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CRAWFORD DANAC, MORGAN ALEXANDERA, DENNY JOSHUAC, ARONOW BRUCEJ, BRENNER STEVENE. PRECISION MEDICINE: FROM DIPLOTYPES TO DISPARITIES TOWARDS IMPROVED HEALTH AND THERAPIES. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018; 23:389-399. [PMID: 29218899 PMCID: PMC6182117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Precision medicine research efforts both in basic science discovery and clinical implementation are well underway and promise to provide individualized preventions and treatments, improving overall health care delivery. To achieve these goals, advances in data capture and analysis are needed spanning different types of 'omic and clinical data. The efforts to enhance precise treatments for all may accentuate healthcare disparities unless specific challenges are identified and addressed. This session of the 2018 Pacific Symposium on Biocomputing presents the latest developments in this transdisciplinary research space of genomics, medicine, and population health.
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Affiliation(s)
- DANA C. CRAWFORD
- Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106 USA,
| | | | - JOSHUA C. DENNY
- Vanderbilt University Medical Center, Nashville, TN 37203 USA,
| | - BRUCE J. ARONOW
- Center for Computational Medicine, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati, Cincinnati, OH 45229 USA,
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Taylor JY, Sun YV, Barcelona de Mendoza V, Ifatunji M, Rafferty J, Fox ER, Musani SK, Sims M, Jackson JS. The combined effects of genetic risk and perceived discrimination on blood pressure among African Americans in the Jackson Heart Study. Medicine (Baltimore) 2017; 96:e8369. [PMID: 29069027 PMCID: PMC5671860 DOI: 10.1097/md.0000000000008369] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Both genomics and environmental stressors play a significant role in increases in blood pressure (BP). In an attempt to further explain the hypertension (HTN) disparity among African Americans (AA), both genetic underpinnings (selected candidate genes) and stress due to perceived racial discrimination (as reported in the literature) have independently been linked to increased BP among AAs. Although Gene x Environment interactions on BP have been examined, the environmental component of these investigations has focused more on lifestyle behaviors such as smoking, diet, and physical activity, and less on psychosocial stressors such as perceived discrimination.The present study uses candidate gene analyses to identify the relationship between Everyday Discrimination (ED) and Major Life Discrimination (MLD) with increases in systolic BP (SBP) and diastolic BP (DBP) among AA in the Jackson Heart Study. Multiple linear regression models reveal no association between discrimination and BP after adjusting for age, sex, body mass index (BMI), antihypertensive medication use, and current smoking status.Subsequent candidate gene analysis identified 5 SNPs (rs7602215, rs3771724, rs1006502, rs1791926, and rs2258119) that interacted with perceived discrimination and SBP, and 3 SNPs (rs2034454, rs7602215, and rs3771724) that interacted with perceived discrimination and DBP. Most notably, there was a significant SNP × discrimination interaction for 2 SNPs on the SLC4A5 gene: rs3771724 (MLD: SBP P = .034, DBP P = .031; ED: DBP: P = .016) and rs1006502 (MLD: SBP P = .034, DBP P = .030; ED: DBP P = .015).This study supports the idea that SNP × discrimination interactions combine to influence clinically relevant traits such as BP. Replication with similar epidemiological samples is required to ascertain the role of genes and psychosocial stressors in the development and expression of high BP in this understudied population.
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Affiliation(s)
| | - Yan V. Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA
- Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, GA
| | | | - Mosi Ifatunji
- Department of Sociology and Carolina Population Center, University of North Carolina, Chapel Hill, NC
| | - Jane Rafferty
- Program for Research on Black Americans, Institute for Social Research, University of Michigan, Ann Arbor, MI
| | - Ervin R. Fox
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS
| | - Solomon K. Musani
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS
| | - Mario Sims
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS
| | - James S. Jackson
- Program for Research on Black Americans, Institute for Social Research, University of Michigan, Ann Arbor, MI
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Taino and African maternal heritage in the Greater Antilles. Gene 2017; 637:33-40. [PMID: 28912065 DOI: 10.1016/j.gene.2017.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/22/2017] [Accepted: 09/04/2017] [Indexed: 01/08/2023]
Abstract
Notwithstanding the general interest and the geopolitical importance of the island countries in the Greater Antilles, little is known about the specific ancestral Native American and African populations that settled them. In an effort to alleviate this lacuna of information on the genetic constituents of the Greater Antilles, we comprehensively compared the mtDNA compositions of Cuba, Dominican Republic, Haiti, Jamaica and Puerto Rico. To accomplish this, the mtDNA HVRI and HVRII regions, as well as coding diagnostic sites, were assessed in the Haitian general population and compared to data from reference populations. The Taino maternal DNA is prominent in the ex-Spanish colonies (61.3%-22.0%) while it is basically non-existent in the ex-French and ex-English colonies of Haiti (0.0%) and Jamaica (0.5%), respectively. The most abundant Native American mtDNA haplogroups in the Greater Antilles are A2, B2 and C1. The African mtDNA component is almost fixed in Haiti (98.2%) and Jamaica (98.5%), and the frequencies of specific African haplogroups vary considerably among the five island nations. The strong persistence of Taino mtDNA in the ex-Spanish colonies (and especially in Puerto Rico), and its absence in the French and English excolonies is likely the result of different social norms regarding mixed marriages with Taino women during the early years after the first contact with Europeans. In addition, this article reports on the results of an integrative approach based on mtDNA analysis and demographic data that tests the hypothesis of a southward shift in raiding zones along the African west coast during the period encompassing the Transatlantic Slave Trade.
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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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What Ancestry Can Tell Us About the Genetic Origins of Inter-Ethnic Differences in Asthma Expression. Curr Allergy Asthma Rep 2017; 16:53. [PMID: 27393700 DOI: 10.1007/s11882-016-0635-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Differences in asthma prevalence have been described across different populations, suggesting that genetic ancestry can play an important role in this disease. In fact, several studies have demonstrated an association between African ancestry with increased asthma susceptibility and severity, higher immunoglobulin E levels, and lower lung function. In contrast, Native American ancestry has been shown to have a protective role for this disease. Genome-wide association studies have allowed the identification of population-specific genetic variants with varying allele frequency among populations. Additionally, the correlation of genetic ancestry at the chromosomal level with asthma and related traits by means of admixture mapping has revealed regions of the genome where ancestry is correlated with the disease. In this review, we discuss the evidence supporting the association of genetic ancestry with asthma susceptibility and asthma-related traits, and highlight the regions of the genome harboring ancestry-specific genetic risk factors.
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Palmer C, Pe’er I. Statistical correction of the Winner's Curse explains replication variability in quantitative trait genome-wide association studies. PLoS Genet 2017; 13:e1006916. [PMID: 28715421 PMCID: PMC5536394 DOI: 10.1371/journal.pgen.1006916] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 07/31/2017] [Accepted: 07/10/2017] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified hundreds of SNPs responsible for variation in human quantitative traits. However, genome-wide-significant associations often fail to replicate across independent cohorts, in apparent inconsistency with their apparent strong effects in discovery cohorts. This limited success of replication raises pervasive questions about the utility of the GWAS field. We identify all 332 studies of quantitative traits from the NHGRI-EBI GWAS Database with attempted replication. We find that the majority of studies provide insufficient data to evaluate replication rates. The remaining papers replicate significantly worse than expected (p < 10-14), even when adjusting for regression-to-the-mean of effect size between discovery- and replication-cohorts termed the Winner's Curse (p < 10-16). We show this is due in part to misreporting replication cohort-size as a maximum number, rather than per-locus one. In 39 studies accurately reporting per-locus cohort-size for attempted replication of 707 loci in samples with similar ancestry, replication rate matched expectation (predicted 458, observed 457, p = 0.94). In contrast, ancestry differences between replication and discovery (13 studies, 385 loci) cause the most highly-powered decile of loci to replicate worse than expected, due to difference in linkage disequilibrium.
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Affiliation(s)
- Cameron Palmer
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Computer Science, Columbia University, New York, New York, United States of America
| | - Itsik Pe’er
- Department of Computer Science, Columbia University, New York, New York, United States of America
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Metti AL, Rosano C, Boudreau R, Massa R, Yaffe K, Satterfield S, Harris T, Rosso AL. Catechol-O-Methyltransferase Genotype and Gait Speed Changes over 10 Years in Older Adults. J Am Geriatr Soc 2017. [PMID: 28640434 DOI: 10.1111/jgs.14980] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To determine the association between catechol-O-methyltransferase (COMT) genotype and 6-m walk time and to determine whether these associations are quadratic in nature, similar to previously reported U-shaped associations between dopamine and gait and cognition. DESIGN Prospective cohort study. SETTING Health, Aging and Body Composition Study. PARTICIPANTS Black (n = 850) and white (n = 1,352) men and women with a mean age of 73.5 ± 2.85 at baseline. MEASUREMENTS Mixed models were used to assess the association between the COMT genotype and 6-m walk time, cross-sectionally and longitudinally over 10 years. Models were assessed unstratified and stratified according to race because allele distributions were different between white and black participants. RESULTS There was a significant U-shaped association between COMT genotype and 6-m walk time: those with higher (Val/Val) and lower (Met/Met) dopamine slowed more over 10 years (0.22 ± 0.02 seconds per visit and 0.23 ± 0.02 seconds per visit, respectively) than those with the intermediate (Met/Val) dopamine (0.20 ± 0.02 seconds per visit) (P = .005). Stratified results showed a significant relationship in black (P = .01) but not white (P = .15) participants. CONCLUSION These findings indicate a role of dopaminergic regulation of gait speed in community-dwelling older adults and of prefrontal cortex involvement in gait performance. Future work should investigate the molecular integrity of dopaminergic networks and gait changes over time and structural changes in the brain with COMT and gait decline in older adults.
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Affiliation(s)
- Andrea L Metti
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Caterina Rosano
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Robert Boudreau
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Robyn Massa
- Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kristine Yaffe
- Department of Psychiatry, University of California San Francisco, San Francisco, California.,Department of Neurology, University of California San Francisco, San Francisco, California.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Suzanne Satterfield
- Department of Preventive Medicine, University of Tennessee at Memphis, Memphis, Tennessee
| | - Tamara Harris
- Laboratory of Epidemiology and Population Sciences, Intramural Research Program, National Institute on Aging, Bethesda, Maryland
| | - Andrea L Rosso
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
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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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Modi BP, Teves ME, Pearson LN, Parikh HI, Chaemsaithong P, Sheth NU, York TP, Romero R, Strauss JF. Rare mutations and potentially damaging missense variants in genes encoding fibrillar collagens and proteins involved in their production are candidates for risk for preterm premature rupture of membranes. PLoS One 2017; 12:e0174356. [PMID: 28346524 PMCID: PMC5367779 DOI: 10.1371/journal.pone.0174356] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 03/07/2017] [Indexed: 12/22/2022] Open
Abstract
Preterm premature rupture of membranes (PPROM) is the leading identifiable cause of preterm birth with ~ 40% of preterm births being associated with PPROM and occurs in 1% - 2% of all pregnancies. We hypothesized that multiple rare variants in fetal genes involved in extracellular matrix synthesis would associate with PPROM, based on the assumption that impaired elaboration of matrix proteins would reduce fetal membrane tensile strength, predisposing to unscheduled rupture. We performed whole exome sequencing (WES) on neonatal DNA derived from pregnancies complicated by PPROM (49 cases) and healthy term deliveries (20 controls) to identify candidate mutations/variants. Genotyping for selected variants from the WES study was carried out on an additional 188 PPROM cases and 175 controls. All mothers were self-reported African Americans, and a panel of ancestry informative markers was used to control for genetic ancestry in all genetic association tests. In support of the primary hypothesis, a statistically significant genetic burden (all samples combined, SKAT-O p-value = 0.0225) of damaging/potentially damaging rare variants was identified in the genes of interest-fibrillar collagen genes, which contribute to fetal membrane strength and integrity. These findings suggest that the fetal contribution to PPROM is polygenic, and driven by an increased burden of rare variants that may also contribute to the disparities in rates of preterm birth among African Americans.
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Affiliation(s)
- Bhavi P. Modi
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Maria E. Teves
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Laurel N. Pearson
- Department of Anthropology, Pennsylvania State University, University Park, PA, United States of America
| | - Hardik I. Parikh
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Piya Chaemsaithong
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute for Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, United States of America
| | - Nihar U. Sheth
- Center for Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Timothy P. York
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Roberto Romero
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute for Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI, United States of America
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, United States of America
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States of America
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States of America
| | - Jerome F. Strauss
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, United States of America
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Polygenic risk assessment reveals pleiotropy between sarcoidosis and inflammatory disorders in the context of genetic ancestry. Genes Immun 2017; 18:88-94. [PMID: 28275240 PMCID: PMC5407914 DOI: 10.1038/gene.2017.3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/07/2016] [Accepted: 11/21/2016] [Indexed: 12/26/2022]
Abstract
Sarcoidosis is a complex disease of unknown etiology characterized by the presence of granulomatous inflammation. Though various immune system pathways have been implicated in disease, the relationship between the genetic determinants of sarcoidosis and other inflammatory disorders has not been characterized. Herein, we examined the degree of genetic pleiotropy common to sarcoidosis and other inflammatory disorders to identify shared pathways and disease systems pertinent to sarcoidosis onset. To achieve this, we quantify the association of common variant polygenic risk scores from nine complex inflammatory disorders with sarcoidosis risk. Enrichment analyses of genes implicated in pleiotropic associations were further used to elucidate candidate pathways. In European-Americans, we identify significant pleiotropy between risk of sarcoidosis and risk of asthma (R2=2.03%; p=8.89×10−9), celiac disease (R2=2.03%; p=8.21×10−9), primary biliary cirrhosis (R2=2.43%; p=2.01×10−10), and rheumatoid arthritis (R2=4.32%; p=2.50×10−17). These associations validate in African Americans only after accounting for the proportion of genome-wide European ancestry, where we demonstrate similar effects of polygenic risk for African-Americans with the highest levels of European ancestry. Variants and genes implicated in European-American pleiotropic associations were enriched for pathways involving interleukin-12, interleukin-27, and cell adhesion molecules, corroborating the hypothesized immunopathogenesis of disease.
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Moreno DJ, Ruiz S, Ríos Á, Lopera F, Ostos H, Via M, Bedoya G. Association of GWAS Top Genes With Late-Onset Alzheimer's Disease in Colombian Population. Am J Alzheimers Dis Other Demen 2017; 32:27-35. [PMID: 28084078 PMCID: PMC10857032 DOI: 10.1177/1533317516679303] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The association of variants in CLU, CR1, PICALM, BIN1, ABCA7, and CD33 genes with late-onset Alzheimer's disease (LOAD) was evaluated and confirmed through genome-wide association study. However, it is unknown whether these associations can be replicated in admixed populations. METHODS The association of 14 single-nucleotide polymorphisms in those genes was evaluated in 280 LOAD cases and 357 controls from the Colombian population. RESULTS In a multivariate analysis using age, gender, APOE∊4 status, and admixture covariates, significant associations were obtained ( P < .05) for variants in BIN1 (rs744373, odds ratio [OR]: 1.42), CLU (rs11136000, OR: 0.66), PICALM (rs541458, OR: 0.69), ABCA7 (rs3764650, OR: 1.7), and CD33 (rs3865444, OR: 1.12). Likewise, a significant interaction effect was observed between CLU and CR1 variants with APOE. CONCLUSION This study replicated the associations previously reported in populations of European ancestry and shows that APOE variants have a regulatory role on the effect that variants in other loci have on LOAD, reflecting the importance of gene-gene interactions in the etiology of neurodegenerative diseases.
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Affiliation(s)
| | - Susana Ruiz
- Grupo de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
| | - Ángela Ríos
- Grupo de Neuropsicología, Universidad Surcolombiana, Neiva, Colombia
| | - Francisco Lopera
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - Henry Ostos
- Grupo de Medicina Genómica, Universidad Surcolombiana, Neiva, Colombia
| | - Marc Via
- Psicologia Clínica i Psicobiologia and Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Gabriel Bedoya
- Grupo de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
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Thakur N, White MJ, Burchard EG. Race and Ethnicity. Respir Med 2017. [DOI: 10.1007/978-3-319-43447-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Circadian rhythms of European and African-Americans after a large delay of sleep as in jet lag and night work. Sci Rep 2016; 6:36716. [PMID: 27819313 PMCID: PMC5098183 DOI: 10.1038/srep36716] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/17/2016] [Indexed: 12/31/2022] Open
Abstract
Jet travel and night shift work produce large changes in when people sleep, work and eat; a challenge that was not encountered during most of our evolution. Successful adaptation would require the internal, master, circadian clock to make large phase shifts to reduce the circadian misalignment between circadian rhythms and the times for sleep, work and meals. We compared African-Americans and non-Hispanic European-Americans in how much their circadian clocks shifted after a 9 hour phase delay of the light/dark, sleep/wake and meal schedule, which has similarities to flying west or sleeping in the daytime after night shifts. We also measured their free-running circadian periods using a forced desynchrony protocol with a 5-h day. European-Americans had longer free-running periods and larger phase delays than African-Americans. Correlations (among all subjects, just African-Americans and just European-Americans) showed that longer circadian periods were associated with larger phase delays. Larger phase delays, facilitated by longer circadian periods, reduce jet lag after westward travel and make it easier to work night shifts and sleep during the daytime after night work. On the other hand, a shorter circadian period, which makes one more of a morning-type person, is better for most people given our early-bird dominated society.
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Rao R, Rivers A, Rahimi A, Wooldridge R, Rao M, Leitch M, Euhus D, Haley BB. Genetic Ancestry using Mitochondrial DNA in patients with Triple-negative breast cancer (GAMiT study). Cancer 2016; 123:107-113. [PMID: 27584945 DOI: 10.1002/cncr.30267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/27/2016] [Accepted: 07/27/2016] [Indexed: 12/26/2022]
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) lacks estrogen, progesterone, and human epidermal growth factor receptor 2 (HER2)/neu receptors, and is aggressive and therapeutically challenging. Genetic ancestry testing is an emerging medical field. Mitochondrial DNA (mtDNA), which is distinct from nuclear DNA, is maternally inherited and allows for origin determination. Patients with TNBC tend to be younger and are more likely to be African American, making this an ideal disease for mtDNA exploration. To the authors' knowledge, the current study is the first to perform mtDNA for self-described African American, White, and Hispanic patients with TNBC to identify mtDNA patterns. METHODS Patients with TNBC who were at any stage of therapy/survivorship were included. Self-reported ethnicity was confirmed at the time of the prospective buccal swab. Haplogroup prediction was performed on sequencing of hypervariable region 1. Using sequence similarity scores and lineage databases, sequence patterns were determined. Data regarding presentation and treatment, tumor features, and outcomes was collected. RESULTS A total of 92 patients were included: 31 self-described African American, 31 White, and 30 Hispanic individuals. Hispanic patients were found to have the largest tumor size (4.5 cm; P = .01) and youngest age (41 years; P<.0001). Eight patients were BRCA1/2 mutation carriers. There were no differences noted among groups with regard to surgery, lymph node metastases, or survival. Analysis revealed Nigerian, Cameroon, or Sierra Leone ancestry and haplogroups A, U, H, or B to be the most common mtDNA patterns. Twelve discordances (13%) between mtDNA analysis and self-described ethnicity were identified among the 92 patients. The highest discordance (26%; 8 patients) was noted in self-described Hispanic patients: 3 had Nigerian ancestry, and 1 individual demonstrated haplogroup K mtDNA (Ashkenazi Jewish ancestry). CONCLUSIONS Discordance between self-reported ethnicity and mtDNA analysis was identified in 13% of patients with TNBC. The identification of mtDNA patterns with a predisposition toward TNBC may allow for risk stratification. Cancer 2017;107-113. © 2016 American Cancer Society.
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Affiliation(s)
- Roshni Rao
- Division of Surgical Oncology, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Aeisha Rivers
- Division of Surgical Oncology, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Asal Rahimi
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Rachel Wooldridge
- Division of Surgical Oncology, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Madhu Rao
- Division of Surgical Oncology, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Marilyn Leitch
- Division of Surgical Oncology, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, Texas
| | - David Euhus
- Division of Surgical Oncology, Department of Surgery, The Johns Hopkins Hospital, Baltimore, Maryland
| | - Barbara B Haley
- Division of Medical Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
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Fox K, Johnsen JM, Coe BP, Frazar CD, Reiner AP, Eichler EE, Nickerson DA. Analysis of exome sequencing data sets reveals structural variation in the coding region ofABOin individuals of African ancestry. Transfusion 2016; 56:2744-2749. [DOI: 10.1111/trf.13797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/06/2016] [Accepted: 07/07/2016] [Indexed: 12/26/2022]
Affiliation(s)
| | - Jill M. Johnsen
- Hematology Division; University of Washington, School of Medicine
- Bloodworks Northwest
| | | | | | - Alexander P. Reiner
- Public Health Sciences Division; Fred Hutchinson Cancer Research Center
- Department of Epidemiology; University of Washington, School of Public Health
| | - Evan E. Eichler
- Department of Genome Sciences
- Howard Hughes Medical Institute; Seattle Washington
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Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity. Sci Rep 2016; 6:31775. [PMID: 27558272 PMCID: PMC4997337 DOI: 10.1038/srep31775] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/27/2016] [Indexed: 12/29/2022] Open
Abstract
The joint impact of pregnancy, environmental, and sociocultural exposures on early life gut microbiome is not yet well-characterized, especially in racially and socioeconomically diverse populations. Gut microbiota of 298 children from a Detroit-based birth cohort were profiled using 16S rRNA sequencing: 130 neonates (median age = 1.2 months) and 168 infants (median age = 6.6 months). Multiple factors were associated with neonatal gut microbiome composition in both single- and multi-factor models, with independent contributions of maternal race-ethnicity, breastfeeding, mode of delivery, marital status, exposure to environmental tobacco smoke, and indoor pets. These findings were consistent in the infants, and networks demonstrating the shared impact of factors on gut microbial composition also showed notable topological similarity between neonates and infants. Further, latent groups defined by these factors explained additional variation, highlighting the importance of combinatorial effects. Our findings also have implications for studies investigating the impact of the early life gut microbiota on disease.
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Muñoz AM, Velásquez CM, Bedoya G. Cardio-metabolic parameters are associated with genetic admixture estimates in a pediatric population from Colombia. BMC Genet 2016; 17:93. [PMID: 27350247 PMCID: PMC4924275 DOI: 10.1186/s12863-016-0402-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 06/17/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND There are different genetic patterns for cardio-metabolic parameters among different populations. Additionally, it has been found that ancestral genetic components (the proportion of Amerindian, European and African) in admixed Latin American populations influence an individual's susceptibility to cardio-metabolic disorders. The aim of this study was to evaluate the effect of ancestral genetic composition on a series of cardio-metabolic risk factors in a young admixed population from Colombia. RESULTS In a sample of 853 Colombian youth, 10 to 18 years old, the mean European contribution was 66.6 % (range: 41-82 %), the mean African contribution was 14 % (range: 4-48 %), and the mean Amerindian contribution was 19.4 % (range: 10-35 %) using a panel of 40 autosomal ancestry-informative markers (AIMs). We assessed the degree of association between ancestral African, Amerindian and European genetic components and measures of body mass index, waist circumference, fasting glucose, fasting insulin, insulin resistance, triglycerides, high-density lipoprotein, and systolic and diastolic blood pressure. Two of the nine measures assessed presented a nominal significant association with ancestral components after adjusting for confounding variables: triglyceride levels were associated with the Amerindian component (OR = 1.06, 98.3 % CI = 1.01-1.11, P = 0.002) and systolic blood pressure was associated with the European component (OR = 0.93, 98.3 % CI = 0.87 to 0.99, P = 0.008) and the African component (OR = 1.07, CI = 1.01-1.14 P = 0.008), although it was not significant following a global Bonferroni correction. Additionally, insulin levels and insulin resistance showed associations with the African component. CONCLUSIONS Our findings support the idea that an Amerindian ancestral component may act as a risk factor for high triglyceride levels. In addition, an African ancestral component confers a risk for high systolic blood pressure, and a European ancestry serves as a protective factor for this condition in a young admixed population from Colombia. However, these results should be confirmed in a larger population.
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Affiliation(s)
- Angélica M Muñoz
- Research Group on Food and Human Nutrition, Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia. .,Laboratorio 413, Sede de Investigación Universitaria (SIU), Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia.
| | - Claudia M Velásquez
- Research Group on Food and Human Nutrition, Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia
| | - Gabriel Bedoya
- Research Group on Molecular Genetic (GENMOL), Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia
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Gichohi-Wainaina WN, Tanaka T, Towers GW, Verhoef H, Veenemans J, Talsma EF, Harryvan J, Boekschoten MV, Feskens EJ, Melse-Boonstra A. Associations between Common Variants in Iron-Related Genes with Haematological Traits in Populations of African Ancestry. PLoS One 2016; 11:e0157996. [PMID: 27332551 PMCID: PMC4917107 DOI: 10.1371/journal.pone.0157996] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 06/08/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Large genome-wide association (GWA) studies of European ancestry individuals have identified multiple genetic variants influencing iron status. Studies on the generalizability of these associations to African ancestry populations have been limited. These studies are important given interethnic differences in iron status and the disproportionate burden of iron deficiency among African ancestry populations. METHODS We tested the associations of 20 previously identified iron status-associated single nucleotide polymorphisms (SNPs) in 628 Kenyans, 609 Tanzanians, 608 South Africans and 228 African Americans. In each study, we examined the associations present between 20 SNPs with ferritin and haemoglobin, adjusting for age, sex and CRP levels. RESULTS In the meta analysis including all 4 African ancestry cohorts, we replicated previously reported associations with lowered haemoglobin concentrations for rs2413450 (β = -0.19, P = 0.02) and rs4820268 (β = -0.16, P = 0.04) in TMPRSS6. An association with increased ferritin concentrations was also confirmed for rs1867504 in TF (β = 1.04, P = <0.0001) in the meta analysis including the African cohorts only. CONCLUSIONS In all meta analyses, we only replicated 4 of the 20 single nucleotide polymorphisms reported to be associated with iron status in large GWA studies of European ancestry individuals. While there is now evidence for the associations of a number of genetic variants with iron status in both European and African ancestry populations, the considerable lack of concordance highlights the importance of continued ancestry-specific studies to elucidate the genetic underpinnings of iron status in ethnically diverse populations.
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Affiliation(s)
- Wanjiku N. Gichohi-Wainaina
- Division of Human Nutrition, Wageningen University, Wageningen, the Netherlands
- International institute of Tropical Agriculture (IITA), Dar es Salaam, Tanzania
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, United States of America
| | - G. Wayne Towers
- Centre of Excellence for Nutrition, North-West University (Potchefstroom campus), Potchefstroom, South Africa
| | - Hans Verhoef
- Cell Biology and Immunology Group, Wageningen University, Wageningen, The Netherlands
- Medical Research Council (MRC) International Nutrition Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Medical Research Council Banjul, The Gambia
| | - Jacobien Veenemans
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands
- Department of Medical Microbiology and Immunology, Admiraal De Ruyter Hospital, Goes The Netherlands
| | - Elise F. Talsma
- Division of Human Nutrition, Wageningen University, Wageningen, the Netherlands
- HarvestPlus, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Jan Harryvan
- Division of Human Nutrition, Wageningen University, Wageningen, the Netherlands
| | - Mark V. Boekschoten
- Nutrition, Metabolism and Genomics group, Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands
| | - Edith J. Feskens
- Division of Human Nutrition, Wageningen University, Wageningen, the Netherlands
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Baharian S, Barakatt M, Gignoux CR, Shringarpure S, Errington J, Blot WJ, Bustamante CD, Kenny EE, Williams SM, Aldrich MC, Gravel S. The Great Migration and African-American Genomic Diversity. PLoS Genet 2016; 12:e1006059. [PMID: 27232753 PMCID: PMC4883799 DOI: 10.1371/journal.pgen.1006059] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/26/2016] [Indexed: 12/23/2022] Open
Abstract
We present a comprehensive assessment of genomic diversity in the African-American population by studying three genotyped cohorts comprising 3,726 African-Americans from across the United States that provide a representative description of the population across all US states and socioeconomic status. An estimated 82.1% of ancestors to African-Americans lived in Africa prior to the advent of transatlantic travel, 16.7% in Europe, and 1.2% in the Americas, with increased African ancestry in the southern United States compared to the North and West. Combining demographic models of ancestry and those of relatedness suggests that admixture occurred predominantly in the South prior to the Civil War and that ancestry-biased migration is responsible for regional differences in ancestry. We find that recent migrations also caused a strong increase in genetic relatedness among geographically distant African-Americans. Long-range relatedness among African-Americans and between African-Americans and European-Americans thus track north- and west-bound migration routes followed during the Great Migration of the twentieth century. By contrast, short-range relatedness patterns suggest comparable mobility of ∼15–16km per generation for African-Americans and European-Americans, as estimated using a novel analytical model of isolation-by-distance. Genetic studies of African-Americans identify functional variants, elucidate historical and genealogical mysteries, and reveal basic biology. However, African-Americans have been under-represented in genetic studies, and relatively little is known about nation-wide patterns of genomic diversity in the population. Here, we study African-American genomic diversity using genotype data from nationally and regionally representative cohorts. Access to these unique cohorts allows us to clarify the role of population structure, admixture, and recent massive migrations in shaping African-American genomic diversity and sheds new light on the genetic history of this population.
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Affiliation(s)
- Soheil Baharian
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Maxime Barakatt
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
- School of Computer Science, McGill University, Montreal, Quebec, Canada
| | - Christopher R. Gignoux
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Suyash Shringarpure
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jacob Errington
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - William J. Blot
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- International Epidemiology Institute, Rockville, Maryland, United States of America
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Eimear E. Kenny
- Department of Genetics and Genomic Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Center for Statistical Genetics, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Scott M. Williams
- Department of Genetics, Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Melinda C. Aldrich
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Thoracic Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Simon Gravel
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
- * E-mail:
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Oetjens MT, Brown-Gentry K, Goodloe R, Dilks HH, Crawford DC. Population Stratification in the Context of Diverse Epidemiologic Surveys Sans Genome-Wide Data. Front Genet 2016; 7:76. [PMID: 27200085 PMCID: PMC4858524 DOI: 10.3389/fgene.2016.00076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 04/18/2016] [Indexed: 01/01/2023] Open
Abstract
Population stratification or confounding by genetic ancestry is a potential cause of false associations in genetic association studies. Estimation of and adjustment for genetic ancestry has become common practice thanks in part to the availability of ancestry informative markers on genome-wide association study (GWAS) arrays. While array data is now widespread, these data are not ubiquitous as several large epidemiologic and clinic-based studies lack genome-wide data. One such large epidemiologic-based study lacking genome-wide data accessible to investigators is the National Health and Nutrition Examination Surveys (NHANES), population-based cross-sectional surveys of Americans linked to demographic, health, and lifestyle data conducted by the Centers for Disease Control and Prevention. DNA samples (n = 14,998) were extracted from biospecimens from consented NHANES participants between 1991-1994 (NHANES III, phase 2) and 1999-2002 and represent three major self-identified racial/ethnic groups: non-Hispanic whites (n = 6,634), non-Hispanic blacks (n = 3,458), and Mexican Americans (n = 3,950). We as the Epidemiologic Architecture for Genes Linked to Environment study genotyped candidate gene and GWAS-identified index variants in NHANES as part of the larger Population Architecture using Genomics and Epidemiology I study for collaborative genetic association studies. To enable basic quality control such as estimation of genetic ancestry to control for population stratification in NHANES san genome-wide data, we outline here strategies that use limited genetic data to identify the markers optimal for characterizing genetic ancestry. From among 411 and 295 autosomal SNPs available in NHANES III and NHANES 1999-2002, we demonstrate that markers with ancestry information can be identified to estimate global ancestry. Despite limited resolution, global genetic ancestry is highly correlated with self-identified race for the majority of participants, although less so for ethnicity. Overall, the strategies outlined here for a large epidemiologic study can be applied to other datasets accessible for genotype-phenotype studies but are sans genome-wide data.
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Affiliation(s)
- Matthew T. Oetjens
- Center for Human Genetics Research Vanderbilt University, NashvilleTN, USA
| | | | - Robert Goodloe
- Center for Human Genetics Research Vanderbilt University, NashvilleTN, USA
| | | | - Dana C. Crawford
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University, ClevelandOH, USA
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Feibus AH, Levy J, McCaslin IR, Doucet ME, Sholl AB, Moparty K, Thomas R, Sartor O, Silberstein JL. Racial variation in prostate needle biopsy templates directed anterior to the peripheral zone. Urol Oncol 2016; 34:336.e1-6. [PMID: 27155916 DOI: 10.1016/j.urolonc.2016.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 03/22/2016] [Accepted: 03/28/2016] [Indexed: 10/21/2022]
Abstract
OBJECTIVES African Americans (AA) have been reported to have both increased incidence and increased aggressiveness of prostate cancer (PCa) located anterior to the peripheral zone (APZ). We sought to evaluate the utility of prostate biopsies directed toward the APZ in a predominantly AA cohort. METHODS AND MATERIALS We reviewed all patients with PCa found on biopsy schema that included needle biopsies directed at both the peripheral zone (PZ) and APZ from 2010 to 2014. Self-identified race was recorded for all patients. To evaluate the reliability of APZ-directed prostate biopsies, we performed pathologic secondary review of 25 radical prostatectomy specimens. A series of the Mann-Whitney U and Chi-square tests were used to compare variables. RESULTS We identified 398 men, of which 277 (70%) were AA. Compared with non-AA, AA had more National Comprehensive Cancer Network-defined intermediate or high-risk (50% vs. 39%, P = 0.25) PCa. Most patients had PCa limited to the PZ only (n = 190) or in both the PZ and APZ (n = 191). For 17 patients (4%), PCa was limited only to the APZ core(s), 14 (5%) AA vs. 3 (2%) non-AA (P = 0.24). Most of these 17 patients (n = 14, 82%) had Gleason 6 disease. Patients with PCa in both the PZ and APZ had higher serum prostate-specific antigen, prostate-specific antigen density, volume of disease, and increased grade and National Comprehensive Cancer Network category (all P<0.01). Of these patients, there were no differences in race (AA = 135, 71% vs. non-AA = 56, 29%; P = 0.48). In only 21 men (11%), without racial variation, APZ tumor grade was greater than PZ. Radical prostatectomy and APZ-directed biopsies demonstrated a concordance rate of 80% (20/25), false positive rate of 8% (2/25), and false negative rate of 12% (3/25). CONCLUSIONS APZ-directed prostate biopsies are rarely the sole location of PCa and do not show a clear racial predilection. In those men with PCa identified in both regions, the APZ biopsy did not frequently change treatment recommendations. Biopsies directed at the APZ are not of greater benefit to AA than non-AA.
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Affiliation(s)
- Allison H Feibus
- Department of Urology, Tulane University School of Medicine, New Orleans, LA; Southeast Louisiana Veterans Health Care Services, New Orleans, LA
| | - Justin Levy
- Department of Urology, Tulane University School of Medicine, New Orleans, LA
| | - Ian R McCaslin
- Department of Urology, Tulane University School of Medicine, New Orleans, LA
| | - Meggie E Doucet
- Department of Pathology, Tulane University School of Medicine, New Orleans, LA
| | - Andrew B Sholl
- Department of Pathology, Tulane University School of Medicine, New Orleans, LA
| | - Krishnarao Moparty
- Department of Urology, Tulane University School of Medicine, New Orleans, LA; Southeast Louisiana Veterans Health Care Services, New Orleans, LA
| | - Raju Thomas
- Department of Urology, Tulane University School of Medicine, New Orleans, LA; Southeast Louisiana Veterans Health Care Services, New Orleans, LA
| | - Oliver Sartor
- Department of Urology, Tulane University School of Medicine, New Orleans, LA
| | - Jonathan L Silberstein
- Department of Urology, Tulane University School of Medicine, New Orleans, LA; Southeast Louisiana Veterans Health Care Services, New Orleans, LA.
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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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Ni X, Guo W, Yuan K, Yang X, Ma Z, Xu S, Zhang S. A Probabilistic Method for Estimating the Sharing of Identity by Descent for Populations with Migration. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:281-290. [PMID: 26394436 DOI: 10.1109/tcbb.2015.2480074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The inference of demographic history of populations is an important undertaking in population genetics. A few recent studies have developed identity-by-descent (IBD) based methods to reveal the signature of the relatively recent historical events. Notably, Pe'er and his colleagues have introduced a novel method (named PIBD here) by employing IBD sharing to infer effective population size and migration rate. However, under island model, PIBD neglects the coalescent information before the time to the most recent common ancestor (tMRCA) which leads to apparent deviations in certain situations. In this paper, we propose a new method, MIBD, by adopting a Markov process to describe the island model and develop a new formula for estimating IBD sharing. The new formula considers the coalescent information before tMRCA and the joint effect of the coalescent and migration events. We apply both MIBD and PIBD to the genome-wide data of two human populations (Palestinian and Bedouin) obtained from the HGDP-CEPH database, and demonstrate that MIBD is competitive to PIBD. Our simulation analyses also show that the results of MIBD are more accurate than those of PIBD especially in the case of small effective population size.
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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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Aleluia MM, Mello MAG, Alcântara LCJ, Rego FFA, de Souza Santos LP, Galvão-Castro B, de Souza Gonçalves M, de Oliveira T, Marin LJ, Sousa SMB, Gadelha SR. The origin of HTLV-1 in southern Bahia by phylogenetic, mtDNA and β-globin analysis. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.virep.2015.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Rocconi RP, Lankes HA, Brady WE, Goodfellow PJ, Ramirez NC, Alvarez RD, Creasman W, Fernández JR. The role of racial genetic admixture with endometrial cancer outcomes: An NRG Oncology/Gynecologic Oncology Group study. Gynecol Oncol 2015; 140:264-9. [PMID: 26603970 DOI: 10.1016/j.ygyno.2015.11.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 10/21/2015] [Accepted: 11/17/2015] [Indexed: 11/19/2022]
Abstract
PURPOSE Racial genetic admixture (RGA), a measure to account for ancestral genetic background that correlates with individual's racial classification, could provide insights on causation of racial disparity in endometrial cancer (EC). Our objective is to evaluate the association of RGA with EC outcomes. METHODS EC patients enrolled onto the GOG-210 protocol were eligible. A randomized subcohort stratified by stage and self-reported race/ethnicity of black or white was used. Genotyping was performed using custom-selected Ancestry Informative Markers to calculate individual admixture estimates of African and European ancestral background. RESULTS A total of 149 patients were evaluated (self-reported race: 70 black & 79 white). Mean RGA for African ancestry for self-reported black patients was 0.65 (range 0.04-0.86); while mean RGA for European ancestry for self-reported white patients was 0.77 (range 0.12-0.88). Progression-free survival (PFS) analysis using proportional hazards models stratified by stage and race revealed that each 0.10 increase in African ancestry was associated with worse PFS with hazard ratio (HR) of 1.11 (95% CI 0.90-1.37). Each 0.10 increase in European RGA was associated with improved PFS with HR of 0.86 (95% CI 0.69-1.07). Using tertiles of African RGA showed increasing risk of progression of death with increasing African RGA (with 0-5% as reference), HR (95% CIs) for top two tertiles are: 6%-66%: 1.38 (0.64, 2.97), and 67%-86%: 2.27 (0.74, 6.95). CONCLUSION RGA demonstrated a trend with PFS in self-reported black and white patients with EC. Patients with increased levels of African ancestry showed a trend towards worse survival after stratifying by stage/race.
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Affiliation(s)
- Rodney P Rocconi
- Mitchell Cancer Institute, University Of South Alabama, Mobile, AL, USA.
| | | | | | | | - Nilsa C Ramirez
- The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.
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Jhun EH, Yao Y, He Y, Mack AK, Wilkie DJ, Molokie RE, Wang ZJ. Prevalence of pain-related single nucleotide polymorphisms in patients of African origin with sickle cell disease. Pharmacogenomics 2015; 16:1795-806. [PMID: 26555434 DOI: 10.2217/pgs.15.126] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Prospective pain genetics research is hindered by a lack of data on the prevalence of polymorphisms in pain-relevant genes for patients with sickle cell disease (SCD). For African-Americans in general, limited information is available in public databases. METHODS We prioritized and examined the genotype and allele frequencies of 115 SNPs from 49 candidate pain genes in 199 adult African-Americans and pediatric patients of African origin with SCD. Analyses were performed and compared with available data from public databases. RESULTS Genotype and allele frequencies of a number of SNPs were found to be different between our cohort and those from the databases and between adult and pediatric subjects. CONCLUSION As pain therapy is inadequate in a significant percentage of patients with SCD, candidate pain genetic studies may aid in designing precision pain medicine. We provide prevalence data as a reference for prospective genetic studies in this population.
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Affiliation(s)
- Ellie H Jhun
- Department of Biopharmaceutical Sciences, University of Illinois at Chicago College of Pharmacy, Chicago, IL, USA
| | - Yingwei Yao
- Department of Biobehavioral Nursing Science, University of Florida College of Nursing, Gainsville, FL, USA.,Department of Biobehavioral Health Science, University of Illinois at Chicago College of Nursing, Chicago, IL, USA
| | - Ying He
- Department of Biopharmaceutical Sciences, University of Illinois at Chicago College of Pharmacy, Chicago, IL, USA
| | - A Kyle Mack
- Northwestern University-Feinberg School of Medicine, Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Children's Memorial Hospital, Chicago, IL, USA
| | - Diana J Wilkie
- Department of Biobehavioral Nursing Science, University of Florida College of Nursing, Gainsville, FL, USA.,Department of Biobehavioral Health Science, University of Illinois at Chicago College of Nursing, Chicago, IL, USA
| | - Robert E Molokie
- Department of Biopharmaceutical Sciences, University of Illinois at Chicago College of Pharmacy, Chicago, IL, USA
| | - Zaijie Jim Wang
- Department of Biopharmaceutical Sciences, University of Illinois at Chicago College of Pharmacy, Chicago, IL, USA
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Zheng J, Rao DC, Shi G. An update on genome-wide association studies of hypertension. ACTA ACUST UNITED AC 2015. [DOI: 10.1186/s40535-015-0013-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Mersha TB. Mapping asthma-associated variants in admixed populations. Front Genet 2015; 6:292. [PMID: 26483834 PMCID: PMC4586512 DOI: 10.3389/fgene.2015.00292] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/03/2015] [Indexed: 12/19/2022] Open
Abstract
Admixed populations arise when two or more previously isolated populations interbreed. Mapping asthma susceptibility loci in an admixed population using admixture mapping (AM) involves screening the genome of individuals of mixed ancestry for chromosomal regions that have a higher frequency of alleles from a parental population with higher asthma risk as compared with parental population with lower asthma risk. AM takes advantage of the admixture created in populations of mixed ancestry to identify genomic regions where an association exists between genetic ancestry and asthma (in contrast to between the genotype of the marker and asthma). The theory behind AM is that chromosomal segments of affected individuals contain a significantly higher-than-average proportion of alleles from the high-risk parental population and thus are more likely to harbor disease-associated loci. Criteria to evaluate the applicability of AM as a gene mapping approach include: (1) the prevalence of the disease differences in ancestral populations from which the admixed population was formed; (2) a measurable difference in disease-causing alleles between the parental populations; (3) reduced linkage disequilibrium (LD) between unlinked loci across chromosomes and strong LD between neighboring loci; (4) a set of markers with noticeable allele-frequency differences between parental populations that contributes to the admixed population (single nucleotide polymorphisms (SNPs) are the markers of choice because they are abundant, stable, relatively cheap to genotype, and informative with regard to the LD structure of chromosomal segments); and (5) there is an understanding of the extent of segmental chromosomal admixtures and their interactions with environmental factors. Although genome-wide association studies have contributed greatly to our understanding of the genetic components of asthma, the large and increasing degree of admixture in populations across the world create many challenges for further efforts to map disease-causing genes. This review, summarizes the historical context of admixed populations and AM, and considers current opportunities to use AM to map asthma genes. In addition, we provide an overview of the potential limitations and future directions of AM in biomedical research, including joint admixture and association mapping for asthma and asthma-related disorders.
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Affiliation(s)
- Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati Cincinnati, OH, USA
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Rao G, Powell-Wiley TM, Ancheta I, Hairston K, Kirley K, Lear SA, North KE, Palaniappan L, Rosal MC. Identification of Obesity and Cardiovascular Risk in Ethnically and Racially Diverse Populations: A Scientific Statement From the American Heart Association. Circulation 2015; 132:457-72. [PMID: 26149446 DOI: 10.1161/cir.0000000000000223] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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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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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Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort. Genetics 2015; 200:1285-95. [PMID: 26092716 DOI: 10.1534/genetics.115.178616] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 06/02/2015] [Indexed: 01/06/2023] Open
Abstract
Using genome-wide genotypes, we characterized the genetic structure of 103,006 participants in the Kaiser Permanente Northern California multi-ethnic Genetic Epidemiology Research on Adult Health and Aging Cohort and analyzed the relationship to self-reported race/ethnicity. Participants endorsed any of 23 race/ethnicity/nationality categories, which were collapsed into seven major race/ethnicity groups. By self-report the cohort is 80.8% white and 19.2% minority; 93.8% endorsed a single race/ethnicity group, while 6.2% endorsed two or more. Principal component (PC) and admixture analyses were generally consistent with prior studies. Approximately 17% of subjects had genetic ancestry from more than one continent, and 12% were genetically admixed, considering only nonadjacent geographical origins. Self-reported whites were spread on a continuum along the first two PCs, indicating extensive mixing among European nationalities. Self-identified East Asian nationalities correlated with genetic clustering, consistent with extensive endogamy. Individuals of mixed East Asian-European genetic ancestry were easily identified; we also observed a modest amount of European genetic ancestry in individuals self-identified as Filipinos. Self-reported African Americans and Latinos showed extensive European and African genetic ancestry, and Native American genetic ancestry for the latter. Among 3741 genetically identified parent-child pairs, 93% were concordant for self-reported race/ethnicity; among 2018 genetically identified full-sib pairs, 96% were concordant; the lower rate for parent-child pairs was largely due to intermarriage. The parent-child pairs revealed a trend toward increasing exogamy over time; the presence in the cohort of individuals endorsing multiple race/ethnicity categories creates interesting challenges and future opportunities for genetic epidemiologic studies.
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Gebreab SY, Riestra P, Khan RJ, Xu R, Musani SK, Tekola-Ayele F, Correa A, Wilson JG, Rotimi CN, Davis SK. Genetic ancestry is associated with measures of subclinical atherosclerosis in African Americans: the Jackson Heart Study. Arterioscler Thromb Vasc Biol 2015; 35:1271-8. [PMID: 25745061 PMCID: PMC4523273 DOI: 10.1161/atvbaha.114.304855] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/22/2015] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To determine whether genetic ancestry was associated with subclinical atherosclerosis measures after adjustment for traditional cardiovascular disease risk factors, inflammatory marker, socioeconomic status, and psychosocial factors in a large admixed African American population. APPROACH AND RESULTS Participants were drawn from the Jackson Heart Study. Participant's percent of European ancestry (PEA) was estimated based on 1747 genetic markers using HAPMIX. Association of PEA with peripheral arterial disease and common carotid intima-media thickness were investigated among 2168 participants and with coronary artery calcification >0 and abdominal aortic calcification >0 among 1139 participants. The associations were evaluated using multivariable regression models. Our results showed that a 1 SD increase in PEA was associated with a lower peripheral arterial disease prevalence after adjusting for age and sex (prevalence ratio=0.90 [95% CI, 0.82-0.99]; P=0.036). Adjustments for traditional cardiovascular disease risk factors, socioeconomic status, and psychosocial factors attenuated this association (prevalence ratio=0.91 [0.82-1.00]; P=0.046). There was also a nonlinear association between PEA and coronary artery calcification and abdominal aortic calcification. The lowest PEA was associated with a lower coronary artery calcification (prevalence ratio=0.75 [0.58-0.96]; P=0.022) and a lower abdominal aortic calcification [prevalence ratio=0.80 [0.67-0.96]; P=0.016) compared with the reference group (10th-90th percentile) after adjusting for traditional cardiovascular disease risk factors, inflammatory marker, socioeconomic status, and psychosocial factors. However, we found no significant association between PEA and common carotid intima-media thickness. CONCLUSIONS Overall, our findings indicate that genetic ancestry was associated with subclinical atherosclerosis, suggesting unmeasured risk factors and interactions with genetic factors might contribute to the distribution of subclinical atherosclerosis among African Americans.
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Affiliation(s)
- Samson Y Gebreab
- From the National Human Genome Research Institute, Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, Bethesda, MD (S.Y.G., P.R., R.J.K., R.X., F.T.-A., C.N.R., S.K.D.); and Jackson Heart Study (S.K.M., A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson.
| | - Pia Riestra
- From the National Human Genome Research Institute, Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, Bethesda, MD (S.Y.G., P.R., R.J.K., R.X., F.T.-A., C.N.R., S.K.D.); and Jackson Heart Study (S.K.M., A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson
| | - Rumana J Khan
- From the National Human Genome Research Institute, Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, Bethesda, MD (S.Y.G., P.R., R.J.K., R.X., F.T.-A., C.N.R., S.K.D.); and Jackson Heart Study (S.K.M., A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson
| | - Ruihua Xu
- From the National Human Genome Research Institute, Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, Bethesda, MD (S.Y.G., P.R., R.J.K., R.X., F.T.-A., C.N.R., S.K.D.); and Jackson Heart Study (S.K.M., A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson
| | - Solomon K Musani
- From the National Human Genome Research Institute, Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, Bethesda, MD (S.Y.G., P.R., R.J.K., R.X., F.T.-A., C.N.R., S.K.D.); and Jackson Heart Study (S.K.M., A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson
| | - Fasil Tekola-Ayele
- From the National Human Genome Research Institute, Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, Bethesda, MD (S.Y.G., P.R., R.J.K., R.X., F.T.-A., C.N.R., S.K.D.); and Jackson Heart Study (S.K.M., A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson
| | - Adolfo Correa
- From the National Human Genome Research Institute, Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, Bethesda, MD (S.Y.G., P.R., R.J.K., R.X., F.T.-A., C.N.R., S.K.D.); and Jackson Heart Study (S.K.M., A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson
| | - James G Wilson
- From the National Human Genome Research Institute, Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, Bethesda, MD (S.Y.G., P.R., R.J.K., R.X., F.T.-A., C.N.R., S.K.D.); and Jackson Heart Study (S.K.M., A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson
| | - Charles N Rotimi
- From the National Human Genome Research Institute, Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, Bethesda, MD (S.Y.G., P.R., R.J.K., R.X., F.T.-A., C.N.R., S.K.D.); and Jackson Heart Study (S.K.M., A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson
| | - Sharon K Davis
- From the National Human Genome Research Institute, Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, Bethesda, MD (S.Y.G., P.R., R.J.K., R.X., F.T.-A., C.N.R., S.K.D.); and Jackson Heart Study (S.K.M., A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson
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Muñoz I, Henriques D, Johnston JS, Chávez-Galarza J, Kryger P, Pinto MA. Reduced SNP panels for genetic identification and introgression analysis in the dark honey bee (Apis mellifera mellifera). PLoS One 2015; 10:e0124365. [PMID: 25875986 PMCID: PMC4395157 DOI: 10.1371/journal.pone.0124365] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/10/2015] [Indexed: 11/19/2022] Open
Abstract
Beekeeping activities, especially queen trading, have shaped the distribution of honey bee (Apis mellifera) subspecies in Europe, and have resulted in extensive introductions of two eastern European C-lineage subspecies (A. m. ligustica and A. m. carnica) into the native range of the M-lineage A. m. mellifera subspecies in Western Europe. As a consequence, replacement and gene flow between native and commercial populations have occurred at varying levels across western European populations. Genetic identification and introgression analysis using molecular markers is an important tool for management and conservation of honey bee subspecies. Previous studies have monitored introgression by using microsatellite, PCR-RFLP markers and most recently, high density assays using single nucleotide polymorphism (SNP) markers. While the latter are almost prohibitively expensive, the information gained to date can be exploited to create a reduced panel containing the most ancestry-informative markers (AIMs) for those purposes with very little loss of information. The objective of this study was to design reduced panels of AIMs to verify the origin of A. m. mellifera individuals and to provide accurate estimates of the level of C-lineage introgression into their genome. The discriminant power of the SNPs using a variety of metrics and approaches including the Weir & Cockerham’s FST, an FST-based outlier test, Delta, informativeness (In), and PCA was evaluated. This study shows that reduced AIMs panels assign individuals to the correct origin and calculates the admixture level with a high degree of accuracy. These panels provide an essential tool in Europe for genetic stock identification and estimation of admixture levels which can assist management strategies and monitor honey bee conservation programs.
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Affiliation(s)
- Irene Muñoz
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301–855, Bragança, Portugal
| | - Dora Henriques
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301–855, Bragança, Portugal
| | - J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, Texas, 77843–2475, United States of America
| | - Julio Chávez-Galarza
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301–855, Bragança, Portugal
| | - Per Kryger
- Aarhus University, Department of Agroecology, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - M. Alice Pinto
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301–855, Bragança, Portugal
- * E-mail:
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Eckberg K, Kramer H, Wolf M, Durazo-Arvizu R, Tayo B, Luke A, Cooper R. Impact of westernization on fibroblast growth factor 23 levels among individuals of African ancestry. Nephrol Dial Transplant 2015; 30:630-5. [PMID: 25358495 PMCID: PMC4370291 DOI: 10.1093/ndt/gfu342] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 09/24/2014] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION The Western diet is associated with high consumption of processed foods preserved with phosphate. Higher dietary phosphate consumption stimulates production of fibroblast growth factor 23 (FGF23), which heightens risk for cardiovascular disease and mortality. We hypothesized that adults living in a more westernized society have higher levels of FGF23 due to increased phosphate consumption as measured by urinary phosphate excretion. METHODS We measured plasma C-terminal FGF23 levels and urinary phosphate and creatinine levels in timed urine collections among 100 African adults living in the rural area of Igbo-Ora, Nigeria (52 women, 48 men), and 100 African Americans (32 women, 68 men) living in Maywood, IL, an urban suburb of Chicago, IL, USA. Among these 200 participants, urine collections were adequate in 76 and 68 of the Maywood and Igbo-Ora participants, respectively. RESULTS In the total group, the mean age and body mass index, respectively, were 34.6 ± 8.2 years and 22.1 ± 3.9 kg/m(2) in Igbo-Ora, and 42.8 ± 7.2 years and 25.8 ± 6.5 kg/m(2) in Maywood. Demographic characteristics for each site were very similar after excluding participants without adequate urine collections. Among all 200 participants, the median (interquartile range) FGF23 levels were significantly higher in Maywood versus Igbo-Ora [63.8 (45.0-89.9) versus 12.5 RU/mL (8.5-18.5); P < 0.0001] and these differences did not change substantially after excluding nine women from Maywood with FGF23 levels >400 RU/mL or after excluding participants with inadequate urine collections. Among participants with adequate urine collections, the mean 24-h urinary phosphate excretion was significantly higher in Maywood versus Igbo-Ora (810.6 ± 309.0 versus 347.5 ± 153.1 mg; P < 0.001) and FGF23 levels correlated significantly with total urinary phosphate excretion (r = 0.62; P < 0.001) and urinary phosphate-to-creatinine ratios (r = 0.50; P < 0.001). CONCLUSIONS Living in a more westernized society may be associated with greater net phosphate absorption, as reflected by higher urinary phosphate excretion, and higher FGF23 levels.
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Affiliation(s)
- Karl Eckberg
- Department of Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Holly Kramer
- Department of Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
- Division of Nephrology and Hypertension, Department of Medicine, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Myles Wolf
- Division of Nephrology and Hypertension, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ramon Durazo-Arvizu
- Department of Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Bamidele Tayo
- Department of Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Amy Luke
- Department of Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Richard Cooper
- Department of Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
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Johnson RC, Nelson GW, Zagury JF, Winkler CA. ALDsuite: Dense marker MALD using principal components of ancestral linkage disequilibrium. BMC Genet 2015; 16:23. [PMID: 25886794 PMCID: PMC4408589 DOI: 10.1186/s12863-015-0179-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/06/2015] [Indexed: 01/04/2023] Open
Abstract
Background Mapping by admixture linkage disequilibrium (MALD) is a whole genome gene mapping method that uses LD from extended blocks of ancestry inherited from parental populations among admixed individuals to map associations for diseases, that vary in prevalence among human populations. The extended LD queried for marker association with ancestry results in a greatly reduced number of comparisons compared to standard genome wide association studies. As ancestral population LD tends to confound the analysis of admixture LD, the earliest algorithms for MALD required marker sets sufficiently sparse to lack significant ancestral LD between markers. However current genotyping technologies routinely provide dense SNP data, which convey more information than sparse sets, if this information can be efficiently used. There are currently no software solutions that offer both local ancestry inference using dense marker data and disease association statistics. Results We present here an R package, ALDsuite, which accounts for local LD using principal components of haplotypes from surrogate ancestral population data, and includes tools for quality control of data, MALD, downstream analysis of results and visualization graphics. Conclusions ALDsuite offers a fast, accurate estimation of global and local ancestry and comes bundled with the tools needed for MALD, from data quality control through mapping of and visualization of disease genes.
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Affiliation(s)
- Randall C Johnson
- BSP CCR Genetics Core, Leidos Biomedical Research, Inc, Frederick National Laboratory, Frederick, MD, 21702, USA. .,Chaire de Bioinformatique, Conservatiore National des Arts et Metieèrs, Paris, 75003, France.
| | - George W Nelson
- BSP CCR Genetics Core, Leidos Biomedical Research, Inc, Frederick National Laboratory, Frederick, MD, 21702, USA.
| | - Jean-Francois Zagury
- Chaire de Bioinformatique, Conservatiore National des Arts et Metieèrs, Paris, 75003, France.
| | - Cheryl A Winkler
- Basic Research Laboratory, Leidos Biomedical Research, Inc, Frederick National Laboratory, Frederick, MD, 21702, USA.
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Girkin CA, Nievergelt CM, Kuo JZ, Maihofer AX, Huisingh C, Liebmann JM, Ayyagari R, Weinreb RN, Ritch R, Zangwill LM. Biogeographic Ancestry in the African Descent and Glaucoma Evaluation Study (ADAGES): Association With Corneal and Optic Nerve Structure. Invest Ophthalmol Vis Sci 2015; 56:2043-9. [PMID: 25744975 DOI: 10.1167/iovs.14-15719] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
PURPOSE We determined if quantitative measurements of biogeographic ancestry (BGA) correlate with variations in optic disc area, corneal thickness (CCT), and retinal nerve fiber layer (RNFL) thickness. METHODS Data were obtained from 656 participants in the African Descent and Glaucoma Evaluation Study (ADAGES) cohort who consented to BGA testing. Data for CCT, optic disc area, and RNFL thickness were obtained from subjects in the ADAGES study who also had participated in the current substudy. A total of 31 ancestry informative markers (AIMs) with large allele frequencies differences between populations was used to calculate admixture proportion (implemented in STRUCTURE). Correlations with BGA adjusted for diagnosis, age, and sex for CCT and optic disc area using the whole group and RNFL thickness adjusted for age and sex for the normal study participants were determined. RESULTS The mean percentage of African admixture was 79.6% in the self-described African Descent (AD) group and 3.5% in the European Descent (ED) group. Percent African ancestry was significantly correlated with CCT (ρ = -0.27, P < 0.0001) and disc area (ρ = 0.15, P < 0.0001), but only marginally associated with RNFL thickness (ρ = 0.20, P = 0.092) in adjusted models. CONCLUSIONS The BGA correlates with variation in ocular features that significantly differ across racial groups and that have been associated with the development of glaucoma. While BGA can provide an objective measurement of the biologic component of self-described race for ocular research, for most nongenetic epidemiologic studies, self-described race may adequately describe the associations with these ocular characteristics. (ClinicalTrials.gov number, NCT00221923.).
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Affiliation(s)
- Christopher A Girkin
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California, San Diego, San Diego, California, United States
| | - Jane Z Kuo
- Department of Ophthalmology, University of California, San Diego, San Diego, California, United States Pathway Genomics Corporation, San Diego, California, United States
| | - Adam X Maihofer
- Department of Psychiatry, University of California, San Diego, San Diego, California, United States
| | - Carrie Huisingh
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | | | - Radha Ayyagari
- Department of Ophthalmology, University of California, San Diego, San Diego, California, United States
| | - Robert N Weinreb
- Department of Ophthalmology, University of California, San Diego, San Diego, California, United States
| | - Robert Ritch
- Department of Ophthalmology, New York Eye and Ear Infirmary, New York, New York, United States
| | - Linda M Zangwill
- Department of Ophthalmology, University of California, San Diego, San Diego, California, United States
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Franceschini N, Chasman DI, Cooper-DeHoff RM, Arnett DK. Genetics, ancestry, and hypertension: implications for targeted antihypertensive therapies. Curr Hypertens Rep 2015; 16:461. [PMID: 24903233 DOI: 10.1007/s11906-014-0461-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hypertension is the most common chronic condition seen by physicians in ambulatory care and a condition for which life-long medications are commonly prescribed. There is evidence for genetic factors influencing blood pressure variation in populations and response to medications. This review summarizes recent genetic discoveries that surround blood pressure, hypertension, and antihypertensive drug response from genome-wide association studies, while highlighting ancestry-specific findings and any potential implication for drug therapy targets. Genome-wide association studies have identified several novel loci for inter-individual variation of blood pressure and hypertension risk in the general population. Evidence from pharmacogenetic studies suggests that genes influence the blood pressure response to antihypertensive drugs, although results are somewhat inconsistent across studies. There is still much work that remains to be done to identify genes both for efficacy and adverse events of antihypertensive medications.
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Affiliation(s)
- Nora Franceschini
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, 137 E. Franklin St., Suite 306, Chapel Hill, NC, USA,
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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: 70] [Impact Index Per Article: 7.8] [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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Salazar-Flores J, Zuñiga-Chiquette F, Rubi-Castellanos R, Álvarez-Miranda J, Zetina-Hérnandez A, Martínez-Sevilla V, González-Andrade F, Corach D, Vullo C, Álvarez J, Lorente J, Sánchez-Diz P, Herrera R, Cerda-Flores R, Muñoz-Valle J, Rangel-Villalobos H. Admixture and genetic relationships of Mexican Mestizos regarding Latin American and Caribbean populations based on 13 CODIS-STRs. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2015; 66:44-59. [DOI: 10.1016/j.jchb.2014.08.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 08/28/2014] [Indexed: 12/21/2022]
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Loder RT, Shafer C. The demographics of developmental hip dysplasia in the Midwestern United States (Indiana). J Child Orthop 2015; 9:93-8. [PMID: 25690337 PMCID: PMC4340845 DOI: 10.1007/s11832-015-0636-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 01/30/2015] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Today's society is much more mobile than in the past. This increased mobility has resulted in different marriage/parenting groups. We wished to study the demographics of developmental dysplasia of the hip (DDH) in our area and compare/contrast our findings with those in the literature and specifically look for new findings compared to previous studies. METHODS A retrospective review of all children with DDH from 2003 through 2012 was performed. The age at first visit, gestational age, pregnancy number, gender, race, and family history of DDH was collected. Statistical significance was a p-value < 0.05. RESULTS There were 424 children (363 girls, 61 boys). Ethnicity was White in 80.8 %, Hispanic in 13.8 %, Black in 4.0 %, and Indo-Malay and Indo-Mediterranean in 0.7 % each; 66.8 % were unilateral; 14.2 % had a positive family history. The average gestational age was 38.1 weeks; 94.4 % were full term. The child was vertex presentation in 67.6 % and breech in 32.4 %; 52.8 % were delivered vaginally and 47.2 % by Cesarean section. The child was the first-born in 48.3 %. When compared to the birth statistics of our state, there was a higher proportion of Whites and Hispanics with DDH, and a lower, but not inconsequential, proportion of Blacks (p = 0.0018). CONCLUSION Mixing of gene pools and infant carrying methods (lack of swaddling or marked abduction) occurring with societal change likely explains the higher than expected proportion of DDH amongst those of Hispanic ethnicity and a lower than expected, but not rare, proportion in those of African ancestry. LEVEL OF EVIDENCE Level IV-retrospective case series.
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Affiliation(s)
- Randall T Loder
- Department of Orthopaedic Surgery, Indiana School of Medicine, Indiana University, Indianapolis, IN, USA,
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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: 431] [Impact Index Per Article: 47.9] [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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Mersha TB, Abebe T. Self-reported race/ethnicity in the age of genomic research: its potential impact on understanding health disparities. Hum Genomics 2015; 9:1. [PMID: 25563503 PMCID: PMC4307746 DOI: 10.1186/s40246-014-0023-x] [Citation(s) in RCA: 263] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 12/01/2014] [Indexed: 12/02/2022] Open
Abstract
This review explores the limitations of self-reported race, ethnicity, and genetic ancestry in biomedical research. Various terminologies are used to classify human differences in genomic research including race, ethnicity, and ancestry. Although race and ethnicity are related, race refers to a person's physical appearance, such as skin color and eye color. Ethnicity, on the other hand, refers to communality in cultural heritage, language, social practice, traditions, and geopolitical factors. Genetic ancestry inferred using ancestry informative markers (AIMs) is based on genetic/genomic data. Phenotype-based race/ethnicity information and data computed using AIMs often disagree. For example, self-reporting African Americans can have drastically different levels of African or European ancestry. Genetic analysis of individual ancestry shows that some self-identified African Americans have up to 99% of European ancestry, whereas some self-identified European Americans have substantial admixture from African ancestry. Similarly, African ancestry in the Latino population varies between 3% in Mexican Americans to 16% in Puerto Ricans. The implication of this is that, in African American or Latino populations, self-reported ancestry may not be as accurate as direct assessment of individual genomic information in predicting treatment outcomes. To better understand human genetic variation in the context of health disparities, we suggest using "ancestry" (or biogeographical ancestry) to describe actual genetic variation, "race" to describe health disparity in societies characterized by racial categories, and "ethnicity" to describe traditions, lifestyle, diet, and values. We also suggest using ancestry informative markers for precise characterization of individuals' biological ancestry. Understanding the sources of human genetic variation and the causes of health disparities could lead to interventions that would improve the health of all individuals.
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Affiliation(s)
- Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA.
| | - Tilahun Abebe
- Department of Biology, University of Northern Iowa, Cedar Falls, IA, USA.
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Abstract
An extensive literature documents the existence of pervasive and persistent child health, development, and health care disparities by race, ethnicity, and socioeconomic status (SES). Disparities experienced during childhood can result in a wide variety of health and health care outcomes, including adult morbidity and mortality, indicating that it is crucial to examine the influence of disparities across the life course. Studies often collect data on the race, ethnicity, and SES of research participants to be used as covariates or explanatory factors. In the past, these variables have often been assumed to exert their effects through individual or genetically determined biologic mechanisms. However, it is now widely accepted that these variables have important social dimensions that influence health. SES, a multidimensional construct, interacts with and confounds analyses of race and ethnicity. Because SES, race, and ethnicity are often difficult to measure accurately, leading to the potential for misattribution of causality, thoughtful consideration should be given to appropriate measurement, analysis, and interpretation of such factors. Scientists who study child and adolescent health and development should understand the multiple measures used to assess race, ethnicity, and SES, including their validity and shortcomings and potential confounding of race and ethnicity with SES. The American Academy of Pediatrics (AAP) recommends that research on eliminating health and health care disparities related to race, ethnicity, and SES be a priority. Data on race, ethnicity, and SES should be collected in research on child health to improve their definitions and increase understanding of how these factors and their complex interrelationships affect child health. Furthermore, the AAP believes that researchers should consider both biological and social mechanisms of action of race, ethnicity, and SES as they relate to the aims and hypothesis of the specific area of investigation. It is important to measure these variables, but it is not sufficient to use these variables alone as explanatory for differences in disease, morbidity, and outcomes without attention to the social and biologic influences they have on health throughout the life course. The AAP recommends more research, both in the United States and internationally, on measures of race, ethnicity, and SES and how these complex constructs affect health care and health outcomes throughout the life course.
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96
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Rogalla U, Rychlicka E, Derenko MV, Malyarchuk BA, Grzybowski T. Simple and cost-effective 14-loci SNP assay designed for differentiation of European, East Asian and African samples. Forensic Sci Int Genet 2015; 14:42-9. [DOI: 10.1016/j.fsigen.2014.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 08/27/2014] [Accepted: 09/14/2014] [Indexed: 12/19/2022]
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Araujo AB, Yang M, Suarez EA, Dagincourt N, Abraham JR, Chiu G, Holick MF, Bouxsein ML, Zmuda JM. Racial/ethnic and socioeconomic differences in bone loss among men. J Bone Miner Res 2014; 29:2552-60. [PMID: 24984683 DOI: 10.1002/jbmr.2305] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 05/22/2014] [Accepted: 05/29/2014] [Indexed: 11/10/2022]
Abstract
As men age, they lose bone and are susceptible to fracture. Despite having lower fracture rates than women, men have worse fractures than women do. Racial/ethnic and socioeconomic status (SES) disparities in fracture rates exist, yet data on rates of bone loss by race/ethnicity and SES among men are limited. We examined annualized percentage change in bone mineral density (%ΔBMD) at the hip (N = 681), spine (N = 663), and forearm (N = 636) during 7 years of follow-up among men aged 30-79 years at baseline. Multivariable models tested whether race/ethnicity, income, or genetic ancestry predicted annualized %ΔBMD after controlling for an extensive set of covariates. Annualized %ΔBMD ranged from -0.65(0.04)% (femoral neck) to +0.26(0.03)% (1/3 distal radius), and changes were consistent across age groups with the exception of the ultradistal radius, where annualized declines increased with age. Neither self-identified race/ethnicity nor genetic ancestry were associated with annualized %ΔBMD. In contrast, income was strongly associated (dose-response) with annualized %ΔBMD at total hip (independent of confounders, self-identified race/ethnicity, and genetic ancestry). Fully adjusted least-square mean change in annualized %ΔBMD at the total hip were -0.24(0.12)% and -0.16(0.06)% steeper among men with low and moderate incomes, respectively, than among men with higher incomes (overall p = 0.0293). Results show a linear decline in bone that begins relatively early in life among men, that rates of bone loss do not vary with race/ethnicity (self-identified or "objectively" measured), and that income plays an important role in relation to bone loss at the hip. These data suggest that fracture risk in men may be driven in part by income-related differences in bone loss, but also, that the known higher fracture risk among white men is not the result of racial/ethnic differences in bone loss, but rather, early life exposures that lead to attainment of higher peak bone mass among minorities.
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Affiliation(s)
- Andre B Araujo
- Department of Epidemiology, New England Research Institutes, Inc., Watertown, MA, USA; Eli Lilly and Company, Indianapolis, IN, USA
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98
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Inter-ethnic differences in genetic variants within the transmembrane protease, serine 6 (TMPRSS6) gene associated with iron status indicators: a systematic review with meta-analyses. GENES AND NUTRITION 2014; 10:442. [PMID: 25416640 DOI: 10.1007/s12263-014-0442-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 11/11/2014] [Indexed: 10/24/2022]
Abstract
Transmembrane protease, serine 6 (TMPRSS6), is likely to be involved in iron metabolism through its pleiotropic effect on hepcidin concentrations. Recently, genome-wide association studies have identified common variants in the TMPRSS6 gene to be linked to anaemia and low iron status. To get a more precise evaluation of identified TMPRSS6 single nucleotide polymorphism associations with iron status in cohorts of differing continental ancestry, we conducted a systematic review with meta-analyses. We searched the literature using HuGE Navigator, Pubmed and Scopus databases for primarily genome-wide association studies using TMPRSS6 as a free term. Fixed-effects meta-analysis was used to obtain summary estimates of associations. Eleven studies comprised Caucasian populations, four included an Asian population and one study included an African-American population. Differences in minor allele frequencies of 8 TMPRSS6 SNPs (rs855791, rs4820268, rs2111833, rs1421312, rs228921, rs228918, rs228919 and rs575620) across ethnic groups were observed, with the MAF of rs855791 significantly higher in Asian populations than in Caucasians (0.55 vs 0.42, P < 0.0001). In the meta-analysis, the A allele of rs855791 was associated with lower Hb and ferritin concentrations in all populations. This allele was also associated with increased serum transferrin receptor and transferrin concentrations. We observed similar associations for the G allele in rs4820268. Clear disparities in associations were found for the African-American population, although not statistically significant. Associations between TMPRSS6 SNPs and anaemia are consistent across Caucasian and Asian populations. This study highlights the need to conduct studies in African populations where iron deficiency is of utmost public health significance.
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99
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Lopera EA, Baena A, Florez V, Montiel J, Duque C, Ramirez T, Borrero M, Cordoba CM, Rojas F, Pareja R, Bedoya AM, Bedoya G, Sanchez GI. Unexpected inverse correlation between Native American ancestry and Asian American variants of HPV16 in admixed Colombian cervical cancer cases. INFECTION GENETICS AND EVOLUTION 2014; 28:339-48. [PMID: 25446942 DOI: 10.1016/j.meegid.2014.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/18/2014] [Accepted: 10/16/2014] [Indexed: 12/17/2022]
Abstract
BACKGROUND European (E) variants of HPV 16 are evenly distributed among world regions, meanwhile Non-European variants such as European-Asian (EAs), Asian American (AA) and African (Af) are mostly confined to Eastern Asia, The Americas and African regions respectively. Several studies have shown that genetic variation of HPV 16 is associated with the risk of cervical cancer, which also seems to be dependent on the population. This relationship between ethnicity and variants have led to the suggestion that there is co-evolution of variants with humankind. Our aim was to evaluate the relationship between the individual ancestry proportion and infection with HPV 16 variants in cervical cancer. METHODS We examined the association between ancestry and HPV 16 variants in samples of 82 cervical cancer cases from different regions of Colombia. Individual ancestry proportions (European, African and Native American) were estimated by genotyping 106 ancestry informative markers. Variants were identified by PCR amplification of the E6 gene, followed by reverse line blot hybridization (RLB) with variants specific probes. RESULTS Overall European (E) and Asian American (AA) variants frequency was 66.5% and 33.5% respectively. Similar distribution was observed in cases with higher proportions of European or African ancestry. A higher Native American ancestry was significantly associated with higher frequency of E variants (median ancestry>23.6%, Age and place of birth adjusted OR: 3.55, 95% CI: 1.26-10.03, p=0.01). Even further, an inverse geographic correlation between Native American ancestry and frequency of infections with AA variants was observed (ρ=-0.825, p=0.008). Regions with higher proportion of Native American ancestry had a lower frequency of AA variants of HPV 16. CONCLUSIONS This study suggests replacement of AA variants by E variants of human papillomavirus 16 in cervical cancer cases with high Native American ancestry.
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Affiliation(s)
- Esteban A Lopera
- Infection and Cancer Group, School of Medicine and Corporación Académica para el Estudio de Patologías Tropicales, Universidad de Antioquia, UdeA, Calle 70 No 52-21, Medellín, Colombia
| | - Armando Baena
- Infection and Cancer Group, School of Medicine and Corporación Académica para el Estudio de Patologías Tropicales, Universidad de Antioquia, UdeA, Calle 70 No 52-21, Medellín, Colombia
| | - Victor Florez
- Infection and Cancer Group, School of Medicine and Corporación Académica para el Estudio de Patologías Tropicales, Universidad de Antioquia, UdeA, Calle 70 No 52-21, Medellín, Colombia
| | - Jehidys Montiel
- Infection and Cancer Group, School of Medicine and Corporación Académica para el Estudio de Patologías Tropicales, Universidad de Antioquia, UdeA, Calle 70 No 52-21, Medellín, Colombia
| | - Constanza Duque
- Genética Molecular, Universidad de Antioquia, UdeA, Calle 70 No 52-21, Medellín, Colombia; Universidad Cooperativa de Colombia, Carrera 42 No 49-95, Medellín, Colombia
| | - Tatiana Ramirez
- Infection and Cancer Group, School of Medicine and Corporación Académica para el Estudio de Patologías Tropicales, Universidad de Antioquia, UdeA, Calle 70 No 52-21, Medellín, Colombia
| | - Mauricio Borrero
- Infection and Cancer Group, School of Medicine and Corporación Académica para el Estudio de Patologías Tropicales, Universidad de Antioquia, UdeA, Calle 70 No 52-21, Medellín, Colombia; Instituto de Cancerología Las Américas, Carrera 70 No 1-35, Torre 5, Medellín, Colombia; Department of Gynecology and Obstetrics, School of Medicine, Universidad de Antioquia, UdeA, Calle 70 No 52-52, Medellín, Colombia
| | - Carlos M Cordoba
- Department of Gynecology and Obstetrics, School of Medicine, Universidad de Antioquia, UdeA, Calle 70 No 52-52, Medellín, Colombia
| | - Fredy Rojas
- Instituto de Cancerología Las Américas, Carrera 70 No 1-35, Torre 5, Medellín, Colombia
| | - Rene Pareja
- Instituto de Cancerología Las Américas, Carrera 70 No 1-35, Torre 5, Medellín, Colombia
| | - Astrid M Bedoya
- Infection and Cancer Group, School of Medicine and Corporación Académica para el Estudio de Patologías Tropicales, Universidad de Antioquia, UdeA, Calle 70 No 52-21, Medellín, Colombia; Escuela de Microbiología, Universidad de Antioquia UdeA, Calle 70 No 52-21, Medellín, Colombia
| | - Gabriel Bedoya
- Genética Molecular, Universidad de Antioquia, UdeA, Calle 70 No 52-21, Medellín, Colombia
| | - Gloria I Sanchez
- Infection and Cancer Group, School of Medicine and Corporación Académica para el Estudio de Patologías Tropicales, Universidad de Antioquia, UdeA, Calle 70 No 52-21, Medellín, Colombia.
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Germline mutations in BRCA1, BRCA2, CHEK2 and TP53 in patients at high-risk for HBOC: characterizing a Northeast Brazilian Population. Hum Genome Var 2014; 1:14012. [PMID: 27081505 PMCID: PMC4785545 DOI: 10.1038/hgv.2014.12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/11/2014] [Accepted: 07/31/2014] [Indexed: 11/08/2022] Open
Abstract
Considering the importance of BRCA1, BRCA2, CHEK2 and TP53 in the development of hereditary early-onset breast and ovarian cancer and that the genetic susceptibility profile of the Northeast population from Brazil has never been analyzed, this study aimed to verify the frequency of mutations of clinical significance in these genes in high-risk hereditary breast and ovarian cancer (HBOC) syndrome patients from that region. DNA samples from 106 high-risk unrelated patients mostly from Bahia, the biggest state in the Northeast region, were analyzed. These patients underwent full BRCA1 gene sequencing, screening for common founder mutations in the BRCA2, CHEK2 and TP53 genes and genetic ancestry analysis with nine ancestry informative markers. The positive results were confirmed by two sequencing reactions. Three mutations of clinical significance were found: BRCA1 p.R71G (4.71%), 3450del4 (3.77%) and TP53 p.R337H (0.94%). The genetic ancestry analysis showed a high European ancestry contribution (62.2%) as well as considerable African (31.2%) and Amerindian (6.6%) ancestry contributions (r2=0.991); this degree of heterogeneity was also significant in the population structure analysis (r=0.604). This population is highly admixed with a different spectrum of genetic susceptibility, with the Galician founder mutation BRCA1 p.R71G accounting for 50% of all identified mutations in high-risk HBOC patients. TP53 p.R337H was also significantly frequent; thus, the combined screening of BRCA1/2 and TP53 should be offered to high-risk HBOC patients from Northeast Brazil.
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