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Homburger JR, Moreno-Estrada A, Gignoux CR, Nelson D, Sanchez E, Ortiz-Tello P, Pons-Estel BA, Acevedo-Vasquez E, Miranda P, Langefeld CD, Gravel S, Alarcón-Riquelme ME, Bustamante CD. Genomic Insights into the Ancestry and Demographic History of South America. PLoS Genet 2015; 11:e1005602. [PMID: 26636962 PMCID: PMC4670080 DOI: 10.1371/journal.pgen.1005602] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/22/2015] [Indexed: 01/19/2023] Open
Abstract
South America has a complex demographic history shaped by multiple migration and admixture events in pre- and post-colonial times. Settled over 14,000 years ago by Native Americans, South America has experienced migrations of European and African individuals, similar to other regions in the Americas. However, the timing and magnitude of these events resulted in markedly different patterns of admixture throughout Latin America. We use genome-wide SNP data for 437 admixed individuals from 5 countries (Colombia, Ecuador, Peru, Chile, and Argentina) to explore the population structure and demographic history of South American Latinos. We combined these data with population reference panels from Africa, Asia, Europe and the Americas to perform global ancestry analysis and infer the subcontinental origin of the European and Native American ancestry components of the admixed individuals. By applying ancestry-specific PCA analyses we find that most of the European ancestry in South American Latinos is from the Iberian Peninsula; however, many individuals trace their ancestry back to Italy, especially within Argentina. We find a strong gradient in the Native American ancestry component of South American Latinos associated with country of origin and the geography of local indigenous populations. For example, Native American genomic segments in Peruvians show greater affinities with Andean indigenous peoples like Quechua and Aymara, whereas Native American haplotypes from Colombians tend to cluster with Amazonian and coastal tribes from northern South America. Using ancestry tract length analysis we modeled post-colonial South American migration history as the youngest in Latin America during European colonization (9–14 generations ago), with an additional strong pulse of European migration occurring between 3 and 9 generations ago. These genetic footprints can impact our understanding of population-level differences in biomedical traits and, thus, inform future medical genetic studies in the region. South America is home to over 400 million people who share a rich demographic history, including settlement by Native Americans, European colonization, and the African slave trade. We use genomic data to infer which populations from Europe and the Americas contributed to these admixture events. We provide evidence for multiple origins of the Native American ancestry of admixed South American Latinos. The Native American ancestral component correlates strongly with geography, indicating that admixture occurred between European colonists and local Native American populations throughout South America. We also show that the European ancestry of South American Latinos comes mainly from the Iberian peninsula, however, a significant number of Argentinians have European ancestry from other Southern European regions. The genetic signal of European admixture in South American populations is younger than the signal observed in Mexico and the Caribbean. We find evidence for a second pulse of European migration to many regions of South America subsequent to the original colonization. These results demonstrate the heterogeneous nature of the Latino population in South America and help elucidate the complex genetic and admixture events that shaped the population structure of the region.
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Affiliation(s)
- Julian R. Homburger
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Andrés Moreno-Estrada
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
- * E-mail: (AME); (MEAR); (CDB)
| | - Christopher R. Gignoux
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Dominic Nelson
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Elena Sanchez
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Patricia Ortiz-Tello
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | | | - Eduardo Acevedo-Vasquez
- Facultad de Medicina, Universidad Nacional Mayor de San Marcos, Hospital Nacional Guillermo Almenara Irigoyen, Lima, Peru
| | | | - Carl D. Langefeld
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Simon Gravel
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Marta E. Alarcón-Riquelme
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- GENYO, Centre for Genomics and Oncological Research: Pfizer/ University of Granada/ Andalusian Regional Government, Granada, Spain
- * E-mail: (AME); (MEAR); (CDB)
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
- * E-mail: (AME); (MEAR); (CDB)
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Ugarte-Gil M, Garcia-Poma A, Gamboa-Cardenas R, Mora C, Cucho M, Terrazas H, Pastor C, Rhor E, Acevedo-Vasquez E, Segami M. FRI0121 Concordance of 6 composite disease activity measures in a peruvian population with rheumatoid arthritis. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2012-eular.2578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Sánchez E, Rasmussen A, Riba L, Acevedo-Vasquez E, Kelly JA, Langefeld CD, Williams AH, Ziegler JT, Comeau ME, Marion MC, García-De La Torre I, Maradiaga-Ceceña MA, Cardiel MH, Esquivel-Valerio JA, Rodriguez-Amado J, Moctezuma JF, Miranda P, Perandones CE, Castel C, Laborde HA, Alba P, Musuruana JL, Goecke IA, Anaya JM, Kaufman KM, Adler A, Glenn SB, Brown EE, Alarcón GS, Kimberly RP, Edberg JC, Vilá LM, Criswell LA, Gilkeson GS, Niewold TB, Martín J, Vyse TJ, Boackle SA, Ramsey-Goldman R, Scofield RH, Petri M, Merrill JT, Reveille JD, Tsao BP, Orozco L, Baca V, Moser KL, Gaffney PM, James JA, Harley JB, Tusié-Luna T, Pons-Estel BA, Jacob CO, Alarcón-Riquelme ME. Impact of genetic ancestry and sociodemographic status on the clinical expression of systemic lupus erythematosus in American Indian-European populations. ACTA ACUST UNITED AC 2013; 64:3687-94. [PMID: 22886787 DOI: 10.1002/art.34650] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE American Indian-Europeans, Asians, and African Americans have an excess morbidity from systemic lupus erythematosus (SLE) and a higher prevalence of lupus nephritis than do Caucasians. The aim of this study was to analyze the relationship between genetic ancestry and sociodemographic characteristics and clinical features in a large cohort of American Indian-European SLE patients. METHODS A total of 2,116 SLE patients of American Indian-European origin and 4,001 SLE patients of European descent for whom we had clinical data were included in the study. Genotyping of 253 continental ancestry-informative markers was performed on the Illumina platform. Structure and Admixture software were used to determine genetic ancestry proportions of each individual. Logistic regression was used to test the association between genetic ancestry and sociodemographic and clinical characteristics. Odds ratios (ORs) were calculated with 95% confidence intervals (95% CIs). RESULTS The average American Indian genetic ancestry of 2,116 SLE patients was 40.7%. American Indian genetic ancestry conferred increased risks of renal involvement (P < 0.0001, OR 3.50 [95% CI 2.63- 4.63]) and early age at onset (P < 0.0001). American Indian ancestry protected against photosensitivity (P < 0.0001, OR 0.58 [95% CI 0.44-0.76]), oral ulcers (P < 0.0001, OR 0.55 [95% CI 0.42-0.72]), and serositis (P < 0.0001, OR 0.56 [95% CI 0.41-0.75]) after adjustment for age, sex, and age at onset. However, age and sex had stronger effects than genetic ancestry on malar rash, discoid rash, arthritis, and neurologic involvement. CONCLUSION In general, American Indian genetic ancestry correlates with lower sociodemographic status and increases the risk of developing renal involvement and SLE at an earlier age.
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Affiliation(s)
- Elena Sánchez
- Oklahoma Medical Research Foundation, Oklahoma City, USA
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Ponce de Leon D, Acevedo-Vasquez E, Alvizuri S, Gutierrez C, Cucho M, Alfaro J, Perich R, Sanchez-Torres A, Pastor C, Sanchez-Schwartz C, Medina M, Gamboa R, Ugarte M. Comparison of an interferon-gamma assay with tuberculin skin testing for detection of tuberculosis (TB) infection in patients with rheumatoid arthritis in a TB-endemic population. J Rheumatol 2008; 35:776-781. [PMID: 18398944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
OBJECTIVE Tuberculosis (TB) in patients with rheumatoid arthritis (RA) undergoing treatment with anti-tumor necrosis factor (TNF) agents is commonly the result of reactivation of latent TB infection (LTBI); detection and treatment of LTBI is essential before treatment with anti-TNF agents. We reported previously that the tuberculin skin test (TST) is inaccurate for diagnosis of LTBI in patients with RA. Here, we compare the prevalence of LTBI in RA patients and matched controls according to positive TST and QuantiFeron-TB Gold In-Tube version (QFT) results and determine their agreement. METHODS A cross-sectional study of 101 RA patients and 93 controls was conducted in Lima, Perú, where the prevalence of LTBI in the general population has been estimated to be 68%. Blood was drawn for QFT assay followed by TST using 2-TU of RT 23 purified protein derivative. TST was deemed positive at >or= 5 mm for RA patients and >or= 10 mm for controls. RESULTS There were no significant differences between RA patients and controls for age, sex, bacillus Calmette-Guérin vaccination, or history of or contact with TB. 88% of patients had active RA disease and 2 (1.9%) patients had indeterminate QFT results. The number of subjects testing positive with the QuantiFeron assay was comparable between patients and controls (44.6% vs 59.1%, respectively), whereas the TST detected significantly less LTBI among RA patients (26.7%) than controls (65.6%). Thus, the rate of LTBI in RA patients represented 75% and 41% of the rate in their controls using QFT or TST, respectively (p = 0.008). Poor agreement between TST and QFT was seen in RA patients, but in controls, good agreement was observed between these tests. CONCLUSION In a TB-endemic population, the QuantiFeron-TB Gold In-Tube assay seemed to be a more accurate test for detection of LTBI in RA patients compared with the TST, and may potentially improve the targeting of prophylactic therapy before treatment with anti-TNF agents.
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Affiliation(s)
- Dario Ponce de Leon
- Department of Internal Medicine, Hospital Nacional Guillermo Almenara Irigoyen, Lima, Peru
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