1
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Pfennig A, Lachance J. Challenges of accurately estimating sex-biased admixture from X chromosomal and autosomal ancestry proportions. Am J Hum Genet 2023; 110:359-367. [PMID: 36736293 PMCID: PMC9943719 DOI: 10.1016/j.ajhg.2022.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/20/2022] [Indexed: 02/05/2023] Open
Abstract
Sex-biased admixture can be inferred from ancestry-specific proportions of X chromosome and autosomes. In a paper published in the American Journal of Human Genetics, Micheletti et al.1 used this approach to quantify male and female contributions following the transatlantic slave trade. Using a large dataset from 23andMe, they concluded that African and European contributions to gene pools in the Americas were much more sex biased than previously thought. We show that the reported extreme sex-specific contributions can be attributed to unassigned genetic ancestry as well as the limitations of simple models of sex-biased admixture. Unassigned ancestry proportions in the study by Micheletti et al. ranged from ∼1% to 21%, depending on the type of chromosome and geographic region. A sensitivity analysis illustrates how this unassigned ancestry can create false patterns of sex bias and that mathematical models are highly sensitive to slight sampling errors when inferring mean ancestry proportions, making confidence intervals necessary. Thus, unassigned ancestry and the sensitivity of the models effectively prohibit the interpretation of estimated sex biases for many geographic regions in Micheletti et al. Furthermore, Micheletti et al. assumed models of a single admixture event. Using simulations, we find that violations of demographic assumptions, such as subsequent gene flow and/or sex-specific assortative mating, may have confounded the analyses of Micheletti et al., but unassigned ancestry was likely the more important confounding factor. Our findings underscore the importance of using complete ancestry information, sufficiently large sample sizes, and appropriate models when inferring sex-biased patterns of demography. This Matters Arising paper is in response to Micheletti et al.,1 published in American Journal of Human Genetics. See also the response by Micheletti et al.,2 published in this issue.
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Affiliation(s)
- Aaron Pfennig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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2
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Caldwell J, Jackson FLC. Evolutionary perspectives on African North American genetic diversity: Origins and prospects for future investigations. Evol Anthropol 2021; 30:242-252. [PMID: 34388300 DOI: 10.1002/evan.21910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/03/2020] [Accepted: 11/13/2020] [Indexed: 11/07/2022]
Abstract
African-descended peoples of the Americas represent an amalgamation of West, Central, and Southeast African regional and ethnic groups with modest gene flow from specific non-African populations. Despite 16+ generations of residence in the Americas, there is a deficit of evolutionary knowledge about these populations. Focusing on Legacy African American, the African North American descendants of survivors of the transatlantic trade in enslaved Africans, we report on emic evolutionary perspectives of their self-identity gleaned from our interviews of 600 individuals collected over 2 years. Gullah-Geechee peoples of Carolina Coastal regions are a model case study due to their historical antiquity, substantial African retentions, relative geospatial isolation, and proposed progenitor status to other Legacy African American microethnic groups. We identify salient research questions for future studies that will begin to bridge the evolutionary gaps in our knowledge of these diverse peoples and the historical evidence for specific evolutionary processes.
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Affiliation(s)
- Jennifer Caldwell
- Genetics Department, Howard University, Washington, District of Columbia, USA
| | - Fatimah L C Jackson
- Biology Department, Howard University, Washington, District of Columbia, USA
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3
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Zimmerman KD, Schurr TG, Chen W, Nayak U, Mychaleckyj JC, Quet Q, Moultrie LH, Divers J, Keene KL, Kamen DL, Gilkeson GS, Hunt KJ, Spruill IJ, Fernandes JK, Aldrich MC, Reich D, Garvey WT, Langefeld CD, Sale MM, Ramos PS. Genetic landscape of Gullah African Americans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175:905-919. [PMID: 34008864 PMCID: PMC8286328 DOI: 10.1002/ajpa.24333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 03/30/2021] [Accepted: 04/17/2021] [Indexed: 01/20/2023]
Abstract
OBJECTIVES Gullah African Americans are descendants of formerly enslaved Africans living in the Sea Islands along the coast of the southeastern U.S., from North Carolina to Florida. Their relatively high numbers and geographic isolation were conducive to the development and preservation of a unique culture that retains deep African features. Although historical evidence supports a West-Central African ancestry for the Gullah, linguistic and cultural evidence of a connection to Sierra Leone has led to the suggestion of this country/region as their ancestral home. This study sought to elucidate the genetic structure and ancestry of the Gullah. MATERIALS AND METHODS We leveraged whole-genome genotype data from Gullah, African Americans from Jackson, Mississippi, African populations from Sierra Leone, and population reference panels from Africa and Europe to infer population structure, ancestry proportions, and global estimates of admixture. RESULTS Relative to non-Gullah African Americans from the Southeast US, the Gullah exhibited higher mean African ancestry, lower European admixture, a similarly small Native American contribution, and increased male-biased European admixture. A slightly tighter bottleneck in the Gullah 13 generations ago suggests a largely shared demographic history with non-Gullah African Americans. Despite a slightly higher relatedness to populations from Sierra Leone, our data demonstrate that the Gullah are genetically related to many West African populations. DISCUSSION This study confirms that subtle differences in African American population structure exist at finer regional levels. Such observations can help to inform medical genetics research in African Americans, and guide the interpretation of genetic data used by African Americans seeking to explore ancestral identities.
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Affiliation(s)
- Kip D. Zimmerman
- Center for Precision MedicineWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Theodore G. Schurr
- Department of AnthropologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Wei‐Min Chen
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Public Health SciencesUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Uma Nayak
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Josyf C. Mychaleckyj
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Public Health SciencesUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Queen Quet
- Gullah/Geechee NationSt. Helena IslandSouth CarolinaUSA
| | - Lee H. Moultrie
- Lee H. Moultrie & AssociatesNorth CharlestonSouth CarolinaUSA
| | - Jasmin Divers
- Department of Health Services ResearchNew York University Winthrop HospitalMineolaNew YorkUSA
| | - Keith L. Keene
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
- Center for Health DisparitiesEast Carolina University Brody School of MedicineGreenvilleNorth CarolinaUSA
| | - Diane L. Kamen
- Department of MedicineMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Gary S. Gilkeson
- Department of MedicineMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Kelly J. Hunt
- Department of Public Health SciencesMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Ida J. Spruill
- College of NursingMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Jyotika K. Fernandes
- Department of MedicineMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Melinda C. Aldrich
- Department of Thoracic SurgeryVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Vanderbilt Genetics InstituteVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - David Reich
- Department of GeneticsHarvard Medical SchoolBostonMassachusettsUSA
- Howard Hughes Medical InstituteHarvard Medical SchoolBostonMassachusettsUSA
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Department of Human Evolutionary BiologyHarvard UniversityCambridgeMassachusettsUSA
| | - W. Timothy Garvey
- Department of Nutrition ScienceUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Carl D. Langefeld
- Center for Precision MedicineWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Michèle M. Sale
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Public Health SciencesUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Paula S. Ramos
- Department of MedicineMedical University of South CarolinaCharlestonSouth CarolinaUSA
- Department of Public Health SciencesMedical University of South CarolinaCharlestonSouth CarolinaUSA
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4
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Gross JM, Edgar HJH. Geographic and temporal diversity in dental morphology reflects a history of admixture, isolation, and drift in African Americans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175:497-505. [PMID: 33704773 DOI: 10.1002/ajpa.24258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 11/10/2022]
Abstract
OBJECTIVES While genetic studies have documented variation in admixture proportions in contemporary African Americans across the US, relatively little is known about the socio-historical roots of this variation. Our goal in this study is to use dental morphology to explore the socio-historical correlates of admixture, localized gene flow, and drift in African Americans. METHODS Our data are ordinally-graded dental morphological traits scored in 196 Africans, 335 Europeans and European Americans, 291 pre-Spanish-contact Native Americans, and 722 African Americans. The African American data derived from contemporary and historic samples. We eliminated from analysis individuals and traits with greater than 20% missing data. We summarized the major axes of trait variation using principal component analysis (PCA), estimated biological distance, constructed multidimensional scaling (MDS) plots of the distances, and measured the correlation between geographic and biological distance. RESULTS In the PCA, African American groups clustered between Africans and Europeans on PC 1, reflecting admixture between the groups. PC 2 separated African American samples, possibly reflecting movement, isolation, and drift. MDS analyses confirmed the existence of sizable biological distances between African American samples, especially between contemporary and past African American samples. We found no relationship between biological and geographic distances. DISCUSSION We demonstrate that admixture and drift can be inferred from multi-variable analyses of patterns of dental morphology in admixed populations. Localized gene flow has not affected patterns of trait variation in African Americans, but long-range movement, isolation, and drift have. We connect patterns of dental trait variation to efforts to flee oppression during the Great Migration, and the repeal of anti-miscegenation laws.
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Affiliation(s)
- Jessica M Gross
- Department of Anthropology MSC01-1040, Anthropology 1, University of New Mexico, Albuquerque, New Mexico, USA
| | - Heather J H Edgar
- Department of Anthropology MSC01-1040, Anthropology 1, University of New Mexico, Albuquerque, New Mexico, USA
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5
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Teteh DK, Dawkins-Moultin L, Hooker S, Hernandez W, Bonilla C, Galloway D, LaGroon V, Santos ER, Shriver M, Royal CDM, Kittles RA. Genetic ancestry, skin color and social attainment: The four cities study. PLoS One 2020; 15:e0237041. [PMID: 32813691 PMCID: PMC7446776 DOI: 10.1371/journal.pone.0237041] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/17/2020] [Indexed: 12/26/2022] Open
Abstract
Introduction The Black population in the US is heterogeneous but is often treated as monolithic in research, with skin pigmentation being the primary indicator of racial classification. Objective: This paper examines the differences among Blacks by comparing genetic ancestry, skin color and social attainment of 259 residents across four US cities—Norman, Oklahoma; Cincinnati, Ohio; Harlem, New York; and Washington, District of Columbia. Methods Participants were recruited between 2004 and 2006 at community-based forums. Cross-sectional data were analyzed using chi-square tests, correlation analyses and logistic regression. Results There were variations in ancestry, melanin index and social attainment across some cities. Overall, men with darker skin color, and women with lighter skin color were significantly more likely to be married. Darker skin individuals with significantly more West African ancestry reported attainment of graduate degrees, and professional occupations than lighter skin individuals. Conclusions Our findings suggest differences in skin pigmentation by geography and support regional variations in ancestry of US Blacks. Biomedical research should consider genetic ancestry and local historical/social context rather than relying solely on skin pigmentation as a proxy for race.
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Affiliation(s)
- Dede K. Teteh
- Division of Health Equities, Department of Population Sciences, City of Hope Medical Center, Duarte, California, United States of America
| | - Lenna Dawkins-Moultin
- Department of Health Disparities Research, M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Stanley Hooker
- Division of Health Equities, Department of Population Sciences, City of Hope Medical Center, Duarte, California, United States of America
| | - Wenndy Hernandez
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, Illinois, United States of America
| | - Carolina Bonilla
- Departamento de Medicina Preventiva, Faculdade de Medicina, Universidade de São Paulo, Butanta, Brazil
| | - Dorothy Galloway
- Division of Health Equities, Department of Population Sciences, City of Hope Medical Center, Duarte, California, United States of America
| | - Victor LaGroon
- Division of Health Equities, Department of Population Sciences, City of Hope Medical Center, Duarte, California, United States of America
| | | | - Mark Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Charmaine D. M. Royal
- Department of African & African American Studies, Duke University, Durham, North Carolina, United States of America
| | - Rick A. Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope Medical Center, Duarte, California, United States of America
- * E-mail:
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Hernandez W, Danahey K, Pei X, Yeo KTJ, Leung E, Volchenboum SL, Ratain MJ, Meltzer DO, Stranger BE, Perera MA, O'Donnell PH. Pharmacogenomic genotypes define genetic ancestry in patients and enable population-specific genomic implementation. THE PHARMACOGENOMICS JOURNAL 2020; 20:126-135. [PMID: 31506565 PMCID: PMC7184888 DOI: 10.1038/s41397-019-0095-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/02/2019] [Accepted: 07/18/2019] [Indexed: 12/12/2022]
Abstract
The importance of genetic ancestry characterization is increasing in genomic implementation efforts, and clinical pharmacogenomic guidelines are being published that include population-specific recommendations. Our aim was to test the ability of focused clinical pharmacogenomic SNP panels to estimate individual genetic ancestry (IGA) and implement population-specific pharmacogenomic clinical decision-support (CDS) tools. Principle components and STRUCTURE were utilized to assess differences in genetic composition and estimate IGA among 1572 individuals from 1000 Genomes, two independent cohorts of Caucasians and African Americans (AAs), plus a real-world validation population of patients undergoing pharmacogenomic genotyping. We found that clinical pharmacogenomic SNP panels accurately estimate IGA compared to genome-wide genotyping and identify AAs with ≥70 African ancestry (sensitivity >82%, specificity >80%, PPV >95%, NPV >47%). We also validated a new AA-specific warfarin dosing algorithm for patients with ≥70% African ancestry and implemented it at our institution as a novel CDS tool. Consideration of IGA to develop an institutional CDS tool was accomplished to enable population-specific pharmacogenomic guidance at the point-of-care. These capabilities were immediately applied for guidance of warfarin dosing in AAs versus Caucasians, but also provide a real-world model that can be extended to other populations and drugs as actionable genomic evidence accumulates.
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Affiliation(s)
- Wenndy Hernandez
- University of Chicago, Department of Medicine, Section of Genetic Medicine, Section of Cardiology, Chicago, IL, USA
| | - Keith Danahey
- University of Chicago, Center for Personalized Therapeutics, Chicago, IL, USA
- University of Chicago, Center for Research Informatics, Chicago, IL, USA
| | - Xun Pei
- University of Chicago, Center for Personalized Therapeutics, Chicago, IL, USA
- University of Chicago, Department of Pathology, UChicago Advanced Technology Clinical Pharmacogenomics Laboratory, Chicago, IL, USA
| | - Kiang-Teck J Yeo
- University of Chicago, Department of Pathology, UChicago Advanced Technology Clinical Pharmacogenomics Laboratory, Chicago, IL, USA
| | - Edward Leung
- University of Chicago, Department of Pathology, UChicago Advanced Technology Clinical Pharmacogenomics Laboratory, Chicago, IL, USA
- University of Southern California, Keck School of Medicine, Department of Pathology and Laboratory Medicine, Los Angeles, CA, USA
| | | | - Mark J Ratain
- University of Chicago, Center for Personalized Therapeutics, Chicago, IL, USA
- University of Chicago, Department of Medicine, Chicago, IL, USA
- University of Chicago, Committee on Clinical Pharmacology and Pharmacogenomics, Chicago, IL, USA
| | - David O Meltzer
- University of Chicago, Department of Medicine, Chicago, IL, USA
| | - Barbara E Stranger
- University of Chicago, Department of Medicine, Section of Genetic Medicine, Section of Cardiology, Chicago, IL, USA
- University of Chicago, Institute of Genomics and Systems Biology, and Center for Data Intensive Science, Chicago, IL, USA
| | - Minoli A Perera
- Northwestern University, Department of Pharmacology, Chicago, IL, USA
| | - Peter H O'Donnell
- University of Chicago, Center for Personalized Therapeutics, Chicago, IL, USA.
- University of Chicago, Department of Medicine, Chicago, IL, USA.
- University of Chicago, Committee on Clinical Pharmacology and Pharmacogenomics, Chicago, IL, USA.
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7
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Souza AMD, Resende SS, Sousa TND, Brito CFAD. A systematic scoping review of the genetic ancestry of the Brazilian population. Genet Mol Biol 2019; 42:495-508. [PMID: 31188926 PMCID: PMC6905439 DOI: 10.1590/1678-4685-gmb-2018-0076] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 01/16/2019] [Indexed: 12/27/2022] Open
Abstract
The genetic background of the Brazilian population is mainly characterized by
three parental populations: European, African, and Native American. The aim of
this study was to overview the genetic ancestry estimates for different
Brazilian geographic regions and analyze factors involved in these estimates. In
this systematic scoping review were included 51 studies, comprehending 81
populations of 19 states from five regions of Brazil. To reduce the potential of
bias from studies with different sampling methods, we calculated the mean
genetic ancestry weighted by the number of individuals. The weighted mean
proportions of European, African, and Native American ancestries were 68.1%,
19.6%, and 11.6%, respectively. At the regional level, the highest European
contribution occurred in the South, while the highest African and Native
American contributions occurred in the Northeastern and Northern regions,
respectively. Among states in the Northeast region, Bahia and Ceará showed
significant differences, suggesting distinct demographic histories. This review
contributes for a broader understanding of the Brazilian ancestry and indicates
that the ancestry estimates are influenced by the type of molecular marker and
the sampling method.
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Affiliation(s)
- Aracele Maria de Souza
- Research Group in Molecular Biology and Immunology of Malaria, Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil
| | - Sarah Stela Resende
- Research Group in Molecular Biology and Immunology of Malaria, Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil
| | - Taís Nóbrega de Sousa
- Research Group in Molecular Biology and Immunology of Malaria, Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil
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8
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Zhang F, Finkelstein J. Inconsistency in race and ethnic classification in pharmacogenetics studies and its potential clinical implications. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2019; 12:107-123. [PMID: 31308725 PMCID: PMC6612983 DOI: 10.2147/pgpm.s207449] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/30/2019] [Indexed: 12/11/2022]
Abstract
Introduction Racial and ethnic categories are frequently used in pharmacogenetics literature to stratify patients; however, these categories can be inconsistent across different studies. To address the ongoing debate on the applicability of traditional concepts of race and ethnicity in the context of precision medicine, we aimed to review the application of current racial and ethnic categories in pharmacogenetics and its potential impact on clinical care. Methods One hundred and three total pharmacogenetics papers involving the CYP2C9, CYP2C19, and CYP2D6 genes were analyzed for their country of origin, racial, and ethnic categories used, and allele frequency data. Correspondence between the major continental racial categories promulgated by National Institutes of Health (NIH) and those reported by the pharmacogenetics papers was evaluated. Results The racial and ethnic categories used in the papers we analyzed were highly heterogeneous. In total, we found 66 different racial and ethnic categories used which fall under the NIH race category “White”, 47 different racial and ethnic categories for “Asian”, and 62 different categories for “Black”. The number of categories used varied widely based on country of origin: Japan used the highest number of different categories for “White” with 17, Malaysia used the highest number for “Asian” with 24, and the US used the highest number for “Black” with 28. Significant variation in allele frequency between different ethnic subgroups was identified within 3 major continental racial categories. Conclusion Our analysis showed that racial and ethnic classification is highly inconsistent across different papers as well as between different countries. Evidence-based consensus is necessary for optimal use of self-identified race as well as geographical ancestry in pharmacogenetics. Common taxonomy of geographical ancestry which reflects specifics of particular countries and is accepted by the entire scientific community can facilitate reproducible pharmacogenetic research and clinical implementation of its results.
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Affiliation(s)
- Frederick Zhang
- Center for Bioinformatics and Data Analytics, Columbia University Irving Medical Center, New York, NY, USA
| | - Joseph Finkelstein
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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9
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Stojanowski CM, Paul KS, Seidel AC, Duncan WN, Guatelli‐Steinberg D. Quantitative genetic analyses of postcanine morphological crown variation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 168:606-631. [DOI: 10.1002/ajpa.23778] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/20/2018] [Accepted: 12/26/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Christopher M. Stojanowski
- Center for Bioarchaeological Research School of Human Evolution and Social Change, Arizona State University Tempe Arizona
| | - Kathleen S. Paul
- Center for Bioarchaeological Research School of Human Evolution and Social Change, Arizona State University Tempe Arizona
| | - Andrew C. Seidel
- Center for Bioarchaeological Research School of Human Evolution and Social Change, Arizona State University Tempe Arizona
| | - William N. Duncan
- Department of Sociology and Anthropology East Tennessee State University Johnson City Tennessee
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10
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Gross JM, Edgar HJH. Informativeness of dental morphology in ancestry estimation in African Americans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 168:521-529. [DOI: 10.1002/ajpa.23768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/05/2018] [Accepted: 12/09/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Jessica M. Gross
- Department of Anthropology MSC01-1040, Anthropology 1; University of New Mexico; Albuquerque New Mexico 87131
| | - Heather J. H. Edgar
- Department of Anthropology MSC01-1040, Anthropology 1; University of New Mexico; Albuquerque New Mexico 87131
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11
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Bea VJ, Cunningham JE, Alberg AJ, Burshell D, Bauza CE, Knight KD, Hazelton TR, Varner H, Kramer R, Bolick S, Hurley D, Mosley C, Ford ME. Alcohol and Tobacco Use in an Ethnically Diverse Sample of Breast Cancer Patients, Including Sea Island African Americans: Implications for Survivorship. Front Oncol 2018; 8:392. [PMID: 30319964 PMCID: PMC6170649 DOI: 10.3389/fonc.2018.00392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/31/2018] [Indexed: 11/13/2022] Open
Abstract
Background/Objective: Data suggest that modifiable risk factors such as alcohol and tobacco use may increase the risk of breast cancer (BC) recurrence and reduce survival. Female BC mortality in South Carolina is 40% higher among African Americans (AAs) than European Americans (EAs). Given this substantial racial disparity, using a cross-sectional survey design we examined alcohol and tobacco use in an ethnically diverse statewide study of women with recently diagnosed invasive breast cancer. This included a unique South Carolina AA subpopulation, the Sea Islanders (SI), culturally isolated and with the lowest European American genetic admixture of any AA group. Methods: Participants (42 EAs, 66 non-SI AAs, 29 SIs), diagnosed between August 2011 and December 2012, were identified through the South Carolina Central Cancer Registry and interviewed by telephone within 21 months of diagnosis. Self-reported educational status, alcohol consumption and tobacco use were obtained using elements of the Behavior and Risk Factor Surveillance System questionnaire. Results:Alcohol: EAs were approximately twice as likely to consume alcohol (40%) and to be moderate drinkers (29%) than either AA group (consumers: 24% of non-SI AAs, 21% of SIs; moderate drinkers 15 and 10% respectively). Users tended to be younger, significantly among EAs and non-SI AAs, but not SIs, and to have attained more education. Heavy drinking was rare (≤1%) and binge drinking uncommon (≤10%) with no differences by race/ethnicity. Among both AA subgroups but not EAs, alcohol users were six to nine times more likely to have late stage disease (Regional or Distant), statistically significant but with wide confidence intervals. Tobacco: Current cigarette smoking (daily or occasional) was reported by 14% of EAs, 14% of non-SI AAs and 7% of SIs. Smoking was inversely associated with educational attainment. Use of both alcohol and cigarettes was reported by 3–6% of cases. Conclusions: Prevalences of alcohol and cigarette use were similar to those in the general population, with alcohol consumption more common among EAs. Up to half of cases used alcohol and/or tobacco. Given the risks from alcohol for disease recurrence, and implications of smoking for various health outcomes, these utilization rates are of concern.
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Affiliation(s)
- Vivian J Bea
- Department of Breast Surgical Oncology, MD Anderson Cancer Center at Cooper, Camden, NJ, United States
| | - Joan E Cunningham
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States.,Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, United States.,National Coalition of Independent Scholars, San Antonio, TX, United States
| | - Anthony J Alberg
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC, United States
| | - Dana Burshell
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States.,Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Colleen E Bauza
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Kendrea D Knight
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Tonya R Hazelton
- College of Nursing, Medical University of South Carolina, Charleston, SC, United States
| | - Heidi Varner
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Rita Kramer
- Department of Hematology/Oncology, Medical University of South Carolina, Charleston, SC, United States
| | - Susan Bolick
- South Carolina Department of Health and Environmental Control, Columbia, SC, United States
| | - Deborah Hurley
- South Carolina Department of Health and Environmental Control, Columbia, SC, United States
| | - Catishia Mosley
- South Carolina Department of Health and Environmental Control, Columbia, SC, United States
| | - Marvella E Ford
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States.,Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, United States
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12
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Wolf BJ, Ramos PS, Hyer JM, Ramakrishnan V, Gilkeson GS, Hardiman G, Nietert PJ, Kamen DL. An Analytic Approach Using Candidate Gene Selection and Logic Forest to Identify Gene by Environment Interactions (G × E) for Systemic Lupus Erythematosus in African Americans. Genes (Basel) 2018; 9:genes9100496. [PMID: 30326636 PMCID: PMC6211136 DOI: 10.3390/genes9100496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/27/2018] [Accepted: 10/03/2018] [Indexed: 12/17/2022] Open
Abstract
Development and progression of many human diseases, such as systemic lupus erythematosus (SLE), are hypothesized to result from interactions between genetic and environmental factors. Current approaches to identify and evaluate interactions are limited, most often focusing on main effects and two-way interactions. While higher order interactions associated with disease are documented, they are difficult to detect since expanding the search space to all possible interactions of p predictors means evaluating 2p − 1 terms. For example, data with 150 candidate predictors requires considering over 1045 main effects and interactions. In this study, we present an analytical approach involving selection of candidate single nucleotide polymorphisms (SNPs) and environmental and/or clinical factors and use of Logic Forest to identify predictors of disease, including higher order interactions, followed by confirmation of the association between those predictors and interactions identified with disease outcome using logistic regression. We applied this approach to a study investigating whether smoking and/or secondhand smoke exposure interacts with candidate SNPs resulting in elevated risk of SLE. The approach identified both genetic and environmental risk factors, with evidence suggesting potential interactions between exposure to secondhand smoke as a child and genetic variation in the ITGAM gene associated with increased risk of SLE.
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Affiliation(s)
- Bethany J Wolf
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Paula S Ramos
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
- Division of Rheumatology and Immunology, Department of Medicine, Medical Univeristy of South Carolina, Charleston, SC 29425, USA.
| | - J Madison Hyer
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Viswanathan Ramakrishnan
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Gary S Gilkeson
- Division of Rheumatology and Immunology, Department of Medicine, Medical Univeristy of South Carolina, Charleston, SC 29425, USA.
| | - Gary Hardiman
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
- Center for Genomic Medicine, Department of Medicine, Medical Univeristy of South Carolina, Charleston, SC 29425, USA.
- Division of Nephrology, Department of Medicine, Medical Univeristy of South Carolina, Charleston, SC 29425, USA.
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Stranmillis Road, Belfast BT9 5AG, UK.
| | - Paul J Nietert
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Diane L Kamen
- Division of Rheumatology and Immunology, Department of Medicine, Medical Univeristy of South Carolina, Charleston, SC 29425, USA.
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Rebbeck TR. Prostate Cancer Disparities by Race and Ethnicity: From Nucleotide to Neighborhood. Cold Spring Harb Perspect Med 2018; 8:a030387. [PMID: 29229666 PMCID: PMC6120694 DOI: 10.1101/cshperspect.a030387] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Prostate cancer (CaP) incidence, morbidity, and mortality rates vary substantially by race and ethnicity, with African American men experiencing among the highest CaP rates in the world. The causes of these disparities are multifactorial and complex, and likely involve differences in access to screening and treatment, exposure to CaP risk factors, variation in genomic susceptibility, and other biological factors. To date, the proportion of CaP that can be explained by environmental exposures is small and differences in the role factors play by race or ethnicity is poorly understood. In the absence of additional data, it is likely that environmental factors do not contribute greatly to CaP disparities. In contrast, CaP has one of the highest heritabilities of all major cancers and many CaP susceptibility genes have been identified. Some CaP loci, including the risk loci found at chromosome 8q24, have consistent effects in all racial/ethnic groups studied to date. However, replication of many susceptibility loci across race or ethnicity remains limited. It is likely that inequities in health care access strongly influences CaP disparities. CaP is a disease with a complex multifactorial etiology, and therefore any approach attempting to address racial/ethnic disparities in CaP must consider the many sources that influence risk, outcomes, and disparities.
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Affiliation(s)
- Timothy R Rebbeck
- Dana Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215
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Stojanowski CM, Paul KS, Seidel AC, Duncan WN, Guatelli‐Steinberg D. Heritability and genetic integration of anterior tooth crown variants in the South Carolina Gullah. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:124-143. [DOI: 10.1002/ajpa.23612] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/24/2018] [Accepted: 05/04/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Christopher M. Stojanowski
- Center for Bioarchaeological ResearchSchool of Human Evolution and Social Change, Arizona State UniversityTempe Arizona 85287
| | - Kathleen S. Paul
- Center for Bioarchaeological ResearchSchool of Human Evolution and Social Change, Arizona State UniversityTempe Arizona 85287
| | - Andrew C. Seidel
- Center for Bioarchaeological ResearchSchool of Human Evolution and Social Change, Arizona State UniversityTempe Arizona 85287
| | - William N. Duncan
- Department of Sociology and AnthropologyEast Tennessee State UniversityJohnson City Tennessee 37614
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15
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Noel SE, Mangano KM, Griffith JL, Wright NC, Dawson-Hughes B, Tucker KL. Prevalence of Osteoporosis and Low Bone Mass Among Puerto Rican Older Adults. J Bone Miner Res 2018; 33:396-403. [PMID: 29044768 PMCID: PMC5840013 DOI: 10.1002/jbmr.3315] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/10/2017] [Accepted: 10/16/2017] [Indexed: 11/08/2022]
Abstract
Historically, osteoporosis has not been considered a public health priority for the Hispanic population. However, recent data indicate that Mexican Americans are at increased risk for this chronic condition. Although it is well established that there is heterogeneity in social, lifestyle, and health-related factors among Hispanic subgroups, there are currently few studies on bone health among Hispanic subgroups other than Mexican Americans. The current study aimed to determine the prevalence of osteoporosis and low bone mass (LBM) among 953 Puerto Rican adults, aged 47 to 79 years and living on the US mainland, using data from one of the largest cohorts on bone health in this population: The Boston Puerto Rican Osteoporosis Study (BPROS). Participants completed an interview to assess demographic and lifestyle characteristics and bone mineral density measures. To facilitate comparisons with national data, we calculated age-adjusted estimates for osteoporosis and LBM for Mexican American, non-Hispanic white, and non-Hispanic black adults, aged ≥50 years, from the National Health and Nutrition Examination Survey (NHANES). The overall prevalence of osteoporosis and LBM were 10.5% and 43.3% for participants in the BPROS, respectively. For men, the highest prevalence of osteoporosis was among those aged 50 to 59 years (11%) and lowest for men ≥70 years (3.7%). The age-adjusted prevalence of osteoporosis for Puerto Rican men was 8.6%, compared with 2.3% for non-Hispanic white, and 3.9% for Mexican American men. There were no statistically significant differences between age-adjusted estimates for Puerto Rican women (10.7%), non-Hispanic white women (10.1%), or Mexican American women (16%). There is a need to understand specific factors contributing to osteoporosis in Puerto Rican adults, particularly younger men. This will provide important information to guide the development of culturally and linguistically tailored interventions to improve bone health in this understudied and high-risk population. © 2017 American Society for Bone and Mineral Research.
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Affiliation(s)
- Sabrina E Noel
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - Kelsey M Mangano
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - John L Griffith
- Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
| | - Nicole C Wright
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Bess Dawson-Hughes
- Bone Metabolism Laboratory, Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - Katherine L Tucker
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA, USA
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Gross JM. Tests of fit of historically-informed models of African American Admixture. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 165:211-222. [DOI: 10.1002/ajpa.23343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/20/2017] [Accepted: 10/07/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Jessica M Gross
- Department of Anthropology MSC01-1040, Anthropology 1; University of New Mexico; Albuquerque New Mexico
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17
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Koehl AJ, Long JC. The contributions of admixture and genetic drift to diversity among post-contact populations in the Americas. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 165:256-268. [DOI: 10.1002/ajpa.23347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Anthony J. Koehl
- Department of Anthropology; University of New Mexico, MSC01-1040, Anthropology 1; Albuquerque New Mexico 87131
| | - Jeffrey C. Long
- Department of Anthropology; University of New Mexico, MSC01-1040, Anthropology 1; Albuquerque New Mexico 87131
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Adhikari K, Chacón-Duque JC, Mendoza-Revilla J, Fuentes-Guajardo M, Ruiz-Linares A. The Genetic Diversity of the Americas. Annu Rev Genomics Hum Genet 2017; 18:277-296. [DOI: 10.1146/annurev-genom-083115-022331] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kaustubh Adhikari
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Juan Camilo Chacón-Duque
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Javier Mendoza-Revilla
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000009, Chile
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
- Laboratory of Biocultural Anthropology, Law, Ethics, and Health (Centre National de la Recherche Scientifique and Etablissement Français du Sang, UMR-7268), Aix-Marseille University, 13824 Marseille, France
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20
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Heritability and genetic integration of tooth size in the South Carolina Gullah. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:505-521. [DOI: 10.1002/ajpa.23290] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/14/2017] [Accepted: 07/21/2017] [Indexed: 12/15/2022]
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21
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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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Algee-Hewitt BFB. Geographic substructure in craniometric estimates of admixture for contemporary American populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017. [DOI: 10.1002/ajpa.23267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium. Genetics 2016; 205:375-383. [PMID: 27879348 DOI: 10.1534/genetics.116.192138] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 11/01/2016] [Indexed: 01/09/2023] Open
Abstract
Statistical models in medical and population genetics typically assume that individuals assort randomly in a population. While this simplifies model complexity, it contradicts an increasing body of evidence of nonrandom mating in human populations. Specifically, it has been shown that assortative mating is significantly affected by genomic ancestry. In this work, we examine the effects of ancestry-assortative mating on the linkage disequilibrium between local ancestry tracks of individuals in an admixed population. To accomplish this, we develop an extension to the Wright-Fisher model that allows for ancestry-based assortative mating. We show that ancestry-assortment perturbs the distribution of local ancestry linkage disequilibrium (LAD) and the variance of ancestry in a population as a function of the number of generations since admixture. This assortment effect can induce errors in demographic inference of admixed populations when methods assume random mating. We derive closed form formulae for LAD under an assortative-mating model with and without migration. We observe that LAD depends on the correlation of global ancestry of couples in each generation, the migration rate of each of the ancestral populations, the initial proportions of ancestral populations, and the number of generations since admixture. We also present the first direct evidence of ancestry-assortment in African Americans and examine LAD in simulated and real admixed population data of African Americans. We find that demographic inference under the assumption of random mating significantly underestimates the number of generations since admixture, and that accounting for assortative mating using the patterns of LAD results in estimates that more closely agrees with the historical narrative.
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Shringarpure SS, Bustamante CD, Lange K, Alexander DH. Efficient analysis of large datasets and sex bias with ADMIXTURE. BMC Bioinformatics 2016; 17:218. [PMID: 27216439 PMCID: PMC4877806 DOI: 10.1186/s12859-016-1082-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A number of large genomic datasets are being generated for studies of human ancestry and diseases. The ADMIXTURE program is commonly used to infer individual ancestry from genomic data. RESULTS We describe two improvements to the ADMIXTURE software. The first enables ADMIXTURE to infer ancestry for a new set of individuals using cluster allele frequencies from a reference set of individuals. Using data from the 1000 Genomes Project, we show that this allows ADMIXTURE to infer ancestry for 10,920 individuals in a few hours (a 5 × speedup). This mode also allows ADMIXTURE to correctly estimate individual ancestry and allele frequencies from a set of related individuals. The second modification allows ADMIXTURE to correctly handle X-chromosome (and other haploid) data from both males and females. We demonstrate increased power to detect sex-biased admixture in African-American individuals from the 1000 Genomes project using this extension. CONCLUSIONS These modifications make ADMIXTURE more efficient and versatile, allowing users to extract more information from large genomic datasets.
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Affiliation(s)
| | | | - Kenneth Lange
- Department of Biomathematics, UCLA, Los Angeles, California, USA
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25
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Williams RC, Elston RC, Kumar P, Knowler WC, Abboud HE, Adler S, Bowden DW, Divers J, Freedman BI, Igo RP, Ipp E, Iyengar SK, Kimmel PL, Klag MJ, Kohn O, Langefeld CD, Leehey DJ, Nelson RG, Nicholas SB, Pahl MV, Parekh RS, Rotter JI, Schelling JR, Sedor JR, Shah VO, Smith MW, Taylor KD, Thameem F, Thornley-Brown D, Winkler CA, Guo X, Zager P, Hanson RL. Selecting SNPs informative for African, American Indian and European Ancestry: application to the Family Investigation of Nephropathy and Diabetes (FIND). BMC Genomics 2016; 17:325. [PMID: 27142425 PMCID: PMC4855449 DOI: 10.1186/s12864-016-2654-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/22/2016] [Indexed: 01/06/2023] Open
Abstract
Background The presence of population structure in a sample may confound the search for important genetic loci associated with disease. Our four samples in the Family Investigation of Nephropathy and Diabetes (FIND), European Americans, Mexican Americans, African Americans, and American Indians are part of a genome- wide association study in which population structure might be particularly important. We therefore decided to study in detail one component of this, individual genetic ancestry (IGA). From SNPs present on the Affymetrix 6.0 Human SNP array, we identified 3 sets of ancestry informative markers (AIMs), each maximized for the information in one the three contrasts among ancestral populations: Europeans (HAPMAP, CEU), Africans (HAPMAP, YRI and LWK), and Native Americans (full heritage Pima Indians). We estimate IGA and present an algorithm for their standard errors, compare IGA to principal components, emphasize the importance of balancing information in the ancestry informative markers (AIMs), and test the association of IGA with diabetic nephropathy in the combined sample. Results A fixed parental allele maximum likelihood algorithm was applied to the FIND to estimate IGA in four samples: 869 American Indians; 1385 African Americans; 1451 Mexican Americans; and 826 European Americans. When the information in the AIMs is unbalanced, the estimates are incorrect with large error. Individual genetic admixture is highly correlated with principle components for capturing population structure. It takes ~700 SNPs to reduce the average standard error of individual admixture below 0.01. When the samples are combined, the resulting population structure creates associations between IGA and diabetic nephropathy. Conclusions The identified set of AIMs, which include American Indian parental allele frequencies, may be particularly useful for estimating genetic admixture in populations from the Americas. Failure to balance information in maximum likelihood, poly-ancestry models creates biased estimates of individual admixture with large error. This also occurs when estimating IGA using the Bayesian clustering method as implemented in the program STRUCTURE. Odds ratios for the associations of IGA with disease are consistent with what is known about the incidence and prevalence of diabetic nephropathy in these populations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2654-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert C Williams
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, 85014, USA.
| | - Robert C Elston
- Genetic Analysis and Data Coordinating Center, Case Western Reserve University, Cleveland, OH, 44104, USA
| | - Pankaj Kumar
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, 85014, USA
| | - William C Knowler
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, 85014, USA
| | - Hanna E Abboud
- Division of Nephrology, The University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Sharon Adler
- Department of Nephrology, Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Donald W Bowden
- Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Jasmin Divers
- Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | | | - Robert P Igo
- Genetic Analysis and Data Coordinating Center, Case Western Reserve University, Cleveland, OH, 44104, USA
| | - Eli Ipp
- Department of Nephrology, Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Sudha K Iyengar
- Genetic Analysis and Data Coordinating Center, Case Western Reserve University, Cleveland, OH, 44104, USA
| | - Paul L Kimmel
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA
| | - Michael J Klag
- Welch Center for Prevention, Epidemiology, and Clinical Research, Baltimore, MD, 21205, USA
| | - Orly Kohn
- The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | | | - David J Leehey
- Loyola University Medical Center, Chicago, IL, 60153, USA
| | - Robert G Nelson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, 85014, USA
| | - Susanne B Nicholas
- Divisions of Nephrology and Endocrinology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Madeleine V Pahl
- Division of Nephrology and Hypertension, Department of Medicine, UC Irvine School of Medicine, University of California, Orange, 92868, CA, USA
| | - Rulan S Parekh
- Hospital for Sick Children, University Health Network and the University of Toronto, Ontario, M5G1X8, Canada
| | - 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, 90502, USA
| | - Jeffrey R Schelling
- Departments of Medicine and Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44104, USA
| | - John R Sedor
- Departments of Medicine and Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44104, USA
| | - Vallabh O Shah
- The University of New Mexico, Albuquerque, NM, 87131, USA
| | - Michael W Smith
- National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Farook Thameem
- Division of Nephrology, The University of Texas Health Science Center, San Antonio, TX, 78229, USA.,Department of Biochemistry, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | | | - Cheryl A Winkler
- Center for Cancer Research, National Cancer Institute, NIH, Leidos Biomedical, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Phillip Zager
- The University of New Mexico, Albuquerque, NM, 87131, USA
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, 85014, USA
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The mitochondrial landscape of African Americans: An examination of more than 2500 control region haplotypes from 22 U.S. locations. Forensic Sci Int Genet 2016; 22:139-148. [PMID: 26919661 DOI: 10.1016/j.fsigen.2016.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 12/14/2015] [Accepted: 01/06/2016] [Indexed: 01/28/2023]
Abstract
The mitochondrial DNA (mtDNA) control region (16024-576) was Sanger-sequenced for a total of 2563 self-identified African Americans, using automated processing techniques and data review standards exceeding guidelines for forensic applications. Genetic diversity ranged from 0.9952 to 0.9998 in 22 population samples from 20 different states. Haplogroups of African ancestry, found in 82.48% of individuals overall, were most concentrated in the Southeast U.S. and decreased to the north and west. West African and West Central African haplotypes were well-represented in the population samples, especially in the southern U.S. states, while East African haplogroups were observed in low-frequency clusters in a handful of locations across the country. East Asian, Native American, and West Eurasian admixture was present in 3.16%, 2.93%, and 11.43% of samples, respectively. While some geographic substructure was detected across the population samples as clines in admixture frequencies, 20 of the 22 population samples were found to be statistically indistinguishable by pairwise comparisons and AMOVA calculations. Datasets from Hawaii and Idaho, however, were clear outliers. Overall, these more than 2500 control region sequences represent the most comprehensive regional sampling of African American mtDNA diversity to date, and are suitable for use in a forensic mtDNA database. The population data are made available via EMPOP (www.empop.org) and GenBank.
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Clark MA, Guatelli-Steinberg D, Hubbe M, Stout S. Quantification of Maxillary Dental Arcade Curvature and the Estimation of Biological Ancestry in Forensic Anthropology. J Forensic Sci 2016; 61:141-6. [DOI: 10.1111/1556-4029.12910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 01/05/2015] [Accepted: 01/15/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Melissa A. Clark
- Department of Archaeological Sciences; University of Bradford; Bradford Yorkshire BD7 1DP U.K
| | | | - Mark Hubbe
- Department of Anthropology; The Ohio State University; Columbus OH 43210
- Instituto de Investigaciones Arqueológicas y Museo; Universidad Católica del Norte; San Pedro de Atacama Chile
| | - Sam Stout
- Department of Anthropology; The Ohio State University; Columbus OH 43210
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Campbell MC, Hirbo JB, Townsend JP, Tishkoff SA. The peopling of the African continent and the diaspora into the new world. Curr Opin Genet Dev 2015; 29:120-32. [PMID: 25461616 DOI: 10.1016/j.gde.2014.09.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/03/2014] [Accepted: 09/05/2014] [Indexed: 12/22/2022]
Abstract
Africa is the birthplace of anatomically modern humans, and is the geographic origin of human migration across the globe within the last 100,000 years. The history of African populations has consisted of a number of demographic events that have influenced patterns of genetic and phenotypic variation across the continent. With the increasing amount of genomic data and corresponding developments in computational methods, researchers are able to explore long-standing evolutionary questions, expanding our understanding of human history within and outside of Africa. This review will summarize some of the recent findings regarding African demographic history, including the African Diaspora, and will briefly explore their implications for disease susceptibility in populations of African descent.
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De Luca M, Chandler-Laney PC, Wiener H, Fernandez JR. Common variants in the LAMA5 gene associate with fasting plasma glucose and serum triglyceride levels in a cohort of pre-and early pubertal children. J Pediatr Genet 2015; 1. [PMID: 23264881 DOI: 10.3233/pge-12036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Laminins are large glycoproteins found in basement membranes where they play a vital role in tissue architecture and cell behavior. Previously, we reported the association of two LAMA5 polymorphisms (rs659822 and rs944895) with anthropometric traits, fasting lipid profile, and plasma glucose levels in pre-menopausal women and elderly subjects. Furthermore, earlier work in mice showed that Lama5 is involved in organogenesis and placental function during pregnancy. The objective of this study was to investigate whether LAMA5 rs659822 or rs944895 are associated with inter-individual variability in birth weight as well as anthropometric, fasting lipid profile, and fasting glucose levels in children. Two hundred and eighty nine healthy children aged 7-12 years of European, Hispanic, and African-American ancestry were studied. Co-dominant models adjusted for genetic admixture, age, gender, and stages of puberty were used to test for the association of the polymorphisms with each trait. Our analysis showed significant associations of rs659822 with fasting plasma glucose levels (p = 0.0004) and of rs944895 with fasting serum triglycerides (p = 0.004) after Bonferroni correction for multiple testing. Our results corroborate our previous findings that genetic variants in LAMA5 contribute to variation in metabolic phenotypes and provide evidence that this may occur early in life.
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Affiliation(s)
- Maria De Luca
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Abstract
Sex-biased demography, in which parameters governing migration and population size differ between females and males, has been studied through comparisons of X chromosomes, which are inherited sex-specifically, and autosomes, which are not. A common form of sex bias in humans is sex-biased admixture, in which at least one of the source populations differs in its proportions of females and males contributing to an admixed population. Studies of sex-biased admixture often examine the mean ancestry for markers on the X chromosome in relation to the autosomes. A simple framework noting that in a population with equally many females and males, two-thirds of X chromosomes appear in females, suggests that the mean X-chromosomal admixture fraction is a linear combination of female and male admixture parameters, with coefficients 2/3 and 1/3, respectively. Extending a mechanistic admixture model to accommodate the X chromosome, we demonstrate that this prediction is not generally true in admixture models, although it holds in the limit for an admixture process occurring as a single event. For a model with constant ongoing admixture, we determine the mean X-chromosomal admixture, comparing admixture on female and male X chromosomes to corresponding autosomal values. Surprisingly, in reanalyzing African-American genetic data to estimate sex-specific contributions from African and European sources, we find that the range of contributions compatible with the excess African ancestry on the X chromosome compared to autosomes has a wide spread, permitting scenarios either without male-biased contributions from Europe or without female-biased contributions from Africa.
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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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Circadian rhythm phase shifts and endogenous free-running circadian period differ between African-Americans and European-Americans. Sci Rep 2015; 5:8381. [PMID: 25670162 PMCID: PMC4323653 DOI: 10.1038/srep08381] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/19/2015] [Indexed: 12/13/2022] Open
Abstract
Successful adaptation to modern civilization requires the internal circadian clock to make large phase shifts in response to circumstances (e.g., jet travel and shift work) that were not encountered during most of our evolution. We found that the magnitude and direction of the circadian clock's phase shift after the light/dark and sleep/wake/meal schedule was phase-advanced (made earlier) by 9 hours differed in European-Americans compared to African-Americans. European-Americans had larger phase shifts, but were more likely to phase-delay after the 9-hour advance (to phase shift in the wrong direction). The magnitude and direction of the phase shift was related to the free-running circadian period, and European-Americans had a longer circadian period than African-Americans. Circadian period was related to the percent Sub-Saharan African and European ancestry from DNA samples. We speculate that a short circadian period was advantageous during our evolution in Africa and lengthened with northern migrations out of Africa. The differences in circadian rhythms remaining today are relevant for understanding and treating the modern circadian-rhythm-based disorders which are due to a misalignment between the internal circadian rhythms and the times for sleep, work, school and meals.
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Bryc K, Durand EY, Macpherson JM, Reich D, Mountain JL. The genetic ancestry of African Americans, Latinos, and European Americans across the United States. Am J Hum Genet 2015; 96:37-53. [PMID: 25529636 PMCID: PMC4289685 DOI: 10.1016/j.ajhg.2014.11.010] [Citation(s) in RCA: 425] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 11/17/2014] [Indexed: 12/11/2022] Open
Abstract
Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans (brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry differences reflect historical events, such as early Spanish colonization, waves of immigration from many regions of Europe, and forced relocation of Native Americans within the US. This study sheds light on the fine-scale differences in ancestry within and across the United States and informs our understanding of the relationship between racial and ethnic identities and genetic ancestry.
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Affiliation(s)
- Katarzyna Bryc
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; 23andMe, Inc., Mountain View, CA 94043, USA.
| | | | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Association between DRD2/ANKK1 TaqIA polymorphism and common illicit drug dependence: evidence from a meta-analysis. Hum Immunol 2014; 76:42-51. [PMID: 25500252 DOI: 10.1016/j.humimm.2014.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 04/27/2014] [Accepted: 12/03/2014] [Indexed: 11/24/2022]
Abstract
BACKGROUND Growing evidence indicated conflicting results about the dopamine receptor D2 (DRD2)/kinase domain containing 1 gene (ANKK1) TaqIA single nucleotide polymorphism (rs1800497) and common illicit drug dependence risk including stimulants, opioid and marijuana. We conducted a meta-analysis to evaluate the association between the polymorphism and common illicit drug dependence risk. METHOD A total of 25 available studies (26 subgroups) testing the association between the polymorphism and common illicit drug dependence were examined through Oct 2013. Pooled odds ratios (ORs) and 95% confidence intervals (CI) were estimated using fixed- and random-effects models when appropriate. Heterogeneity and publication bias were evaluated. RESULTS We found the DRD2/ANKK1 TaqIA polymorphism was significantly associated with increased risk of opioid dependence under homozygote, dominant, and recessive genetic model, respectively (homozygote: OR=1.546, 95%CI=1.279-1.87; dominant: OR=1.265, 95%CI=1.055-1.516; recessive: OR=1.409, 95%CI=1.182-1.680). Subgroup analyses were similar to the results of the total population by ethnicity and quality score. Besides, we also found that Caucasian and low-quality studies were major sources of heterogeneity for opioid dependence. We failed to find any significant association between the polymorphism and stimulants or marijuana neither in total population nor subgroup analyses under any genetic model. CONCLUSIONS The current meta-analysis suggested that DRD2/ANKK1 TaqIA polymorphism might be associated with opioid dependence risk, but not associated with stimulants or marijuana dependence.
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Menzel S, Rooks H, Zelenika D, Mtatiro SN, Gnanakulasekaran A, Drasar E, Cox S, Liu L, Masood M, Silver N, Garner C, Vasavda N, Howard J, Makani J, Adekile A, Pace B, Spector T, Farrall M, Lathrop M, Thein SL. Global genetic architecture of an erythroid quantitative trait locus, HMIP-2. Ann Hum Genet 2014; 78:434-51. [PMID: 25069958 PMCID: PMC4303951 DOI: 10.1111/ahg.12077] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/20/2014] [Indexed: 12/16/2022]
Abstract
HMIP-2 is a human quantitative trait locus affecting peripheral numbers, size and hemoglobin composition of red blood cells, with a marked effect on the persistence of the fetal form of hemoglobin, HbF, in adults. The locus consists of multiple common variants in an enhancer region for MYB (chr 6q23.3), which encodes the hematopoietic transcription factor cMYB. Studying a European population cohort and four African-descended groups of patients with sickle cell anemia, we found that all share a set of two spatially separate HbF-promoting alleles at HMIP-2, termed “A” and “B.” These typically occurred together (“A–B”) on European chromosomes, but existed on separate homologous chromosomes in Africans. Using haplotype signatures for “A” and “B,” we interrogated public population datasets. Haplotypes carrying only “A” or “B” were typical for populations in Sub-Saharan Africa. The “A–B” combination was frequent in European, Asian, and Amerindian populations. Both alleles were infrequent in tropical regions, possibly undergoing negative selection by geographical factors, as has been reported for malaria with other hematological traits. We propose that the ascertainment of worldwide distribution patterns for common, HbF-promoting alleles can aid their further genetic characterization, including the investigation of gene–environment interaction during human migration and adaptation.
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Affiliation(s)
| | | | | | - Siana N Mtatiro
- King's College London, London, UK.,Muhimbili University, Dar es Salaam, Tanzania
| | | | - Emma Drasar
- King's College London, London, UK.,King's College Hospital NHS Foundation Trust, London, UK
| | - Sharon Cox
- Muhimbili University, Dar es Salaam, Tanzania
| | - Li Liu
- University of Texas at Dallas, Richardson, TX, USA
| | | | | | - Chad Garner
- University of California Irvine School of Medicine, Irvine, CA, USA
| | | | - Jo Howard
- King's College London, London, UK.,Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | | | | | - Betty Pace
- Georgia Regents University, Augusta, GA, USA
| | | | - Martin Farrall
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Swee Lay Thein
- King's College London, London, UK.,King's College Hospital NHS Foundation Trust, London, UK
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Zhang J, Stram DO. The role of local ancestry adjustment in association studies using admixed populations. Genet Epidemiol 2014; 38:502-15. [PMID: 25043967 PMCID: PMC5079159 DOI: 10.1002/gepi.21835] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/25/2014] [Accepted: 05/19/2014] [Indexed: 01/11/2023]
Abstract
Association analysis using admixed populations imposes challenges and opportunities for disease mapping. By developing some explicit results for the variance of an allele of interest conditional on either local or global ancestry and by simulation of recently admixed genomes we evaluate power and false-positive rates under a variety of scenarios concerning linkage disequilibrium (LD) and the presence of unmeasured variants. Pairwise LD patterns were compared between admixed and nonadmixed populations using the HapMap phase 3 data. Based on the above, we showed that as follows:
For causal variants with similar effect size in all populations, power is generally higher in a study using admixed population than using nonadmixed population, especially for highly differentiated SNPs. This gain of power is achieved with adjustment of global ancestry, which completely removes any cross-chromosome inflation of type I error rates, and addresses much of the intrachromosome inflation. If reliably estimated, adjusting for local ancestry precisely recovers the localization that could have been achieved in a stratified analysis of source populations. Improved localization is most evident for highly differentiated SNPs; however, the advantage of higher power is lost on exactly the same differentiated SNPs. In the real admixed populations such as African Americans and Latinos, the expansion of LD is not as dramatic as in our simulation. While adjustment for global ancestry is required prior to announcing a novel association seen in an admixed population, local ancestry adjustment may best be regarded as a localization tool not strictly required for discovery purposes.
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Affiliation(s)
- Jianqi Zhang
- Division of Biostatistics, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
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Barnado A, Wheless L, Meyer AK, Gilkeson GS, Kamen DL. Pregnancy outcomes among African-American patients with systemic lupus erythematosus compared with controls. Lupus Sci Med 2014; 1:e000020. [PMID: 25360323 PMCID: PMC4211631 DOI: 10.1136/lupus-2014-000020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 11/21/2022]
Abstract
Objective In a study of Gullah African–Americans, we compared pregnancy outcomes before and after systemic lupus erythematosus (SLE) diagnosis to controls to test whether there is a predisease state that negativelyaffects pregnancy outcomes. Design Cases and controls reporting at least one pregnancy were included. Controls were all Gullah African-American females. We collected demographic, socioeconomic and pregnancy data. We modelled pregnancy outcome associations with case status using multiple logistic regression to calculate ORs. Results After adjustment for age, years of education, medical coverage and pregnancy number, compared with controls, cases were more likely to have any adverse outcome (OR 2.35, 95% CI 1.78 to 3.10), including stillbirth (OR 4.55, 95% CI 1.53 to 13.50), spontaneous abortion (OR 2.05, 95% CI 1.40 to 3.00), preterm birth (OR 2.58, 95% CI 1.58 to 4.20), low birth weight (OR 2.64, 95% CI 1.61 to 4.34) and preeclampsia (OR 1.80, 95% CI 1.08 to 3.01). The odds of adverse pregnancy outcomes all increased after SLE diagnosis compared with before diagnosis, even after adjustment for age, years of education, pregnancy number and medical coverage. Conclusion From a large cohort of African–American women, our findings suggest there may be a predisease state that predisposes to adverse pregnancy outcomes.
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Affiliation(s)
- April Barnado
- Division of Rheumatology, Department of Medicine , Medical University of South Carolina , Charleston, South Carolina , USA
| | - Lee Wheless
- Department of Public Health Sciences , Medical University of South Carolina , Charleston, South Carolina , USA
| | - Anna K Meyer
- Division of Rheumatology, Department of Medicine , Medical University of South Carolina , Charleston, South Carolina , USA
| | - Gary S Gilkeson
- Division of Rheumatology, Department of Medicine , Medical University of South Carolina , Charleston, South Carolina , USA
| | - Diane L Kamen
- Division of Rheumatology, Department of Medicine , Medical University of South Carolina , Charleston, South Carolina , USA
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Bidulescu A, Choudhry S, Musani SK, Buxbaum SG, Liu J, Rotimi CN, Wilson JG, Taylor HA, Gibbons GH. Associations of adiponectin with individual European ancestry in African Americans: the Jackson Heart Study. Front Genet 2014; 5:22. [PMID: 24575123 PMCID: PMC3918651 DOI: 10.3389/fgene.2014.00022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/21/2014] [Indexed: 12/23/2022] Open
Abstract
Background: Compared with European Americans, African Americans (AAs) exhibit lower levels of the cardio-metabolically protective adiponectin even after accounting for adiposity measures. Because few studies have examined in AA the association between adiponectin and genetic admixture, a dense panel of ancestry informative markers (AIMs) was used to estimate the individual proportions of European ancestry (PEA) for the AAs enrolled in a large community-based cohort, the Jackson Heart Study (JHS). We tested the hypothesis that plasma adiponectin and PEA are directly associated and assessed the interaction with a series of cardio-metabolic risk factors. Methods: Plasma specimens from 1439 JHS participants were analyzed by ELISA for adiponectin levels. Using pseudo-ancestral population genotype data from the HapMap Consortium, PEA was estimated with a panel of up to 1447 genome-wide preselected AIMs by a maximum likelihood approach. Interaction assessment, stepwise linear and cubic multivariable-adjusted regression models were used to analyze the cross-sectional association between adiponectin and PEA. Results: Among the study participants (62% women; mean age 48 ± 12 years), the median (interquartile range) of PEA was 15.8 (9.3)%. Body mass index (BMI) (p = 0.04) and insulin resistance (p = 0.0001) modified the association between adiponectin and PEA. Adiponectin was directly and linearly associated with PEA (β = 0.62 ± 0.28, p = 0.03) among non-obese (n = 673) and insulin sensitive participants (n = 1141; β = 0.74 ± 0.23, p = 0.001), but not among those obese or with insulin resistance. No threshold point effect was detected for non-obese participants. Conclusions: In a large AA population, the individual proportion of European ancestry was linearly and directly associated with plasma adiponectin among non-obese and non insulin-resistant participants, pointing to the interaction of genetic and metabolic factors influencing adiponectin levels.
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Affiliation(s)
- Aurelian Bidulescu
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health - Bloomington Bloomington, IN, USA
| | - Shweta Choudhry
- Department of Urology, University of California San Francisco, CA, USA
| | - Solomon K Musani
- Jackson Heart Study, University of Mississippi Medical Center Jackson, MS, USA
| | - Sarah G Buxbaum
- Department of Health Sciences, Jackson State University Jackson, MS, USA
| | - Jiankang Liu
- Jackson Heart Study, University of Mississippi Medical Center Jackson, MS, USA
| | - Charles N Rotimi
- National Human Genome Research Institute, National Institutes of Health Bethesda, MD, USA
| | - James G Wilson
- Jackson Heart Study, University of Mississippi Medical Center Jackson, MS, USA
| | - Herman A Taylor
- Jackson Heart Study, University of Mississippi Medical Center Jackson, MS, USA
| | - Gary H Gibbons
- National Heart Lung and Blood Institute, National Institutes of Health Bethesda, MD, USA
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Gontijo CC, Guerra Amorim CE, Godinho NMO, Toledo RCP, Nunes A, Silva W, Da Fonseca Moura MM, De Oliveira JCC, Pagotto RC, De Nazaré Klautau-Guimarães M, De Oliveira SF. Brazilian quilombos: A repository of Amerindian alleles. Am J Hum Biol 2014; 26:142-50. [DOI: 10.1002/ajhb.22501] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/05/2013] [Accepted: 12/15/2013] [Indexed: 11/05/2022] Open
Affiliation(s)
- Carolina Carvalho Gontijo
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de Ciências Biológicas, Universidade de Brasília; 70910-900 Brasília DF Brazil
| | - Carlos Eduardo Guerra Amorim
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de Ciências Biológicas, Universidade de Brasília; 70910-900 Brasília DF Brazil
| | - Neide Maria Oliveira Godinho
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de Ciências Biológicas, Universidade de Brasília; 70910-900 Brasília DF Brazil
- Instituto de Criminalística Leonardo Rodrigues; 74425-030 Goiânia GO Brazil
| | - Rafaela Cesare Parmezan Toledo
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de Ciências Biológicas, Universidade de Brasília; 70910-900 Brasília DF Brazil
| | - Adriana Nunes
- Departamento de Arqueologia; Universidade Federal de Rondônia; 76801-059 Porto Velho RO Brazil
| | - Wellington Silva
- Faculdade Adventista da Bahia; Caixa Postal 18 44300-000 Cachoeira BA Brazil
| | | | | | - Rubiani C. Pagotto
- Departamento de Biologia; Universidade Federal de Rondônia; 76801-059 Porto Velho RO Brazil
| | - Maria De Nazaré Klautau-Guimarães
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de Ciências Biológicas, Universidade de Brasília; 70910-900 Brasília DF Brazil
| | - Silviene Fabiana De Oliveira
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de Ciências Biológicas, Universidade de Brasília; 70910-900 Brasília DF Brazil
- Jackson Laboratory for Genomic Medicine; University of Connecticut Health Center; 06032 Farmington CT, USA
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Detecting Sex-Biased Gene Flow in African-Americans through the Analysis of Intra- and Inter-Population Variation at Mitochondrial DNA and Y- Chromosome Microsatellites. Balkan J Med Genet 2013; 15:7-14. [PMID: 24052726 PMCID: PMC3776662 DOI: 10.2478/bjmg-2013-0001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
This study reports on variations at the mitochondrial DNA (mtDNA) hypervariable region 1 (HVR-1) and at seven Y-chromosome microsatellites in an African-American population sample from Chicago, IL, USA. Our results support the hypothesis that the population studied had undergone a European male-biased gene flow. We show that comparisons of intra-and inter-population diversity parameters between African-Americans, Europeans and Africans may help detect sex-biased gene flow, providing a complement to quantitative methods to estimate genetic admixture.
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Hernandez W, Gamazon ER, Aquino-Michaels K, Patel S, O'Brien TJ, Harralson AF, Kittles RA, Barbour A, Tuck M, McIntosh SD, Douglas JN, Nicolae D, Cavallari LH, Perera MA. Ethnicity-specific pharmacogenetics: the case of warfarin in African Americans. THE PHARMACOGENOMICS JOURNAL 2013; 14:223-8. [PMID: 24018621 DOI: 10.1038/tpj.2013.34] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 07/18/2013] [Accepted: 07/22/2013] [Indexed: 01/05/2023]
Abstract
Using a derivation cohort (N=349), we developed the first warfarin dosing algorithm that includes recently discovered polymorphisms in VKORC1 and CYP2C9 associated with warfarin dose requirement in African Americans (AAs). We tested our novel algorithm in an independent cohort of 129 AAs and compared the dose prediction to the International Warfarin Pharmacogenetics Consortium (IWPC) dosing algorithms. Our algorithm explains more of the phenotypic variation (R(2)=0.27) than the IWPC pharmacogenomics (R(2)=0.15) or clinical (R(2)=0.16) algorithms. Among high-dose patients, our algorithm predicted a higher proportion of patients within 20% of stable warfarin dose (45% vs 29% and 2% in the IWPC pharmacogenomics and clinical algorithms, respectively). In contrast to our novel algorithm, a significant inverse correlation between predicted dose and percent West African ancestry was observed for the IWPC pharmacogenomics algorithm among patients requiring ⩾60 mg per week (β=-2.04, P=0.02).
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Affiliation(s)
- W Hernandez
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - E R Gamazon
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - K Aquino-Michaels
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - S Patel
- Department of Pharmacy, University of Illinois, Chicago, IL, USA
| | - T J O'Brien
- Department of Pharmacology and Physiology, The George Washington University, Washington DC, USA
| | - A F Harralson
- 1] Department of Pharmacology and Physiology, The George Washington University, Washington DC, USA [2] Department of Pharmacogenomics, Bernard J. Dunn School of Pharmacy, Shenandoah University, Ashburn, VA, USA
| | - R A Kittles
- Department of Medicine, Institute of Human Genetics, University of Illinois, Chicago, IL, USA
| | - A Barbour
- Department of Medicine, The George Washington University, Washington DC, USA
| | - M Tuck
- Department of Veterans Affairs, Uniformed Services University of the Health Sciences, Washington DC, USA
| | - S D McIntosh
- 1] Department of Medicine, The George Washington University, Washington DC, USA [2] Department of Veterans Affairs, Uniformed Services University of the Health Sciences, Washington DC, USA
| | - J N Douglas
- Department of Veterans Affairs, Uniformed Services University of the Health Sciences, Washington DC, USA
| | - D Nicolae
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - L H Cavallari
- Department of Pharmacy, University of Illinois, Chicago, IL, USA
| | - M A Perera
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
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Clarke TK, Bloch PJ, Ambrose-Lanci LM, Ferraro TN, Berrettini WH, Kampman KM, Dackis CA, Pettinati HM, O'Brien CP, Oslin DW, Lohoff FW. Further evidence for association of polymorphisms in the CNR1 gene with cocaine addiction: confirmation in an independent sample and meta-analysis. Addict Biol 2013; 18:702-8. [PMID: 21790903 DOI: 10.1111/j.1369-1600.2011.00346.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetic research on cocaine dependence (CD) may help clarify our understanding of the disorder as well as provide insights for effective treatment. As endocannabinoid signaling and dopamine neurotransmission have been shown to be involved in drug reward, genes related to these systems are plausible candidates for susceptibility to CD. The cannabinoid receptor 1 protein regulates both the endocannabinoid and dopaminergic neurobiological systems, and polymorphisms in the cannabinoid receptor gene, CNR1, have been associated previously with substance dependence. In this study, we attempt to replicate findings associating CNR1 with CD in African Americans. Cocaine-addicted individuals (n=860) and unaffected controls (n=334) of African descent were genotyped for two single nucleotide polymorphisms (SNPs) in CNR1 (rs6454674, rs806368). We observed a significant difference in genotype frequencies between cases and controls for both SNPs (P≤0.042). A meta-analysis was also performed combining our data with that of Zuo et al. who also studied these polymorphisms in African American cocaine addicts (total n=1253 cases versus 543 controls). When our data were combined, rs6454674 increased in significance to P=0.027; however, rs806368 was no longer significant. This study confirms the association between rs6454674 and CD. However, because there is considerable co-morbidity of CD with other drugs of abuse, additional studies are necessary to determine whether polymorphisms in CNR1 induce a general susceptibility to substance dependence or are specific to cocaine addiction. Furthermore, as this population consists of American individuals of African descent, the possibility of population stratification should not be excluded.
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Affiliation(s)
- Toni-Kim Clarke
- Psychiatric Pharmacogenetics Laboratory Center for Neurobiology and Behavior Treatment Research Center Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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43
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Ramos PS, Oates JC, Kamen DL, Williams AH, Gaffney PM, Kelly JA, Kaufman KM, Kimberly RP, Niewold TB, Jacob CO, Tsao BP, Alarcón GS, Brown EE, Edberg JC, Petri MA, Ramsey-Goldman R, Reveille JD, Vilá LM, James JA, Guthridge JM, Merrill JT, Boackle SA, Freedman BI, Scofield RH, Stevens AM, Vyse TJ, Criswell LA, Moser KL, Alarcón-Riquelme ME, Langefeld CD, Harley JB, Gilkeson GS. Variable association of reactive intermediate genes with systemic lupus erythematosus in populations with different African ancestry. J Rheumatol 2013; 40:842-9. [PMID: 23637325 DOI: 10.3899/jrheum.120989] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Little is known about the genetic etiology of systemic lupus erythematosus (SLE) in individuals of African ancestry, despite its higher prevalence and greater disease severity. Overproduction of nitric oxide (NO) and reactive oxygen species are implicated in the pathogenesis and severity of SLE, making NO synthases and other reactive intermediate-related genes biological candidates for disease susceptibility. We analyzed variation in reactive intermediate genes for association with SLE in 2 populations with African ancestry. METHODS A total of 244 single-nucleotide polymorphisms (SNP) from 53 regions were analyzed in non-Gullah African Americans (AA; 1432 cases and 1687 controls) and the genetically more homogeneous Gullah of the Sea Islands of South Carolina (133 cases and 112 controls). Single-marker, haplotype, and 2-locus interaction tests were computed for these populations. RESULTS The glutathione reductase gene GSR (rs2253409; p = 0.0014, OR 1.26, 95% CI 1.09-1.44) was the most significant single SNP association in AA. In the Gullah, the NADH dehydrogenase NDUFS4 (rs381575; p = 0.0065, OR 2.10, 95% CI 1.23-3.59) and NO synthase gene NOS1 (rs561712; p = 0.0072, OR 0.62, 95% CI 0.44-0.88) were most strongly associated with SLE. When both populations were analyzed together, GSR remained the most significant effect (rs2253409; p = 0.00072, OR 1.26, 95% CI 1.10-1.44). Haplotype and 2-locus interaction analyses also uncovered different loci in each population. CONCLUSION These results suggest distinct patterns of association with SLE in African-derived populations; specific loci may be more strongly associated within select population groups.
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Affiliation(s)
- Paula S Ramos
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
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44
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Long J, Zhang B, Signorello LB, Cai Q, Deming-Halverson S, Shrubsole MJ, Sanderson M, Dennis J, Michailidou K, Michailiou K, Easton DF, Shu XO, Blot WJ, Zheng W. Evaluating genome-wide association study-identified breast cancer risk variants in African-American women. PLoS One 2013; 8:e58350. [PMID: 23593120 PMCID: PMC3620157 DOI: 10.1371/journal.pone.0058350] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 02/03/2013] [Indexed: 12/25/2022] Open
Abstract
Genome-wide association studies (GWAS), conducted mostly in European or Asian descendants, have identified approximately 67 genetic susceptibility loci for breast cancer. Given the large differences in genetic architecture between the African-ancestry genome and genomes of Asians and Europeans, it is important to investigate these loci in African-ancestry populations. We evaluated index SNPs in all 67 breast cancer susceptibility loci identified to date in our study including up to 3,300 African-American women (1,231 cases and 2,069 controls), recruited in the Southern Community Cohort Study (SCCS) and the Nashville Breast Health Study (NBHS). Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the same direction as previously reported: rs10069690 (5p15/TERT), rs999737 (14q24/RAD51L1), rs13387042 (2q35/TNP1), rs1219648 (10q26/FGFR2), rs8170 (19p13/BABAM1), rs17817449 (16q12/FTO), and rs13329835 (16q23/DYL2). A marginally significant association (P<0.10) was found for three additional SNPs: rs1045485 (2q33/CASP8), rs4849887 (2q14/INHBB), and rs4808801 (19p13/ELL). Three additional SNPs, including rs1011970 (9p21/CDKN2A/2B), rs941764 (14q32/CCDC88C), and rs17529111 (6q14/FAM46A), showed a significant association in analyses conducted by breast cancer subtype. The risk of breast cancer was elevated with an increasing number of risk variants, as measured by quintile of the genetic risk score, from 1.00 (reference), to 1.75 (1.30-2.37), 1.56 (1.15-2.11), 2.02 (1.50-2.74) and 2.63 (1.96-3.52), respectively, (P = 7.8 × 10(-10)). Results from this study highlight the need for large genetic studies in AAs to identify risk variants impacting this population.
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Affiliation(s)
- Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.
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Sora ND, Marlow NM, Bandyopadhyay D, Leite RS, Slate EH, Fernandes JK. Metabolic syndrome and periodontitis in Gullah African Americans with type 2 diabetes mellitus. J Clin Periodontol 2013; 40:599-606. [PMID: 23557538 DOI: 10.1111/jcpe.12104] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2013] [Indexed: 12/29/2022]
Abstract
AIM To assess associations of metabolic syndrome, and its individual components, with extent of severe periodontitis among patients with type 2 diabetes mellitus (T2DM). MATERIALS & METHODS We performed a secondary data analysis (N = 283) using a cross-sectional study population of Gullah African Americans with T2DM. Extent of severe periodontitis was assessed as total diseased tooth-sites/person [evaluated as separate outcomes: 6+mm clinical attachment level (CAL), 5+mm periodontal probing depth (PPD)] using negative binomial regression techniques. Primary independent variables assessed in separate models included metabolic syndrome (yes/no), each metabolic syndrome component (low HDL, hypertension, high triglycerides, large waist circumference) and glycemic control (poor/good). RESULTS Multivariable CAL-model results showed a significant association for metabolic syndrome status with extent of severe periodontitis (RR = 2.77, p = 0.03). The separate multivariable CAL-model including each metabolic syndrome component showed marginally increased rates among those with large waist circumference (RR = 2.33, p = 0.09) and those with HbA1c ≥ 7% (RR = 1.73, p = 0.06). Multivariable PPD-models showed marginally increased rates among those with metabolic syndrome (RR = 2.18, p = 0.06). CONCLUSION Metabolic syndrome is associated with the extent of severe periodontitis in this Gullah population with T2DM.
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Affiliation(s)
- Nicoleta D Sora
- Division of Endocrinology, Diabetes & Medical Genetics, College of Medicine, Medical University of South Carolina, Charleston, SC, USA
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Leite R, Hudson C, West L, Carpenter E, Andrews JO. Assessment of oral health needs and barriers to care in a Gullah community: Hollywood smiles. Prog Community Health Partnersh 2013; 7:201-8. [PMID: 23793251 PMCID: PMC4097834 DOI: 10.1353/cpr.2013.0016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVES To assess the oral health (OH) needs and barriers to OH care in Gullah African American communities. METHODS A community advisory board (CAB) was formed to guide the research study. Five focus groups (n = 27 participants) were conducted to explore the OH needs/barriers. Participants completed demographic surveys and participated in discussions facilitated by open-ended questions. All sessions were audio-recorded, transcribed and analyzed using NVivo8. RESULTS Facilitators of OH included positive experiences and modeling. Fear and access to care were the most cited barriers. Tooth extraction was the dental treatment of choice. Intervention recommendations included improving clinic access, using the churches to socially influence receipt of OH care, providing group educational sessions with OH specialists, and having local "lay people" to provide support and help to navigate OH care systems. CONCLUSIONS The design of a multilevel, culturally and locally relevant intervention may lead to a decrease in OH disparities in Gullah communities.
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Affiliation(s)
- Renata Leite
- Division of Periodontics, College of Dental Medicine, Medical University of South Carolina
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47
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Adeyanju O, Okou D, Huang C, Kumar A, Sauer C, Galloway C, Prasad M, Waters J, Cutler D, Zwick M, Dhere T, Kugathasan S. Common NOD2 risk variants in African Americans with Crohn's disease are due exclusively to recent Caucasian admixture. Inflamm Bowel Dis 2012; 18:2357-9. [PMID: 22447396 PMCID: PMC3392535 DOI: 10.1002/ibd.22944] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 02/14/2012] [Indexed: 12/09/2022]
Abstract
BACKGROUND Crohn's disease (CD) is highly heritable. NOD2 has emerged as the main susceptibility gene among individuals of European ancestry; however, NOD2 does not appear to contribute to CD susceptibility among many non-European populations. Today's African American (AA) population represents an admixture of West African (80%) and European (20%) ancestry. Since genotype-based tools are becoming increasingly available for CD, it is important that we validate the risk variants in different populations, such as admixed AAs. METHODS We analyzed the NOD2 variants among admixed AAs (n = 321, 240 with CD and 111 healthy controls [HCs]) and nonadmixed West Africans (n = 40) by genotyping four known disease-causing NOD variants. We extracted the publicly available 1000 Genomes data on NOD2 variants from 500 subjects of West African origin. Association with disease was evaluated by logistic regression. RESULTS An association with CD was found for the classical single nucleotide polymorphism (SNP) 1007fs (2.6% CD, 0% HC, P = 0.012); there was no association when the genotypic and allelic frequencies of the risk alleles were compared for SNPs R702W and G908R. No known NOD2 risk alleles were seen in either the West African cohort or in subjects of African ancestry from the 1000 Genomes project. CONCLUSIONS The NOD2 gene is a risk for CD in AAs, although the allele frequencies and the attributable risk are much lower compared with Caucasians. The risk alleles are not seen in the West African population, suggesting that the risk for CD contributed by NOD2 among AAs is due exclusively to recent European admixture.
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Affiliation(s)
- Oloruntosin Adeyanju
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - David Okou
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Clifton Huang
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,Children’s Health Care of Atlanta, Atlanta, GA
| | - Archana Kumar
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Cary Sauer
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,Children’s Health Care of Atlanta, Atlanta, GA
| | - Courtney Galloway
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Mahadev Prasad
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Jon Waters
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - David Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
| | - Michael Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
| | - Tanvi Dhere
- Division of Gastroenterology and Hepatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Subra Kugathasan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,Children’s Health Care of Atlanta, Atlanta, GA
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Quanjer PH, Stanojevic S, Cole TJ, Baur X, Hall GL, Culver BH, Enright PL, Hankinson JL, Ip MSM, Zheng J, Stocks J. Multi-ethnic reference values for spirometry for the 3-95-yr age range: the global lung function 2012 equations. Eur Respir J 2012; 40:1324-43. [PMID: 22743675 PMCID: PMC3786581 DOI: 10.1183/09031936.00080312] [Citation(s) in RCA: 3714] [Impact Index Per Article: 309.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The aim of the Task Force was to derive continuous prediction equations and their lower limits of normal for spirometric indices, which are applicable globally. Over 160,000 data points from 72 centres in 33 countries were shared with the European Respiratory Society Global Lung Function Initiative. Eliminating data that could not be used (mostly missing ethnic group, some outliers) left 97,759 records of healthy nonsmokers (55.3% females) aged 2.5-95 yrs. Lung function data were collated and prediction equations derived using the LMS method, which allows simultaneous modelling of the mean (mu), the coefficient of variation (sigma) and skewness (lambda) of a distribution family. After discarding 23,572 records, mostly because they could not be combined with other ethnic or geographic groups, reference equations were derived for healthy individuals aged 3-95 yrs for Caucasians (n=57,395), African-Americans (n=3,545), and North (n=4,992) and South East Asians (n=8,255). Forced expiratory value in 1 s (FEV(1)) and forced vital capacity (FVC) between ethnic groups differed proportionally from that in Caucasians, such that FEV(1)/FVC remained virtually independent of ethnic group. For individuals not represented by these four groups, or of mixed ethnic origins, a composite equation taken as the average of the above equations is provided to facilitate interpretation until a more appropriate solution is developed. Spirometric prediction equations for the 3-95-age range are now available that include appropriate age-dependent lower limits of normal. They can be applied globally to different ethnic groups. Additional data from the Indian subcontinent and Arabic, Polynesian and Latin American countries, as well as Africa will further improve these equations in the future.
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Affiliation(s)
- Philip H Quanjer
- Dept of Pulmonary Diseases and Dept of Paediatrics, Erasmus Medical Centre, Erasmus University, Rotterdam, the Netherlands
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Beleza S, Campos J, Lopes J, Araújo II, Hoppfer Almada A, Correia e Silva A, Parra EJ, Rocha J. The admixture structure and genetic variation of the archipelago of Cape Verde and its implications for admixture mapping studies. PLoS One 2012; 7:e51103. [PMID: 23226471 PMCID: PMC3511383 DOI: 10.1371/journal.pone.0051103] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 10/30/2012] [Indexed: 11/18/2022] Open
Abstract
Recently admixed populations offer unique opportunities for studying human history and for elucidating the genetic basis of complex traits that differ in prevalence between human populations. Historical records, classical protein markers, and preliminary genetic data indicate that the Cape Verde islands in West Africa are highly admixed and primarily descended from European males and African females. However, little is known about the variation in admixture levels, admixture dynamics and genetic diversity across the islands, or about the potential of Cape Verde for admixture mapping studies. We have performed a detailed analysis of phenotypic and genetic variation in Cape Verde based on objective skin color measurements, socio-economic status (SES) evaluations and data for 50 autosomal, 34 X-chromosome, and 21 non-recombinant Y-chromosome (NRY) markers in 845 individuals from six islands of the archipelago. We find extensive genetic admixture between European and African ancestral populations (mean West African ancestry = 0.57, sd = 0.08), with individual African ancestry proportions varying considerably among the islands. African ancestry proportions calculated with X and Y-chromosome markers confirm that the pattern of admixture has been sex-biased. The high-resolution NRY-STRs reveal additional patterns of variation among the islands that are most consistent with differentiation after admixture. The differences in the autosomal admixture proportions are clearly evident in the skin color distribution across the islands (Pearson r = 0.54, P-value<2e–16). Despite this strong correlation, there are significant interactions between SES and skin color that are independent of the relationship between skin color and genetic ancestry. The observed distributions of admixture, genetic variation and skin color and the relationship of skin color with SES relate to historical and social events taking place during the settlement history of Cape Verde, and have implications for the design of association studies using this population.
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Affiliation(s)
- Sandra Beleza
- IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.
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50
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Jin W, Wang S, Wang H, Jin L, Xu S. Exploring population admixture dynamics via empirical and simulated genome-wide distribution of ancestral chromosomal segments. Am J Hum Genet 2012; 91:849-62. [PMID: 23103229 DOI: 10.1016/j.ajhg.2012.09.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 06/01/2012] [Accepted: 09/11/2012] [Indexed: 12/22/2022] Open
Abstract
The processes of genetic admixture determine the haplotype structure and linkage disequilibrium patterns of the admixed population, which is important for medical and evolutionary studies. However, most previous studies do not consider the inherent complexity of admixture processes. Here we proposed two approaches to explore population admixture dynamics, and we demonstrated, by analyzing genome-wide empirical and simulated data, that the approach based on the distribution of chromosomal segments of distinct ancestry (CSDAs) was more powerful than that based on the distribution of individual ancestry proportions. Analysis of 1,890 African Americans showed that a continuous gene flow model, in which the African American population continuously received gene flow from European populations over about 14 generations, best explained the admixture dynamics of African Americans among several putative models. Interestingly, we observed that some African Americans had much more European ancestry than the simulated samples, indicating substructures of local ancestries in African Americans that could have been caused by individuals from some particular lineages having repeatedly admixed with people of European ancestry. In contrast, the admixture dynamics of Mexicans could be explained by a gradual admixture model in which the Mexican population continuously received gene flow from both European and Amerindian populations over about 24 generations. Our results also indicated that recent gene flows from Sub-Saharan Africans have contributed to the gene pool of Middle Eastern populations such as Mozabite, Bedouin, and Palestinian. In summary, this study not only provides approaches to explore population admixture dynamics, but also advances our understanding on population history of African Americans, Mexicans, and Middle Eastern populations.
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Affiliation(s)
- Wenfei Jin
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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