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Jaramillo‐Valverde L, Levano KS, Tarazona DD, Capristano S, Sanchez C, Poterico JA, Tarazona‐Santos E, Guio H. Pharmacogenetic variability of tuberculosis biomarkers in native and mestizo Peruvian populations. Pharmacol Res Perspect 2024; 12:e1179. [PMID: 38666760 PMCID: PMC11047445 DOI: 10.1002/prp2.1179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/25/2023] [Accepted: 01/27/2024] [Indexed: 04/29/2024] Open
Abstract
In Peru, 29 292 people were diagnosed with tuberculosis in 2022. Although tuberculosis treatments are effective, 3.4%-13% are associated with significant adverse drug reactions, with drug-induced liver injury (DILI) considered the most predominant. Among the first-line antituberculosis drugs, isoniazid is the main drug responsible for the appearance of DILI. In liver, isoniazid (INH) is metabolized by N-acetyltransferase-2 (NAT2) and cytochrome P450 2E1 (CYP2E1). Limited information exists on genetic risk factors associated with the presence of DILI to antituberculosis drugs in Latin America, and even less is known about these factors in the native and mestizo Peruvian population. The aim of this study was to determine the prevalence of NAT2 and CYP2E1 genotypes in native and mestizo population. An analytical cross-sectional analysis was performed using genetic data from mestizo population in Lima and native participants from south of Peru. NAT2 metabolizer was determined as fast, intermediate and slow, and CYP2E1 genotypes were classified as c1/c1, c1/c2 and c2/c2, from molecular tests and bioinformatic analyses. Of the 472 participants, 36 and 6 NAT2 haplotypes were identified in the mestizo and native population, respectively. In mestizo population, the most frequent NAT2*5B and NAT2*7B haplotypes were associated with DILI risk; while in natives, NAT2*5G and NAT2*13A haplotypes were associated with decreased risk of DILI. For CYP2E1, c1/c1 and c1/c2 genotypes are the most frequent in natives and mestizos, respectively. The linkage disequilibrium of NAT2 single nucleotide polymorphisms (SNPs) was estimated, detecting a block between all SNPs natives. In addition, a block between rs1801280 and rs1799929 for NAT2 was detected in mestizos. Despite the limitations of a secondary study, it was possible to report associations between NAT2 and CYP2E alleles with Peruvian native and mestizo by prevalence ratios. The results of this study will help the development of new therapeutic strategies for a Tuberculosis efficient control between populations.
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Affiliation(s)
- Luis Jaramillo‐Valverde
- Laboratorio de Biotecnología y Biología MolecularInstituto Nacional de SaludLimaPeru
- School of MedicineUniversidad ContinentalLimaPeru
- INBIOMEDIC Research and Technological CenterLimaPeru
| | - Kelly S. Levano
- Laboratorio de Biotecnología y Biología MolecularInstituto Nacional de SaludLimaPeru
- Science DepartmentHelene Fuld College of NursingNew YorkNew YorkUSA
| | - David D. Tarazona
- Laboratorio de Biotecnología y Biología MolecularInstituto Nacional de SaludLimaPeru
| | - Silvia Capristano
- Laboratorio de Biotecnología y Biología MolecularInstituto Nacional de SaludLimaPeru
| | - Cesar Sanchez
- Laboratorio de Biotecnología y Biología MolecularInstituto Nacional de SaludLimaPeru
| | - Julio A. Poterico
- INBIOMEDIC Research and Technological CenterLimaPeru
- Universidad de HuánucoHuánucoPeru
| | - Eduardo Tarazona‐Santos
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e EvoluçãoBelo HorizonteMinas GeraisBrazil
| | - Heinner Guio
- Laboratorio de Biotecnología y Biología MolecularInstituto Nacional de SaludLimaPeru
- INBIOMEDIC Research and Technological CenterLimaPeru
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Carvalho VHV, Rodrigues JCG, Vinagre LWMS, Pereira EEB, Monte N, Fernandes MR, Ribeiro-Dos-Santos AM, Guerreiro JF, Ribeiro-Dos-Santos Â, Dos Santos SEB, Dos Santos NPC. Genomic investigation on genes related to mercury metabolism in Amazonian indigenous populations. Sci Total Environ 2024; 923:171232. [PMID: 38402986 DOI: 10.1016/j.scitotenv.2024.171232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Studies have identified elevated levels of mercury in Amazonian Indigenous individuals, highlighting them as one of the most exposed to risks. In the unique context of the Brazilian Indigenous population, it is crucial to identify genetic variants with clinical significance to better understand vulnerability to mercury and its adverse effects. Currently, there is a lack of research on the broader genomic profile of Indigenous people, particularly those from the Amazon region, concerning mercury contamination. Therefore, the aim of this study was to assess the genomic profile related to the processes of mercury absorption, distribution, metabolism, and excretion in 64 Indigenous individuals from the Brazilian Amazon. We aimed to determine whether these individuals exhibit a higher susceptibility to mercury exposure. Our study identified three high-impact variants (GSTA1 rs1051775, GSTM1 rs1183423000, and rs1241704212), with the latter two showing a higher frequency in the study population compared to global populations. Additionally, we discovered seven new variants with modifier impact and a genomic profile different from the worldwide populations. These genetic variants may predispose the study population to more harmful mercury exposure compared to global populations. As the first study to analyze broader genomics of mercury metabolism pathways in Brazilian Amazonian Amerindians, we emphasize that our research aims to contribute to public policies by utilizing genomic investigation as a method to identify populations with a heightened susceptibility to mercury exposure.
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Affiliation(s)
- Victor Hugo Valente Carvalho
- Núecleo de Pesquisas em Oncologia, Unidade de Alta Complexidade em Oncologia, Hospital Universitário João de Barros Barreto, 66073-005 Belém, Pará, Brazil.
| | - Juliana Carla Gomes Rodrigues
- Núecleo de Pesquisas em Oncologia, Unidade de Alta Complexidade em Oncologia, Hospital Universitário João de Barros Barreto, 66073-005 Belém, Pará, Brazil
| | - Lui Wallacy Morikawa Souza Vinagre
- Núecleo de Pesquisas em Oncologia, Unidade de Alta Complexidade em Oncologia, Hospital Universitário João de Barros Barreto, 66073-005 Belém, Pará, Brazil
| | - Esdras Edgar Batista Pereira
- Núecleo de Pesquisas em Oncologia, Unidade de Alta Complexidade em Oncologia, Hospital Universitário João de Barros Barreto, 66073-005 Belém, Pará, Brazil
| | - Natasha Monte
- Núecleo de Pesquisas em Oncologia, Unidade de Alta Complexidade em Oncologia, Hospital Universitário João de Barros Barreto, 66073-005 Belém, Pará, Brazil
| | - Marianne Rodrigues Fernandes
- Núecleo de Pesquisas em Oncologia, Unidade de Alta Complexidade em Oncologia, Hospital Universitário João de Barros Barreto, 66073-005 Belém, Pará, Brazil
| | - André Maurício Ribeiro-Dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-110, Belém, Pará, Brazil
| | - João Farias Guerreiro
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-110, Belém, Pará, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-110, Belém, Pará, Brazil
| | - Sidney Emanuel Batista Dos Santos
- Núecleo de Pesquisas em Oncologia, Unidade de Alta Complexidade em Oncologia, Hospital Universitário João de Barros Barreto, 66073-005 Belém, Pará, Brazil
| | - Ney Pereira Carneiro Dos Santos
- Núecleo de Pesquisas em Oncologia, Unidade de Alta Complexidade em Oncologia, Hospital Universitário João de Barros Barreto, 66073-005 Belém, Pará, Brazil
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Espitia Fajardo M, Rivera Franco N, Braga Y, Barreto G. New Y-SNPs in QM3 indigenous populations of Colombia. PLoS One 2023; 18:e0294516. [PMID: 38055663 PMCID: PMC10699635 DOI: 10.1371/journal.pone.0294516] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023] Open
Abstract
In evolutionary studies of human populations based on the Y chromosome, the majority of Native Americans belong to the QM3 lineage. Therefore, to study the history of groups inhabiting northern South America, it is necessary to have a higher resolution of the tree. The objective of this work was to identify new SNPs of the QM3 lineage that would allow the evaluation of the phylogenetic relationships between Andean and Amazonian populations of Colombia. Sequences previously obtained from two Y chromosomes of Amazonian populations were used, from which 13 potential SNPs were selected and typed in 171 Amazonian samples from the Vaupés region and in 60 samples from the Pasto, Nasa, Embera, Arhuaco and Kogüi ethnic groups of the Andean region. In addition, the main SNPs/markers (L56, L54, M346, M848, Z780, CTS11780) defining autochthonous Q lineages were typed, along with others defined by different SNPs/markers as reported in the literature (CTS11357, SA05, Z19319, Z5915, and Z19384). It was found that all the new SNPs are present in the Amazonian samples and only 2 of them are shared with the Embera, Nasa and Pasto, but none with the Kogüi and Arhuaco from the northern Andes, in the Colombian Caribbean. Combining the 13 variants of the present study with 14 previously reported and using TMRCA, a new QM3 tree proposal is generated. This method makes it possible to increase the number of sublineages of QM3 with a higher resolution and to detect differences between the different populations of Vaupés in the Amazon, as in the case of the Kubeos and Pisamiras, the latter of which is in grave danger of extinction. These new sublineages are useful for microevolutionary studies of the Amerindian populations of South America.
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Affiliation(s)
- Marisol Espitia Fajardo
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
| | - Nelson Rivera Franco
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
| | - Yamid Braga
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
- Research Group in Biology, Languages and History, IMGB, Corpodihva, Mitú, Colombia
| | - Guillermo Barreto
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
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Abstract
South America is home to one of the most culturally diverse present-day native populations. However, the dispersion pattern, genetic substructure, and demographic complexity within South America are still poorly understood. Based on genome-wide data of 58 native populations, we provide a comprehensive scenario of South American indigenous groups considering the genomic, environmental, and linguistic data. Clear patterns of genetic structure were inferred among the South American natives, presenting at least four primary genetic clusters in the Amazonian and savanna regions and three clusters in the Andes and Pacific coast. We detected a cline of genetic variation along a west-east axis, contradicting a hard Andes-Amazon divide. This longitudinal genetic variation seemed to have been shaped by both serial population bottlenecks and isolation by distance. Results indicated that present-day South American substructures recapitulate ancient macroregional ancestries and western Amazonia groups show genetic evidence of cultural exchanges that led to language replacement in precontact times. Finally, demographic inferences pointed to a higher resilience of the western South American groups regarding population collapses caused by the European invasion and indicated precontact population reductions and demic expansions in South America.
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Affiliation(s)
- Marcos Araújo Castro e Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago Ferraz
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Cainã M Couto-Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Renan B Lemes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - David Comas
- Departament de Ciències, Institut de Biologia Evolutiva, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Barozet E, Valenzuela CY, Cifuentes L, Verdugo RA, Herrera L, Acuña M, Llop E, Moraga M, Berríos S, Di Genova A, Digman D, Symon A, Asenjo S, López P, Bustamante ML, Pezo-Valderrama P, Suazo J, Caba F, Villalón M, Alvarado S, Cáceres D, Salgado K, Portales P, Loira N, Maas A. The Chilean socio-ethno-genomic cline. Biodemography Soc Biol 2021; 66:156-171. [PMID: 34182852 DOI: 10.1080/19485565.2021.1879626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Studies of the current Chilean population performed using classical genetic markers have established that the Chilean population originated primarily from the admixture of European people, particularly Spaniards, and Amerindians. A socioeconomic-ethno-genetic cline was established soon after the conquest. Spaniards born in Spain or Chile occupied the highest Socioeconomic Strata, while Amerindians belonged to the lowest. The intermediate strata consisted of people with different degrees of ethnic admixture; the larger the European admixture, the higher the Socioeconomic Level. The present study of molecular genomic markers sought to calculate the percentage of Amerindian admixture and revealed a finer distribution of this cline, as well as differences between two Amerindian groups: Aymara and Mapuche. The use of two socioeconomic classifications - Class and Socioeconomic Level - reveals important differences. Furthermore, Self-reported Ethnicity (self-assignment to an ethnic group) and Self-reported Ancestry (self-recognition of Amerindian ancestors) show variations and differing relationships between socioeconomic classifications and genomic Amerindian Admixture. These data constitute a valuable input for the formulation of public healthcare policy and show that the notions of Ethnicity, Socioeconomic Strata and Class should always be a consideration in policy development.
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Affiliation(s)
- E Barozet
- Departamento de Sociología, Facultad de Ciencias Sociales, Universidad de Chile, Centro de Estudios de Conflicto y Cohesión, Social, Santiago, Chile
| | - C Y Valenzuela
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - L Cifuentes
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - R A Verdugo
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - L Herrera
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - M Acuña
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - E Llop
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - M Moraga
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - S Berríos
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - A Di Genova
- Mathomics, Centro de Modelamiento Matemático y Centro Para la Regulación del Genoma, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - D Digman
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - A Symon
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - S Asenjo
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - P López
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - M L Bustamante
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Psiquiatría y Salud Mental Norte, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - P Pezo-Valderrama
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - J Suazo
- Instituto de Investigación en Ciencias Odontológicas, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - F Caba
- Escuela de Puericultura, Facultad de Ciencias Médicas, Universidad Bernardo O'Higgins, Chile
| | - M Villalón
- Instituto de Salud Poblacional "Escuela de Salud Pública", Universidad de Chile, Santiago, Chile
| | - S Alvarado
- Instituto de Salud Poblacional "Escuela de Salud Pública", Universidad de Chile, Santiago, Chile
| | - D Cáceres
- Instituto de Salud Poblacional "Escuela de Salud Pública", Universidad de Chile, Santiago, Chile
| | - K Salgado
- Escuela de Puericultura, Facultad de Ciencias Médicas, Universidad Bernardo O'Higgins, Chile
| | - P Portales
- Corporación Municipal de Desarrollo Social, Iquique, Chile
| | - N Loira
- Mathomics, Centro de Modelamiento Matemático y Centro Para la Regulación del Genoma, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - A Maas
- Mathomics, Centro de Modelamiento Matemático y Centro Para la Regulación del Genoma, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Matemática, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
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Guevara EK, Palo JU, Översti S, King JL, Seidel M, Stoljarova M, Wendt FR, Bus MM, Guengerich A, Church WB, Guillén S, Roewer L, Budowle B, Sajantila A. Genetic assessment reveals no population substructure and divergent regional and sex-specific histories in the Chachapoyas from northeast Peru. PLoS One 2020; 15:e0244497. [PMID: 33382772 PMCID: PMC7774974 DOI: 10.1371/journal.pone.0244497] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 05/27/2020] [Accepted: 12/10/2020] [Indexed: 12/31/2022] Open
Abstract
Many native populations in South America have been severely impacted by two relatively recent historical events, the Inca and the Spanish conquest. However decisive these disruptive events may have been, the populations and their gene pools have been shaped markedly also by the history prior to the conquests. This study focuses mainly on the Chachapoya peoples that inhabit the montane forests on the eastern slopes of the northern Peruvian Andes, but also includes three distinct neighboring populations (the Jívaro, the Huancas and the Cajamarca). By assessing mitochondrial, Y-chromosomal and autosomal diversity in the region, we explore questions that have emerged from archaeological and historical studies of the regional culture (s). These studies have shown, among others, that Chachapoyas was a crossroads for Coast-Andes-Amazon interactions since very early times. In this study, we examine the following questions: 1) was there pre-Hispanic genetic population substructure in the Chachapoyas sample? 2) did the Spanish conquest cause a more severe population decline on Chachapoyan males than on females? 3) can we detect different patterns of European gene flow in the Chachapoyas region? and, 4) did the demographic history in the Chachapoyas resemble the one from the Andean area? Despite cultural differences within the Chachapoyas region as shown by archaeological and ethnohistorical research, genetic markers show no significant evidence for past or current population substructure, although an Amazonian gene flow dynamic in the northern part of this territory is suggested. The data also indicates a bottleneck c. 25 generations ago that was more severe among males than females, as well as divergent population histories for populations in the Andean and Amazonian regions. In line with previous studies, we observe high genetic diversity in the Chachapoyas, despite the documented dramatic population declines. The diverse topography and great biodiversity of the northeastern Peruvian montane forests are potential contributing agents in shaping and maintaining the high genetic diversity in the Chachapoyas region.
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Affiliation(s)
- Evelyn K. Guevara
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- * E-mail: (EKG); (AS)
| | - Jukka U. Palo
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Genetics Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Sanni Översti
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jonathan L. King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Maria Seidel
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Monika Stoljarova
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Frank R. Wendt
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Department of Psychiatry, Yale University School of Medicine and VA Connecticut Healthcare System, West Haven, Connecticut, United States of America
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Magdalena M. Bus
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Anna Guengerich
- Eckerd College, Saint Petersburg, Florida, United States of America
| | - Warren B. Church
- Department of Earth and Space Sciences, Columbus State University, Columbus, Georgia, United States of America
| | | | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- * E-mail: (EKG); (AS)
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7
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Vicuña L, Klimenkova O, Norambuena T, Martinez FI, Fernandez MI, Shchur V, Eyheramendy S. Postadmixture Selection on Chileans Targets Haplotype Involved in Pigmentation, Thermogenesis and Immune Defense against Pathogens. Genome Biol Evol 2020; 12:1459-1470. [PMID: 32614437 PMCID: PMC7487163 DOI: 10.1093/gbe/evaa136] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2020] [Indexed: 12/13/2022] Open
Abstract
Detection of positive selection signatures in populations around the world is helping to uncover recent human evolutionary history as well as the genetic basis of diseases. Most human evolutionary genomic studies have been performed in European, African, and Asian populations. However, populations with Native American ancestry have been largely underrepresented. Here, we used a genome-wide local ancestry enrichment approach complemented with neutral simulations to identify postadmixture adaptations underwent by admixed Chileans through gene flow from Europeans into local Native Americans. The top significant hits (P = 2.4×10-7) are variants in a region on chromosome 12 comprising multiple regulatory elements. This region includes rs12821256, which regulates the expression of KITLG, a well-known gene involved in lighter hair and skin pigmentation in Europeans as well as in thermogenesis. Another variant from that region is associated with the long noncoding RNA RP11-13A1.1, which has been specifically involved in the innate immune response against infectious pathogens. Our results suggest that these genes were relevant for adaptation in Chileans following the Columbian exchange.
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Affiliation(s)
- Lucas Vicuña
- Faculty of Engineering and Sciences, Universidad Adolfo Ibañez, Peñalolén, Santiago, Chile
| | - Olga Klimenkova
- National Research University Higher School of Economics, Russian Federation, Moscow, Russia
| | - Tomás Norambuena
- Faculty of Engineering and Sciences, Universidad Adolfo Ibañez, Peñalolén, Santiago, Chile
| | - Felipe I Martinez
- Center for Intercultural and Indigenous Research, School of Anthropology, Faculty of Social Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mario I Fernandez
- Department of Urology, Clínica Alemana, Santiago, Chile
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Vladimir Shchur
- National Research University Higher School of Economics, Russian Federation, Moscow, Russia
| | - Susana Eyheramendy
- Faculty of Engineering and Sciences, Universidad Adolfo Ibañez, Peñalolén, Santiago, Chile
- Instituto Milenio de Investigación sobre los Fundamentos de los Datos (IMFD)
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8
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Boekstegers F, Marcelain K, Barahona Ponce C, Baez Benavides PF, Müller B, de Toro G, Retamales J, Barajas O, Ahumada M, Morales E, Rojas A, Sanhueza V, Loader D, Rivera MT, Gutiérrez L, Bernal G, Ortega A, Montalvo D, Portiño S, Bertrán ME, Gabler F, Spencer L, Olloquequi J, González Silos R, Fischer C, Scherer D, Jenab M, Aleksandrova K, Katzke V, Weiderpass E, Moradi T, Fischer K, Bossers W, Brenner H, Hveem K, Eklund N, Völker U, Waldenberger M, Fuentes Guajardo M, Gonzalez-Jose R, Bedoya G, Bortolini MC, Canizales S, Gallo C, Ruiz Linares A, Rothhammer F, Lorenzo Bermejo J. ABCB1/4 gallbladder cancer risk variants identified in India also show strong effects in Chileans. Cancer Epidemiol 2020; 65:101643. [PMID: 32058310 DOI: 10.1016/j.canep.2019.101643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The first large-scale genome-wide association study of gallbladder cancer (GBC) recently identified and validated three susceptibility variants in the ABCB1 and ABCB4 genes for individuals of Indian descent. We investigated whether these variants were also associated with GBC risk in Chileans, who show the highest incidence of GBC worldwide, and in Europeans with a low GBC incidence. METHODS This population-based study analysed genotype data from retrospective Chilean case-control (255 cases, 2042 controls) and prospective European cohort (108 cases, 181 controls) samples consistently with the original publication. RESULTS Our results confirmed the reported associations for Chileans with similar risk effects. Particularly strong associations (per-allele odds ratios close to 2) were observed for Chileans with high Native American (=Mapuche) ancestry. No associations were noticed for Europeans, but the statistical power was low. CONCLUSION Taking full advantage of genetic and ethnic differences in GBC risk may improve the efficiency of current prevention programs.
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Affiliation(s)
- Felix Boekstegers
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Germany
| | - Katherine Marcelain
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Chile
| | - Carol Barahona Ponce
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Germany; Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Chile
| | | | - Bettina Müller
- Servicio de Oncología Médica, Instituto Nacional del Cáncer, Santiago, Chile
| | - Gonzalo de Toro
- Servicio de Anatomía Patológica, Hospital de Puerto Montt, Puerto Montt, Chile
| | - Javier Retamales
- Servicio de Oncología Médica, Instituto Nacional del Cáncer, Santiago, Chile
| | - Olga Barajas
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Chile; Oncology, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Monica Ahumada
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Chile; Oncology, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Erik Morales
- Servicio de Anatomía Patológica, Hospital Regional, Talca, Chile
| | - Armando Rojas
- Biomedical Research Labs, Medicine Faculty, Catholic University of Maule, Talca, Chile
| | - Verónica Sanhueza
- Servicio de Anatomía Patológica, Hospital Padre Hurtado, Santiago, Chile
| | - Denisse Loader
- Servicio de Anatomía Patológica, Hospital Padre Hurtado, Santiago, Chile
| | | | - Lorena Gutiérrez
- Servicio de Anatomía Patológica, Hospital San Juan de Dios, Santiago, Chile
| | - Giuliano Bernal
- Laboratory of Molecular and Cellular Biology of Cancer (CancerLab), Department of Biomedical Sciences, Faculty of Medicine, Universidad Católica del Norte, Coquimbo, Chile
| | - Alejandro Ortega
- Servicio de Anatomía Patológica, Hospital Regional, Arica, Chile
| | | | - Sergio Portiño
- Oncology, Hospital Clínico Universidad de Chile, Santiago, Chile
| | | | - Fernando Gabler
- Servicio de Anatomía Patológica, Hospital San Borja Arriarán, Santiago, Chile
| | - Loreto Spencer
- Servicio de Anatomía Patológica, Hospital Regional Guillermo Grant Benavente, Concepción, Chile
| | - Jordi Olloquequi
- Laboratory of Cellular and Molecular Pathology, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
| | - Rosa González Silos
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Germany
| | | | - Dominique Scherer
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Germany
| | - Mazda Jenab
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Krasimira Aleksandrova
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany; University of Potsdam, Institute of Nutritional Science, Potsdam, Germany
| | - Verena Katzke
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elisabete Weiderpass
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Tahereh Moradi
- Division of Epidemiology, Department of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Krista Fischer
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kristian Hveem
- The Nord-Trøndelag Health (HUNT) Research Centre, Norwegian University of Science and Technology (NTNU), Trondheim, K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Norway
| | - Niina Eklund
- Genomics and biobank, National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Uwe Völker
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Universitätsmedizin Greifswald, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology and Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Rolando Gonzalez-Jose
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Gabriel Bedoya
- Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Maria C Bortolini
- Instituto de Biociências, Universidad Federal do Rio Grande do Sul, Puerto Alegre, Brazil
| | - Samuel Canizales
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Carla Gallo
- Unidad de Neurobiología Molecular y Genética, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Andres Ruiz Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200433, China; Aix-Marseille Univ, CNRS, EFS, ADES, Marseille 13007, France
| | | | - Justo Lorenzo Bermejo
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Germany.
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Guzmán-Castañeda SJ, Ortega-Vega EL, de la Cuesta-Zuluaga J, Velásquez-Mejía EP, Rojas W, Bedoya G, Escobar JS. Gut microbiota composition explains more variance in the host cardiometabolic risk than genetic ancestry. Gut Microbes 2019; 11:191-204. [PMID: 31311405 PMCID: PMC7053924 DOI: 10.1080/19490976.2019.1634416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/10/2019] [Accepted: 06/16/2019] [Indexed: 02/03/2023] Open
Abstract
Cardiometabolic affections greatly contribute to the global burden of disease. The susceptibility to obesity, cardiovascular disease, and type-2 diabetes, conditions that add to the cardiometabolic syndrome (CMS), was associated with the ancestral genetic composition and gut microbiota. Studies explicitly testing associations between genetic ancestry and gut microbes are growing. We here examined whether the host genetic ancestry was associated with gut microbiota composition, and distinguished the effects of genetic ancestry and non-genetic factors on human cardiometabolic health. We performed a cross-sectional study with 441 community-dwelling Colombian mestizos from five cities spanning the Andes, Pacific, and Caribbean coasts. We characterized the host genetic ancestry by genotyping 40 ancestry informative markers; characterized gut microbiota through 16S rRNA gene sequencing; assessed diet intake, physical activity, cigarette, and medicament consumption; and measured cardiometabolic outcomes that allowed calculating a CMS risk scale. On average, each individual of our cohort was 67 ± 6% European, 21 ± 5% Native American and 12 ± 5% African. Multivariable-adjusted generalized linear models showed that individuals with higher Native American and African ancestries had increased fasting insulin, body mass index and CMS risk, as assessed by the CMS risk scale. Furthermore, we identified 21 OTUs associated to the host genetic ancestry and 20 to cardiometabolic health. While we highlight novel associations between genetic ancestry and gut microbiota, we found that the effect of intestinal microbes was more likely to explain the variance in CMS risk scale than the contributions of European, Native American and African genetic backgrounds.
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Affiliation(s)
- Sandra J. Guzmán-Castañeda
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Esteban L. Ortega-Vega
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Jacobo de la Cuesta-Zuluaga
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eliana P. Velásquez-Mejía
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Winston Rojas
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Gabriel Bedoya
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Juan S. Escobar
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
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Soejima M, Koda Y. Genetic variation of FUT2 in a Peruvian population: identification of a novel LTR-mediated deletion and characterization of 4 nonsynonymous single-nucleotide polymorphisms. Transfusion 2019; 59:2415-2421. [PMID: 30957248 DOI: 10.1111/trf.15298] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/17/2023]
Abstract
BACKGROUND The human FUT2 gene, which encodes a secretor type α(1,2)fucosyltransferase, is reported to have several population-specific single-nucleotide polymorphisms (SNPs) and copy number variations. However, little is known about genetic variation of FUT2 in Native Americans. STUDY DESIGN AND METHODS To detect SNPs and copy number variations of the FUT2 gene in Peruvians, direct sequencing and digital polymerase chain reaction were performed. Haplotypes of observed SNPs were estimated by PHASE software or cloning into plasmids. The functional significance of nonsynonymous SNPs was examined by transient transfection assay. RESULTS We identified three novel nonfunctional alleles (se178,357 , se841 , and sedel4 ) due to two nonsynonymous SNPs (178C > T and 841G > A) and a novel long terminal repeat-mediated recombination with a 4.3-kb deletion in 70 Peruvians. The frequency of nonfunctional alleles was relative low (20.7%). Because se841 has a relatively high frequency (5.7%), it might be a suitable genetic marker for Peruvians. CONCLUSION We identified three novel nonfunctional alleles in 70 Peruvians. To our knowledge, this is the first time a long terminal repeat-mediated gene recombination event at the FUT2 locus has been detected.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, Japan
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12
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Chacón-Duque JC, Adhikari K, Fuentes-Guajardo M, Mendoza-Revilla J, Acuña-Alonzo V, Barquera R, Quinto-Sánchez M, Gómez-Valdés J, Everardo Martínez P, Villamil-Ramírez H, Hünemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Villena M, Vásquez R, Llop E, Sandoval JR, Salazar-Granara AA, Parolin ML, Sandoval K, Peñaloza-Espinosa RI, Rangel-Villalobos H, Winkler CA, Klitz W, Bravi C, Molina J, Corach D, Barrantes R, Gomes V, Resende C, Gusmão L, Amorim A, Xue Y, Dugoujon JM, Moral P, González-José R, Schuler-Faccini L, Salzano FM, Bortolini MC, Canizales-Quinteros S, Poletti G, Gallo C, Bedoya G, Rothhammer F, Balding D, Hellenthal G, Ruiz-Linares A. Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance. Nat Commun 2018; 9:5388. [PMID: 30568240 PMCID: PMC6300600 DOI: 10.1038/s41467-018-07748-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [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: 02/02/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
Abstract
Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample.
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Affiliation(s)
- Juan-Camilo Chacón-Duque
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000009, Chile
| | - Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Mirsha Quinto-Sánchez
- Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Jorge Gómez-Valdés
- Posgrado en Antropología Física, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
| | - Paola Everardo Martínez
- Posgrado en Antropología, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, 04510, Mexico
| | - Tábita Hünemeier
- Departamento de Genética e Biología Evolutiva, Instituto de Biociências, Universidade de São Paulo, Sao Paulo, 05508-090, Brazil
| | - Virginia Ramallo
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Caio C Silva de Cerqueira
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Mercedes Villena
- Instituto Boliviano de Biología de Altura (IBBA), Universidad Mayor de San Andrés (UMSA), La Paz, 2070, Bolivia
| | - René Vásquez
- Instituto Boliviano de Biología de Altura (IBBA), Universidad Autónoma Tomás Frías, Potosí, 53820, Bolivia
| | - Elena Llop
- Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 1027, Chile
| | - José R Sandoval
- Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, 12, Peru
| | | | - Maria-Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
| | - Karla Sandoval
- National Laboratory of Genomics and Biodiversity (LANGEBIO), CINVESTAV, Irapuato, 36821, Mexico
| | - Rosenda I Peñaloza-Espinosa
- Department of Biological Systems, Division of Biological and Health Sciences, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, 04960, Mexico
| | - Hector Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara, Ocotlán, 1115, Mexico
| | - Cheryl A Winkler
- Basic Research Laboratory, National Cancer Institute, Frederick National Laboratory, Frederick, MD, 21702, USA
| | - William Klitz
- Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Claudio Bravi
- Instituto Multidisciplinario de Biología Celular, CONICET, La Plata, B1906APO, Argentina
| | - Julio Molina
- Centro de Investigaciones Biomédicas de Guatemala, Ciudad de Guatemala, 01011, Guatemala
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas and CONICET, Universidad de Buenos Aires, Buenos Aires, C1113AAD, Argentina
| | - Ramiro Barrantes
- Escuela de Biología, Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Verónica Gomes
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
| | - Carlos Resende
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
| | - Leonor Gusmão
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
- DNA Diagnostic Laboratory (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, 23968-000, Brazil
| | - Antonio Amorim
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, 4169-007, Portugal
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Jean-Michel Dugoujon
- Centre National de la Recherche Scientifique, Université Toulouse 3 Paul Sabatier, Toulouse, 31330, France
| | - Pedro Moral
- Departamento de Biología Evolutiva, Ecología y Ciencias Ambientales, Universitat de Barcelona, Barcelona, 08007, Spain
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, 04510, Mexico
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Gabriel Bedoya
- Genética Molecular (GENMOL), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Francisco Rothhammer
- Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 1027, Chile
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, 1000009, Chile
| | - David Balding
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200433, China.
- Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, 13007, France.
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Alonso Morales LA, Casas-Vargas A, Rojas Castro M, Resque R, Ribeiro-dos-Santos ÂK, Santos S, Gusmão L, Usaquén W. Paternal portrait of populations of the middle Magdalena River region (Tolima and Huila, Colombia): New insights on the peopling of Central America and northernmost South America. PLoS One 2018; 13:e0207130. [PMID: 30439976 PMCID: PMC6237345 DOI: 10.1371/journal.pone.0207130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 05/09/2018] [Accepted: 10/25/2018] [Indexed: 11/18/2022] Open
Abstract
The valley of the Magdalena River is one of the main population pathways in Colombia. The gene pool and spatial configuration of human groups in this territory have been outlined throughout three historical stages: the Native pre-Hispanic world, Spanish colonization, and XIX century migrations. This research was designed with the goal of characterizing the diversity and distribution pattern of Y-chromosome lineages that are currently present in the Tolima and Huila departments (middle Magdalena River region). Historic cartography was used to identify the main geographic sites where the paternal lineages belonging to this area have gathered. Twelve municipalities were chosen, and a survey that included genealogical information was administered. Samples collected from 83 male volunteers were analyzed for 48 Y-SNPs and 17 Y-STRs. The results showed a highly diverse region characterized by the presence of 16 sublineages within the major clades R, Q, J, G, T and E and revealed that 93% (n = 77) of haplotypes were different. Among these haplogroups, European-specific R1b-M269 lineages were the most representative (57.83%), with six different subhaplogroups and 43 unique haplotypes. Native American paternal ancestry was also detected based on the presence of the Q1a2-M3*(xM19, M194, M199) and Q1a2-M346*(xM3) lineages. Interestingly, all Q1a2-M346*(xM3) samples (n = 7, with five different haplotypes) carried allele six at the DYS391 locus. This allele has a worldwide frequency of 0.169% and was recently associated with a new Native subhaplogroup. An in-depth phylogenetic analysis of these samples suggests the Tolima and Huila region to be the principal area in all Central and South America where this particular Native lineage is found. This lineage has been present in the region for at least 1,809 (+/- 0,5345) years.
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Affiliation(s)
- Luz Angela Alonso Morales
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
- * E-mail: (LAAM); (WU)
| | - Andrea Casas-Vargas
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Madelyn Rojas Castro
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Rafael Resque
- Laboratório de Toxicologia e Química Farmacêutica, Departamento de Ciências da Saúde e Biológicas, Universidade Federal do Amapá, Macapá, Brazil
| | - Ândrea Kelly Ribeiro-dos-Santos
- Human and Medical Genetics Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará - UFPA), Belém, state of Pará (PA), Brazil
| | - Sidney Santos
- Human and Medical Genetics Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará - UFPA), Belém, state of Pará (PA), Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - William Usaquén
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
- * E-mail: (LAAM); (WU)
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14
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Abstract
Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the nonrecombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic exogamy, a marital practice in which men are required to marry women speaking a different language. We identified 2,969 SNPs in the NRY sequences, only 925 of which were previously described. The NRY and mtDNA data showed different sex-specific demographic histories: female effective population size has been larger than that of males through time, which might reflect larger variance in male reproductive success. Both markers show an increase in lineage diversification beginning ∼5,000 years ago, which may reflect the intensification of agriculture, technological innovations, and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, we find similar excesses of NRY versus mtDNA between-population divergence at both the local and continental scale, suggesting long-term stability of female versus male migration. We also find evidence of the impact of sociocultural practices on diversity patterns. Finally, our study highlights the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between sexes.
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Affiliation(s)
- Leonardo Arias
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Laboratorio de Genética Molecular Humana, Departamento de Biología, Universidad del Valle, Cali, Colombia
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Guillermo Barreto
- Laboratorio de Genética Molecular Humana, Departamento de Biología, Universidad del Valle, Cali, Colombia
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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15
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Lindo J, Haas R, Hofman C, Apata M, Moraga M, Verdugo RA, Watson JT, Viviano Llave C, Witonsky D, Beall C, Warinner C, Novembre J, Aldenderfer M, Di Rienzo A. The genetic prehistory of the Andean highlands 7000 years BP though European contact. Sci Adv 2018; 4:eaau4921. [PMID: 30417096 PMCID: PMC6224175 DOI: 10.1126/sciadv.aau4921] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/12/2018] [Indexed: 05/02/2023]
Abstract
The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation datasets from both highland and lowland populations. We infer three significant features: a split between low- and high-elevation populations that occurred between 9200 and 8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. We do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.
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Affiliation(s)
- John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Randall Haas
- Department of Anthropology, University of California, Davis, CA 95616, USA
| | - Courtney Hofman
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
| | - Mario Apata
- Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, Chile
| | - Mauricio Moraga
- Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, Chile
- Departamento de Antropología, Universidad de Chile, Santiago, Chile
| | - Ricardo A. Verdugo
- Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, Chile
- Departamento de Oncología Básico-Clínica, Universidad de Chile, Santiago, Chile
| | - James T. Watson
- Arizona State Museum and School of Anthropology, University of Arizona, Tucson, AZ 85721, USA
| | | | - David Witonsky
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Cynthia Beall
- Department of Anthropology, Case Western University, Cleveland, OH 44106, USA
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Mark Aldenderfer
- School of Social Sciences, Humanities, and Arts, University of California, Merced, Merced, CA 95343, USA
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
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16
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Criollo-Rayo AA, Bohórquez M, Prieto R, Howarth K, Culma C, Carracedo A, Tomlinson I, Echeverry de Polnaco MM, Carvajal Carmona LG. Native American gene continuity to the modern admixed population from the Colombian Andes: Implication for biomedical, population and forensic studies. Forensic Sci Int Genet 2018; 36:e1-e7. [PMID: 29909140 DOI: 10.1016/j.fsigen.2018.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/05/2018] [Accepted: 06/05/2018] [Indexed: 12/14/2022]
Abstract
Andean populations have variable degrees of Native American and European ancestry, representing an opportunity to study admixture dynamics in the populations from Latin America (also known as Hispanics). We characterized the genetic structure of two indigenous (Nasa and Pijao) and three admixed (Ibagué, Ortega and Planadas) groups from Tolima, in the Colombian Andes. DNA samples from 348 individuals were genotyped for six mitochondrial DNA (mtDNA), seven non-recombining Y-chromosome (NRY) region and 100 autosomal ancestry informative markers. Nasa and Pijao had a predominant Native American ancestry at the autosomal (92%), maternal (97%) and paternal (70%) level. The admixed groups had a predominant Native American mtDNA ancestry (90%), a substantial frequency of European NRY haplotypes (72%) and similar autosomal contributions from Europeans (51%) and Amerindians (45%). Pijao and nearby Ortega were indistinguishable at the mtDNA and autosomal level, suggesting a genetic continuity between them. Comparisons with multiple Native American populations throughout the Americas revealed that Pijao, had close similarities with Carib-speakers from distant parts of the continent, suggesting an ancient correlation between language and genes. In summary, our study aimed to understand Hispanic patterns of migration, settlement and admixture, supporting an extensive contribution of local Amerindian women to the gene pool of admixed groups and consistent with previous reports of European-male driven admixture in Colombia.
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Affiliation(s)
- Angel A Criollo-Rayo
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Facultad de Ciencias y Facultad de Ciencias de la Salud, Universidad del Tolima, Ibagué, Colombia
| | - Mabel Bohórquez
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Facultad de Ciencias y Facultad de Ciencias de la Salud, Universidad del Tolima, Ibagué, Colombia
| | - Rodrigo Prieto
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Facultad de Ciencias y Facultad de Ciencias de la Salud, Universidad del Tolima, Ibagué, Colombia
| | - Kimberley Howarth
- Institute of Cancer and Genomics Sciences, University of Birmingham, UK
| | - Cesar Culma
- Comite Regional Indígena del Tolima, Ibagué, Tolima, Colombia
| | - Angel Carracedo
- Fundación Pública Galega de Medicina Xenómica (SERGAS)-CIBERER, Universidad de Santiago de Compostela, Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ian Tomlinson
- Institute of Cancer and Genomics Sciences, University of Birmingham, UK
| | - Maria M Echeverry de Polnaco
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Facultad de Ciencias y Facultad de Ciencias de la Salud, Universidad del Tolima, Ibagué, Colombia
| | - Luis G Carvajal Carmona
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Facultad de Ciencias y Facultad de Ciencias de la Salud, Universidad del Tolima, Ibagué, Colombia; Fundación de Genética y Genómica, Medellin, Colombia; Corporación Universitaria Remington, Medellin, Colombia; Genome Center and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, GBSF, 451 Health Science Drive Davis, CA, 95616-8816, USA.
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17
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Sandoval JR, Lacerda DR, Jota MS, Elward R, Acosta O, Pinedo D, Danos P, Cuellar C, Revollo S, Santos FR, Fujita R. Genetic ancestry of families of putative Inka descent. Mol Genet Genomics 2018; 293:873-881. [PMID: 29502256 PMCID: PMC6061041 DOI: 10.1007/s00438-018-1427-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/26/2018] [Indexed: 11/17/2022]
Abstract
This study focuses on the descendants of the royal Inka family. The Inkas ruled Tawantinsuyu, the largest pre-Columbian empire in South America, which extended from southern Colombia to central Chile. The origin of the royal Inkas is currently unknown. While the mummies of the Inka rulers could have been informative, most were destroyed by Spaniards and the few remaining disappeared without a trace. Moreover, no genetic studies have been conducted on present-day descendants of the Inka rulers. In the present study, we analysed uniparental DNA markers in 18 individuals predominantly from the districts of San Sebastian and San Jerónimo in Cusco (Peru), who belong to 12 families of putative patrilineal descent of Inka rulers, according to documented registries. We used single-nucleotide polymorphisms and short tandem repeat (STR) markers of the Y chromosome (Y-STRs), as well as mitochondrial DNA D-loop sequences, to investigate the paternal and maternal descent of the 18 alleged Inka descendants. Two Q-M3* Y-STR clusters descending from different male founders were identified. The first cluster, named AWKI-1, was associated with five families (eight individuals). By contrast, the second cluster, named AWKI-2, was represented by a single individual; AWKI-2 was part of the Q-Z19483 sub-lineage that was likely associated with a recent male expansion in the Andes, which probably occurred during the Late Intermediate Period (1000-1450 AD), overlapping the Inka period. Concerning the maternal descent, different mtDNA lineages associated with each family were identified, suggesting a high maternal gene flow among Andean populations, probably due to changes in the last 1000 years.
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Affiliation(s)
- José R Sandoval
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres (USMP), Lima, Peru.
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Daniela R Lacerda
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marilza S Jota
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Oscar Acosta
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres (USMP), Lima, Peru
| | - Donaldo Pinedo
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres (USMP), Lima, Peru
| | - Pierina Danos
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres (USMP), Lima, Peru
| | | | | | - Fabricio R Santos
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ricardo Fujita
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres (USMP), Lima, Peru
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18
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Brandini S, Bergamaschi P, Cerna MF, Gandini F, Bastaroli F, Bertolini E, Cereda C, Ferretti L, Gómez-Carballa A, Battaglia V, Salas A, Semino O, Achilli A, Olivieri A, Torroni A. The Paleo-Indian Entry into South America According to Mitogenomes. Mol Biol Evol 2018; 35:299-311. [PMID: 29099937 PMCID: PMC5850732 DOI: 10.1093/molbev/msx267] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Recent and compelling archaeological evidence attests to human presence ∼14.5 ka at multiple sites in South America and a very early exploitation of extreme high-altitude Andean environments. Considering that, according to genetic evidence, human entry into North America from Beringia most likely occurred ∼16 ka, these archeological findings would imply an extremely rapid spread along the double continent. To shed light on this issue from a genetic perspective, we first completely sequenced 217 novel modern mitogenomes of Native American ancestry from the northwestern area of South America (Ecuador and Peru); we then evaluated them phylogenetically together with other available mitogenomes (430 samples, both modern and ancient) from the same geographic area and, finally, with all closely related mitogenomes from the entire double continent. We detected a large number (N = 48) of novel subhaplogroups, often branching into further subclades, belonging to two classes: those that arose in South America early after its peopling and those that instead originated in North or Central America and reached South America with the first settlers. Coalescence age estimates for these subhaplogroups provide time boundaries indicating that early Paleo-Indians probably moved from North America to the area corresponding to modern Ecuador and Peru over the short time frame of ∼1.5 ka comprised between 16.0 and 14.6 ka.
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Affiliation(s)
- Stefania Brandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Paola Bergamaschi
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Servizio di Immunoematologia e Medicina Trasfusionale, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marco Fernando Cerna
- Biotechnology Laboratory, Salesian Polytechnic University of Ecuador, Quito, Ecuador
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | | | - Emilie Bertolini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, National Neurological Institute C. Mondino, Pavia, Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alberto Gómez-Carballa
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Unidade de Xenética, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Galicia, Spain
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, Galicia, Spain
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Antonio Salas
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Unidade de Xenética, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Galicia, Spain
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
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19
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Blanco R, Suazo J, Santos JL, Paredes M, Sung H, Carreño H, Jara L. Association between 10 Microsatellite Markers and Nonsyndromic Cleft Lip Palate in the Chilean Population. Cleft Palate Craniofac J 2017; 41:163-7. [PMID: 14989688 DOI: 10.1597/02-147] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objective The objective of this case-control study was to evaluate the possible association between nonsyndromic cleft lip/palate (NSCLP) and 10 genetic markers in four chromosomal regions in the admixed Spanish-Amerindian Chilean population. Setting Study participants included 56 patients with NSCLP identified and interviewed for positive family history during the course of clinical examinations at different rehabilitation centers in the cities of Santiago and Talca, Chile. A control group of 59 normal individuals without known familial antecedents of clefting was obtained from blood bank donors of the University Hospital, University of Chile. Cases and controls belonged to low- to low-middle socioeconomic strata. Results Ten markers from chromosome 4p, 4q, 6p, 17q, and 19q were assessed (MSX1, D4S175, D4S192, F13A1, EDN1, D6S89, D6S105, D6S109, D17S579, BCL3). Four of them showed significant deviations from Hardy-Weinberg expectations in controls, according to the exact test (D4S192, BCL3, F13A1, and D6S89). The case-control comparison by means of the CLUMP program showed significant differences only in BCL3, and D6S109 almost reached statistical significance. Conclusions Most of the genetic regions with positive results in Caucasian populations may not be involved in NSCLP in Chile, regardless of the positive evidence for the candidate region on chromosome 19. Similar findings have been reported recently in the Chinese population.
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Affiliation(s)
- Rafael Blanco
- Human Genetics Program, Institute of Biomedical Sciences, School of Medicine, University of Chile, Santiago, Chile.
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20
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Ossa H, Aquino J, Pereira R, Ibarra A, Ossa RH, Pérez LA, Granda JD, Lattig MC, Groot H, Fagundes de Carvalho E, Gusmão L. Outlining the Ancestry Landscape of Colombian Admixed Populations. PLoS One 2016; 11:e0164414. [PMID: 27736937 PMCID: PMC5063461 DOI: 10.1371/journal.pone.0164414] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/23/2016] [Indexed: 12/17/2022] Open
Abstract
The ancestry of the Colombian population comprises a large number of well differentiated Native communities belonging to diverse linguistic groups. In the late fifteenth century, a process of admixture was initiated with the arrival of the Europeans, and several years later, Africans also became part of the Colombian population. Therefore, the genepool of the current Colombian population results from the admixture of Native Americans, Europeans and Africans. This admixture occurred differently in each region of the country, producing a clearly stratified population. Considering the importance of population substructure in both clinical and forensic genetics, we sought to investigate and compare patterns of genetic ancestry in Colombia by studying samples from Native and non-Native populations living in its 5 continental regions: the Andes, Caribe, Amazonia, Orinoquía, and Pacific regions. For this purpose, 46 AIM-Indels were genotyped in 761 non-related individuals from current populations. Previously published genotype data from 214 Colombian Natives from five communities were used for population comparisons. Significant differences were observed between Native and non-Native populations, among non-Native populations from different regions and among Native populations from different ethnic groups. The Pacific was the region with the highest African ancestry, Amazonia harboured the highest Native ancestry and the Andean and Orinoquían regions showed the highest proportion of European ancestry. The Andean region was further sub-divided into 6 sub-regions: North East, Central West, Central East, West, South West and South East. Among these regions, the South West region showed a significantly lower European admixture than the other regions. Hardy-Weinberg equilibrium and variance values of ancestry among individuals within populations showed a potential stratification of the Pacific population.
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Affiliation(s)
- Humberto Ossa
- Pontificia Universidad Javeriana, Facultad de Ciencias, Bogotá, Colombia
- Laboratório de Genética y Biología Molecular, Bogotá, Colombia
| | - Juliana Aquino
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Rui Pereira
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal
| | - Adriana Ibarra
- IdentiGEN - Genetic Identification Laboratory and Research Group of Genetic Identification, Institute of Biology, School of Natural and Exact Sciences (FCEN), University of Antioquia, Medellin, Antioquia, Colombia
| | - Rafael H Ossa
- Laboratório de Genética y Biología Molecular, Bogotá, Colombia
- Universidad El Bosque, Facultad de Medicina, Bogotá, Colombia
| | - Luz Adriana Pérez
- Laboratorio de genética humana, Universidad de los Andes, Bogotá, Colombia
| | - Juan David Granda
- IdentiGEN - Genetic Identification Laboratory and Research Group of Genetic Identification, Institute of Biology, School of Natural and Exact Sciences (FCEN), University of Antioquia, Medellin, Antioquia, Colombia
| | | | - Helena Groot
- Laboratorio de genética humana, Universidad de los Andes, Bogotá, Colombia
| | | | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal
- * E-mail:
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21
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Abstract
BACKGROUND Amerindian admixture is an important parameter to consider in epidemiological studies in American countries, to make a proper selection of cases and controls. AIM To compare Amerindian admixture estimates obtained using ABO*A and ABO*O blood group alleles and ancestral identity markers (AIMs) in the mixed Chilean population. SUBJECTS AND METHODS Amerindian admixture rates were determined in 720 Chilean volunteers residing in Arica and born in the 15 regions of the country, using ABO*O and ABO*A alleles and 40 AIMs selected from more than 500,000 single nucleotide polymorphisms (SNPs). RESULTS Mean admixture estimates obtained using ABO*O and ABO*A alleles and AIMs were 35, 47% and 48% respectively. There was concordance in estimates, with the exception of the admixture based on ABO*O allele and AIMs. CONCLUSIONS In Chile, Amerindian admixture estimates obtained using ABO*A could be used as an alternative to AIMs in justified cases provided the sample size is reasonably large.
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22
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Nishi T, Nakamura T, Honda K. Detection of a novel X-chromosomal short tandem repeat marker in Xq28 in four ethnic groups. Leg Med (Tokyo) 2016; 19:43-6. [PMID: 26980253 DOI: 10.1016/j.legalmed.2016.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 12/28/2015] [Accepted: 01/27/2016] [Indexed: 12/17/2022]
Abstract
DNA testing of X-chromosomal short tandem repeat (X-STR) polymorphisms has been the focus of attention in several studies, mainly due to its applicability in the investigation of complex kinship cases. Studies of X-STR in analyses of DNA sequences, population studies and DNA testing applications have been reported. We performed detection and population genetic study of a novel tetranucleotide X-STR locus in the present study. We identified a unique X-STR locus consisting of two tetranucleotides in Xq28. Although the STR is a simple tetranucleotide, its polymorphism was comparatively high [polymorphism information content (PIC)=0.7140] in Japanese subjects. In addition, the STR varied in structure among ethnic groups. We conclude that this locus will be useful for forensic DNA testing and anthropological studies.
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Affiliation(s)
- Takeki Nishi
- Department of Forensic Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, 105-8461 Tokyo, Japan.
| | - Takako Nakamura
- Department of Legal Medicine, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Katuya Honda
- Department of Legal Medicine, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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23
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Roco A, Quiñones LA, Sepúlveda P, Donoso H, Lapostol C, Alarcón R, Torres ME, Véliz PC, Acuña G, Wilke O, Acevedo C. Prevalence of seven cardiovascular-related genetic polymorphisms in a Chilean mestizo healthy population. Acta Cardiol 2015; 70:528-35. [PMID: 26567812 DOI: 10.2143/ac.70.5.3110513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
OBJECTIVE Among the genetic factors associated with cardiovascular disease (CVD), determining polymorphic genotypes could help to understand the appearance of the illness. Ethnic differences in these polymorphisms could explain population variability in susceptibility to CVD. The main goal of this research is to study the presence of more relevant genetic variants of ApoE, CETP, ACE, PAI-1, MTHFR, FII and FVL of the coagulation cascade, to describe the presence of cardiovascular-related variants in a mestizo group of the Chilean people. METHODS AND RESULTS The studied population comprised 146 unrelated subjects from the general population, diagnosed as healthy, who were genotyped through conventional and/or real-time PCR. The allele frequencies for the Chilean population were: Apo E, ε2: 0.036, ε3: 0.875 and ε4: 0.089; CETP, B1: 0.51 and B2: 0.49; MTHFR, C: 0.52 and T: 0.48; ACE, I: 0.603 and D: 0.397; PAI-1, 4G: 0.381 and 5G: 0.619; FII, G: 0.97 and A: 0.03, and FV Leiden, G: 0.97 and A: 0.03. CONCLUSIONS This study contributes to establish a first picture in the Chilean mestizo population about the frequencies of these variants, which could act as single or complementary risk factors to trigger CVD. The obtained allele frequencies show great differences in relation to other South American populations.
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Bégat C, Bailly P, Chiaroni J, Mazières S. Revisiting the Diego Blood Group System in Amerindians: Evidence for Gene-Culture Comigration. PLoS One 2015; 10:e0132211. [PMID: 26148209 PMCID: PMC4493026 DOI: 10.1371/journal.pone.0132211] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 06/12/2015] [Indexed: 11/24/2022] Open
Abstract
Six decades ago the DI*A allele of the Diego blood group system was instrumental in proving Native American populations originated from Siberia. Since then, it has received scant attention. The present study was undertaken to reappraise distribution of the DI*A allele in 144 Native American populations based on current knowledge. Using analysis of variance tests, frequency distribution was studied according to geographical, environmental, and cultural parameters. Frequencies were highest in Amazonian populations. In contrast, DI*A was undetectable in subarctic, Fuegian, Panamanian, Chaco and Yanomama populations. Closer study revealed a correlation that this unequal distribution was correlated with language, suggesting that linguistic divergence was a driving force in the expansion of DI*A among Native Americans. The absence of DI*A in circumpolar Eskimo-Aleut and Na-Dene speakers was consistent with a late migratory event confined to North America. Distribution of DI*A in subtropical areas indicated that gene and culture exchanges were more intense within than between ecozones. Bolstering the utility of classical genetic markers in biological anthropology, the present study of the expansion of Diego blood group genetic polymorphism in Native Americans shows strong evidence of gene-culture comigration.
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Affiliation(s)
- Christophe Bégat
- Aix Marseille Université, CNRS, EFS, ADES UMR 7268, 13916 Marseille, France
| | - Pascal Bailly
- Aix Marseille Université, CNRS, EFS, ADES UMR 7268, 13916 Marseille, France
- Etablissement Français du Sang Alpes Méditerranée, 13392 Marseille cedex 5, France
| | - Jacques Chiaroni
- Aix Marseille Université, CNRS, EFS, ADES UMR 7268, 13916 Marseille, France
- Etablissement Français du Sang Alpes Méditerranée, 13392 Marseille cedex 5, France
| | - Stéphane Mazières
- Aix Marseille Université, CNRS, EFS, ADES UMR 7268, 13916 Marseille, France
- * E-mail:
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Black FL, Schiffman G, Pandey JP. HLA, Gm, and Km polymorphisms and immunity to infectious diseases in South Amerinds. Exp Clin Immunogenet 2015; 12:206-16. [PMID: 8534507 DOI: 10.1159/000424873] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Isolated South Amerinds, a population at very high risk from infectious disease, mount good immune responses to pneumococcal polysaccharides, viral antigens and other immunogens. No unusual immunoglobulin allotype or HLA antigen, which might explain the high risk from infectious disease, was found among them. Responses are examined in relation to the immunogenetic markers that are most prevalent. Amerinds with Gm 1,2,17,21 responded less well than persons without this haplotype to 10 of 12 pneumococcal polysaccharides, and those who were homozygous at the HLA class I loci responded less well to viral antigens. However, these differences are not strong and there are few such findings relative to the number of possibilities examined. The most distinctive immunogenetic characteristic of these populations is their low level of polymorphism at all tested loci. Their susceptibility to infectious agents can be attributed to this genetic uniformity and a consequent ability of pathogens to adapt to the population.
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Affiliation(s)
- F L Black
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Conn. 06520-8034, USA
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Rothhammer F, Fuentes-Guajardo M, Chakraborty R, Lorenzo Bermejo J, Dittmar M. Neonatal variables, altitude of residence and Aymara ancestry in northern Chile. PLoS One 2015; 10:e0121834. [PMID: 25885573 PMCID: PMC4401771 DOI: 10.1371/journal.pone.0121834] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/04/2015] [Indexed: 11/18/2022] Open
Abstract
Studies performed in the Andean plateau, one of the highest inhabited areas in the world, have reported that reduced availability of oxygen is associated to fetal growth retardation and lower birth weight, which are established predictors of morbidity and mortality during the first year of life. To test this hypothesis, perinatal variables of neonates born at the Juan Noé Hospital of Arica, Chile, were analyzed in relation to altitude of residence and Aymara ancestry of their mothers. The study population comprised the offspring of 5,295 mothers born between February 2004 and August 2010. Information included birth weight, height, head circumference, gestational age, altitude of residence and socioeconomic status, and was obtained from medical records. Mother´s ancestry was assessed based on surnames which were linked to percentages of Aymara admixture estimates relying on 40 selected ancestry informative markers. After correcting for the effect of multicollinearity among predictor variables, neonates born to mothers with an increased component of Aymara ancestry showed significantly higher birth weight and height at sea level, a marginally significant (p-value 0.06) decrease of birth weight and a significant decrease of height with altitude in comparison with the offspring of mothers with low Aymara ancestry. Since observed tendencies are suggestive of a possible genetic adaptation to hypoxia of the Chilean Aymara, we discuss briefly preliminary evidence related to fetal oxygen transport, particularly polymorphisms in the promoters of the HBG1 and HBG2 genes that are modulators of HbF synthesis, obtained in this ethnic group.
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Affiliation(s)
- Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
- Centro de Investigaciones del Hombre en el Desierto (CIHDE), Arica, Chile
- * E-mail:
| | - Macarena Fuentes-Guajardo
- Departmento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Ranajit Chakraborty
- Center for Computational Genomics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, United State of America
| | - Justo Lorenzo Bermejo
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Manuela Dittmar
- Department of Human Biology, Zoological Institute, Christian Albrechts-University, Kiel, Germany
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Xavier C, Builes JJ, Gomes V, Ospino JM, Aquino J, Parson W, Amorim A, Gusmão L, Goios A. Admixture and genetic diversity distribution patterns of non-recombining lineages of Native American ancestry in Colombian populations. PLoS One 2015; 10:e0120155. [PMID: 25775361 PMCID: PMC4361580 DOI: 10.1371/journal.pone.0120155] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/20/2015] [Indexed: 11/19/2022] Open
Abstract
Genetic diversity of present American populations results from very complex demographic events involving different types and degrees of admixture. Through the analysis of lineage markers such as mtDNA and Y chromosome it is possible to recover the original Native American haplotypes, which remained identical since the admixture events due to the absence of recombination. However, the decrease in the effective population sizes and the consequent genetic drift effects suffered by these populations during the European colonization resulted in the loss or under-representation of a substantial fraction of the Native American lineages. In this study, we aim to clarify how the diversity and distribution of uniparental lineages vary with the different demographic characteristics (size, degree of isolation) and the different levels of admixture of extant Native groups in Colombia. We present new data resulting from the analyses of mtDNA whole control region, Y chromosome SNP haplogroups and STR haplotypes, and autosomal ancestry informative insertion-deletion polymorphisms in Colombian individuals from different ethnic and linguistic groups. The results demonstrate that populations presenting a high proportion of non-Native American ancestry have preserved nevertheless a substantial diversity of Native American lineages, for both mtDNA and Y chromosome. We suggest that, by maintaining the effective population sizes high, admixture allowed for a decrease in the effects of genetic drift due to Native population size reduction and thus resulting in an effective preservation of the Native American non-recombining lineages.
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Affiliation(s)
- Catarina Xavier
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Juan José Builes
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
- Laboratorio Genes Ltda, Medellín, Colombia
| | - Verónica Gomes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | | | - Juliana Aquino
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
- Eberly College of Science, Penn State University, University Park, PA, United States of America
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Leonor Gusmão
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Ana Goios
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- * E-mail:
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Céspedes-Garro C, Jiménez-Arce G, Naranjo MEG, Barrantes R, Llerena A. Ethnic background and CYP2D6 genetic polymorphisms in Costa Ricans. REV BIOL TROP 2014; 62:1659-1671. [PMID: 25720195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
CYP2D6 differences have already been demonstrated within Latin American populations by the CEIBA.FP Consortium of the Ibero-American Network of Pharmacogenetics (RIBEF, as per the acronym in Spanish). However, within the population of Costa Rica, no research has been conducted until now, even though this population has a trihybrid component ancestry that represents an interesting condition. Thus, the present study was aimed to determine the frequency of Ultra-rapid Metabolizers (UMs) and Poor Metabolizers (PMs) in a Costa Rican population, as well as to determine whether there are differences in the CYP2D6-predicted phenotype frequencies among three Costa Rican groups with different ethnic backgrounds. Additionally, these frequencies of PMs and UMs obtained were compared with Ibero-American populations published data. Finally, we also aimed to describe allele frequencies among different Costa Rican ethnic groups. This research has been undertaken within the framework of the RIBEF CEIBA Consortium studies on Latin American populations. A total of 385 individuals were included in the study: 139 mestizos, 197 Amerindians, and 49 Afro-Caribbeans. CYP2D6 genotypes were determined by XL-PCR and Real-Time PCR. The CYP2D6 variant alleles *2, *3, *4, *5, *6, *10, "17, *29, *35 and *41 were also determined. For the entire Costa Rican population, the frequency of PMs and UMs was 6% and 6.5%, respectively. The percentage of UMs in the mestizo population was higher than in the Amerindian population. CYP2D6 UMs vary from 3.6% to 10.1% and PMs from 1.4% to 10.2% among three Costa Rican groups. The highest frequencies of UMs (10.1%) and PMs (10.2%) were found in the mestizo and Amerindian populations, respectively. In conclusion, the frequencies of UMs and PMs for CYP2D6 varied widely across the mestizo, Amerindian and Afro-Caribbean Costa Rican populations. Future research in this population should be oriented to identify new CYP2D6 variants through sequencing methods, as well as to determine CYP2D6 phenotype, in order to establish the phenotype-genotype relation. Finally, further studies involving genetic markers of ancestry are needed in the Costa Rican population.
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Malaspinas AS, Lao O, Schroeder H, Rasmussen M, Raghavan M, Moltke I, Campos PF, Sagredo FS, Rasmussen S, Gonçalves VF, Albrechtsen A, Allentoft ME, Johnson PLF, Li M, Reis S, Bernardo DV, DeGiorgio M, Duggan AT, Bastos M, Wang Y, Stenderup J, Moreno-Mayar JV, Brunak S, Sicheritz-Ponten T, Hodges E, Hannon GJ, Orlando L, Price TD, Jensen JD, Nielsen R, Heinemeier J, Olsen J, Rodrigues-Carvalho C, Lahr MM, Neves WA, Kayser M, Higham T, Stoneking M, Pena SDJ, Willerslev E. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil. Curr Biol 2014; 24:R1035-7. [PMID: 25455029 PMCID: PMC4370112 DOI: 10.1016/j.cub.2014.09.078] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [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: 12/01/2022]
Abstract
Understanding the peopling of the Americas remains an important and challenging question. Here, we present (14)C dates, and morphological, isotopic and genomic sequence data from two human skulls from the state of Minas Gerais, Brazil, part of one of the indigenous groups known as 'Botocudos'. We find that their genomic ancestry is Polynesian, with no detectable Native American component. Radiocarbon analysis of the skulls shows that the individuals had died prior to the beginning of the 19th century. Our findings could either represent genomic evidence of Polynesians reaching South America during their Pacific expansion, or European-mediated transport.
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Affiliation(s)
- Anna-Sapfo Malaspinas
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Oscar Lao
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark; Faculty of Archaeology, Leiden University, PO Box 9515, 2300 Leiden, The Netherlands
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Ida Moltke
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløesvej 5, Copenhagen 2200, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Francisca Santana Sagredo
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, South Parks Road, Dyson Perrins Building, Oxford University, OX1 3QY, UK
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby, DK-2800, Denmark
| | - Vanessa F Gonçalves
- Centre for Addiction and Mental Health, Toronto, Canada, Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløesvej 5, Copenhagen 2200, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Philip L F Johnson
- Department of Biology, Emory University, 1510 Clifton Rd NE, Rm 2006, Atlanta, GA 30322
| | - Mingkun Li
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Silvia Reis
- Setor de Antropologia Biológica, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Danilo V Bernardo
- Instituto de Ciências Humanas e da Informação - ICHI, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Michael DeGiorgio
- Department of Biology, Pennsylvania State University, 502 Wartik Laboratory, University Park, Pennsylvania 16802, USA
| | - Ana T Duggan
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Murilo Bastos
- Setor de Antropologia Biológica, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yong Wang
- Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140; Ancestry.com DNA LLC, San Francisco, CA 94107, USA
| | - Jesper Stenderup
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - J Victor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby, DK-2800, Denmark
| | - Thomas Sicheritz-Ponten
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby, DK-2800, Denmark
| | - Emily Hodges
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA, Howard Hughes Medical Institute
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA, Howard Hughes Medical Institute
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - T Douglas Price
- Department of Anthropology 5240 W.H. Sewell Social Science Building 1180 Observatory Dr. University of Wisconsin Madison, WI 53706, USA
| | - Jeffrey D Jensen
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Station 15, CH-1015 Lausanne, Switzerland
| | - Rasmus Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark; Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140
| | - Jan Heinemeier
- AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - Jesper Olsen
- AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - Claudia Rodrigues-Carvalho
- Setor de Antropologia Biológica, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marta Mirazón Lahr
- LCHES, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam St, Cambridge CB2 1QH, UK
| | - Walter A Neves
- Laboratory for Human Evolutionary Studies, Department of Genetics and Evolutionary Biology, Institute of Bioscience, University of São Paulo, Brazil
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, South Parks Road, Dyson Perrins Building, Oxford University, OX1 3QY, UK
| | - Mark Stoneking
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Deutscher Platz 6, D-04103 Leipzig, Germany.
| | - Sergio D J Pena
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil.
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.
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León-Velarde F, Villafuerte FC. Con: All dwellers at high altitude are persons of impaired physical and mental powers: the view from the Andes. High Alt Med Biol 2014; 14:212-3. [PMID: 24067177 DOI: 10.1089/ham.2013.1039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Fabiola León-Velarde
- Universidad Peruana Cayetano Heredia, Facultad de Ciencias y Filosofía, Departmento de Ciencias Biológicas y Fisiológicas , Lima, Perú
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Chiurillo MA. Role of gene polymorphisms in gastric cancer and its precursor lesions: Current knowledge and perspectives in Latin American countries. World J Gastroenterol 2014; 20:4503-4515. [PMID: 24782603 PMCID: PMC4000487 DOI: 10.3748/wjg.v20.i16.4503] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/23/2013] [Accepted: 03/13/2014] [Indexed: 02/07/2023] Open
Abstract
Latin America shows one of the highest incidence rates of gastric cancer in the world, with variations in mortality rates among nations or even within countries belonging to this region. Gastric cancer is the result of a multifactorial complex process, for which a multistep model of carcinogenesis is currently accepted. Additionally to the infection with Helicobacter pylori, that plays a major role, environmental factors as well as genetic susceptibility factors are significant players at different stages in the gastric cancer process. The differences in population origin, demographic structure, socio-economic development, and the impact of globalization lifestyles experienced in Latin America in the last decades, all together offer opportunities for studying in this context the influence of genetic polymorphisms in the susceptibility to gastric cancer. The aim of this article is to discuss current trends on gastric cancer in Latin American countries and to review the available published information about studies of association of gene polymorphisms involved in gastric cancer susceptibility from this region of the world. A total of 40 genes or genomic regions and 69 genetic variants, 58% representing markers involved in inflammatory response, have been used in a number of studies in which predominates a low number of individuals (cases and controls) included. Polymorphisms of IL-1B (-511 C/T, 14 studies; -31 T/C, 10 studies) and IL-1RN (variable number of tandem repeats, 17 studies) are the most represented ones in the reviewed studies. Other genetic variants recently evaluated in large meta-analyses and associated with gastric cancer risk were also analyzed in a few studies [e.g., prostate stem cell antigen (PSCA), CDH1, Survivin]. Further and better analysis centered in gene polymorphisms linked to other covariates, epidemiological studies and the information provided by meta-analyses and genome-wide association studies should help to improve our understanding of gastric cancer etiology in order to develop appropriate health programs in Latin America.
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Coutinho A, Valverde G, Fehren-Schmitz L, Cooper A, Barreto Romero MI, Espinoza IF, Llamas B, Haak W. AmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas. PLoS One 2014; 9:e93292. [PMID: 24671218 PMCID: PMC3966882 DOI: 10.1371/journal.pone.0093292] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 03/04/2014] [Indexed: 11/18/2022] Open
Abstract
Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible.
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Affiliation(s)
- Alexandra Coutinho
- Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Guido Valverde
- Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lars Fehren-Schmitz
- Historical Anthropology and Human Ecology, Johann-Friedrich-Blumenbach Department of Zoology and Anthropology, University Goettingen, Goettingen, Germany
- Department of Anthropology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | | | | | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
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Ibarra A, Restrepo T, Rojas W, Castillo A, Amorim A, Martínez B, Burgos G, Ostos H, Álvarez K, Camacho M, Suarez Z, Pereira R, Gusmão L. Evaluating the X chromosome-specific diversity of Colombian populations using insertion/deletion polymorphisms. PLoS One 2014; 9:e87202. [PMID: 24498042 PMCID: PMC3909073 DOI: 10.1371/journal.pone.0087202] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 12/23/2013] [Indexed: 12/20/2022] Open
Abstract
The European and African contribution to the pre-existing Native American background has influenced the complex genetic pool of Colombia. Because colonisation was not homogeneous in this country, current populations are, therefore, expected to have different proportions of Native American, European and African ancestral contributions. The aim of this work was to examine 11 urban admixed populations and a Native American group, called Pastos, for 32 X chromosome indel markers to expand the current knowledge concerning the genetic background of Colombia. The results revealed a highly diverse genetic background comprising all admixed populations, harbouring important X chromosome contributions from all continental source populations. In addition, Colombia is genetically sub-structured, with different proportions of European and African influxes depending on the regions. The samples from the North Pacific and Caribbean coasts have a high African ancestry, showing the highest levels of diversity. The sample from the South Andean region showed the lowest diversity and significantly higher proportion of Native American ancestry than the other samples from the North Pacific and Caribbean coasts, Central-West and Central-East Andean regions, and the Orinoquian region. The results of admixture analysis using X-chromosomal markers suggest that the high proportion of African ancestry in the North Pacific coast was primarily male driven. These men have joined to females with higher Native American and European ancestry (likely resulting from a classic colonial asymmetric mating type: European male x Amerindian female). This high proportion of male-mediated African contributions is atypical of colonial settings, suggesting that the admixture occurred during a period when African people were no longer enslaved. In the remaining regions, the African contribution was primarily female-mediated, whereas the European counterpart was primarily male driven and the Native American ancestry contribution was not gender biased.
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Affiliation(s)
- Adriana Ibarra
- IdentiGEN - Genetic Identification Laboratory and Research Group of Genetic Identification, Institute of Biology, School of Natural and Exact Sciences (FCEN), University of Antioquia, Medellin, Antioquia, Colombia
- * E-mail:
| | - Tomás Restrepo
- IdentiGEN - Genetic Identification Laboratory and Research Group of Genetic Identification, Institute of Biology, School of Natural and Exact Sciences (FCEN), University of Antioquia, Medellin, Antioquia, Colombia
| | - Winston Rojas
- Laboratory of Molecular Genetics, Institute of Biology, University of Antioquia, Medellin, Antioquia, Colombia
| | - Adriana Castillo
- Laboratorio de Genética, Universidad Industrial de Santander (UIS), Bucaramanga, Santander, Colombia
| | - António Amorim
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FCUP - Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Beatriz Martínez
- Molecular Genetics Laboratory, Institute for Immunological Research, University of Cartagena, Cartagena, Bolivar, Colombia
| | - German Burgos
- Molecular Genetics Laboratory, Cruz Vital, Ecuadorian Red Cross, Quito, Ecuador
| | - Henry Ostos
- Genomic Medicine Laboratory, Health Faculty, Surcolombiana University, Neiva, Huila, Colombia
| | - Karen Álvarez
- IdentiGEN - Genetic Identification Laboratory and Research Group of Genetic Identification, Institute of Biology, School of Natural and Exact Sciences (FCEN), University of Antioquia, Medellin, Antioquia, Colombia
| | - Mauricio Camacho
- Institute of Legal Medicine and Forensic Sciences, Northeast Regional, Arauca, Colombia
| | - Zuleyma Suarez
- Clinical Laboratory Olga Zuleima Suárez Molina, Cucuta, Norte de Santander, Colombia
| | - Rui Pereira
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Leonor Gusmão
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
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Ribeiro-dos-Santos AM, de Souza JES, Almeida R, Alencar DO, Barbosa MS, Gusmão L, Silva WA, de Souza SJ, Silva A, Ribeiro-dos-Santos Â, Darnet S, Santos S. High-throughput sequencing of a South American Amerindian. PLoS One 2013; 8:e83340. [PMID: 24386182 PMCID: PMC3875439 DOI: 10.1371/journal.pone.0083340] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 10/30/2013] [Indexed: 11/18/2022] Open
Abstract
The emergence of next-generation sequencing technologies allowed access to the vast amounts of information that are contained in the human genome. This information has contributed to the understanding of individual and population-based variability and improved the understanding of the evolutionary history of different human groups. However, the genome of a representative of the Amerindian populations had not been previously sequenced. Thus, the genome of an individual from a South American tribe was completely sequenced to further the understanding of the genetic variability of Amerindians. A total of 36.8 giga base pairs (Gbp) were sequenced and aligned with the human genome. These Gbp corresponded to 95.92% of the human genome with an estimated miscall rate of 0.0035 per sequenced bp. The data obtained from the alignment were used for SNP (single-nucleotide) and INDEL (insertion-deletion) calling, which resulted in the identification of 502,017 polymorphisms, of which 32,275 were potentially new high-confidence SNPs and 33,795 new INDELs, specific of South Native American populations. The authenticity of the sample as a member of the South Native American populations was confirmed through the analysis of the uniparental (maternal and paternal) lineages. The autosomal comparison distinguished the investigated sample from others continental populations and revealed a close relation to the Eastern Asian populations and Aboriginal Australian. Although, the findings did not discard the classical model of America settlement; it brought new insides to the understanding of the human population history. The present study indicates a remarkable genetic variability in human populations that must still be identified and contributes to the understanding of the genetic variability of South Native American populations and of the human populations history.
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Affiliation(s)
| | - Jorge Estefano Santana de Souza
- Centro Regional de Hemoterapia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- Institute of Bioinformatics and Biotechnology, São Paulo, São Paulo, Brazil
| | - Renan Almeida
- Institute of Bioinformatics and Biotechnology, São Paulo, São Paulo, Brazil
| | - Dayse O. Alencar
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | - Leonor Gusmão
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
- Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Wilson A. Silva
- Centro Regional de Hemoterapia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Sandro J. de Souza
- Institute of Bioinformatics and Biotechnology, São Paulo, São Paulo, Brazil
- Brain Institute, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Artur Silva
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | - Sylvain Darnet
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Sidney Santos
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
- * E-mail: /
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Sandoval JR, Lacerda DR, Jota MSA, Salazar-Granara A, Vieira PPR, Acosta O, Cuellar C, Revollo S, Fujita R, Santos FR. The genetic history of indigenous populations of the Peruvian and Bolivian Altiplano: the legacy of the Uros. PLoS One 2013; 8:e73006. [PMID: 24039843 PMCID: PMC3770642 DOI: 10.1371/journal.pone.0073006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [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: 02/27/2013] [Accepted: 07/22/2013] [Indexed: 11/10/2022] Open
Abstract
The Altiplano region of the South American Andes is marked by an inhospitable climate to which the autochthonous human populations adapted and then developed great ancient civilizations, such as the Tiwanaku culture and the Inca Empire. Since pre-Columbian times, different rulers established themselves around the Titicaca and Poopo Lakes. By the time of the arrival of Spaniards, Aymara and Quechua languages were predominant on the Altiplano under the rule of the Incas, although the occurrence of other spoken languages, such as Puquina and Uruquilla, suggests the existence of different ethnic groups in this region. In this study, we focused on the pre-Columbian history of the autochthonous Altiplano populations, particularly the Uros ethnic group, which claims to directly descend from the first settlers of the Andes, and some linguists suggest they might otherwise be related to Arawak speaking groups from the Amazon. Using phylogeographic, population structure and spatial genetic analyses of Y-chromosome and mtDNA data, we inferred the genetic relationships among Uros populations (Los Uros from Peru, Uru-Chipaya and Uru-Poopo from Bolivia), and compared their haplotype profiles with eight Aymara, nine Quechua and two Arawak (Machiguenga and Yanesha) speaking populations from Peru and Bolivia. Our results indicated that Uros populations stand out among the Altiplano populations, while appearing more closely related to the Aymara and Quechua from Lake Titicaca and surrounding regions than to the Amazon Arawaks. Moreover, the Uros populations from Peru and Bolivia are genetically differentiated from each other, indicating a high heterogeneity in this ethnic group. Finally, our results support the distinctive ancestry for the Uros populations of Peru and Bolivia, which are likely derived from ancient Andean lineages that were partially replaced during more recent farming expansion events and the establishment of complex civilizations in the Andes.
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Affiliation(s)
- José Raul Sandoval
- Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- Universidad San Martin de Porres (USMP), Lima, Peru
| | | | | | | | | | - Oscar Acosta
- Universidad San Martin de Porres (USMP), Lima, Peru
| | | | | | | | - Fabrício R. Santos
- Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- * E-mail:
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Battaglia V, Grugni V, Perego UA, Angerhofer N, Gomez-Palmieri JE, Woodward SR, Achilli A, Myres N, Torroni A, Semino O. The first peopling of South America: new evidence from Y-chromosome haplogroup Q. PLoS One 2013; 8:e71390. [PMID: 23990949 PMCID: PMC3749222 DOI: 10.1371/journal.pone.0071390] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/03/2013] [Indexed: 01/13/2023] Open
Abstract
Recent progress in the phylogenetic resolution of the Y-chromosome phylogeny permits the male demographic dynamics and migratory events that occurred in Central and Southern America after the initial human spread into the Americas to be investigated at the regional level. To delve further into this issue, we examined more than 400 Native American Y chromosomes (collected in the region ranging from Mexico to South America) belonging to haplogroup Q – virtually the only branch of the Y phylogeny observed in modern-day Amerindians of Central and South America – together with 27 from Mongolia and Kamchatka. Two main founding lineages, Q1a3a1a-M3 and Q1a3a1-L54(xM3), were detected along with novel sub-clades of younger age and more restricted geographic distributions. The first was also observed in Far East Asia while no Q1a3a1-L54(xM3) Y chromosome was found in Asia except the southern Siberian-specific sub-clade Q1a3a1c-L330. Our data not only confirm a southern Siberian origin of ancestral populations that gave rise to Paleo-Indians and the differentiation of both Native American Q founding lineages in Beringia, but support their concomitant arrival in Mesoamerica, where Mexico acted as recipient for the first wave of migration, followed by a rapid southward migration, along the Pacific coast, into the Andean region. Although Q1a3a1a-M3 and Q1a3a1-L54(xM3) display overlapping general distributions, they show different patterns of evolution in the Mexican plateau and the Andean area, which can be explained by local differentiations due to demographic events triggered by the introduction of agriculture and associated with the flourishing of the Great Empires.
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Affiliation(s)
- Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
| | - Viola Grugni
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
| | - Ugo Alessandro Perego
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | - Norman Angerhofer
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | | | - Scott Ray Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- AncestryDNA, Provo, Utah, United States of America
| | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Natalie Myres
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- AncestryDNA, Provo, Utah, United States of America
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
- Centro Interdipartimentale “Studi di Genere”, Università di Pavia, Pavia, Italy
- * E-mail:
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Sevini F, Yao DY, Lomartire L, Barbieri A, Vianello D, Ferri G, Moretti E, Dasso MC, Garagnani P, Pettener D, Franceschi C, Luiselli D, Franceschi ZA. Analysis of population substructure in two sympatric populations of Gran Chaco, Argentina. PLoS One 2013; 8:e64054. [PMID: 23717528 PMCID: PMC3661677 DOI: 10.1371/journal.pone.0064054] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 04/10/2013] [Indexed: 01/26/2023] Open
Abstract
Sub-population structure and intricate kinship dynamics might introduce biases in molecular anthropology studies and could invalidate the efforts to understand diseases in highly admixed populations. In order to clarify the previously observed distribution pattern and morbidity of Chagas disease in Gran Chaco, Argentina, we studied two populations (Wichí and Criollos) recruited following an innovative bio-cultural model considering their complex cultural interactions. By reconstructing the genetic background and the structure of these two culturally different populations, the pattern of admixture, the correspondence between genealogical and genetic relationships, this integrated perspective had the power to validate data and to link the gap usually relying on a singular discipline. Although Wichí and Criollos share the same area, these sympatric populations are differentiated from the genetic point of view as revealed by Non Recombinant Y Chromosome genotyping resulting in significantly high Fst values and in a lower genetic variability in the Wichí population. Surprisingly, the Amerindian and the European components emerged with comparable amounts (20%) among Criollos and Wichí respectively. The detailed analysis of mitochondrial DNA showed that the two populations have as much as 87% of private haplotypes. Moreover, from the maternal perspective, despite a common Amerindian origin, an Andean and an Amazonian component emerged in Criollos and in Wichí respectively. Our approach allowed us to highlight that quite frequently there is a discrepancy between self-reported and genetic kinship. Indeed, if self-reported identity and kinship are usually utilized in population genetics as a reliable proxy for genetic identity and parental relationship, in our model populations appear to be the result not only and not simply of the genetic background but also of complex cultural determinants. This integrated approach paves the way to a rigorous reconstruction of demographic and cultural history as well as of bioancestry and propensity to diseases of Wichí and Criollos.
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Affiliation(s)
- Federica Sevini
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Università di Bologna, Bologna, Italy
- Centro Interdipartimentale “Luigi Galvani” (CIG), Università di Bologna, Bologna, Italy
| | - Daniele Yang Yao
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA) – Sezione di Biologia, University of Bologna, Bologna, Italy
| | - Laura Lomartire
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Università di Bologna, Bologna, Italy
- Centro Interdipartimentale “Luigi Galvani” (CIG), Università di Bologna, Bologna, Italy
| | - Annalaura Barbieri
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Università di Bologna, Bologna, Italy
- Centro Interdipartimentale “Luigi Galvani” (CIG), Università di Bologna, Bologna, Italy
| | - Dario Vianello
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Università di Bologna, Bologna, Italy
- Centro Interdipartimentale “Luigi Galvani” (CIG), Università di Bologna, Bologna, Italy
| | - Gianmarco Ferri
- Dipartimento ad Attività Integrata di Laboratori, Anatomia Patologica, Medicina Legale – U.O. Struttura Complessa di Medicina Legale, Azienda Ospedaliero – Universitaria di Modena, Modena, Italy
| | - Edgardo Moretti
- Coordinación Nacional de Control de Vectores, Córdoba, Argentina
| | - Maria Cristina Dasso
- Centro de Investigaciones en Antropologia Filosofica y Cultural (CIAFIC), Buenos Aires, Argentina
- Centro Universitario Interdisciplinario sobre la Enfermedad de Chagas (CUNIDEC), BuenosAires, Argentina
| | - Paolo Garagnani
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Università di Bologna, Bologna, Italy
- Centro Interdipartimentale “Luigi Galvani” (CIG), Università di Bologna, Bologna, Italy
| | - Davide Pettener
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA) – Sezione di Biologia, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Università di Bologna, Bologna, Italy
- Centro Interdipartimentale “Luigi Galvani” (CIG), Università di Bologna, Bologna, Italy
| | - Donata Luiselli
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA) – Sezione di Biologia, University of Bologna, Bologna, Italy
- * E-mail:
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Roewer L, Nothnagel M, Gusmão L, Gomes V, González M, Corach D, Sala A, Alechine E, Palha T, Santos N, Ribeiro-Dos-Santos A, Geppert M, Willuweit S, Nagy M, Zweynert S, Baeta M, Núñez C, Martínez-Jarreta B, González-Andrade F, Fagundes de Carvalho E, da Silva DA, Builes JJ, Turbón D, Lopez Parra AM, Arroyo-Pardo E, Toscanini U, Borjas L, Barletta C, Ewart E, Santos S, Krawczak M. Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans. PLoS Genet 2013; 9:e1003460. [PMID: 23593040 PMCID: PMC3623769 DOI: 10.1371/journal.pgen.1003460] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 03/04/2013] [Indexed: 01/07/2023] Open
Abstract
Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans. In the largest population genetic study of South Americans to date, we analyzed the Y-chromosomal makeup of more than 1,000 male natives. We found that the male-specific genetic variation of Native Americans lacks any clear structure that could sensibly be related to their geographic and/or linguistic relationships. This finding is consistent with a rapid initial peopling of South America, followed by long periods of isolation in small tribal groups. The observed continent-wide decoupling of geography, spoken language, and genetics contrasts strikingly with previous reports of such correlation from many parts of Europe and Asia. Moreover, we identified a cluster of Native American founding lineages of Y chromosomes, called C-M217 (C3*), within a restricted area of Ecuador in North-Western South America. The same haplogroup occurs at high frequency in Central, East, and North East Asia, but is virtually absent from North (except Alaska) and Central America. Possible scenarios for the introduction of C-M217 (C3*) into Ecuador may thus include a coastal or trans-Pacific route, an idea also supported by occasional archeological evidence and the recent coalescence of the C3* haplotypes, estimated from our data to have occurred some 6,000 years ago.
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Affiliation(s)
- Lutz Roewer
- Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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Augusto DG, Piovezan BZ, Tsuneto LT, Callegari-Jacques SM, Petzl-Erler ML. KIR gene content in amerindians indicates influence of demographic factors. PLoS One 2013; 8:e56755. [PMID: 23451080 PMCID: PMC3581531 DOI: 10.1371/journal.pone.0056755] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 01/14/2013] [Indexed: 11/18/2022] Open
Abstract
Although the KIR gene content polymorphism has been studied worldwide, only a few isolated or Amerindian populations have been analyzed. This extremely diverse gene family codifies receptors that are expressed mainly in NK cells and bind HLA class I molecules. KIR-HLA combinations have been associated to several diseases and population studies are important to comprehend their evolution and their role in immunity. Here we analyzed, by PCR-SSP (specific sequencing priming), 327 individuals from four isolated groups of two of the most important Brazilian Amerindian populations: Kaingang and Guarani. The pattern of KIR diversity among these and other ten Amerindian populations disclosed a wide range of variation for both KIR haplotypes and gene frequencies, indicating that demographic factors, such as bottleneck and founder effects, were the most important evolutionary factors in shaping the KIR polymorphism in these populations.
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Affiliation(s)
| | - Bruno Zagonel Piovezan
- Laboratório de Genética Molecular Humana, Universidade Federal do Paraná, Curitiba, Brazil
| | - Luiza Tamie Tsuneto
- Laboratório de Imunogenética, Universidade Estadual de Maringá, Maringá, Brazil
| | | | - Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Universidade Federal do Paraná, Curitiba, Brazil
- * E-mail:
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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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He Y, Wang WR, Li R, Wang S, Jin L. Genetic divergence disclosing a rapid prehistorical dispersion of Native Americans in Central and South America. PLoS One 2012; 7:e44788. [PMID: 22970308 PMCID: PMC3435283 DOI: 10.1371/journal.pone.0044788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 08/13/2012] [Indexed: 12/04/2022] Open
Abstract
An accurate estimate of the divergence time between Native Americans is important for understanding the initial entry and early dispersion of human beings in the New World. Current methods for estimating the genetic divergence time of populations could seriously depart from a linear relationship with the true divergence for multiple populations of a different population size and significant population expansion. Here, to address this problem, we propose a novel measure to estimate the genetic divergence time of populations. Computer simulation revealed that the new measure maintained an excellent linear correlation with the population divergence time in complicated multi-population scenarios with population expansion. Utilizing the new measure and microsatellite data of 21 Native American populations, we investigated the genetic divergences of the Native American populations. The results indicated that genetic divergences between North American populations are greater than that between Central and South American populations. None of the divergences, however, were large enough to constitute convincing evidence supporting the two-wave or multi-wave migration model for the initial entry of human beings into America. The genetic affinity of the Native American populations was further explored using Neighbor-Net and the genetic divergences suggested that these populations could be categorized into four genetic groups living in four different ecologic zones. The divergence of the population groups suggests that the early dispersion of human beings in America was a multi-step procedure. Further, the divergences suggest the rapid dispersion of Native Americans in Central and South Americas after a long standstill period in North America.
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Affiliation(s)
- Yungang He
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Wei R. Wang
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Ran Li
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Sijia Wang
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Li Jin
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, China
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Kuhn PC, Horimoto ARVR, Sanches JM, Vieira Filho JPB, Franco L, Fabbro AD, Franco LJ, Pereira AC, Moises RS. Genome-wide analysis in Brazilian Xavante Indians reveals low degree of admixture. PLoS One 2012; 7:e42702. [PMID: 22900041 PMCID: PMC3416854 DOI: 10.1371/journal.pone.0042702] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 07/10/2012] [Indexed: 11/20/2022] Open
Abstract
Characterization of population genetic variation and structure can be used as tools for research in human genetics and population isolates are of great interest. The aim of the present study was to characterize the genetic structure of Xavante Indians and compare it with other populations. The Xavante, an indigenous population living in Brazilian Central Plateau, is one of the largest native groups in Brazil. A subset of 53 unrelated subjects was selected from the initial sample of 300 Xavante Indians. Using 86,197 markers, Xavante were compared with all populations of HapMap Phase III and HGDP-CEPH projects and with a Southeast Brazilian population sample to establish its population structure. Principal Components Analysis showed that the Xavante Indians are concentrated in the Amerindian axis near other populations of known Amerindian ancestry such as Karitiana, Pima, Surui and Maya and a low degree of genetic admixture was observed. This is consistent with the historical records of bottlenecks experience and cultural isolation. By calculating pair-wise Fst statistics we characterized the genetic differentiation between Xavante Indians and representative populations of the HapMap and from HGDP-CEPH project. We found that the genetic differentiation between Xavante Indians and populations of Ameridian, Asian, European, and African ancestry increased progressively. Our results indicate that the Xavante is a population that remained genetically isolated over the past decades and can offer advantages for genome-wide mapping studies of inherited disorders.
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Affiliation(s)
- Patricia C. Kuhn
- Disciplina de Endocrinologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Andréa R. V. Russo. Horimoto
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School of University of São Paulo, São Paulo, Brazil
| | - José Maurício Sanches
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School of University of São Paulo, São Paulo, Brazil
| | - João Paulo B. Vieira Filho
- Disciplina de Endocrinologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Luciana Franco
- Disciplina de Endocrinologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Amaury Dal Fabbro
- Departamento de Medicina Social, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Laercio Joel Franco
- Departamento de Medicina Social, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Alexandre C. Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School of University of São Paulo, São Paulo, Brazil
| | - Regina S Moises
- Disciplina de Endocrinologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- * E-mail:
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Pereira L, Zamudio R, Soares-Souza G, Herrera P, Cabrera L, Hooper CC, Cok J, Combe JM, Vargas G, Prado WA, Schneider S, Kehdy F, Rodrigues MR, Chanock SJ, Berg DE, Gilman RH, Tarazona-Santos E. Socioeconomic and nutritional factors account for the association of gastric cancer with Amerindian ancestry in a Latin American admixed population. PLoS One 2012; 7:e41200. [PMID: 22870209 PMCID: PMC3411699 DOI: 10.1371/journal.pone.0041200] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [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: 03/01/2012] [Accepted: 06/18/2012] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer is one of the most lethal types of cancer and its incidence varies worldwide, with the Andean region of South America showing high incidence rates. We evaluated the genetic structure of the population from Lima (Peru) and performed a case-control genetic association study to test the contribution of African, European, or Native American ancestry to risk for gastric cancer, controlling for the effect of non-genetic factors. A wide set of socioeconomic, dietary, and clinic information was collected for each participant in the study and ancestry was estimated based on 103 ancestry informative markers. Although the urban population from Lima is usually considered as mestizo (i.e., admixed from Africans, Europeans, and Native Americans), we observed a high fraction of Native American ancestry (78.4% for the cases and 74.6% for the controls) and a very low African ancestry (<5%). We determined that higher Native American individual ancestry is associated with gastric cancer, but socioeconomic factors associated both with gastric cancer and Native American ethnicity account for this association. Therefore, the high incidence of gastric cancer in Peru does not seem to be related to susceptibility alleles common in this population. Instead, our result suggests a predominant role for ethnic-associated socioeconomic factors and disparities in access to health services. Since Native Americans are a neglected group in genomic studies, we suggest that the population from Lima and other large cities from Western South America with high Native American ancestry background may be convenient targets for epidemiological studies focused on this ethnic group.
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Affiliation(s)
- Latife Pereira
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Roxana Zamudio
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Giordano Soares-Souza
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Catherine C. Hooper
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jaime Cok
- Departamento de Patología, Hospital Nacional Cayetano Heredia, Lima, Peru
| | - Juan M. Combe
- Departamento de Gastroenterologia, Instituto Nacional de Enfermedades Neopláscas, Lima, Peru
| | - Gloria Vargas
- Servicio de Gastroenterologia, Hospital Nacional Arzobispo Loayza, Lima, Peru
| | | | - Silvana Schneider
- Departamento de Estatística, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernanda Kehdy
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maira R. Rodrigues
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Stephen J. Chanock
- Laboratory of Translational Genomics of the Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland, United States of America
| | - Douglas E. Berg
- Department of Molecular Microbiology, Washington University Medical School, St Louis, Missouri, United States of America
| | - Robert H. Gilman
- Asociación Benéfica PRISMA, Lima, Peru
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
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Palha T, Gusmão L, Ribeiro-Rodrigues E, Guerreiro JF, Ribeiro-Dos-Santos A, Santos S. Disclosing the genetic structure of Brazil through analysis of male lineages with highly discriminating haplotypes. PLoS One 2012; 7:e40007. [PMID: 22808085 PMCID: PMC3393733 DOI: 10.1371/journal.pone.0040007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Accepted: 05/30/2012] [Indexed: 11/18/2022] Open
Abstract
In a large variety of genetic studies, probabilistic inferences are made based on information available in population databases. The accuracy of the estimates based on population samples are highly dependent on the number of chromosomes being analyzed as well as the correct representation of the reference population. For frequency calculations the size of a database is especially critical for haploid markers, and for countries with complex admixture histories it is important to assess possible substructure effects that can influence the coverage of the database. Aiming to establish a representative Brazilian population database for haplotypes based on 23 Y chromosome STRs, more than 2,500 Y chromosomes belonging to Brazilian, European and African populations were analyzed. No matter the differences in the colonization history of the five geopolitical regions that currently exist in Brazil, for the Y chromosome haplotypes of the 23 studied Y-STRs, a lack of genetic heterogeneity was found, together with a predominance of European male lineages in all regions of the country. Therefore, if we do not consider the diverse Native American or Afro-descendent isolates, which are spread through the country, a single Y chromosome haplotype frequency database will adequately represent the urban populations in Brazil. In comparison to the most commonly studied group of 17 Y-STRs, the 23 markers included in this work allowed a high discrimination capacity between haplotypes from non-related individuals within a population and also increased the capacity to discriminate between paternal relatives. Nevertheless, the expected haplotype mutation rate is still not enough to distinguish the Y chromosome profiles of paternally related individuals. Indeed, even for rapidly mutating Y-STRs, a very large number of markers will be necessary to differentiate male lineages from paternal relatives.
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Affiliation(s)
- Teresinha Palha
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.
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Abstract
It is now generally accepted that Polynesia was first settled by peoples from southeast Asia. An alternative that eastern parts of Polynesia were first inhabited by Amerindians has found little support. There are, however, many indications of a 'prehistoric' (i.e. before Polynesia was discovered by Europeans) contact between Polynesia and the Americas, but genetic evidence of a prehistoric Amerindian contribution to the Polynesian gene pool has been lacking. We recently carried out genomic HLA (human leucocyte antigen) typing as well as typing for mitochondrial DNA (mtDNA) and Y chromosome markers of blood samples collected in 1971 and 2008 from reputedly non-admixed Easter Islanders. All individuals carried HLA alleles and mtDNA types previously found in Polynesia, and most of the males carried Y chromosome markers of Polynesian origin (a few had European Y chromosome markers), further supporting an initial Polynesian population on Easter Island. The HLA investigations revealed, however, that some individuals also carried HLA alleles which have previously almost only been found in Amerindians. We could trace the introduction of these Amerindian alleles to before the Peruvian slave trades, i.e. before the 1860s, and provide suggestive evidence that they were introduced already in prehistoric time. Our results demonstrate an early Amerindian contribution to the Polynesian gene pool on Easter Island, and illustrate the usefulness of typing for immunogenetic markers such as HLA to complement mtDNA and Y chromosome analyses in anthropological investigations.
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Affiliation(s)
- Erik Thorsby
- Institute of Immunology, Oslo University Hospital, Rikshospitalet, and University of Oslo, Oslo, Norway.
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46
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Mata IF, Wilhoite GJ, Yearout D, Bacon JA, Cornejo-Olivas M, Mazzetti P, Marca V, Ortega O, Acosta O, Cosentino C, Torres L, Medina AC, Perez-Pastene C, Díaz-Grez F, Vilariño-Güell C, Venegas P, Miranda M, Trujillo-Godoy O, Layson L, Avello R, Dieguez E, Raggio V, Micheli F, Perandones C, Alvarez V, Segura-Aguilar J, Farrer MJ, Zabetian CP, Ross OA. Lrrk2 p.Q1111H substitution and Parkinson's disease in Latin America. Parkinsonism Relat Disord 2011; 17:629-31. [PMID: 21632271 DOI: 10.1016/j.parkreldis.2011.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 03/16/2011] [Accepted: 05/05/2011] [Indexed: 11/18/2022]
Abstract
Mutations in the LRRK2 gene are the most common genetic cause of Parkinson's disease, with frequencies displaying a high degree of population-specificity. Although more than 100 coding substitutions have been identified, only seven have been proven to be highly penetrant pathogenic mutations. Studies however are lacking in non-white populations. Recently, Lrrk2 p.Q1111H (rs78365431) was identified in two affected Hispanic brothers and absent in 386 non-Hispanic white healthy controls. We therefore screened this variant in 1460 individuals (1150 PD patients and 310 healthy controls) from 4 Latin American countries (Peru, Chile, Uruguay and Argentina). In our case-control series from Peru and Chile we observed an increased frequency of Lrrk2 p.Q1111H in patients (7.9%) compared to controls (5.4%) although the difference did not reach significance (OR 1.38; p = 0.10). In addition, the frequency of Lrrk2 p.Q1111H varied greatly between populations and further screening in a set of pure Amerindian and pure Spanish controls suggested that this variant likely originated in an Amerindian population. Further studies in other Latin American populations are warranted to assess its role as a risk factor for Parkinson's disease. Screening in Parkinson's disease patients from under-represented populations will increase our understanding of the role of LRRK2 variants in disease risk worldwide.
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Affiliation(s)
- Ignacio F Mata
- Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108, USA.
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Amorim CEG, Wang S, Marrero AR, Salzano FM, Ruiz-Linares A, Bortolini MC. X-chromosomal genetic diversity and linkage disequilibrium patterns in Amerindians and non-Amerindian populations. Am J Hum Biol 2011; 23:299-304. [PMID: 21294208 DOI: 10.1002/ajhb.21110] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Revised: 09/08/2010] [Accepted: 09/14/2010] [Indexed: 11/12/2022] Open
Affiliation(s)
- Carlos Eduardo G Amorim
- Programa de Pós-Graduação em Genética e Biologia Molecular and Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970, Porto Alegre, RS, Brazil
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Vasunilashorn S, Finch CE, Crimmins EM, Vikman SA, Stieglitz J, Gurven M, Kaplan H, Allayee H. Inflammatory gene variants in the Tsimane, an indigenous Bolivian population with a high infectious load. Biodemography Soc Biol 2011; 57:33-52. [PMID: 21845926 PMCID: PMC3529658 DOI: 10.1080/19485565.2011.564475] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The Tsimane of lowland Bolivia are an indigenous forager-farmer population living under conditions resembling pre-industrial European populations, with high infectious morbidity, high infection and inflammation, and shortened life expectancy. Analysis of 917 persons ages 5 to 60+ showed that allele frequencies of 9 SNPs examined in the apolipoprotein E (apoE), C-reactive protein (CRP), and interleukin-6 (IL-6) genes differed from some European, African, and north Asian-derived populations. The apoE2 allele was absent, whereas four SNPs related to CRP and IL-6 were monomorphic: CRP (rs1800947, rs3093061, and rs3093062) and IL-6 (rs1800795). No significant differences in apoE, CRP, and IL-6 variants across age were found CRP levels were higher in carriers of two CRP proinflammatory SNPs, whereas they were lower in carriers of apoE4. Taken together the evidence for (1) different allele frequencies between the Tsimane and other populations and (2) the correlations of CRP and apoE alleles with blood CRP may suggest that these variants are under selection in response to a high infection environment.
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Palha TDJBF, Ribeiro-Rodrigues EM, Ribeiro-dos-Santos A, Guerreiro JF, de Moura LSS, Santos S. Male ancestry structure and interethnic admixture in African-descent communities from the Amazon as revealed by Y-chromosome Strs. Am J Phys Anthropol 2010; 144:471-8. [PMID: 21302273 DOI: 10.1002/ajpa.21436] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 09/10/2010] [Indexed: 11/07/2022]
Abstract
Some genetic markers on both the Y chromosome and mtDNA are highly polymorphic and population-specific in humans, representing useful tools for reconstructing the past history of populations with poor historical records. Such lack of information is usually true in the case of recent African-descent populations of the New World founded by fugitive slaves throughout the slavery period in the Americas, particularly in Brazil, where those communities are known as quilombos. Aiming to recover male-derived ethnic structure of nine quilombos from the Brazilian Amazon, a total of 300 individuals, belonging to Mazagão Velho (N = 24), Curiaú (N = 48), Mazagão (N = 36), Trombetas (N = 20), Itacoã (N = 22), Saracura (N = 46), Marajó (N = 58), Pitimandeua (N = 26), and Pontal (N = 20), were investigated for nine Y-STRs (DYS393, DYS19, DYS390, DYS389 I, DYS389 II, DYS392, DYS391, DYS385 I/II). From the 169 distinct haplotypes obtained, 120 were singletons. The results suggest the West African coast as the main origin of slaves brought to Brazil (54% of male contribution); the European contribution was high (41%), while the Amerindian's was low (5%). Those results contrast with previous mtDNA data that showed high Amerindian female contribution (46.6%) in African-descent populations. AMOVA suggests that the genetic differentiation among the quilombos is mainly influenced by admixture with European. However, when restricting AMOVA to African-specific haplotypes, low differentiation was detected, suggesting great genetic homogeneity of the African founding populations and/or a later homogenization by intense slave trade inside Brazil.
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Affiliation(s)
- Teresinha de Jesus Brabo Ferreira Palha
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará 1, Cidade Universitária Prof. José da Silva Neto, Belém-Pará, Brazil
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Paiva L, Hernández A, Martínez V, Creus A, Quinteros D, Marcos R. Association between GSTO2 polymorphism and the urinary arsenic profile in copper industry workers. Environ Res 2010; 110:463-468. [PMID: 20045512 DOI: 10.1016/j.envres.2009.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 11/19/2009] [Accepted: 12/09/2009] [Indexed: 05/28/2023]
Abstract
Two members of the recently identified Omega class glutathione S-transferase enzymes (GSTO1 and GSTO2) have been proposed to play a role in the response to arsenic exposure. Therefore, polymorphisms in these genes could be related with variations in the arsenic excretion profile and, consequently, with the individual response to chronic exposure. Exons and flanking regions of GSTO2 gene have been screened in two different ethnic groups (20 Europeans and 20 Chilean Indians), and the urinary arsenic patterns and the GSTO2 Asn142Asp polymorphism have been investigated in 207 copper mine workers occupationally exposed to arsenic. Three polymorphisms of GSTO2 already described were detected in Europeans and Chilean Indians, although with significant different allele frequencies. The genotyping for the Asn142Asp polymorphism revealed that almost no significant association exists between this change and the arsenic excretion profile. However, 142Asp change seems to be correlated with an increase in DMA excretion after age and total urinary arsenic adjustment (OR=3.61; P=0.05). Altogether, our findings indicate that ethnical differences should be taken into account for correlation studies between GST Omega polymorphisms and arsenic susceptibility, and that the 142Asp allozyme could modulate arsenic biotransformation and thereby arsenic toxicity.
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Affiliation(s)
- Leiliane Paiva
- Grup de Mutagènesi, Departament de Genètica i de Microbiologia, Edifici Cn, Facultat de Biociències, Universitat Autònoma de Barcelona, Campus de Bellaterra, 08193 Cerdanyola del Vallès, Bellaterra, Spain
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