detected association at low-frequency African-specific variants that mapped predominantly to the gene PCDH7, which is most highly expressed in aorta. Our results suggest that these regions may harbor genetic variants that contribute to the different prevalence of hypertension.
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Affiliation(s)
- Zhi Liu
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nancy F. Hansen
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - James C. Mullikin
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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12
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Influence of Genetic Ancestry on Human Serum Proteome. Am J Hum Genet 2020; 106:303-314. [PMID: 32059761 DOI: 10.1016/j.ajhg.2020.01.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/14/2020] [Indexed: 02/02/2023] Open
Abstract
Disease risk varies significantly between ethnic groups, however, the clinical significance and implications of these observations are poorly understood. Investigating ethnic differences within the human proteome may shed light on the impact of ancestry on disease risk. We used admixture mapping to explore the impact of genetic ancestry on 237 cardiometabolic biomarkers in 2,216 Latin Americans within the Outcomes Reduction with an Initial Glargine Intervention (ORIGIN) study. We developed a variance component model in order to determine the proportion of variance explained by inter-ancestry differences, and we applied it to the biomarker panel. Multivariable linear regression was used to identify and localize genetic loci affecting biomarker variability between ethnicities. Variance component analysis revealed that 5% of biomarkers were significantly impacted by genetic admixture (p < 0.05/237), including C-peptide, apolipoprotein-E, and intercellular adhesion molecule 1. We also identified 46 regional associations across 40 different biomarkers (p < 1.13 × 10-6). An independent analysis revealed that 34 of these 46 regions were associated at genome-wide significance (p < 5 × 10-8) with their respective biomarker in either Europeans or Latin populations. Additional analyses revealed that an admixture mapping signal associated with increased C-peptide levels was also associated with an increase in diabetes risk (odds ratio [OR] = 6.07 per SD, 95% confidence interval [CI] 1.44 to 25.56, p = 0.01) and surrogate measures of insulin resistance. Our results demonstrate the impact of ancestry on biomarker levels, suggesting that some of the observed differences in disease prevalence have a biological basis, and that reference intervals for those biomarkers should be tailored to ancestry. Specifically, our results point to a strong role of ancestry in insulin resistance and diabetes risk.
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13
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Abstract
Local ancestry, defined as the genetic ancestry at a genomic location of an admixed individual, is widely used as a genetic marker in genetic association and evolutionary genetics studies. Many methods have been developed to infer the local ancestries in a set of unrelated individuals, a few of them have been extended to small nuclear families, but none can be applied to large (e.g. three-generation) pedigrees. In this study, we developed a method, FamANC, that can improve the accuracy of local ancestry inference in large pedigrees by: (1) using an existing algorithm to infer local ancestries for all individuals in a family, assuming (contrary to fact) they are unrelated, and (2) improving its accuracy by correcting inference errors using pedigree structure. Applied on African-American pedigrees from the Cleveland Family Study, FamANC was able to correct all identified Mendelian errors and most of double crossovers.
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14
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Do AN, Zhao W, Baldridge AS, Raffield LM, Wiggins KL, Shah SJ, Aslibekyan S, Tiwari HK, Limdi N, Zhi D, Sitlani CM, Taylor KD, Psaty BM, Sotoodehnia N, Brody JA, Rasmussen‐Torvik LJ, Lloyd‐Jones D, Lange LA, Wilson JG, Smith JA, Kardia SLR, Mosley TH, Vasan RS, Arnett DK, Irvin MR. Genome-wide meta-analysis of SNP and antihypertensive medication interactions on left ventricular traits in African Americans. Mol Genet Genomic Med 2019; 7:e00788. [PMID: 31407531 PMCID: PMC6785453 DOI: 10.1002/mgg3.788] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/14/2019] [Accepted: 04/22/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Left ventricular (LV) hypertrophy affects up to 43% of African Americans (AAs). Antihypertensive treatment reduces LV mass (LVM). However, interindividual variation in LV traits in response to antihypertensive treatments exists. We hypothesized that genetic variants may modify the association of antihypertensive treatment class with LV traits measured by echocardiography. METHODS We evaluated the main effects of the three most common antihypertensive treatments for AAs as well as the single nucleotide polymorphism (SNP)-by-drug interaction on LVM and relative wall thickness (RWT) in 2,068 participants across five community-based cohorts. Treatments included thiazide diuretics (TDs), angiotensin converting enzyme inhibitors (ACE-Is), and dihydropyridine calcium channel blockers (dCCBs) and were compared in a pairwise manner. We performed fixed effects inverse variance weighted meta-analyses of main effects of drugs and 2.5 million SNP-by-drug interaction estimates. RESULTS We observed that dCCBs versus TDs were associated with higher LVM after adjusting for covariates (p = 0.001). We report three SNPs at a single locus on chromosome 20 that modified the association between RWT and treatment when comparing dCCBs to ACE-Is with consistent effects across cohorts (smallest p = 4.7 × 10-8 , minor allele frequency range 0.09-0.12). This locus has been linked to LV hypertrophy in a previous study. A marginally significant locus in BICD1 (rs326641) was validated in an external population. CONCLUSIONS Our study identified one locus having genome-wide significant SNP-by-drug interaction effect on RWT among dCCB users in comparison to ACE-I users. Upon additional validation in future studies, our findings can enhance the precision of medical approaches in hypertension treatment.
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Affiliation(s)
- Anh N. Do
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Wei Zhao
- Department of EpidemiologyUniversity of MichiganAnn ArborMichiganUSA
| | | | - Laura M. Raffield
- Department of GeneticsUniversity of North CarolinaChapel HillNorth CarolinaUSA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Sanjiv J. Shah
- Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Stella Aslibekyan
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Hemant K. Tiwari
- Department of BiostatisticsUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Nita Limdi
- Department of NeurologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Degui Zhi
- School of Biomedical InformaticsUniversity of Texas Health Sciences Center at HoustonHoustonTexasUSA
| | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Department of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Kent D. Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population SciencesLABioMed at Harbor‐UCLA Medical CenterSeattleWashingtonUSA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health ServicesUniversity of WashingtonSeattleWashingtonUSA
- Kaiser Permanente Washington Health Research InstituteSeattleWashingtonUSA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, Departments of Medicine and EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Laura J. Rasmussen‐Torvik
- Department of Preventive Medicine Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | | | - Leslie A. Lange
- Department of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - James G. Wilson
- Department of Physiology and BiophysicsUniversity of Mississippi Medical CenterJacksonMississippiUSA
| | - Jennifer A. Smith
- Department of EpidemiologyUniversity of MichiganAnn ArborMichiganUSA
| | | | - Thomas H. Mosley
- Department of MedicineUniversity of Mississippi Medical CenterJacksonMississippiUSA
| | - Ramachandran S. Vasan
- Departments of Medicine and Preventive MedicineBoston University School of MedicineBostonMassachusettsUSA
| | - Donna K. Arnett
- College of Public HealthUniversity of KentuckyLexingtonKentuckyUSA
| | - Marguerite R. Irvin
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
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15
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Zilbermint M, Gaye A, Berthon A, Hannah-Shmouni F, Faucz FR, Lodish MB, Davis AR, Gibbons GH, Stratakis CA. ARMC 5 Variants and Risk of Hypertension in Blacks: MH- GRID Study. J Am Heart Assoc 2019; 8:e012508. [PMID: 31266387 PMCID: PMC6662143 DOI: 10.1161/jaha.119.012508] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background We recently found that ARMC5 variants may be associated with primary aldosteronism in blacks. We investigated a cohort from the MH‐GRID (Minority Health Genomics and Translational Research Bio‐Repository Database) and tested the association between ARMC5 variants and blood pressure in blacks. Methods and Results Whole exome sequencing data of 1377 blacks were analyzed. Target single‐variant and gene‐based association analyses of hypertension were performed for ARMC5, and replicated in a subset of 3015 individuals of African descent from the UK Biobank cohort. Sixteen rare variants were significantly associated with hypertension (P=0.0402) in the gene‐based (optimized sequenced kernel association test) analysis; the 16 and one other, rs116201073, together, showed a strong association (P=0.0003) with blood pressure in this data set. The presence of the rs116201073 variant was associated with lower blood pressure. We then used human embryonic kidney 293 and adrenocortical H295R cells transfected with an ARMC5 construct containing rs116201073 (c.*920T>C). The latter was common in both the discovery (MH‐GRID) and replication (UK Biobank) data and reached statistical significance (P=0.044 [odds ratio, 0.7] and P=0.007 [odds ratio, 0.76], respectively). The allele carrying rs116201073 increased levels of ARMC5 mRNA, consistent with its protective effect in the epidemiological data. Conclusions ARMC5 shows an association with hypertension in blacks when rare variants within the gene are considered. We also identified a protective variant of the ARMC5 gene with an effect on ARMC5 expression confirmed in vitro. These results extend our previous report of ARMC5’s possible involvement in the determination of blood pressure in blacks.
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Affiliation(s)
- Mihail Zilbermint
- 1 Section on Endocrinology and Genetics Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda MD.,2 Division of Endocrinology, Diabetes, and Metabolism Johns Hopkins University School of Medicine Baltimore MD.,3 Johns Hopkins Community Physicians at Suburban Hospital Bethesda MD.,4 Johns Hopkins University Carey Business School Baltimore MD
| | - Amadou Gaye
- 5 Genomics of Metabolic, Cardiovascular and Inflammatory Disease Branch, Cardiovascular Section National Human Genome Research Institute Bethesda MD
| | - Annabel Berthon
- 1 Section on Endocrinology and Genetics Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda MD
| | - Fady Hannah-Shmouni
- 1 Section on Endocrinology and Genetics Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda MD
| | - Fabio R Faucz
- 1 Section on Endocrinology and Genetics Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda MD
| | - Maya B Lodish
- 1 Section on Endocrinology and Genetics Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda MD
| | - Adam R Davis
- 6 Technological Research and Innovation Uniformed Services University Bethesda MD
| | - Gary H Gibbons
- 5 Genomics of Metabolic, Cardiovascular and Inflammatory Disease Branch, Cardiovascular Section National Human Genome Research Institute Bethesda MD.,7 National Heart, Lung, and Blood Institute Bethesda MD
| | - Constantine A Stratakis
- 1 Section on Endocrinology and Genetics Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda MD
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16
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Abstract
Risk of disease is multifactorial and can be shaped by socio-economic, demographic, cultural, environmental and genetic factors. Our understanding of the genetic determinants of disease risk has greatly advanced with the advent of genome-wide association studies (GWAS), which detect associations between genetic variants and complex traits or diseases by comparing populations of cases and controls. However, much of this discovery has occurred through GWAS of individuals of European ancestry, with limited representation of other populations, including from Africa, The Americas, Asia and Oceania. Population demography, genetic drift and adaptation to environments over thousands of years have led globally to the diversification of populations. This global genomic diversity can provide new opportunities for discovery and translation into therapies, as well as a better understanding of population disease risk. Large-scale multi-ethnic and representative biobanks and population health resources provide unprecedented opportunities to understand the genetic determinants of disease on a global scale.
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17
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Wang H, Cade BE, Sofer T, Sands SA, Chen H, Browning SR, Stilp AM, Louie TL, Thornton TA, Johnson WC, Below JE, Conomos MP, Evans DS, Gharib SA, Guo X, Wood AC, Mei H, Yaffe K, Loredo JS, Ramos AR, Barrett-Connor E, Ancoli-Israel S, Zee PC, Arens R, Shah NA, Taylor KD, Tranah GJ, Stone KL, Hanis CL, Wilson JG, Gottlieb DJ, Patel SR, Rice K, Post WS, Rotter JI, Sunyaev SR, Cai J, Lin X, Purcell SM, Laurie CC, Saxena R, Redline S, Zhu X. Admixture mapping identifies novel loci for obstructive sleep apnea in Hispanic/Latino Americans. Hum Mol Genet 2019; 28:675-687. [PMID: 30403821 DOI: 10.1093/hmg/ddy387] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/05/2018] [Indexed: 01/11/2023] Open
Abstract
Obstructive sleep apnea (OSA) is a common disorder associated with increased risk of cardiovascular disease and mortality. Its prevalence and severity vary across ancestral background. Although OSA traits are heritable, few genetic associations have been identified. To identify genetic regions associated with OSA and improve statistical power, we applied admixture mapping on three primary OSA traits [the apnea hypopnea index (AHI), overnight average oxyhemoglobin saturation (SaO2) and percentage time SaO2 < 90%] and a secondary trait (respiratory event duration) in a Hispanic/Latino American population study of 11 575 individuals with significant variation in ancestral background. Linear mixed models were performed using previously inferred African, European and Amerindian local genetic ancestry markers. Global African ancestry was associated with a lower AHI, higher SaO2 and shorter event duration. Admixture mapping analysis of the primary OSA traits identified local African ancestry at the chromosomal region 2q37 as genome-wide significantly associated with AHI (P < 5.7 × 10-5), and European and Amerindian ancestries at 18q21 suggestively associated with both AHI and percentage time SaO2 < 90% (P < 10-3). Follow-up joint ancestry-SNP association analyses identified novel variants in ferrochelatase (FECH), significantly associated with AHI and percentage time SaO2 < 90% after adjusting for multiple tests (P < 8 × 10-6). These signals contributed to the admixture mapping associations and were replicated in independent cohorts. In this first admixture mapping study of OSA, novel associations with variants in the iron/heme metabolism pathway suggest a role for iron in influencing respiratory traits underlying OSA.
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Affiliation(s)
- Heming Wang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.,Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.,Broad Institute, Cambridge, MA 02142, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.,Broad Institute, Cambridge, MA 02142, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Scott A Sands
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Precision Health, School of Public Health & School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Tin L Louie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alexis C Wood
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Hao Mei
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Kristine Yaffe
- Departments of Psychiatry and Neurology, University of California, San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Jose S Loredo
- Division of Pulmonary Critical Care and Sleep Medicine, Department of Medicine, UC San Diego School of Medicine, La Jolla, CA, USA
| | - Alberto R Ramos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Sonia Ancoli-Israel
- Departments of Medicine and Psychiatry, University of California, San Diego, CA, USA.,Department of Veterans Affairs, San Diego Center of Excellence for Stress and Mental Health, San Diego, CA, USA
| | - Phyllis C Zee
- Department of Neurology and Sleep Medicine Center, Northwestern University, Chicago, IL, USA
| | - Raanan Arens
- The Children's Hospital at Montefiore, Division of Respiratory and Sleep Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Neomi A Shah
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Katie L Stone
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Craig L Hanis
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - James G Wilson
- Physiology and Biophysics, University of Mississippi, Jackson, MS, USA
| | - Daniel J Gottlieb
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.,VA Boston Healthcare System, Boston, MA, USA
| | - Sanjay R Patel
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Ken Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Wendy S Post
- Division of Cardiology, Johns Hopkins University, Baltimore, MD, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Shamil R Sunyaev
- Broad Institute, Cambridge, MA 02142, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.,Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Shaun M Purcell
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Broad Institute, Cambridge, MA 02142, USA.,Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Richa Saxena
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.,Broad Institute, Cambridge, MA 02142, USA.,Center for Genomic Medicine and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
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18
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Qin H, Zhao J, Zhu X. Identifying Rare Variant Associations in Admixed Populations. Sci Rep 2019; 9:5458. [PMID: 30931973 PMCID: PMC6443736 DOI: 10.1038/s41598-019-41845-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 03/12/2019] [Indexed: 12/27/2022] Open
Abstract
An admixed population and its ancestral populations bear different burdens of a complex disease. The ancestral populations may have different haplotypes of deleterious alleles and thus ancestry-gene interaction can influence disease risk in the admixed population. Among admixed individuals, deleterious haplotypes and their ancestries are dependent and can provide non-redundant association information. Herein we propose a local ancestry boosted sum test (LABST) for identifying chromosomal blocks that harbor rare variants but have no ancestry switches. For such a stable ancestral block, our LABST exploits ancestry-gene interaction and the number of rare alleles therein. Under the null of no genetic association, the test statistic asymptotically follows a chi-square distribution with one degree of freedom (1-df). Our LABST properly controlled type I error rates under extensive simulations, suggesting that the asymptotic approximation was accurate for the null distribution of the test statistic. In terms of power for identifying rare variant associations, our LABST uniformly outperformed several famed methods under four important modes of disease genetics over a large range of relative risks. In conclusion, exploiting ancestry-gene interaction can boost statistical power for rare variant association mapping in admixed populations.
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Affiliation(s)
- Huaizhen Qin
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street, New Orleans, LA, 70112, USA
| | - Jinying Zhao
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio, 44106, USA.
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19
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Grinde KE, Brown LA, Reiner AP, Thornton TA, Browning SR. Genome-wide Significance Thresholds for Admixture Mapping Studies. Am J Hum Genet 2019; 104:454-465. [PMID: 30773276 PMCID: PMC6407497 DOI: 10.1016/j.ajhg.2019.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/17/2019] [Indexed: 01/25/2023] Open
Abstract
Admixture mapping studies have become more common in recent years, due in part to technological advances and growing international efforts to increase the diversity of genetic studies. However, many open questions remain about appropriate implementation of admixture mapping studies, including how best to control for multiple testing, particularly in the presence of population structure. In this study, we develop a theoretical framework to characterize the correlation of local ancestry and admixture mapping test statistics in admixed populations with contributions from any number of ancestral populations and arbitrary population structure. Based on this framework, we develop an analytical approach for obtaining genome-wide significance thresholds for admixture mapping studies. We validate our approach via analysis of simulated traits with real genotype data for 8,064 unrelated African American and 3,425 Hispanic/Latina women from the Women's Health Initiative SNP Health Association Resource (WHI SHARe). In an application to these WHI SHARe data, our approach yields genome-wide significant p value thresholds of 2.1 × 10-5 and 4.5 × 10-6 for admixture mapping studies in the African American and Hispanic/Latina cohorts, respectively. Compared to other commonly used multiple testing correction procedures, our method is fast, easy to implement (using our publicly available R package), and controls the family-wise error rate even in structured populations. Importantly, we note that the appropriate admixture mapping significance threshold depends on the number of ancestral populations, generations since admixture, and population structure of the sample; as a result, significance thresholds are not, in general, transferable across studies.
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Affiliation(s)
- Kelsey E Grinde
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
| | - Lisa A Brown
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA; Seattle Genetics, Bothell, WA 98021, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
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20
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Zilbermint M, Hannah-Shmouni F, Stratakis CA. Genetics of Hypertension in African Americans and Others of African Descent. Int J Mol Sci 2019; 20:ijms20051081. [PMID: 30832344 PMCID: PMC6429313 DOI: 10.3390/ijms20051081] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/19/2019] [Accepted: 02/21/2019] [Indexed: 02/07/2023] Open
Abstract
Hypertension is the leading cause of cardiovascular disease in the United States, affecting up to one-third of adults. When compared to other ethnic or racial groups in the United States, African Americans and other people of African descent show a higher incidence of hypertension and its related comorbidities; however, the genetics of hypertension in these populations has not been studied adequately. Several genes have been identified to play a role in the genetics of hypertension. They include genes regulating the renin-aldosterone-angiotensin system (RAAS), such as Sodium Channel Epithelial 1 Beta Subunit (SCNN1B), Armadillo Repeat Containing 5 (ARMC5), G Protein-Coupled Receptor Kinase 4 (GRK4), and Calcium Voltage-Gated Channel Subunit Alpha1 D (CACNA1D). In this review, we focus on recent genetic findings available in the public domain for potential differences between African Americans and other populations. We also cover some recent and relevant discoveries in the field of low-renin hypertension from our laboratory at the National Institutes of Health. Understanding the different genetics of hypertension among various groups is essential for effective precision-guided medical therapy of high blood pressure.
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Affiliation(s)
- Mihail Zilbermint
- Section on Endocrinology and Genetics, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, BG 31 RM 2A46, 31 Center Dr, Bethesda, MD 20892, USA.
- Division of Endocrinology, Diabetes, and Metabolism, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
- Johns Hopkins Community Physicians at Suburban Hospital, Bethesda, MD 20814, USA.
- Johns Hopkins University Carey Business School, Baltimore, MD 21202, USA.
| | - Fady Hannah-Shmouni
- Section on Endocrinology and Genetics, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, BG 31 RM 2A46, 31 Center Dr, Bethesda, MD 20892, USA.
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, BG 31 RM 2A46, 31 Center Dr, Bethesda, MD 20892, USA.
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21
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He KY, Li X, Kelly TN, Liang J, Cade BE, Assimes TL, Becker LC, Beitelshees AL, Bress AP, Chang YPC, Chen YDI, de Vries PS, Fox ER, Franceschini N, Furniss A, Gao Y, Guo X, Haessler J, Hwang SJ, Irvin MR, Kalyani RR, Liu CT, Liu C, Martin LW, Montasser ME, Muntner PM, Mwasongwe S, Palmas W, Reiner AP, Shimbo D, Smith JA, Snively BM, Yanek LR, Boerwinkle E, Correa A, Cupples LA, He J, Kardia SLR, Kooperberg C, Mathias RA, Mitchell BD, Psaty BM, Vasan RS, Rao DC, Rich SS, Rotter JI, Wilson JG, Chakravarti A, Morrison AC, Levy D, Arnett DK, Redline S, Zhu X. Leveraging linkage evidence to identify low-frequency and rare variants on 16p13 associated with blood pressure using TOPMed whole genome sequencing data. Hum Genet 2019; 138:199-210. [PMID: 30671673 PMCID: PMC6404531 DOI: 10.1007/s00439-019-01975-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 01/10/2019] [Indexed: 01/05/2023]
Abstract
In this study, we investigated low-frequency and rare variants associated with blood pressure (BP) by focusing on a linkage region on chromosome 16p13. We used whole genome sequencing (WGS) data obtained through the NHLBI Trans-Omics for Precision Medicine (TOPMed) program on 395 Cleveland Family Study (CFS) European Americans (CFS-EA). By analyzing functional coding variants and non-coding rare variants with CADD score > 10 residing within the chromosomal region in families with linkage evidence, we observed 25 genes with nominal statistical evidence (burden or SKAT p < 0.05). One of the genes is RBFOX1, an evolutionarily conserved RNA-binding protein that regulates tissue-specific alternative splicing that we previously reported to be associated with BP using exome array data in CFS. After follow-up analysis of the 25 genes in ten independent TOPMed studies with individuals of European, African, and East Asian ancestry, and Hispanics (N = 29,988), we identified variants in SLX4 (p = 2.19 × 10-4) to be significantly associated with BP traits when accounting for multiple testing. We also replicated the associations previously reported for RBFOX1 (p = 0.007). Follow-up analysis with GTEx eQTL data shows SLX4 variants are associated with gene expression in coronary artery, multiple brain tissues, and right atrial appendage of the heart. Our study demonstrates that linkage analysis of family data can provide an efficient approach for detecting rare variants associated with complex traits in WGS data.
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Affiliation(s)
- Karen Y. He
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xiaoyin Li
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Tanika N. Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Jingjing Liang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, 02115, USA,Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Lewis C. Becker
- GeneSTAR Research Program, Department of Medicine, Divisions of Cardiology and General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Amber L. Beitelshees
- Division of Endocrinology Diabetes and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Adam P. Bress
- Department of Population Health Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Yen-Pei Christy Chang
- Division of Endocrinology Diabetes and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Ervin R. Fox
- Division of Cardiovascular Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Nora Franceschini
- Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, NC, 27599, USA
| | - Anna Furniss
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Yan Gao
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Shih-Jen Hwang
- Boston University’s and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, 01702, USA
| | - Marguerite Ryan Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AB, 35294, USA
| | - Rita R. Kalyani
- GeneSTAR Research Program, Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ching-Ti Liu
- Boston University’s and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, 01702, USA
| | - Chunyu Liu
- Boston University’s and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, 01702, USA
| | - Lisa Warsinger Martin
- Division of Cardiology, Department of Medicine, George Washington University, Washington, DC, 20052, USA
| | - May E. Montasser
- Division of Endocrinology Diabetes and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Paul M. Muntner
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AB, 35294, USA
| | | | - Walter Palmas
- Division of General Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA
| | - Daichi Shimbo
- Division of General Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Beverly M. Snively
- Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, 27101, USA
| | - Lisa R. Yanek
- GeneSTAR Research Program, Department of Medicine, Division of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Adolfo Correa
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - L. Adrienne Cupples
- Boston University’s and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, 01702, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Rasika A. Mathias
- GeneSTAR Research Program, Department of Medicine, Divisions of Allergy and Clinical Immunology and General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Braxton D. Mitchell
- Division of Endocrinology Diabetes and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA,Geriatrics Research and Education Clinical Center, Veterans Affairs Medical Center, Baltimore, MD, 21201, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, 98195, USA,Kaiser Permanente Washington Health Research Institute, Seattle, WA, 98101, USA
| | - Ramachandran S. Vasan
- Boston University’s and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, 01702, USA
| | - DC Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | | | - Aravinda Chakravarti
- Center for Human Genetics & Genomics, Department of Medicine, New York University Langone Health, New York, NY, 10016, USA
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Daniel Levy
- Boston University’s and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, 01702, USA,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Donna K. Arnett
- University of Kentucky College of Public Health, Lexington, KY, 40508, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, 02115, USA,Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA,Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA,Correspondence: Xiaofeng Zhu, PhD; ; Phone: (216) 368-0201
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22
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Mengesha HG, Welegerima AH, Hadgu A, Temesgen H, Otieno MG, Tsegay K, Fisseha T, Getachew S, Merha Z, Tewodros H, Dabessa J, Gebreegzabher B, Petrucka P. Comparative effectiveness of antihypertensive drugs prescribed in Ethiopian healthcare practice: A pilot prospective, randomized, open label study. PLoS One 2018; 13:e0203166. [PMID: 30204768 PMCID: PMC6133365 DOI: 10.1371/journal.pone.0203166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 08/15/2018] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Previous research has been highly suggestive that patients of African ancestry are less responsive to beta-blockers and angiotensin converting enzyme inhibitors. However, clinical practice within Ethiopia has continued to recommend all drugs for treatment of hypertension despite the lack of evidentiary support. Therefore this study aims to compare the effectiveness of the three major antihypertensive drugs currently prescribed in an Ethiopian health care setting to further the potential for evidence based prescribing practices. METHODS A prospective, randomized, open label comparative study was used to determine the mean reduction in blood pressure (primary outcome) and assess cardiovascular events (secondary outcomes) among patients receiving one or more of three common antihypertensive drugs (i.e., nifedipine, hydrochlorothiazide, and enalapril) in routine clinical practice between November 2016 and April 2017. Patients were followed for three months. Analysis was based on an intention-to-treat approach. One way analysis of covariance was used to compare the difference in therapeutic effectiveness in reducing blood pressure. RESULT A total of 141 patients were randomized to one of three recipient groups-nifedipine (n = 47), enalapril (n = 47) or hydrochlorothiazide (n = 47). Three months after randomization, 44 patients in each group completed the follow-up. Patients randomized to nifedipine had significantly higher mean reduction in systolic blood pressure than those randomized to enalapril(p = 0.003) or hydrochlorothiazide(p = 0.036). The mean reduction in systolic blood pressure was -37.35(CI:-40, -34.2) in the nifedipine group; -30.3(CI: -33.5, -27.1) in patients receiving enalapril; and -32.1(CI:-35, -29.3) in patients assigned hydrochlorothiazide. However, nifedipine did not have a significance difference in reduction of mean diastolic blood pressure compared than those receiving enalapril (p = 0.57) or hydrochlorthiazide (p = 0.99). CONCLUSION This study revealed that amongst the three drugs nifedipine was found to be the most effective drug in reduction of systolic blood pressure. Hydrochlorothiazide and enalapril did not show a difference in reduction of mean blood pressure. Further, long term randomized trials are highly recommended to inform revision of Ethiopia-centric hypertension treatment guidelines.
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Affiliation(s)
| | | | - Abera Hadgu
- Departement of Pharmacology and Toxicology, School of Pharmacy, Mekelle University, Mekelle, Ethiopia
| | - Haftom Temesgen
- School of Public Health, Mekelle University, Mekelle, Ethiopia
| | - Mala George Otieno
- College of Health Science, Department of Medical Biochemistry, Mekelle University, Mekelle, Ethiopia
| | - Kiflom Tsegay
- Adwa Hospital, Internal Medicine Unit, Adwa, Ethiopia
| | - Tedros Fisseha
- Adigrat Hospital, Internal Medicine Unit, Adigrat, Ethiopia
| | | | - Zekarias Merha
- Kidst Mariam Hospital, Internal Medicine Unit, Axum, Ethiopa
| | - Helen Tewodros
- Mekelle Hospital, Internal Medicine Unit, Mekelle, Ethiopia
| | - Jiksa Dabessa
- Ayder Referral Hospital, Internal Medicine Unit, Mekelle, Ethiopia
| | | | - Pammla Petrucka
- University of Saskatchewan, College of Nursing, Saskatchewan, Canada
- Adjunct Nelson Mandela African Institute of Science and Technology, Arusha, Tanzania
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23
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Das R, Upadhyai P. An Ancestry Informative Marker Set Which Recapitulates the Known Fine Structure of Populations in South Asia. Genome Biol Evol 2018; 10:2408-2416. [PMID: 30184103 PMCID: PMC6143162 DOI: 10.1093/gbe/evy182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2018] [Indexed: 12/16/2022] Open
Abstract
The inference of genomic ancestry using ancestry informative markers (AIMs) can be useful for a range of studies in evolutionary genetics, biomedical research, and forensic analyses. However, the determination of AIMs for highly admixed populations with complex ancestries has remained a formidable challenge. Given the immense genetic heterogeneity and unique population structure of the Indian subcontinent, here we sought to derive AIMs that would yield a cohesive and faithful understanding of South Asian genetic origins. To discern the most optimal strategy for extracting AIMs for South Asians we compared three commonly used AIMs-determining methods namely, Infocalc, FST, and Smart Principal Component Analysis with ADMIXTURE, using previously published whole genome data from the Indian subcontinent. Our findings suggest that the Infocalc approach is likely most suitable for delineation of South Asian AIMs. In particular, Infocalc-2,000 (N = 2,000) appeared as the most informative South Asian AIMs panel that recapitulated the finer structure within South Asian genomes with high degree of sensitivity and precision, whereas a negative control with an equivalent number of randomly selected markers when used to interrogate the South Asian populations, failed to do so. We discuss the utility of all approaches under evaluation for AIMs derivation and interpreting South Asian genomic ancestries. Notably, this is the first report of an AIMs panel for South Asian ancestry inference. Overall these findings may aid in developing cost-effective resources for large-scale demographic analyses and foster expansion of our knowledge of human origins and disease, in the South Asian context.
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Affiliation(s)
- Ranajit Das
- Manipal Centre for Natural Sciences (MCNS), Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
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24
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Ojji DB, Poulter N, Damasceno A, Sliwa K, Smythe W, Kramer N, Badri M, Francis V, Aje A, Barasa F, Dzudie A, Jones E, Kana SS, Mntla P, Mondo C, Ogah O, Ogola EN, Ogunbanjo G, Okpechi I, Shedul G, Sani MU, Shedul G, Mayosi BM. Rationale and design of the comparison of 3 combination therapies in lowering blood pressure in black Africans (CREOLE study): 2 × 3 factorial randomized single-blind multicenter trial. Am Heart J 2018; 202:5-12. [PMID: 29800784 DOI: 10.1016/j.ahj.2018.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 03/13/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Current hypertension guidelines recommend the use of combination therapy as first-line treatment or early in the management of hypertensive patients. Although there are many possible combinations of blood pressure(BP)-lowering therapies, the best combination for the black population is still a subject of debate because no large randomized controlled trials have been conducted in this group to compare the efficacy of different combination therapies to address this issue. METHODS The comparison of 3 combination therapies in lowering BP in the black Africans (CREOLE) study is a randomized single-blind trial that will compare the efficacy of amlodipine plus hydrochlorothiazide versus amlodipine plus perindopril and versus perindopril plus hydrochlorothiazide in blacks residing in sub-Saharan Africa (SSA). Seven hundred two patients aged 30-79 years with a sitting systolic BP of 140 mm Hg and above, and less than 160 mm Hg on antihypertensive monotherapy, or sitting systolic BP of 150 mm Hg and above, and less than 180 mm Hg on no treatment, will be centrally randomized into any of the 3 arms (234 into each arm). The CREOLE study is taking place in 10 sites in SSA, and the primary outcome measure is change in ambulatory systolic BP from baseline to 6 months. The first patient was randomized in June 2017, and the trial will be concluded by 2019. CONCLUSIONS The CREOLE trial will provide unique information as to the most efficacious 2-drug combination in blacks residing in SSA and thereby inform the development of clinical guidelines for the treatment of hypertension in this subregion.
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Affiliation(s)
- Dike B Ojji
- Department of Medicine, Faculty of Clinical Sciences, University of Abuja/University of Abuja Teaching Hospital, Gwagwalada, Abuja, Nigeria
| | - Neil Poulter
- Imperial Clinical Trials Unit, School of Public Health, Imperial College London, London, United Kingdom
| | | | - Karen Sliwa
- Hatter Institute of Cardiovascular Research in Africa, Cape Town, South Africa
| | - Wynand Smythe
- Clinical Research Centre, Faculty of Clinical Sciences, University of Cape Town, Cape Town, South Africa
| | - Nicky Kramer
- Clinical Research Centre, Faculty of Clinical Sciences, University of Cape Town, Cape Town, South Africa
| | - Motasim Badri
- Department of Basic Sciences, College of Sciences & Health Professions King Saud Bin Abdul-Aziz University for Health Sciences NGHA, Riyadh, Saudi Arabia; Department of Medicine, Faculty of Clinical Sciences, University of Cape Town, Cape Town, South Africa
| | - Veronica Francis
- Clinical Research Centre, Faculty of Clinical Sciences, University of Cape Town, Cape Town, South Africa
| | | | | | | | - Erika Jones
- Department of Medicine, Faculty of Clinical Sciences, University of Cape Town, Cape Town, South Africa
| | - Shehu S Kana
- Department of Medicine, Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Pindile Mntla
- Department of Cardiology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | | | | | - Elijah N Ogola
- Department of Clinical Medicine and Therapeutics, University of Nairobi, Nairobi, Kenya
| | - Gboyega Ogunbanjo
- Department of Family Medicine & Primary Health Care, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Ikechi Okpechi
- Department of Medicine, Faculty of Clinical Sciences, University of Cape Town, Cape Town, South Africa
| | - Gabriel Shedul
- Department of Family Medicine, University of Abuja Teaching Hospital, Gwagwalada, Abuja
| | | | - Grace Shedul
- Department of Pharmacy, University of Abuja Teaching Hospital, Gwagwalada, Abuja, Nigeria
| | - Bongani M Mayosi
- Department of Medicine, Faculty of Clinical Sciences, University of Cape Town, Cape Town, South Africa.
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25
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The impact of estrogen alone hormone therapy on breast cancer risk and health outcomes: reassurance for the treatment of climacteric symptoms in black women? Menopause 2018; 24:124-125. [PMID: 28072609 DOI: 10.1097/gme.0000000000000821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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26
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Muzzio M, Motti JMB, Paz Sepulveda PB, Yee MC, Cooke T, Santos MR, Ramallo V, Alfaro EL, Dipierri JE, Bailliet G, Bravi CM, Bustamante CD, Kenny EE. Population structure in Argentina. PLoS One 2018; 13:e0196325. [PMID: 29715266 PMCID: PMC5929549 DOI: 10.1371/journal.pone.0196325] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/11/2018] [Indexed: 11/19/2022] Open
Abstract
We analyzed 391 samples from 12 Argentinian populations from the Center-West, East and North-West regions with the Illumina Human Exome Beadchip v1.0 (HumanExome-12v1-A). We did Principal Components analysis to infer patterns of populational divergence and migrations. We identified proportions and patterns of European, African and Native American ancestry and found a correlation between distance to Buenos Aires and proportion of Native American ancestry, where the highest proportion corresponds to the Northernmost populations, which is also the furthest from the Argentinian capital. Most of the European sources are from a South European origin, matching historical records, and we see two different Native American components, one that spreads all over Argentina and another specifically Andean. The highest percentages of African ancestry were in the Center West of Argentina, where the old trade routes took the slaves from Buenos Aires to Chile and Peru. Subcontinentaly, sources of this African component are represented by both West Africa and groups influenced by the Bantu expansion, the second slightly higher than the first, unlike North America and the Caribbean, where the main source is West Africa. This is reasonable, considering that a large proportion of the ships arriving at the Southern Hemisphere came from Mozambique, Loango and Angola.
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Affiliation(s)
- Marina Muzzio
- Instituto Multidisciplinario de Biología Celular (IMBICE) CCT-La Plata CONICET-CICPBA, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Josefina M. B. Motti
- Universidad Nacional del Centro de la Provincia de Buenos Aires, FACSO, NEIPHPA, Quequén, Buenos Aires, Argentina
| | - Paula B. Paz Sepulveda
- Instituto Multidisciplinario de Biología Celular (IMBICE) CCT-La Plata CONICET-CICPBA, La Plata, Buenos Aires, Argentina
| | - Muh-ching Yee
- Stanford University, Stanford, California, United States of America
| | - Thomas Cooke
- Stanford University, Stanford, California, United States of America
| | - María R. Santos
- Instituto Multidisciplinario de Biología Celular (IMBICE) CCT-La Plata CONICET-CICPBA, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | | | - Emma L. Alfaro
- INECOA (Instituto de Ecorregiones Andinas) UNJu-CONICET, Instituto de Biología de la Altura, Universidad Nacional de Jujuy, San Salvador de Jujuy, Jujuy, Argentina
| | - Jose E. Dipierri
- INECOA (Instituto de Ecorregiones Andinas) UNJu-CONICET, Instituto de Biología de la Altura, Universidad Nacional de Jujuy, San Salvador de Jujuy, Jujuy, Argentina
| | - Graciela Bailliet
- Instituto Multidisciplinario de Biología Celular (IMBICE) CCT-La Plata CONICET-CICPBA, La Plata, Buenos Aires, Argentina
| | - Claudio M. Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE) CCT-La Plata CONICET-CICPBA, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | | | - Eimear E. Kenny
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States
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Sun X, Chandar AK, Canto MI, Thota PN, Brock M, Shaheen NJ, Beer DG, Wang JS, Falk GW, Iyer PG, Abrams JA, Venkat-Ramani M, Veigl M, Miron A, Willis J, Patil DT, Nalbantoglu I, Guda K, Markowitz SD, Zhu X, Elston R, Chak A. Genomic regions associated with susceptibility to Barrett's esophagus and esophageal adenocarcinoma in African Americans: The cross BETRNet admixture study. PLoS One 2017; 12:e0184962. [PMID: 29073141 PMCID: PMC5657624 DOI: 10.1371/journal.pone.0184962] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/04/2017] [Indexed: 12/20/2022] Open
Abstract
Background Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC) are far more prevalent in European Americans than in African Americans. Hypothesizing that this racial disparity in prevalence might represent a genetic susceptibility, we used an admixture mapping approach to interrogate disease association with genomic differences between European and African ancestry. Methods Formalin fixed paraffin embedded samples were identified from 54 African Americans with BE or EAC through review of surgical pathology databases at participating Barrett’s Esophagus Translational Research Network (BETRNet) institutions. DNA was extracted from normal tissue, and genotyped on the Illumina OmniQuad SNP chip. Case-only admixture mapping analysis was performed on the data from both all 54 cases and also on a subset of 28 cases with high genotyping quality. Haplotype phases were inferred with Beagle 3.3.2, and local African and European ancestries were inferred with SABER plus. Disease association was tested by estimating and testing excess European ancestry and contrasting it to excess African ancestry. Results Both datasets, the 54 cases and the 28 cases, identified two admixture regions. An association of excess European ancestry on chromosome 11p reached a 5% genome-wide significance threshold, corresponding to -log10(P) = 4.28. A second peak on chromosome 8q reached -log10(P) = 2.73. The converse analysis examining excess African ancestry found no genetic regions with significant excess African ancestry associated with BE and EAC. On average, the regions on chromosomes 8q and 11p showed excess European ancestry of 15% and 20%, respectively. Conclusions Chromosomal regions on 11p15 and 8q22-24 are associated with excess European ancestry in African Americans with BE and EAC. Because GWAS have not reported any variants in these two regions, low frequency and/or rare disease associated variants that confer susceptibility to developing BE and EAC may be driving the observed European ancestry association evidence.
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Affiliation(s)
- Xiangqing Sun
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Apoorva K. Chandar
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Marcia I. Canto
- Division of Gastroenterology and Hepatology, Johns Hopkins Medical Institutions, Baltimore, MD, United States of America
| | - Prashanthi N. Thota
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH, United States of America
| | - Malcom Brock
- Department of Cardiology and Thoracic Surgery, Johns Hopkins Medical Institutions, Baltimore, MD, United States of America
| | - Nicholas J. Shaheen
- Center for Esophageal Diseases & Swallowing, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States of America
| | - David G. Beer
- Thoracic Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI, United States of America
| | - Jean S. Wang
- Division of Gastroenterology, Washington University School of Medicine, St Louis, MO, United States of America
| | - Gary W. Falk
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United states of America
| | - Prasad G. Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Julian A. Abrams
- Department of Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Medha Venkat-Ramani
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Martina Veigl
- Division of General Medical Sciences (Oncology), Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Alexander Miron
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Joseph Willis
- Department of Pathology, University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Deepa T. Patil
- Department of Pathology, Cleveland Clinic, Cleveland, OH, United States of America
| | - Ilke Nalbantoglu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Kishore Guda
- Division of General Medical Sciences (Oncology), Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Sanford D. Markowitz
- Division of Oncology and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Robert Elston
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Amitabh Chak
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
- Division of General Medical Sciences (Oncology), Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
- * E-mail:
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Taylor JY, Sun YV, Barcelona de Mendoza V, Ifatunji M, Rafferty J, Fox ER, Musani SK, Sims M, Jackson JS. The combined effects of genetic risk and perceived discrimination on blood pressure among African Americans in the Jackson Heart Study. Medicine (Baltimore) 2017; 96:e8369. [PMID: 29069027 PMCID: PMC5671860 DOI: 10.1097/md.0000000000008369] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Both genomics and environmental stressors play a significant role in increases in blood pressure (BP). In an attempt to further explain the hypertension (HTN) disparity among African Americans (AA), both genetic underpinnings (selected candidate genes) and stress due to perceived racial discrimination (as reported in the literature) have independently been linked to increased BP among AAs. Although Gene x Environment interactions on BP have been examined, the environmental component of these investigations has focused more on lifestyle behaviors such as smoking, diet, and physical activity, and less on psychosocial stressors such as perceived discrimination.The present study uses candidate gene analyses to identify the relationship between Everyday Discrimination (ED) and Major Life Discrimination (MLD) with increases in systolic BP (SBP) and diastolic BP (DBP) among AA in the Jackson Heart Study. Multiple linear regression models reveal no association between discrimination and BP after adjusting for age, sex, body mass index (BMI), antihypertensive medication use, and current smoking status.Subsequent candidate gene analysis identified 5 SNPs (rs7602215, rs3771724, rs1006502, rs1791926, and rs2258119) that interacted with perceived discrimination and SBP, and 3 SNPs (rs2034454, rs7602215, and rs3771724) that interacted with perceived discrimination and DBP. Most notably, there was a significant SNP × discrimination interaction for 2 SNPs on the SLC4A5 gene: rs3771724 (MLD: SBP P = .034, DBP P = .031; ED: DBP: P = .016) and rs1006502 (MLD: SBP P = .034, DBP P = .030; ED: DBP P = .015).This study supports the idea that SNP × discrimination interactions combine to influence clinically relevant traits such as BP. Replication with similar epidemiological samples is required to ascertain the role of genes and psychosocial stressors in the development and expression of high BP in this understudied population.
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Affiliation(s)
| | - Yan V. Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA
- Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, GA
| | | | - Mosi Ifatunji
- Department of Sociology and Carolina Population Center, University of North Carolina, Chapel Hill, NC
| | - Jane Rafferty
- Program for Research on Black Americans, Institute for Social Research, University of Michigan, Ann Arbor, MI
| | - Ervin R. Fox
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS
| | - Solomon K. Musani
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS
| | - Mario Sims
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS
| | - James S. Jackson
- Program for Research on Black Americans, Institute for Social Research, University of Michigan, Ann Arbor, MI
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Chen TK, Estrella MM, Vittinghoff E, Lin F, Gutierrez OM, Kramer H, Lewis CE, Kopp JB, Allen NB, Winkler CA, Bibbins-Domingo KB, Peralta CA. APOL1 genetic variants are not associated with longitudinal blood pressure in young black adults. Kidney Int 2017; 92:964-971. [PMID: 28545715 PMCID: PMC5610603 DOI: 10.1016/j.kint.2017.03.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/08/2017] [Accepted: 03/16/2017] [Indexed: 01/13/2023]
Abstract
Whether APOL1 polymorphisms contribute to the excess risk of hypertension among blacks is unknown. To assess this we evaluated whether self-reported race and, in blacks, APOL1 risk variants (high-risk [2 risk alleles] versus low-risk [0-1 risk allele]) were associated with longitudinal blood pressure. Blood pressure trajectories were determined using linear mixed-effects (slope) and latent class models (5 distinct groups) during 25 years of follow-up in the Coronary Artery Risk Development in Young Adults Study. Associations of race and APOL1 genotypes with blood pressure change, separately, using linear mixed-effects and multinomial logistic regression models, adjusting for demographic, socioeconomic, and traditional hypertension risk factors, anti-hypertensive medication use, and kidney function were evaluated. Among 1700 whites and 1330 blacks (13% APOL1 high-risk, mean age 25 years; 46% male) mean mid-, ([systolic + diastolic blood pressure]/2), systolic, and diastolic blood pressures were 89, 110, and 69 mm Hg, respectively. One percent of participants used anti-hypertensive medications at baseline. Compared to whites, blacks, regardless of APOL1 genotype, had significantly greater increases in mid-blood pressure and were more likely to experience significantly increasing mid-blood pressure trajectories with adjusted relative risk ratios of 5.21 and 7.27 for moderate-increasing and elevated-increasing versus low-stable blood pressure, respectively. Among blacks, longitudinal mid-blood pressure changes and mid-blood pressure trajectory classification were similar by APOL1 risk status. Modeling systolic and diastolic blood pressure as outcomes yielded similar findings. From young adulthood to mid-life, blacks have greater blood pressure increases versus whites that are not fully explained by traditional risk factors. Thus APOL1 variants are not associated with longitudinal blood pressure in blacks.
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Affiliation(s)
- Teresa K Chen
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
| | - Michelle M Estrella
- Kidney Health Research Collaborative, Department of Medicine, University of California, San Francisco, California, USA; San Francisco VA Medical Center, San Francisco, California, USA
| | - Eric Vittinghoff
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Feng Lin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Orlando M Gutierrez
- Division of Preventative Medicine, Department of Medicine, University of Alabama at Birmingham, Alabama, USA
| | - Holly Kramer
- Division of Nephrology, Department of Medicine, Loyola University, Maywood, Illinois, USA
| | - Cora E Lewis
- Division of Preventative Medicine, Department of Medicine, University of Alabama at Birmingham, Alabama, USA
| | - Jeffrey B Kopp
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Norrina B Allen
- Division of Epidemiology, Department of Preventative Medicine, Northwestern University, Chicago, Illinois, USA
| | - Cheryl A Winkler
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health and Leidos Biomedical Research, Frederick National Laboratory, Frederick, Maryland, USA
| | - Kirsten B Bibbins-Domingo
- Kidney Health Research Collaborative, Department of Medicine, University of California, San Francisco, California, USA
| | - Carmen A Peralta
- Kidney Health Research Collaborative, Department of Medicine, University of California, San Francisco, California, USA; San Francisco VA Medical Center, San Francisco, California, USA
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PROX1 gene CC genotype as a major determinant of early onset of type 2 diabetes in slavic study participants from Action in Diabetes and Vascular Disease: Preterax and Diamicron MR Controlled Evaluation study. J Hypertens 2017; 35 Suppl 1:S24-S32. [PMID: 28060188 PMCID: PMC5377997 DOI: 10.1097/hjh.0000000000001241] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The prevalence of diabetic nephropathy varies according to ethnicity. Environmental as well as genetic factors contribute to the heterogeneity in the presentation of diabetic nephropathy. Our objective was to evaluate this heterogeneity within the Caucasian population. METHODS The geo-ethnic origin of the 3409 genotyped Caucasian type 2 diabetes (T2D) patients of Action in Diabetes and Vascular Disease: Preterax and Diamicron MR Controlled Evaluation was determined using principal component analysis. Genome-wide association studies analyses of age of onset of T2D were performed for geo-ethnic groups separately and combined. RESULTS The first principal component separated the Caucasian study participants into Slavic and Celtic ethnic origins. Age of onset of diabetes was significantly lower in Slavic patients (P = 7.3 × 10), whereas the prevalence of hypertension (P = 4.9 × 10) and albuminuria (5.1 × 10) were significantly higher. Age of onset of T2D and albuminuria appear to have an important genetic component as the values of these traits were also different between Slavic and Celtic individuals living in the same countries. Common and geo-ethnic-specific loci were found to be associated to age of onset of diabetes. Among the latter, the PROX1/PROX1-AS1 genes (rs340841) had the highest impact. Single-nucleotide polymorphism rs340841 CC genotype was associated with a 4.4 year earlier onset of T2D in Slavic patients living or not in countries with predominant Slavic populations. CONCLUSION These results reveal the presence of distinct genetic architectures between Caucasian ethnic groups that likely have clinical relevance, among them PROX1 gene is a strong candidate of early onset of diabetes with variations depending on ethnicity.
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31
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Noel SE, Arevalo S, Smith CE, Lai CQ, Dawson-Hughes B, Ordovas JM, Tucker KL. Genetic admixture and body composition in Puerto Rican adults from the Boston Puerto Rican Osteoporosis Study. J Bone Miner Metab 2017; 35:448-455. [PMID: 27628044 PMCID: PMC5400727 DOI: 10.1007/s00774-016-0775-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/30/2016] [Indexed: 01/17/2023]
Abstract
Population admixture plays a role in the risk of chronic conditions that are related to body composition; however, our understanding of these associations in Puerto Ricans, a population characterized by multiple ancestries, is limited. This study investigated the relationship between genetic admixture and body composition in 652 Puerto Ricans from the Boston Puerto Rican Osteoporosis Study. Genetic ancestry was estimated from 100 ancestry-informative markers. Body composition measures were obtained from dual-energy X-ray absorptiometry. Multivariable linear regression analyses examined associations between bone mineral density (BMD) of the hip and lumbar spine and percent fat mass and lean mass with genetic admixture. In Puerto Ricans living on the US mainland, European ancestry was associated with lower BMD at the trochanter (P = 0.039) and femoral neck (P = 0.01), and Native American ancestry was associated with lower BMD of the trochanter (P = 0.04). African ancestry was associated with a higher BMD at the trochanter (P = 0.004) and femoral neck (P = 0.001). Ancestry was not associated with percent fat mass or lean mass or waist circumference. Our findings are consistent with existing research demonstrating inverse associations between European and Native American ancestries and BMD and positive relationships between African ancestry and BMD. This work contributes to our understanding of the high prevalence of chronic disease experienced by this population and has implications for other ethnic minority groups, particularly those with multiple ancestries. Future research should consider interactions between ancestry and environmental factors, as this may provide individualized approaches for disease prevention.
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Affiliation(s)
- Sabrina E Noel
- Department of Clinical Laboratory and Nutritional Sciences, University of Massachusetts Lowell, 3 Solomont Way, Suite 4, Lowell, MA, 01854, USA.
| | - Sandra Arevalo
- Department of Clinical Laboratory and Nutritional Sciences, University of Massachusetts Lowell, 3 Solomont Way, Suite 4, Lowell, MA, 01854, USA
| | - Caren E Smith
- Nutrition and Genomics Laboratory, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, 711 Washington Street, Boston, MA, 02111, USA
| | - Chao-Qiang Lai
- Nutrition and Genomics Laboratory, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, 711 Washington Street, Boston, MA, 02111, USA
| | - Bess Dawson-Hughes
- Bone Metabolism Laboratory, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, 711 Washington Street, Boston, MA, 02111, USA
| | - Jose M Ordovas
- Nutrition and Genomics Laboratory, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, 711 Washington Street, Boston, MA, 02111, USA
- IMDEA Food, Ctra. de Cantoblanco, num. 8 Ancient Central Pavilion of the Cantoblanco Hospital (Building num. 7), 28049, Madrid, Spain
| | - Katherine L Tucker
- Department of Clinical Laboratory and Nutritional Sciences, University of Massachusetts Lowell, 3 Solomont Way, Suite 4, Lowell, MA, 01854, USA
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Liang J, Le TH, Edwards DRV, Tayo BO, Gaulton KJ, Smith JA, Lu Y, Jensen RA, Chen G, Yanek LR, Schwander K, Tajuddin SM, Sofer T, Kim W, Kayima J, McKenzie CA, Fox E, Nalls MA, Young JH, Sun YV, Lane JM, Cechova S, Zhou J, Tang H, Fornage M, Musani SK, Wang H, Lee J, Adeyemo A, Dreisbach AW, Forrester T, Chu PL, Cappola A, Evans MK, Morrison AC, Martin LW, Wiggins KL, Hui Q, Zhao W, Jackson RD, Ware EB, Faul JD, Reiner AP, Bray M, Denny JC, Mosley TH, Palmas W, Guo X, Papanicolaou GJ, Penman AD, Polak JF, Rice K, Taylor KD, Boerwinkle E, Bottinger EP, Liu K, Risch N, Hunt SC, Kooperberg C, Zonderman AB, Laurie CC, Becker DM, Cai J, Loos RJF, Psaty BM, Weir DR, Kardia SLR, Arnett DK, Won S, Edwards TL, Redline S, Cooper RS, Rao DC, Rotter JI, Rotimi C, Levy D, Chakravarti A, Zhu X, Franceschini N. Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations. PLoS Genet 2017; 13:e1006728. [PMID: 28498854 PMCID: PMC5446189 DOI: 10.1371/journal.pgen.1006728] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/26/2017] [Accepted: 03/30/2017] [Indexed: 02/07/2023] Open
Abstract
Hypertension is a leading cause of global disease, mortality, and disability. While individuals of African descent suffer a disproportionate burden of hypertension and its complications, they have been underrepresented in genetic studies. To identify novel susceptibility loci for blood pressure and hypertension in people of African ancestry, we performed both single and multiple-trait genome-wide association analyses. We analyzed 21 genome-wide association studies comprised of 31,968 individuals of African ancestry, and validated our results with additional 54,395 individuals from multi-ethnic studies. These analyses identified nine loci with eleven independent variants which reached genome-wide significance (P < 1.25×10-8) for either systolic and diastolic blood pressure, hypertension, or for combined traits. Single-trait analyses identified two loci (TARID/TCF21 and LLPH/TMBIM4) and multiple-trait analyses identified one novel locus (FRMD3) for blood pressure. At these three loci, as well as at GRP20/CDH17, associated variants had alleles common only in African-ancestry populations. Functional annotation showed enrichment for genes expressed in immune and kidney cells, as well as in heart and vascular cells/tissues. Experiments driven by these findings and using angiotensin-II induced hypertension in mice showed altered kidney mRNA expression of six genes, suggesting their potential role in hypertension. Our study provides new evidence for genes related to hypertension susceptibility, and the need to study African-ancestry populations in order to identify biologic factors contributing to hypertension.
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Affiliation(s)
- Jingjing Liang
- Department of Epidemiology & Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
| | - Thu H. Le
- Department of Medicine, Division of Nephrology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Digna R. Velez Edwards
- Department of Obstetrics and Gynecology, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Bamidele O. Tayo
- Department of Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, United States of America
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- The Genetics of Obesity and Related Metabolic Traits Program, Ichan School of Medicine at Mount Sinai, New York City, New York, United States of America
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Richard A. Jensen
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Karen Schwander
- Division of Biostatistics, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Salman M. Tajuddin
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Wonji Kim
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - James Kayima
- Division of Adult Cardiology, Uganda Heart Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Colin A. McKenzie
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Ervin Fox
- Department of Preventive Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Michael A. Nalls
- Data Tecnica International, Glen Echo, MD, United States of America and Laboratory of Neurogenetics, National Institute on Aging, National Institute of Health, Bethesda, Maryland, United States of America
| | - J. Hunter Young
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yan V. Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Jacqueline M. Lane
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Sylvia Cechova
- Department of Medicine, Division of Nephrology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Myriam Fornage
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Solomon K. Musani
- Department of Preventive Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Heming Wang
- Department of Epidemiology & Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
| | - Juyoung Lee
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Cheongju, Republic of Korea
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Albert W. Dreisbach
- Department of Preventive Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Terrence Forrester
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Pei-Lun Chu
- Department of Internal Medicine, Graduate Institute of Biomedical and Pharmaceutical Science, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Anne Cappola
- Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States of America
| | - Michele K. Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Alanna C. Morrison
- Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Lisa W. Martin
- The George Washington University School of Medicine and Health Sciences, Washington DC. United States of America
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Qin Hui
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Rebecca D. Jackson
- Department of Internal Medicine, Ohio State University, Columbus, Ohio, United States of America
| | - Erin B. Ware
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
- Survey Research Center, Institute for Social Research, University of Michigan Ann Arbor, Michigan, United States of America
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan Ann Arbor, Michigan, United States of America
| | - Alex P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael Bray
- Department of Obstetrics and Gynecology, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Joshua C. Denny
- Department of Biomedical Informatics, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Thomas H. Mosley
- Department of Preventive Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Walter Palmas
- Department of Medicine, Columbia University, New York City, New York, United States of America
| | - Xiuqing Guo
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - George J. Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alan D. Penman
- Department of Preventive Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Joseph F. Polak
- Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Ken D. Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Erwin P. Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Kiang Liu
- Department of Preventive Medicine, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Neil Risch
- Institute for Human Genetics, University of California, San Francisco, California, United States of America
| | - Steven C. Hunt
- Cardiovascular Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Alan B. Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Cathy C. Laurie
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Diane M. Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jianwen Cai
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States of America
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- The Genetics of Obesity and Related Metabolic Traits Program, Ichan School of Medicine at Mount Sinai, New York City, New York, United States of America
- The Mindich Child Health and Development Institute, Ichan School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, United States of America
| | - David R. Weir
- Survey Research Center, Institute for Social Research, University of Michigan Ann Arbor, Michigan, United States of America
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Donna K. Arnett
- University of Kentucky, College of Public Health, Lexington, KY
| | - Sungho Won
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Department of Public Health Science, Seoul National University, Seoul, Republic of Korea
| | - Todd L. Edwards
- Division of Epidemiology, Department of Medicine, Institute of Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilit University Medical Center, Nashville, Tennessee, United States of America
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard S. Cooper
- Department of Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, United States of America
| | - D. C. Rao
- Division of Biostatistics, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute of the National Institutes of Health, Bethesda, MD, and the Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Xiaofeng Zhu
- Department of Epidemiology & Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
| | - Nora Franceschini
- Epidemiology, Gilling School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
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Shendre A, Irvin MR, Wiener H, Zhi D, Limdi NA, Overton ET, Shrestha S. Local Ancestry and Clinical Cardiovascular Events Among African Americans From the Atherosclerosis Risk in Communities Study. J Am Heart Assoc 2017; 6:JAHA.116.004739. [PMID: 28396569 PMCID: PMC5532995 DOI: 10.1161/jaha.116.004739] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Local ancestry in relation to clinical cardiovascular events (CVEs) among African Americans can provide insight into their genetic susceptibility to the disease. METHODS AND RESULTS We examined local European ancestry (LEA) association with CVEs among 3000 African Americans from the Atherosclerosis Risk in Communities Study (ARIC). We estimated LEA using Local Ancestry Inference in adMixed Populations using Linkage Disequilibrium (LAMP-LD) and examined its association with myocardial infarction, stroke, coronary heart disease and its composite and cardiovascular disease composite using logistic regression. Genome-wide significance was achieved by 121 LEA regions in relation to myocardial infarction and 2 in relation to the cardiovascular disease composite. The LEA region downstream of 4q32.1 was significantly associated with 2 times higher odds of myocardial infarction (P=1.45×10-6). The LEA region upstream of 6q11.1 was associated with 0.37 times lower odds of fatal coronary heart disease (P=7.34×10-4), whereas the LEA region downstream of 21q21.1 was associated with 1.55 times higher odds of composite coronary heart disease (P=3.45×10-4). Association of LEA with stroke was observed in the region upstream of 6p22.3 with a 1.57 times higher odds of stroke (P=9.69×10-4). Likewise, the LEA region on 4q32.3 was associated with a 1.53 times higher odds of composite cardiovascular disease (P=3.04×10-4). We also found 20 of the LEA regions at previously significant cardiovascular disease single-nucleotide polymorphisms to be associated with CVE in our study. CONCLUSIONS Future studies are needed to replicate and/or determine the causal variants driving our associations and explore clinical applications for those consistently associated with CVEs.
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Affiliation(s)
- Aditi Shendre
- Department of Epidemiology, University of Alabama at Birmingham, AL
| | | | - Howard Wiener
- Department of Epidemiology, University of Alabama at Birmingham, AL
| | - Degui Zhi
- Department of Biostatistics, University of Alabama at Birmingham, AL
| | - Nita A Limdi
- Department of Neurology, University of Alabama at Birmingham, AL
| | - Edgar T Overton
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, AL
| | - Sadeep Shrestha
- Department of Epidemiology, University of Alabama at Birmingham, AL
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Cyr DD, Allen AS, Du GJ, Ruffin F, Adams C, Thaden JT, Maskarinec SA, Souli M, Guo S, Dykxhoorn DM, Scott WK, Fowler VG. Evaluating genetic susceptibility to Staphylococcus aureus bacteremia in African Americans using admixture mapping. Genes Immun 2017; 18:95-99. [PMID: 28332560 PMCID: PMC5435963 DOI: 10.1038/gene.2017.6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/14/2017] [Accepted: 02/16/2017] [Indexed: 12/12/2022]
Abstract
The incidence of Staphylococcus aureus bacteremia (SAB) is significantly higher in African American (AA) than in European-descended populations. We used admixture mapping (AM) to test the hypothesis that genomic variations with different frequencies in European and African ancestral genomes influence susceptibility to SAB in AAs. A total of 565 adult AAs (390 cases with SAB; 175 age-matched controls) were genotyped for AM analysis. A case-only admixture score and a mixed χ2(1df) score (MIX) to jointly evaluate both single-nucleotide polymorphism (SNP) and admixture association (P<5.00e-08) were computed using MIXSCORE. In addition, a permutation scheme was implemented to derive multiplicity adjusted P-values (genome-wide 0.05 significance threshold: P<9.46e-05). After empirical multiplicity adjustment, one region on chromosome 6 (52 SNPs, P=4.56e-05) in the HLA class II region was found to exhibit a genome-wide statistically significant increase in European ancestry. This region encodes genes involved in HLA-mediated immune response and these results provide additional evidence for genetic variation influencing HLA-mediated immunity, modulating susceptibility to SAB.
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Affiliation(s)
- D D Cyr
- Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, USA
| | - A S Allen
- Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, USA.,Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - G-J Du
- Duke Center for Genomic and Computational Biology, Durham, NC, USA
| | - F Ruffin
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - C Adams
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - J T Thaden
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - S A Maskarinec
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - M Souli
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA.,School of Medicine, National and Kapodistrian University of Athens, Chaidari, Greece
| | - S Guo
- Dr John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - D M Dykxhoorn
- Dr John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - W K Scott
- Dr John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - V G Fowler
- Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, USA.,Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
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Kayima J, Liang J, Natanzon Y, Nankabirwa J, Ssinabulya I, Nakibuuka J, Katamba A, Mayanja-Kizza H, Miron A, Li C, Zhu X. Association of genetic variation with blood pressure traits among East Africans. Clin Genet 2017; 92:487-494. [PMID: 28105631 DOI: 10.1111/cge.12974] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/15/2017] [Accepted: 01/16/2017] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Genetic variation may play explain some of the disparity in prevalence and control of hypertension across Sub-Saharan Africa. However, there have been very few studies to characterize genetic variation of blood pressure traits. AIM To determine whether a set of blood pressure-associated genetic loci can be replicated among samples East African samples. METHODS Twenty-seven blood pressures (BP)-related single nucleotide polymorphisms (SNPs) were genotyped among 2881 samples from participants in the Medical Education Partnership Initiative for Cardiovascular Disease (MEPI-CVD) survey. Associations with known BP variants were evaluated for systolic blood pressure (SBP), diastolic blood pressure (DBP) and pulse pressure (PP) as continuous variables and for hypertension (HTN) as a binary variable. RESULTS Eleven SNPS were associated with at least 1 BP trait (P < .05). Four SNPs; rs2004776, rs7726475, rs11837544 and rs2681492, whose nearest genes are AGT, NPR3/SUB1, PLXNC1 and ATP2B1, respectively, were associated with SBP. Six SNPs, rs2004776, rs11977526, rs11191548, rs381815, rs2681492 and rs1327235, close to AGT, IGFBP3, CYP17A1, PLEKHA7, ATP2B1 and JAG, respectively, were associated with DBP while 2 SNPs located within AGT and IGFBP-3 genes associated with HTN. For PP, 4 variants rs1458038, rs11725861, rs7726475 and rs11953630 whose corresponding genes are FGF5, CHIC2, SUB1/NPR3 and EBF1 reached significance (P < .05). Eight SNPs were replicated in the same effect direction as the parent studies. Risk scores defined using published effect sizes were significantly associated with both SBP (P = .0026) and DBP (P = .0214). CONCLUSION The replication of multiple BP variants among East Africans suggests that these variants may have universal effects across ethnic populations.
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Affiliation(s)
- J Kayima
- Division of Adult Cardiology, Uganda Heart Institute, Kampala, Uganda.,Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - J Liang
- Department of Epidemiology & Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Y Natanzon
- Department of Epidemiology & Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - J Nankabirwa
- Clinical Epidemiology Unit, Department of Medicine, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - I Ssinabulya
- Division of Adult Cardiology, Uganda Heart Institute, Kampala, Uganda.,Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - J Nakibuuka
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - A Katamba
- Clinical Epidemiology Unit, Department of Medicine, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - H Mayanja-Kizza
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - A Miron
- Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - C Li
- Department of Epidemiology & Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - X Zhu
- Department of Epidemiology & Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
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He KY, Wang H, Cade BE, Nandakumar P, Giri A, Ware EB, Haessler J, Liang J, Smith JA, Franceschini N, Le TH, Kooperberg C, Edwards TL, Kardia SLR, Lin X, Chakravarti A, Redline S, Zhu X. Rare variants in fox-1 homolog A (RBFOX1) are associated with lower blood pressure. PLoS Genet 2017; 13:e1006678. [PMID: 28346479 PMCID: PMC5386302 DOI: 10.1371/journal.pgen.1006678] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 04/10/2017] [Accepted: 03/09/2017] [Indexed: 12/23/2022] Open
Abstract
Many large genome-wide association studies (GWAS) have identified common blood pressure (BP) variants. However, most of the identified BP variants do not overlap with the linkage evidence observed from family studies. We thus hypothesize that multiple rare variants contribute to the observed linkage evidence. We performed linkage analysis using 517 individuals in 130 European families from the Cleveland Family Study (CFS) who have been genotyped on the Illumina OmniExpress Exome array. The largest linkage peak was observed on chromosome 16p13 (MLOD = 2.81) for systolic blood pressure (SBP). Follow-up conditional linkage and association analyses in the linkage region identified multiple rare, coding variants in RBFOX1 associated with reduced SBP. In a 17-member CFS family, carriers of the missense variant rs149974858 are normotensive despite being obese (average BMI = 60 kg/m2). Gene-based association test of rare variants using SKAT-O showed significant association with SBP (p-value = 0.00403) and DBP (p-value = 0.0258) in the CFS participants and the association was replicated in large independent replication studies (N = 57,234, p-value = 0.013 for SBP, 0.0023 for PP). RBFOX1 is expressed in brain tissues, the atrial appendage and left ventricle in the heart, and in skeletal muscle tissues, organs/tissues which are potentially related to blood pressure. Our study showed that associations of rare variants could be efficiently detected using family information.
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Affiliation(s)
- Karen Y. He
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Heming Wang
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Priyanka Nandakumar
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Ayush Giri
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Erin B. Ware
- Biosocial Methods Collaborative, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jingjing Liang
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nora Franceschini
- Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, North Carolina, United States of America
| | - Thu H. Le
- Department of Medicine, Division of Nephrology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Todd L. Edwards
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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Genetic Loci and Novel Discrimination Measures Associated with Blood Pressure Variation in African Americans Living in Tallahassee. PLoS One 2016; 11:e0167700. [PMID: 28002425 PMCID: PMC5176163 DOI: 10.1371/journal.pone.0167700] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 11/18/2016] [Indexed: 02/06/2023] Open
Abstract
Sequencing of the human genome and decades of genetic association and linkage studies have dramatically improved our understanding of the etiology of many diseases. However, the multiple causes of complex diseases are still not well understood, in part because genetic and sociocultural risk factors are not typically investigated concurrently. Hypertension is a leading risk factor for cardiovascular disease and afflicts more African Americans than any other racially defined group in the US. Few genetic loci for hypertension have been replicated across populations, which may reflect population-specific differences in genetic variants and/or inattention to relevant sociocultural factors. Discrimination is a salient sociocultural risk factor for poor health and has been associated with hypertension. Here we use a biocultural approach to study blood pressure (BP) variation in African Americans living in Tallahassee, Florida by genotyping over 30,000 single nucleotide polymorphisms (SNPs) and capturing experiences of discrimination using novel measures of unfair treatment of self and others (n = 157). We perform a joint admixture and genetic association analysis for BP that prioritizes regions of the genome with African ancestry. We only report significant SNPs that were confirmed through our simulation analyses, which were performed to determine the false positive rate. We identify eight significant SNPs in five genes that were previously associated with cardiovascular diseases. When we include measures of unfair treatment and test for interactions between SNPs and unfair treatment, we identify a new class of genes involved in multiple phenotypes including psychosocial distress and mood disorders. Our results suggest that inclusion of culturally relevant stress measures, like unfair treatment in African Americans, may reveal new genes and biological pathways relevant to the etiology of hypertension, and may also improve our understanding of the complexity of gene-environment interactions that underlie complex diseases.
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Ruiz-Narváez EA, Sucheston-Campbell L, Bensen JT, Yao S, Haddad S, Haiman CA, Bandera EV, John EM, Bernstein L, Hu JJ, Ziegler RG, Deming SL, Olshan AF, Ambrosone CB, Palmer JR, Lunetta KL. Admixture Mapping of African-American Women in the AMBER Consortium Identifies New Loci for Breast Cancer and Estrogen-Receptor Subtypes. Front Genet 2016; 7:170. [PMID: 27708667 PMCID: PMC5030764 DOI: 10.3389/fgene.2016.00170] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/07/2016] [Indexed: 12/13/2022] Open
Abstract
Recent genetic admixture coupled with striking differences in incidence of estrogen receptor (ER) breast cancer subtypes, as well as severity, between women of African and European ancestry, provides an excellent rationale for performing admixture mapping in African American women with breast cancer risk. We performed the largest breast cancer admixture mapping study with in African American women to identify novel genomic regions associated with the disease. We conducted a genome-wide admixture scan using 2,624 autosomal ancestry informative markers (AIMs) in 3,629 breast cancer cases (including 1,968 ER-positive, 1093 ER-negative, and 601 triple-negative) and 4,658 controls from the African American Breast Cancer Epidemiology and Risk (AMBER) Consortium, a collaborative study of four large geographically different epidemiological studies of breast cancer in African American women. We used an independent case-control study to test for SNP association in regions with genome-wide significant admixture signals. We found two novel genome-wide significant regions of excess African ancestry, 4p16.1 and 17q25.1, associated with ER-positive breast cancer. Two regions known to harbor breast cancer variants, 10q26 and 11q13, were also identified with excess of African ancestry. Fine-mapping of the identified genome-wide significant regions suggests the presence of significant genetic associations with ER-positive breast cancer in 4p16.1 and 11q13. In summary, we identified three novel genomic regions associated with breast cancer risk by ER status, suggesting that additional previously unidentified variants may contribute to the racial differences in breast cancer risk in the African American population.
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Affiliation(s)
| | - Lara Sucheston-Campbell
- College of Pharmacy, The Ohio State University, ColumbusOH, USA
- College of Veterinary Medicine, The Ohio State University, ColumbusOH, USA
| | - Jeannette T. Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel HillNC, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, BuffaloNY, USA
| | - Stephen Haddad
- Slone Epidemiology Center, Boston University, BostonMA, USA
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los AngelesCA, USA
| | | | - Esther M. John
- Cancer Prevention Institute of California, FremontCA, USA
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Science, Beckman Research Institute, City of Hope, DuarteCA, USA
| | - Jennifer J. Hu
- Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, University of Miami Miller School of Medicine, MiamiFL, USA
| | - Regina G. Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, BethesdaMD, USA
| | - Sandra L. Deming
- Vanderbilt Epidemiology Center, Vanderbilt University and the Vanderbilt-Ingram Cancer Center, NashvilleTN, USA
| | - Andrew F. Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel HillNC, USA
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, BuffaloNY, USA
| | | | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, BostonMA, USA
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Gupta J, Johansson E, Bernstein JA, Chakraborty R, Khurana Hershey GK, Rothenberg ME, Mersha TB. Resolving the etiology of atopic disorders by using genetic analysis of racial ancestry. J Allergy Clin Immunol 2016; 138:676-699. [PMID: 27297995 PMCID: PMC5014679 DOI: 10.1016/j.jaci.2016.02.045] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 02/09/2016] [Accepted: 02/25/2016] [Indexed: 12/23/2022]
Abstract
Atopic dermatitis (AD), food allergy, allergic rhinitis, and asthma are common atopic disorders of complex etiology. The frequently observed atopic march from early AD to asthma, allergic rhinitis, or both later in life and the extensive comorbidity of atopic disorders suggest common causal mechanisms in addition to distinct ones. Indeed, both disease-specific and shared genomic regions exist for atopic disorders. Their prevalence also varies among races; for example, AD and asthma have a higher prevalence in African Americans when compared with European Americans. Whether this disparity stems from true genetic or race-specific environmental risk factors or both is unknown. Thus far, the majority of the genetic studies on atopic diseases have used populations of European ancestry, limiting their generalizability. Large-cohort initiatives and new analytic methods, such as admixture mapping, are currently being used to address this knowledge gap. Here we discuss the unique and shared genetic risk factors for atopic disorders in the context of ancestry variations and the promise of high-throughput "-omics"-based systems biology approach in providing greater insight to deconstruct their genetic and nongenetic etiologies. Future research will also focus on deep phenotyping and genotyping of diverse racial ancestry, gene-environment, and gene-gene interactions.
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Affiliation(s)
- Jayanta Gupta
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Elisabet Johansson
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Jonathan A Bernstein
- Division of Immunology/Allergy Section, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Ranajit Chakraborty
- Center for Computational Genomics, Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Tex
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio.
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Pacheco-Sierra G, Gompert Z, Domínguez-Laso J, Vázquez-Domínguez E. Genetic and morphological evidence of a geographically widespread hybrid zone between two crocodile species,Crocodylus acutusandCrocodylus moreletii. Mol Ecol 2016; 25:3484-98. [DOI: 10.1111/mec.13694] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 04/07/2016] [Accepted: 05/02/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Gualberto Pacheco-Sierra
- Departamento de Ecología de la Biodiversidad; Instituto de Ecología; Universidad Nacional Autónoma de México; Ap. Postal 70-275 Ciudad Universitaria México DF 04510 México
- Posgrado en Ciencias Biológicas; Universidad Nacional Autónoma de México; Coyoacán México DF 04510 México
| | - Zachariah Gompert
- Department of Biology and Ecology Center; Utah State University; Logan UT 84322 USA
| | | | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad; Instituto de Ecología; Universidad Nacional Autónoma de México; Ap. Postal 70-275 Ciudad Universitaria México DF 04510 México
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Muñoz AM, Velásquez CM, Bedoya G. Cardio-metabolic parameters are associated with genetic admixture estimates in a pediatric population from Colombia. BMC Genet 2016; 17:93. [PMID: 27350247 PMCID: PMC4924275 DOI: 10.1186/s12863-016-0402-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 06/17/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND There are different genetic patterns for cardio-metabolic parameters among different populations. Additionally, it has been found that ancestral genetic components (the proportion of Amerindian, European and African) in admixed Latin American populations influence an individual's susceptibility to cardio-metabolic disorders. The aim of this study was to evaluate the effect of ancestral genetic composition on a series of cardio-metabolic risk factors in a young admixed population from Colombia. RESULTS In a sample of 853 Colombian youth, 10 to 18 years old, the mean European contribution was 66.6 % (range: 41-82 %), the mean African contribution was 14 % (range: 4-48 %), and the mean Amerindian contribution was 19.4 % (range: 10-35 %) using a panel of 40 autosomal ancestry-informative markers (AIMs). We assessed the degree of association between ancestral African, Amerindian and European genetic components and measures of body mass index, waist circumference, fasting glucose, fasting insulin, insulin resistance, triglycerides, high-density lipoprotein, and systolic and diastolic blood pressure. Two of the nine measures assessed presented a nominal significant association with ancestral components after adjusting for confounding variables: triglyceride levels were associated with the Amerindian component (OR = 1.06, 98.3 % CI = 1.01-1.11, P = 0.002) and systolic blood pressure was associated with the European component (OR = 0.93, 98.3 % CI = 0.87 to 0.99, P = 0.008) and the African component (OR = 1.07, CI = 1.01-1.14 P = 0.008), although it was not significant following a global Bonferroni correction. Additionally, insulin levels and insulin resistance showed associations with the African component. CONCLUSIONS Our findings support the idea that an Amerindian ancestral component may act as a risk factor for high triglyceride levels. In addition, an African ancestral component confers a risk for high systolic blood pressure, and a European ancestry serves as a protective factor for this condition in a young admixed population from Colombia. However, these results should be confirmed in a larger population.
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Affiliation(s)
- Angélica M Muñoz
- Research Group on Food and Human Nutrition, Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia. .,Laboratorio 413, Sede de Investigación Universitaria (SIU), Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia.
| | - Claudia M Velásquez
- Research Group on Food and Human Nutrition, Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia
| | - Gabriel Bedoya
- Research Group on Molecular Genetic (GENMOL), Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia
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Palmer ND, Divers J, Lu L, Register TC, Carr JJ, Hicks PJ, Smith SC, Xu J, Judd SE, Irvin MR, Gutierrez OM, Bowden DW, Wagenknecht LE, Langefeld CD, Freedman BI. Admixture mapping of serum vitamin D and parathyroid hormone concentrations in the African American-Diabetes Heart Study. Bone 2016; 87:71-7. [PMID: 27032714 PMCID: PMC4862915 DOI: 10.1016/j.bone.2016.01.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/17/2015] [Accepted: 01/19/2016] [Indexed: 10/22/2022]
Abstract
Vitamin D and intact parathyroid hormone (iPTH) concentrations differ between individuals of African and European descent and may play a role in observed racial differences in bone mineral density (BMD). These findings suggest that mapping by admixture linkage disequilibrium (MALD) may be informative for identifying genetic variants contributing to these ethnic disparities. Admixture mapping was performed for serum 25-hydroxyvitamin D, 1,25-dihydroxyvitamin D, vitamin D-binding protein (VDBP), bioavailable vitamin D, and iPTH concentrations and computed tomography measured thoracic and lumbar vertebral volumetric BMD in 552 unrelated African Americans with type 2 diabetes from the African American-Diabetes Heart Study. Genotyping was performed using a custom Illumina ancestry informative marker (AIM) panel. For each AIM, the probability of inheriting 0, 1, or 2 copies of a European-derived allele was determined. Non-parametric linkage analysis was performed by testing for association between each AIM using these probabilities among phenotypes, accounting for global ancestry, age, and gender. Fine-mapping of MALD peaks was facilitated by genome-wide association study (GWAS) data. VDBP levels were significantly linked in proximity to the protein coding locus (rs7689609, LOD=11.05). Two loci exhibited significant linkage signals for 1,25-dihydroxyvitamin D on 13q21.2 (rs1622710, LOD=3.20) and 12q13.2 (rs11171526, LOD=3.10). iPTH was significantly linked on 9q31.3 (rs7854368, LOD=3.14). Fine-mapping with GWAS data revealed significant known (rs7041 with VDBP, P=1.38×10(-82)) and novel (rs12741813 and rs10863774 with VDBP, P<6.43×10(-5)) loci with plausible biological roles. Admixture mapping in combination with fine-mapping has focused efforts to identify loci contributing to ethnic differences in vitamin D-related traits.
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Affiliation(s)
- Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA; Center for Diabetes Research, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA; Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA; Center for Public Health Genomics, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA.
| | - Jasmin Divers
- Center for Public Health Genomics, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA; Department of Biostatistical Sciences, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA.
| | - Lingyi Lu
- Center for Public Health Genomics, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA; Department of Biostatistical Sciences, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA.
| | - Thomas C Register
- Department of Pathology, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA.
| | - J Jeffrey Carr
- Department of Radiology, Vanderbilt University School of Medicine, 2525 West End Ave, Suite 300-B, Nashville, TN 37203, USA.
| | - Pamela J Hicks
- Department of Biochemistry, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA.
| | - S Carrie Smith
- Department of Biochemistry, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA.
| | - Jianzhao Xu
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA.
| | - Suzanne E Judd
- Department of Biostatistics, University of Alabama at Birmingham, 1665 University Boulevard, Birmingham, AL 35294, USA.
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, 1665 University Boulevard, Birmingham, AL 35294, USA.
| | - Orlando M Gutierrez
- Department of Epidemiology, University of Alabama at Birmingham, 1665 University Boulevard, Birmingham, AL 35294, USA; Department of Medicine, University of Alabama at Birmingham, 1665 University Boulevard, Birmingham, AL, 35294, USA.
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA; Center for Diabetes Research, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA; Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA.
| | - Lynne E Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA.
| | - Carl D Langefeld
- Center for Public Health Genomics, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA; Department of Biostatistical Sciences, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA.
| | - Barry I Freedman
- Center for Diabetes Research, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA; Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA; Center for Public Health Genomics, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA; Department of Internal Medicine-Section on Nephrology, Wake Forest School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA.
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Aschard H, Gusev A, Brown R, Pasaniuc B. Leveraging local ancestry to detect gene-gene interactions in genome-wide data. BMC Genet 2015; 16:124. [PMID: 26498930 PMCID: PMC4619349 DOI: 10.1186/s12863-015-0283-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/19/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Although genome-wide association studies have successfully identified thousands of variants associated to complex traits, these variants only explain a small amount of the entire heritability of the trait. Gene-gene interactions have been proposed as a source to explain a significant percentage of the missing heritability. However, detecting gene-gene interactions has proven to be very difficult due to computational and statistical challenges. The vast number of possible interactions that can be tested induces very stringent multiple hypotheses corrections that limit the power of detection. These issues have been mostly highlighted for the identification of pairwise effects and are even more challenging when addressing higher order interaction effects. In this work we explore the use of local ancestry in recently admixed individuals to find signals of gene-gene interaction on human traits and diseases. RESULTS We introduce statistical methods that leverage the correlation between local ancestry and the hidden unknown causal variants to find distant gene-gene interactions. We show that the power of this test increases with the number of causal variants per locus and the degree of differentiation of these variants between the ancestral populations. Overall, our simulations confirm that local ancestry can be used to detect gene-gene interactions, solving the computational bottleneck. When compared to a single nucleotide polymorphism (SNP)-based interaction screening of the same sample size, the power of our test was lower on all settings we considered. However, accounting for the dramatic increase in sample size that can be achieve when genotyping only a set of ancestry informative markers instead of the whole genome, we observe substantial gain in power in several scenarios. CONCLUSION Local ancestry-based interaction tests offer a new path to the detection of gene-gene interaction effects. It would be particularly useful in scenarios where multiple differentiated variants at the interacting loci act in a synergistic manner.
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Affiliation(s)
- Hugues Aschard
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA.
| | - Alexander Gusev
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA.
| | - Robert Brown
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA.
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA.
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Mersha TB. Mapping asthma-associated variants in admixed populations. Front Genet 2015; 6:292. [PMID: 26483834 PMCID: PMC4586512 DOI: 10.3389/fgene.2015.00292] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/03/2015] [Indexed: 12/19/2022] Open
Abstract
Admixed populations arise when two or more previously isolated populations interbreed. Mapping asthma susceptibility loci in an admixed population using admixture mapping (AM) involves screening the genome of individuals of mixed ancestry for chromosomal regions that have a higher frequency of alleles from a parental population with higher asthma risk as compared with parental population with lower asthma risk. AM takes advantage of the admixture created in populations of mixed ancestry to identify genomic regions where an association exists between genetic ancestry and asthma (in contrast to between the genotype of the marker and asthma). The theory behind AM is that chromosomal segments of affected individuals contain a significantly higher-than-average proportion of alleles from the high-risk parental population and thus are more likely to harbor disease-associated loci. Criteria to evaluate the applicability of AM as a gene mapping approach include: (1) the prevalence of the disease differences in ancestral populations from which the admixed population was formed; (2) a measurable difference in disease-causing alleles between the parental populations; (3) reduced linkage disequilibrium (LD) between unlinked loci across chromosomes and strong LD between neighboring loci; (4) a set of markers with noticeable allele-frequency differences between parental populations that contributes to the admixed population (single nucleotide polymorphisms (SNPs) are the markers of choice because they are abundant, stable, relatively cheap to genotype, and informative with regard to the LD structure of chromosomal segments); and (5) there is an understanding of the extent of segmental chromosomal admixtures and their interactions with environmental factors. Although genome-wide association studies have contributed greatly to our understanding of the genetic components of asthma, the large and increasing degree of admixture in populations across the world create many challenges for further efforts to map disease-causing genes. This review, summarizes the historical context of admixed populations and AM, and considers current opportunities to use AM to map asthma genes. In addition, we provide an overview of the potential limitations and future directions of AM in biomedical research, including joint admixture and association mapping for asthma and asthma-related disorders.
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Affiliation(s)
- Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati Cincinnati, OH, USA
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45
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Jack J, Havener TM, McLeod HL, Motsinger-Reif AA, Foster M. Evaluating the role of admixture in cancer therapy via in vitro drug response and multivariate genome-wide associations. Pharmacogenomics 2015; 16:1451-63. [PMID: 26314407 DOI: 10.2217/pgs.15.85] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
AIM We investigate the role of ethnicity and admixture in drug response across a broad group of chemotherapeutic drugs. Also, we generate hypotheses on the genetic variants driving differential drug response through multivariate genome-wide association studies. METHODS Immortalized lymphoblastoid cell lines from 589 individuals (Hispanic or non-Hispanic/Caucasian) were used to investigate dose-response for 28 chemotherapeutic compounds. Univariate and multivariate statistical models were used to elucidate associations between genetic variants and differential drug response as well as the role of ethnicity in drug potency and efficacy. RESULTS & CONCLUSION For many drugs, the variability in drug response appears to correlate with self-reported race and estimates of genetic ancestry. Additionally, multivariate genome-wide association analyses offered interesting hypotheses governing these differential responses.
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Affiliation(s)
- John Jack
- Department of Statistics, North Carolina State University, 2601 Stinson Drive, Raleigh, NC 27695, USA.,Bioinformatics Research Center, North Carolina State University, 2601 Stinson Drive, Raleigh, NC 27695, USA
| | - Tammy M Havener
- Center for Pharmacogenomics & Individualized Therapy, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC 27514, USA
| | - Howard L McLeod
- DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Pharmacogenetics for Every Nation Initiative, 1119 Oxbridge Drive, Tampa, FL 33549, USA
| | - Alison A Motsinger-Reif
- Department of Statistics, North Carolina State University, 2601 Stinson Drive, Raleigh, NC 27695, USA.,Bioinformatics Research Center, North Carolina State University, 2601 Stinson Drive, Raleigh, NC 27695, USA
| | - Matthew Foster
- Lineberger Comprehensive Cancer Center, University of North Carolina, 101 Manning Drive, Chapel Hill, NC 27514, USA
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46
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Cardena MMSG, Ribeiro-Dos-Santos AK, Santos SEB, Mansur AJ, Bernardez-Pereira S, Santos PCJL, Pereira AC, Fridman C. Mitochondrial and genomic ancestry are associated with etiology of heart failure in Brazilian patients. J Hum Hypertens 2015; 30:120-3. [PMID: 25947276 DOI: 10.1038/jhh.2015.39] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/25/2015] [Accepted: 03/31/2015] [Indexed: 01/19/2023]
Abstract
There is a high prevalence of heart failure (HF) in the general population, but it is more common in black people. We evaluated the association between genomic ancestry and mitochondrial haplogroups (mt-haplogroups) with HF etiology in 503 Brazilian patients. We elicited Mt-haplogroups by analyzing the control region of mitochondrial DNA, and genomic ancestry, by using 48 autosomal insertion-deletion ancestry informative markers. Hypertensive (28.6%, n=144) and ischemic (28.4%, n=143) etiologies of HF were the most prevalent herein. Our results showed that 233 individuals (46.3%) presented African mitochondrial (mt)-haplogroups, and the major contribution in the genomic ancestry analysis was the European ancestry (57.5% (±22.1%)). African mt-haplogroups were positively associated with a diagnosis of hypertensive cardiomyopathy (odds ratio, OR 1.55, confidence interval, CI 95% 1.04-2.44, P=0.04) when compared with European mt-haplogroups. Regarding the genomic ancestry, the African ancestry variant had higher risks (OR 7.84, 95% CI 2.81-21.91, P<0.001), whereas the European ancestry variant had lower risks (OR 0.14, 95% CI 0.04-5.00, P<0.001) for developing the hypertensive etiology. In addition, European ancestry showed an OR of 4.05 (CI 95% 1.53-10.74, P=0.005), whereas African ancestry showed an OR of 0.17 (CI 95% 0.06-0.48, P=0.001) for developing ischemic etiology. In conclusion, this study supports the importance of using ancestry informative markers and mitochondrial DNA to study the genetics of complex diseases in admixed populations to improve the management, treatment and prevention of these illnesses. Therefore, the ancestry informative markers and mt-haplogroups could provide new biomarkers to be associated with HF etiologies and be used as a premise for more specific management.
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Affiliation(s)
- M M S G Cardena
- Department of Legal Medicine, Ethics and Occupational Health, Medical School, University of São Paulo, São Paulo, Brazil
| | - A K Ribeiro-Dos-Santos
- Laboratory of Human Genetics and Medicine, Federal University of Pará, Belém, Pará, Brazil
| | - S E B Santos
- Laboratory of Human Genetics and Medicine, Federal University of Pará, Belém, Pará, Brazil
| | - A J Mansur
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School, University of São Paulo, São Paulo, Brazil
| | - S Bernardez-Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School, University of São Paulo, São Paulo, Brazil.,Fluminense Federal University, Rio de Janeiro, Rio de Janeiro, Brazil
| | - P C J L Santos
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School, University of São Paulo, São Paulo, Brazil
| | - A C Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School, University of São Paulo, São Paulo, Brazil
| | - C Fridman
- Department of Legal Medicine, Ethics and Occupational Health, Medical School, University of São Paulo, São Paulo, Brazil
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Gomez F, Wang L, Abel H, Zhang Q, Province MA, Borecki IB. Admixture mapping of coronary artery calcification in African Americans from the NHLBI family heart study. BMC Genet 2015; 16:42. [PMID: 25902833 PMCID: PMC4417236 DOI: 10.1186/s12863-015-0196-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 04/06/2015] [Indexed: 12/29/2022] Open
Abstract
Background Coronary artery calcification (CAC) is an imaging biomarker of coronary atherosclerosis. In European Americans, genome-wide association studies (GWAS) have identified several regions associated with coronary artery disease. However, few large studies have been conducted in African Americans. The largest meta-analysis of CAC in African Americans failed to identify genome-wide significant variants despite being powered to detect effects comparable to effects identified in European Americans. Because CAC is different in prevalence and severity in African Americans and European Americans, admixture mapping is a useful approach to identify loci missed by GWAS. Results We applied admixture mapping to the African American cohort of the Family Heart Study and identified one genome-wide significant region on chromosome 12 and three potential regions on chromosomes 6, 15, and 19 that are associated with CAC. Follow-up studies using previously reported GWAS meta-analysis data suggest that the regions identified on chromosome 6 and 15 contain variants that are possibly associated with CAC. The associated region on chromosome 6 contains the gene for BMP-6, which is expressed in vascular calcific lesions. Conclusions Our results suggest that admixture mapping can be a useful hypothesis-generating tool to identify genomic regions that contribute to complex diseases in genetically admixed populations. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0196-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Felicia Gomez
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St Louis, 4444 Forest Park Blvd, Campus Box 8506, St Louis, MO, 63108, USA.
| | - Lihua Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St Louis, 4444 Forest Park Blvd, Campus Box 8506, St Louis, MO, 63108, USA.
| | - Haley Abel
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St Louis, 4444 Forest Park Blvd, Campus Box 8506, St Louis, MO, 63108, USA.
| | - Qunyuan Zhang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St Louis, 4444 Forest Park Blvd, Campus Box 8506, St Louis, MO, 63108, USA.
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St Louis, 4444 Forest Park Blvd, Campus Box 8506, St Louis, MO, 63108, USA.
| | - Ingrid B Borecki
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St Louis, 4444 Forest Park Blvd, Campus Box 8506, St Louis, MO, 63108, USA.
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Girkin CA, Nievergelt CM, Kuo JZ, Maihofer AX, Huisingh C, Liebmann JM, Ayyagari R, Weinreb RN, Ritch R, Zangwill LM. Biogeographic Ancestry in the African Descent and Glaucoma Evaluation Study (ADAGES): Association With Corneal and Optic Nerve Structure. Invest Ophthalmol Vis Sci 2015; 56:2043-9. [PMID: 25744975 DOI: 10.1167/iovs.14-15719] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
PURPOSE We determined if quantitative measurements of biogeographic ancestry (BGA) correlate with variations in optic disc area, corneal thickness (CCT), and retinal nerve fiber layer (RNFL) thickness. METHODS Data were obtained from 656 participants in the African Descent and Glaucoma Evaluation Study (ADAGES) cohort who consented to BGA testing. Data for CCT, optic disc area, and RNFL thickness were obtained from subjects in the ADAGES study who also had participated in the current substudy. A total of 31 ancestry informative markers (AIMs) with large allele frequencies differences between populations was used to calculate admixture proportion (implemented in STRUCTURE). Correlations with BGA adjusted for diagnosis, age, and sex for CCT and optic disc area using the whole group and RNFL thickness adjusted for age and sex for the normal study participants were determined. RESULTS The mean percentage of African admixture was 79.6% in the self-described African Descent (AD) group and 3.5% in the European Descent (ED) group. Percent African ancestry was significantly correlated with CCT (ρ = -0.27, P < 0.0001) and disc area (ρ = 0.15, P < 0.0001), but only marginally associated with RNFL thickness (ρ = 0.20, P = 0.092) in adjusted models. CONCLUSIONS The BGA correlates with variation in ocular features that significantly differ across racial groups and that have been associated with the development of glaucoma. While BGA can provide an objective measurement of the biologic component of self-described race for ocular research, for most nongenetic epidemiologic studies, self-described race may adequately describe the associations with these ocular characteristics. (ClinicalTrials.gov number, NCT00221923.).
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Affiliation(s)
- Christopher A Girkin
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California, San Diego, San Diego, California, United States
| | - Jane Z Kuo
- Department of Ophthalmology, University of California, San Diego, San Diego, California, United States Pathway Genomics Corporation, San Diego, California, United States
| | - Adam X Maihofer
- Department of Psychiatry, University of California, San Diego, San Diego, California, United States
| | - Carrie Huisingh
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | | | - Radha Ayyagari
- Department of Ophthalmology, University of California, San Diego, San Diego, California, United States
| | - Robert N Weinreb
- Department of Ophthalmology, University of California, San Diego, San Diego, California, United States
| | - Robert Ritch
- Department of Ophthalmology, New York Eye and Ear Infirmary, New York, New York, United States
| | - Linda M Zangwill
- Department of Ophthalmology, University of California, San Diego, San Diego, California, United States
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Meta-analysis of correlated traits via summary statistics from GWASs with an application in hypertension. Am J Hum Genet 2015; 96:21-36. [PMID: 25500260 DOI: 10.1016/j.ajhg.2014.11.011] [Citation(s) in RCA: 232] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/17/2014] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified many genetic variants underlying complex traits. Many detected genetic loci harbor variants that associate with multiple-even distinct-traits. Most current analysis approaches focus on single traits, even though the final results from multiple traits are evaluated together. Such approaches miss the opportunity to systemically integrate the phenome-wide data available for genetic association analysis. In this study, we propose a general approach that can integrate association evidence from summary statistics of multiple traits, either correlated, independent, continuous, or binary traits, which might come from the same or different studies. We allow for trait heterogeneity effects. Population structure and cryptic relatedness can also be controlled. Our simulations suggest that the proposed method has improved statistical power over single-trait analysis in most of the cases we studied. We applied our method to the Continental Origins and Genetic Epidemiology Network (COGENT) African ancestry samples for three blood pressure traits and identified four loci (CHIC2, HOXA-EVX1, IGFBP1/IGFBP3, and CDH17; p < 5.0 × 10(-8)) associated with hypertension-related traits that were missed by a single-trait analysis in the original report. Six additional loci with suggestive association evidence (p < 5.0 × 10(-7)) were also observed, including CACNA1D and WNT3. Our study strongly suggests that analyzing multiple phenotypes can improve statistical power and that such analysis can be executed with the summary statistics from GWASs. Our method also provides a way to study a cross phenotype (CP) association by using summary statistics from GWASs of multiple phenotypes.
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50
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Shetty PB, Tang H, Feng T, Tayo B, Morrison AC, Kardia SLR, Hanis CL, Arnett DK, Hunt SC, Boerwinkle E, Rao DC, Cooper RS, Risch N, Zhu X. Variants for HDL-C, LDL-C, and triglycerides identified from admixture mapping and fine-mapping analysis in African American families. ACTA ACUST UNITED AC 2014; 8:106-13. [PMID: 25552592 DOI: 10.1161/circgenetics.114.000481] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Admixture mapping of lipids was followed-up by family-based association analysis to identify variants for cardiovascular disease in African Americans. METHODS AND RESULTS The present study conducted admixture mapping analysis for total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides. The analysis was performed in 1905 unrelated African American subjects from the National Heart, Lung and Blood Institute's Family Blood Pressure Program (FBPP). Regions showing admixture evidence were followed-up with family-based association analysis in 3556 African American subjects from the FBPP. The admixture mapping and family-based association analyses were adjusted for age, age(2), sex, body mass index, and genome-wide mean ancestry to minimize the confounding caused by population stratification. Regions that were suggestive of local ancestry association evidence were found on chromosomes 7 (low-density lipoprotein cholesterol), 8 (high-density lipoprotein cholesterol), 14 (triglycerides), and 19 (total cholesterol and triglycerides). In the fine-mapping analysis, 52 939 single-nucleotide polymorphisms (SNPs) were tested and 11 SNPs (8 independent SNPs) showed nominal significant association with high-density lipoprotein cholesterol (2 SNPs), low-density lipoprotein cholesterol (4 SNPs), and triglycerides (5 SNPs). The family data were used in the fine-mapping to identify SNPs that showed novel associations with lipids and regions, including genes with known associations for cardiovascular disease. CONCLUSIONS This study identified regions on chromosomes 7, 8, 14, and 19 and 11 SNPs from the fine-mapping analysis that were associated with high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides for further studies of cardiovascular disease in African Americans.
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Affiliation(s)
- Priya B Shetty
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Hua Tang
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Tao Feng
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Bamidele Tayo
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Alanna C Morrison
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Sharon L R Kardia
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Craig L Hanis
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Donna K Arnett
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Steven C Hunt
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Eric Boerwinkle
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | | | - Dabeeru C Rao
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Richard S Cooper
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Neil Risch
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Xiaofeng Zhu
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.).
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