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Mut P, Bertoni B, Sapiro R, Hidalgo PC, Torres A, Azambuja C, Sans M. Insights into the Y chromosome human diversity in Uruguay. Am J Hum Biol 2023; 35:e23963. [PMID: 37493343 DOI: 10.1002/ajhb.23963] [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: 11/17/2022] [Revised: 04/26/2023] [Accepted: 07/04/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND With regard to the origin of its population and microevolutionary processes, Uruguay exhibits distinctive features that distinguish it from other countries in Latin America, while at the same time sharing several similarities. In this article, we will focus on the variability of paternal genetic lineages in two geographical regions with different histories that can be considered as examples of distinct populations for the continent. In general terms, the genetic diversity is a result of different demographic processes related to the American conquest and colonisation. These resulted in distinct ancestral components which vary geographical and depend on the distribution by sex within these components. In Uruguay, native maternal haplogroups are significantly more frequent in the North. Although there are several studies about the geneticvariability of Uruguay, little is known about male genetic lineages. AIMS The aim of this work is to present an updated study of the male genetic variability of the Uruguayan population. METHODS We analyzed 13 biallelic markers and 27 STRs located in the male-specific region of the Y chromosome for 157 males: 98 from the capital, Montevideo, and 59 from Tacuarembó. RESULTS Almost all haplogroups found in both locations are European (99% and 93.2% respectively). One Sub-Saharan African haplogroup was found in Montevideo (1%) and 2 in Tacuarembó (3%), while Native haplogroups were found only in Tacuarembó, evidencing a strong sex-biased admixture. By crossing genetic and genealogical information we could relate European haplogroups with different waves and times of migrations. DISCUSSION Network analysis indicated a very diverse male population, suggesting that European migrants came from heterogeneous geographic locations and in different waves. Tacuarembó has closer population affinities with Iberian populations while Montevideo is more diverse. Male population expansion expansion, can be explained by the large number of migrants that arrived during the XIX century and the first half of the XX century. CONCLUSIONS The Uruguayan male gene pool is the result of several migration waves with diverse origins, with strong sex-biased admixture that can be explained by the European migration, the violence against the indigenous males, and the segregation of the Africansadmixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation of hte Africans.
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Affiliation(s)
- Patricia Mut
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, UdelaR, Montevideo, Uruguay
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Rossana Sapiro
- Departamento de Histología y Embriología, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Pedro C Hidalgo
- Polo de Desarrollo Universitario Diversidad Genética Humana, Centro Universitario Noreste, Tacuarembó, Uruguay
| | | | | | - Mónica Sans
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, UdelaR, Montevideo, Uruguay
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Pezo P, Orellana-Soto M, de la Fuente C, Leiva X, Herrera L, Flores-Alvarado S, Galimany J, de Saint Pierre M, Bravi C, Moraga M. Native American mitochondrial lineages in admixed populations from Chile: Detecting recent migrations during post-Columbian times using geographically restricted lineages. Am J Biol Anthropol 2022; 178:504-512. [PMID: 36790622 DOI: 10.1002/ajpa.24513] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVES To analyze the mitochondrial diversity in three admixed populations and evaluate the historical migration effect of native southern population movement to Santiago (capital of Chile). The intensity of migration was quantified using three mitochondrial lineages restricted to South-Central native groups. METHODS D-loop sequences were genotyped in 550 unrelated individuals from San Felipe-Los Andes (n = 108), Santiago (n = 217), and Concepción (n = 225). Sequence processing, alignment, and haplogroup inference were carried out, and different genetic structure analyses were performed for haplogroup frequencies and D-loop sequences. RESULTS The Native lineages B2i2, C1b13, and D1g were the most frequent haplogroups, especially in Santiago (71.8%). Despite the distance, this city showed a high-genetic affinity with southern populations, including Concepción (~500 km distant) and native groups, rather than with those from San Felipe-Los Andes (<100 km distant). In fact, there was a negative correlation between geographical and genetic distance among these cities (r corr = -0.5593, p value = 0.8387). Network analysis revealed shared haplotypes between Santiago, Concepción, and other southern populations. Finally, we found lineages from Concepción acting as ancestral nodes in the northern clade. CONCLUSIONS Considering the geographic distances from these cities, the results were not consistent with a model of genetic isolation by geographic distance, revealing the effects of a historical migration process from the south to the capital. We also show evidence of possible north-to-south migration during admixture onset in Concepción and in addition, we were able to identify previously unreported mitochondrial diversity in urban populations that became lost in Native groups post-European contact.
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Affiliation(s)
- Patricio Pezo
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Michael Orellana-Soto
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | - Ximena Leiva
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Luisa Herrera
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sandra Flores-Alvarado
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Programa de Bioestadística, Instituto de Salud Poblacional, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Jacqueline Galimany
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Michelle de Saint Pierre
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Claudio Bravi
- CCT La Plata, IMBICE, La Plata, Argentina.,Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Mauricio Moraga
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
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3
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Reyes-Madrid M, Flores-Alvarado S, Pezo-Valderrama P, Orellana-Soto M, Apata M, Moraga M, de Saint Pierre M. An approach on the migratory processes in the north of Chile based on Y chromosome analysis. Am J Hum Biol 2022; 34:e23736. [PMID: 35263492 DOI: 10.1002/ajhb.23736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/23/2021] [Accepted: 02/12/2022] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES Northern Chile is an area characterized by a complex cultural and demographic trajectory. During the last few centuries, this complex trajectory has become the destination of intra- and intercontinental migratory waves. In this study, we analyzed the Y chromosome to evaluate how migratory and admixture patterns have affected the genetic composition of the populations in northern Chile compared with other populations of the country. METHODS A total of 311 people from urban (Antofagasta and Calama), rural (Azapa and Camarones), and Native (Aymara and Atacameño) populations from northern Chile were characterized by 26 SNPs and the STR DYS393 of the Y chromosome, along with 69 individuals from Native populations (Mapuche, Pehuenche, and Huilliche) from southern Chile. In addition to characterizing the paternal lineages, multivariate analyses were performed to compare with published data from other Chilean populations. RESULTS Both the Antofagasta and Calama populations show differences compared with the rest of the Chilean population. On one side, Antofagasta shows a high diversity of non-Amerindian lineages, including the highest value for haplogroup I (12%) for all Chileans populations. Otherwise, Calama has the highest value of any Chilean urban population (31.9%) for Amerindian lineages, including the only Q-M3 sub-lineage detected in the entire sample. Regarding the Native population, Aymara presents the highest percentage of Q-M3 (94.4%). CONCLUSIONS The Y chromosome haplogroup distribution allowed us to identify recent migratory processes typical of the northern populations studied. These have shaped the demographic and cultural dynamics of local and migrant groups in the territory.
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Affiliation(s)
- Margarita Reyes-Madrid
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Sandra Flores-Alvarado
- Programa de Bioestadística, Instituto de Salud Pública, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | - Michael Orellana-Soto
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mario Apata
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mauricio Moraga
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile.,Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Michelle de Saint Pierre
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
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4
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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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5
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Lardone MC, Ortega V, Ortiz E, Flórez M, Piottante A, Ebensperger M, Flores S, Pezo P, Orellana M, Moraga M, Castro A. Partial-AZFc deletions in Chilean men with primary spermatogenic impairment: gene dosage and Y-chromosome haplogroups. J Assist Reprod Genet 2020; 37:3109-19. [PMID: 33034826 DOI: 10.1007/s10815-020-01957-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/25/2020] [Indexed: 10/23/2022] Open
Abstract
PURPOSE To investigate the association of partial-AZFc deletions in Chilean men with primary spermatogenic failure and their testicular histopathological phenotypes, analyzing the contribution of DAZ dosage, CDY1 copies, and Y-chromosome haplogroups. SUBJECTS AND METHODS We studied 479 Chilean men: 334 infertile patients with histological examination (233 cases with spermatogenic defects and 101 normal spermatogenesis, obstructive controls, OC), and 145 normozoospermic controls (NC). AZFc subdeletions were detected by single-tagged sequences and single nucleotide variants analysis. DAZ-copy number was quantified by real-time qPCR. Y-chromosome haplogroups (Y-hg) were hierarchically genotyped through 16 biallelic-markers. RESULTS The prevalence of AZFc-partial deletions was increased in cases (6%) compared with NC (1.4%) (P = 0.035). There was no difference between 143 Sertoli-cell only syndrome, 35 maturation arrest, or 35 mix atrophy patients and controls. However, gr/gr deletions were more frequent in 16 subjects with hypospermatogenesis compared with NC (P = 0.003) and OC (P = 0.013). Y-hg R was the most prevalent (~ 50%), but decreased among gr/gr deletions (21%, P = 0.03). The prevalence of Y-hg M increased in cases versus controls, both in total and non-deleted men (3.9 and 3.7% versus 0.4%, P = 0.009 and P = 0.016, respectively). Among gr/gr deletions, Y-hg H increased compared with non-deleted men (14.3% versus 0.4%, P = 0.0047). CONCLUSION Partial-AZFc deletions in a Chilean admixed population are associated with secretory azo/oligozoospermia and might have a role in the development of hypospermatogenesis. Low represented haplogroups, Y-hg M and Y-hg H, show an association with the occurrence of spermatogenic failure and gr/gr deletions respectively; however, additional studies are required.
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Verdugo RA, Di Genova A, Herrera L, Moraga M, Acuña M, Berríos S, Llop E, Valenzuela CY, Bustamante ML, Digman D, Symon A, Asenjo S, López P, Blanco A, Suazo J, Barozet E, Caba F, Villalón M, Alvarado S, Cáceres D, Salgado K, Portales P, Moreno-Estrada A, Gignoux CR, Sandoval K, Bustamante CD, Eng C, Huntsman S, Burchard EG, Loira N, Maass A, Cifuentes L. Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components. Biol Res 2020; 53:15. [PMID: 32299502 PMCID: PMC7161194 DOI: 10.1186/s40659-020-00284-5] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
Background Current South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. Individual variation in relative proportions of each of these ancestries may be confounded with socio-economic factors due to population stratification. Therefore, ancestry is a potential confounder variable that should be considered in epidemiologic studies and in public health plans. However, there are few studies that have assessed the ancestry of the current admixed Chilean population. This is partly due to the high cost of genome-scale technologies commonly used to estimate ancestry. In this study we have designed a small panel of SNPs to accurately assess ancestry in the largest sampling to date of the Chilean mestizo population (n = 3349) from eight cities. Our panel is also able to distinguish between the two main Amerindian components of Chileans: Aymara from the north and Mapuche from the south. Results A panel of 150 ancestry-informative markers (AIMs) of SNP type was selected to maximize ancestry informativeness and genome coverage. Of these, 147 were successfully genotyped by KASPar assays in 2843 samples, with an average missing rate of 0.012, and a 0.95 concordance with microarray data. The ancestries estimated with the panel of AIMs had relative high correlations (0.88 for European, 0.91 for Amerindian, 0.70 for Aymara, and 0.68 for Mapuche components) with those obtained with AXIOM LAT1 array. The country’s average ancestry was 0.53 ± 0.14 European, 0.04 ± 0.04 African, and 0.42 ± 0.14 Amerindian, disaggregated into 0.18 ± 0.15 Aymara and 0.25 ± 0.13 Mapuche. However, Mapuche ancestry was highest in the south (40.03%) and Aymara in the north (35.61%) as expected from the historical location of these ethnic groups. We make our results available through an online app and demonstrate how it can be used to adjust for ancestry when testing association between incidence of a disease and nongenetic risk factors. Conclusions We have conducted the most extensive sampling, across many different cities, of current Chilean population. Ancestry varied significantly by latitude and human development. The panel of AIMs is available to the community for estimating ancestry at low cost in Chileans and other populations with similar ancestry.
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Affiliation(s)
- Ricardo A Verdugo
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.,Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Alex 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
| | - Luisa Herrera
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Mauricio Moraga
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Mónica Acuña
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Soledad Berríos
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Elena Llop
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Carlos Y Valenzuela
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - M Leonor Bustamante
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.,Departamento de Psiquiatría, y Salud Mental Norte, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Dayhana Digman
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Adriana Symon
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Soledad Asenjo
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Pamela López
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Alejandro Blanco
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - José Suazo
- Instituto de Investigación en Ciencias Odontológicas, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - Emmanuelle Barozet
- Departamento de Sociología, Facultad de Ciencias Sociales, Universidad de Chile, Centro de Estudios de Conflicto y Cohesión, Social, Santiago, Chile
| | - Fresia Caba
- Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Marcelo Villalón
- Instituto de Salud Poblacional "Escuela de Salud Pública", Universidad de Chile, Santiago, Chile
| | - Sergio Alvarado
- Instituto de Salud Poblacional "Escuela de Salud Pública", Universidad de Chile, Santiago, Chile
| | - Dante Cáceres
- Instituto de Salud Poblacional "Escuela de Salud Pública", Universidad de Chile, Santiago, Chile
| | - Katherine Salgado
- Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Pilar Portales
- Corporación Municipal de Desarrollo Social, Iquique, Chile
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, 36821, Mexico
| | | | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, 36821, Mexico
| | | | - Celeste Eng
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Nicolás Loira
- Mathomics, Centro de Modelamiento Matemático y Centro para la Regulación del Genoma, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Alejandro Maass
- 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
| | - Lucía Cifuentes
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.
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7
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Vidal EA, Moyano TC, Bustos BI, Pérez-Palma E, Moraga C, Riveras E, Montecinos A, Azócar L, Soto DC, Vidal M, Di Genova A, Puschel K, Nürnberg P, Buch S, Hampe J, Allende ML, Cambiazo V, González M, Hodar C, Montecino M, Muñoz-Espinoza C, Orellana A, Reyes-Jara A, Travisany D, Vizoso P, Moraga M, Eyheramendy S, Maass A, De Ferrari GV, Miquel JF, Gutiérrez RA. Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans. Sci Rep 2019; 9:2132. [PMID: 30765821 PMCID: PMC6376018 DOI: 10.1038/s41598-019-39391-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 × 106 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations.
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Affiliation(s)
- Elena A Vidal
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Tomás C Moyano
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bernabé I Bustos
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Eduardo Pérez-Palma
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Carol Moraga
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eleodoro Riveras
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro Montecinos
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Lorena Azócar
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Daniela C Soto
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mabel Vidal
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alex Di Genova
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Matemática del Genoma (LBMG-Mathomics), Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Klaus Puschel
- Departamento de Medicina Familiar, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Stephan Buch
- Medical Department I, University Hospital Dresden, TU Dresden, Germany
| | - Jochen Hampe
- Medical Department I, University Hospital Dresden, TU Dresden, Germany
| | - Miguel L Allende
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Verónica Cambiazo
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Christian Hodar
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Martín Montecino
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Claudia Muñoz-Espinoza
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Ariel Orellana
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Angélica Reyes-Jara
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Dante Travisany
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Matemática del Genoma (LBMG-Mathomics), Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Paula Vizoso
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Propagación y Conservación Vegetal (CEPROVEG), Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Mauricio Moraga
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Susana Eyheramendy
- Departmento de Estadística, Facultad de Matemáticas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro Maass
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Medicina Familiar, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Giancarlo V De Ferrari
- FONDAP Center for Genome Regulation, Santiago, Chile. .,Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile.
| | - Juan Francisco Miquel
- FONDAP Center for Genome Regulation, Santiago, Chile. .,Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Santiago, Chile. .,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
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8
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Vieira-Machado CD, Tostes M, Alves G, Nazer J, Martinez L, Wettig E, Pizarro Rivadeneira O, Diaz Caamaño M, Larenas Ascui J, Pavez P, Dutra MDG, Castilla EE, Orioli IM. Uniparental ancestry markers in Chilean populations. Genet Mol Biol 2016; 39:573-579. [PMID: 27561109 PMCID: PMC5127147 DOI: 10.1590/1678-4685-gmb-2015-0273] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 02/23/2016] [Indexed: 11/29/2022] Open
Abstract
The presence of Native Americans, Europeans, and Africans has led to the development
of a multi-ethnic, admixed population in Chile. This study aimed to contribute to the
characterization of the uniparental genetic structure of three Chilean regions.
Newborns from seven hospitals in Independencia, Providencia, Santiago, Curicó,
Cauquenes, Valdívia, and Puerto Montt communes, belonging to the Chilean regions of
Santiago, Maule, and Los Lagos, were studied. The presence of Native American
mitochondrial DNA (mtDNA) haplogroups and two markers present in the non-recombinant
region of the Y chromosome, DYS199 and DYS287, indicative of Native American and
African ancestry, respectively, was determined. A high Native American matrilineal
contribution and a low Native American and African patrilineal contributions were
found in all three studied regions. As previously found in Chilean admixed
populations, the Native American matrilineal contribution was lower in Santiago than
in the other studied regions. However, there was an unexpectedly higher contribution
of Native American ancestry in one of the studied communes in Santiago, probably due
to the high rate of immigration from other regions of the country. The population
genetic sub-structure we detected in Santiago using few uniparental markers requires
further confirmation, owing to possible stratification for autosomal and X-chromosome
markers.
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Affiliation(s)
- Camilla Dutra Vieira-Machado
- Latin American Collaborative Study of Congenital Malformations (ECLAMC) and National Institute of Population Medical Genetics (INAGEMP), Departmento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Maluah Tostes
- Latin American Collaborative Study of Congenital Malformations (ECLAMC) and National Institute of Population Medical Genetics (INAGEMP), Departmento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Gabrielle Alves
- Latin American Collaborative Study of Congenital Malformations (ECLAMC) and National Institute of Population Medical Genetics (INAGEMP), Departmento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Julio Nazer
- Neonatal Service, Department of Obstetrics and Gynecology, Hospital Clínico de La Universidad del Chile, Santiago, Chile
| | | | | | | | | | | | | | - Maria da Graça Dutra
- Latin American Collaborative Study of Congenital Malformations (ECLAMC) and National Institute of Population Medical Genetics (INAGEMP), Laboratory of Congenital Malformations Epidemiology (LEMC), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Eduardo Enrique Castilla
- Latin American Collaborative Study of Congenital Malformations (ECLAMC) and National Institute of Population Medical Genetics (INAGEMP), Laboratory of Congenital Malformations Epidemiology (LEMC), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Latin American Collaborative Study of Congenital Malformations (ECLAMC) Center for Medical Education and Clinical Research (CEMIC) Buenos Aires, Argentina
| | - Ieda Maria Orioli
- Latin American Collaborative Study of Congenital Malformations (ECLAMC) and National Institute of Population Medical Genetics (INAGEMP), Departmento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
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9
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Toscanini U, Brisighelli F, Moreno F, Pantoja-Astudillo JA, Morales EA, Bustos P, Pardo-Seco J, Salas A. Analysis of Y-chromosome STRs in Chile confirms an extensive introgression of European male lineages in urban populations. Forensic Sci Int Genet 2015; 21:76-80. [PMID: 26736138 DOI: 10.1016/j.fsigen.2015.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 12/05/2015] [Accepted: 12/09/2015] [Indexed: 12/09/2022]
Abstract
We analyzed the Y chromosome haplotypes (Yfiler) of 978 non-related Chilean males grouped in five sampling regions (Iquique, Santiago de Chile, Concepción, Temuco and Punta Arenas) covering main geo-political regions. Overall, 803 different haplotypes and 688 singletons were observed. Molecular diversity was moderately lower than in other neighboring countries (e.g. Argentina); and AMOVA analysis on Y-STR haplotypes showed that among variation within Chile accounted for only 0.25% of the total variation. Punta Arenas, in the southern cone, showed the lowest haplotype diversity, and discrimination capacity, and also the highest matching probability of the five Chilean samples, probably reflecting its more marked geographic isolation compared to the other regions. Multidimensional scaling (MDS) analysis based on RST genetic distances suggested a close proximity of Chilean Y-chromosome profiles to European ones. Consistently, haplogroups inferred from Y-STR profiles revealed that the Native American component constituted only 8% of all the haplotypes, and this component ranged from 5% in the Centre of the country to 9-10% in the South and 13% in the North, which is in good agreement with the distribution of Native American communities in these regions. AMOVA computed on inferred haplogroups confirmed the very low among variation observed in Chilean populations. The present project provides the first Chilean dataset to the international Y-chromosome STR Haplotype Reference Database (YHRD) and it is also the first reference database for Y-chromosome forensic casework of the country.
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Affiliation(s)
- Ulises Toscanini
- Pricai-Fundación Favaloro, Buenos Aires, Argentina; Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain; Infectious Diseases and Vaccines Unit, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Francesca Brisighelli
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain; Sezione di Medicina Legale-Istituto di Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Fabián Moreno
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain; Servicio Medico Legal, Ministerio de Justicia, Santiago, Chile
| | | | - Eugenia Aguirre Morales
- Servicio Medico Legal, Ministerio de Justicia, Santiago, Chile; Infectious Diseases and Vaccines Unit, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Patricio Bustos
- Servicio Medico Legal, Ministerio de Justicia, Santiago, Chile
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain; Infectious Diseases and Vaccines Unit, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain; Infectious Diseases and Vaccines Unit, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain.
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10
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Eyheramendy S, Martinez FI, Manevy F, Vial C, Repetto GM. Genetic structure characterization of Chileans reflects historical immigration patterns. Nat Commun 2015; 6:6472. [PMID: 25778948 DOI: 10.1038/ncomms7472] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 01/30/2015] [Indexed: 12/25/2022] Open
Abstract
Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography. Chileans are genetically admixed. Here, the authors find that the average admixing time is around 10 generations ago and show the contribution of European men and Native-American women to the Chilean population.
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11
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Abstract
A general introduction to the origins and history of Latin American populations is followed by a systematic review of the data from molecular autosomal assessments of the ethnic/continental (European, African, Amerindian) ancestries for 24 Latin American countries or territories. The data surveyed are of varying quality but provide a general picture of the present constitution of these populations. A brief discussion about the applications of these results (admixture mapping) is also provided. Latin American populations can be viewed as natural experiments for the investigation of unique anthropological and epidemiological issues.
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Affiliation(s)
- Francisco Mauro Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Mónica Sans
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay
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12
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Le TN, Elsea SH, Romero R, Chaiworapongsa T, Francis GL. Prolactin receptor gene polymorphisms are associated with gestational diabetes. Genet Test Mol Biomarkers 2013; 17:567-71. [PMID: 23651351 DOI: 10.1089/gtmb.2013.0009] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIMS Human placental lactogen (hPL) acts via the prolactin receptor (PRLR) on maternal β-cells to mediate increases in β-cell mass and function during normal pregnancy. This interaction between hPL and PRLR is essential to maintain normal glucose homeostasis and to address the increased metabolic demands of pregnancy. Given the importance of the PRLR-hPL axis in pancreatic islet cell adaptation to pregnancy, we hypothesized that genetic variation in the PRLR gene could influence risk of development of gestational diabetes mellitus (GDM). DNA samples from 96 mothers affected by GDM and 96 unaffected cases were genotyped for 8 selected single nucleotide polymorphisms (SNPs) in PRLR. RESULTS Significant associations were identified in two SNPs analyzed. The minor alleles of PRLR SNPs rs10068521 and rs9292578 were more frequently observed in GDM cases than controls and were associated with a 2.36-fold increased risk for GDM in those carrying the minor allele. CONCLUSION SNPs of the PRLR gene 5' UTR and promoter region are associated with increased risk for GDM in a population of Chilean subjects.
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Affiliation(s)
- Trang N Le
- Department of Pediatrics, Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, Virginia 23298, USA.
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13
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Lardone MC, Marengo A, Parada-Bustamante A, Cifuentes L, Piottante A, Ebensperger M, Valdevenito R, Castro A. Greater prevalence of Y chromosome Q1a3a haplogroup in Y-microdeleted Chilean men: a case-control study. J Assist Reprod Genet 2013; 30:531-8. [PMID: 23388839 DOI: 10.1007/s10815-013-9950-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 01/28/2013] [Indexed: 10/27/2022] Open
Abstract
PURPOSE To determine the prevalence of South Amerindian Y chromosome in Chilean patients with spermatogenic failure and their association with classical and/or AZFc-partial Y chromosome deletions. METHODS We studied 400 men, 218 with secretory azo/oligozoospermia (cases) and 182 controls (116 fertile and/or normozoospermic, and 66 azoospermic with normal spermatogenesis). After a complete testicular characterization (physical evaluation, hormonal and/or biopsy) peripheral blood was drawn to obtain DNA for Y chromosome microdeletions, AZFc-partial deletions and biallelic analysis by allele specific polymerase chain reaction (PCR) of the M3 (rs3894) single nucleotide polymorphism (SNP). RESULTS Classical AZF microdeletions were found in 23 cases (Y-microdeleted). AZFc-partial deletions were observed in 10 cases (6 "gr/gr", 3 "b2/b3" and 1 "b1/b3") and 4 controls (4 "gr/gr"). The AZFc-partial deletions were mainly associated with the absence of DAZ1/DAZ2 (64 %). No significant differences in the prevalence of AZFc-partial deletions were observed between cases and controls. We observed a significant higher proportion of the Q1a3a haplogroup in Y-microdeleted men compared to patients with spermatogenic failure without deletions and control men (P<0.01 and P<0.05, respectively by Bonferroni test). Among them, patients with AZFb deletions had an increased prevalence of the Q1a3a haplogroup compared to controls, cases without deletions and to those with complete or partial-AZFc deletions (P<0.01, Bonferroni test). CONCLUSIONS The Q1a3a South Amerindian lineage seems to increase the susceptibility to non AZFc microdeletions. On the other hand, in Chilean population the AZFc-partial deletions ("gr/gr", "b1/b3" and/or "b2/b3") does not seem to predispose to severe spermatogenic impairment.
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Affiliation(s)
- María C Lardone
- Institute of Maternal and Child Research, School of Medicine, University of Chile, Santa Rosa 1234, Santiago, Chile
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14
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Barrai I, Rodriguez-Larralde A, Dipierri J, Alfaro E, Acevedo N, Mamolini E, Sandri M, Carrieri A, Scapoli C. Surnames in Chile: A study of the population of Chile through isonymy. Am J Phys Anthropol 2012; 147:380-8. [PMID: 22271503 DOI: 10.1002/ajpa.22000] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 11/22/2011] [Indexed: 11/09/2022]
Affiliation(s)
- I Barrai
- Dipartimento di Biologia ed Evoluzione, Università di Ferrara, 44121 Ferrara, Italy
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15
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Poggi H, Vera A, Lagos M, Solari S, Rodríguez P L, Pérez CM. HLA-B*5701 frequency n Chilean HIV-infected patients and in general population. Braz J Infect Dis 2010; 14:510-512. [DOI: 10.1016/s1413-8670(10)70102-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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16
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Gonzalez-Gronow M, Cuchacovich M, Francos R, Cuchacovich S, Fernandez Mdel P, Blanco A, Bowers EV, Kaczowka S, Pizzo SV. Antibodies against the voltage-dependent anion channel (VDAC) and its protective ligand hexokinase-I in children with autism. J Neuroimmunol 2010; 227:153-61. [PMID: 20576296 DOI: 10.1016/j.jneuroim.2010.06.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 04/09/2010] [Accepted: 06/01/2010] [Indexed: 12/27/2022]
Abstract
Autistic children show elevated serum levels of autoantibodies to several proteins essential for the function of normal brains. The voltage-dependent anion channel (VDAC) and hexokinase-I, a VDAC protective ligand, were identified as targets of this autoimmunity in autistic children. These autoantibodies were purified using immunoaffinity chromatographic techniques. Both antibodies induce apoptosis of cultured human neuroblastoma cells. Because VDAC and hexokinase-I are essential for brain protection from ischemic damage, the presence of these autoantibodies suggests a possible causal role in the neurologic pathogenesis of autism.
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17
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Cuchacovich M, Solanes F, Díaz G, Cermenati T, Avila S, Verdaguer J, Verdaguer JI, Carpentier C, Stopel J, Rojas B, Traipe L, Gallardo P, Sabugo F, Zanoli M, Merino G, Villarroel F. Comparison of the Clinical Efficacy of Two Different Immunosuppressive Regimens in Patients with Chronic Vogt-Koyanagi-Harada Disease. Ocul Immunol Inflamm 2010; 18:200-7. [DOI: 10.3109/09273941003587541] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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18
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Abstract
OBJECTIVES To study the variability at the myotonic dystrophy protein kinase (DMPK) gene in a Chilean sample of healthy people. DM1 is an autosomal dominant disorder caused by an expansion of a (CTG) repeat at the 3'-UTR of the gene DMPK. Healthy individuals have alleles under 35 repeats and diseased individuals have over 50. METHODS Genotyping the number of (CTG) repeats at this gene in a sample of healthy Chilean people. RESULTS Allele frequencies were significantly different from those of other populations. The most frequent allele was with five repeats. The frequency of larger alleles (>18 CTG repeats) was 11%, close to the European frequency (12%) and higher than the Japanese (8%) and Aboriginal Pehuenche samples (8%). CONCLUSIONS Allelic frequencies in the Chilean sample studied were intermediate between those of the two ancestral populations (European and Pehuenche).
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Affiliation(s)
- F Amenabar
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile
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Gómez A, Ávila SJ, Briceño I. De genotipos e isonimias: análisis de correlación entre el apellido y el patrimonio genético heredado en el cromosoma Y en la población de tres departamentos del suroccidente colombiano. biomedica 2008; 28:357. [DOI: 10.7705/biomedica.v28i3.74] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lardone MC, Parodi DA, Ebensperger M, Peñaloza P, Cornejo V, Valdevenito R, Pommer R, Castro A. AZFc partial deletions in Chilean men with severe spermatogenic failure. Fertil Steril 2007; 88:1318-26. [PMID: 17416365 DOI: 10.1016/j.fertnstert.2007.01.038] [Citation(s) in RCA: 20] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Revised: 01/04/2007] [Accepted: 01/05/2007] [Indexed: 11/18/2022]
Abstract
OBJECTIVE To determine the prevalence of AZFc subdeletions in infertile Chilean men with severe spermatogenic impairment. DESIGN Prospective analysis. SETTING University infertility clinic. PATIENT(S) Ninety-five secretory azo/oligozoospermic men without AZFc Y chromosome microdeletions: 71 whose testicular histology showed severe spermatogenic impairment and 24 who exhibited reduced testicular volume and elevated serum FSH levels. As controls, we studied 77 men (50 fertile and/or normozoospermic, and 27 with azoospermia and normal spermatogenesis). INTERVENTION(S) Peripheral blood was drawn to obtain genomic DNA for polymerase chain reaction (PCR) digestion assays of DAZ-sequence nucleotide variants and for AZFc-STS PCR after a complete testicular characterization (biopsy, hormonal, and physical evaluation). MAIN OUTCOME MEASURE(S) DAZ genes and AZFc subdeletion types. RESULT(S) In cases we observed two "gr/gr" subdeletions (2.1%), one with absence of DAZ1/DAZ2 (g1/g2 subtype), and the other with absence of DAZ3/DAZ4 (r2/r4 subtype). Additionally, we found a g1/g3 subdeletion in a patient with Sertoli-cell-only syndrome. In controls, we observed two gr/gr subdeletions with absence of DAZ1/DAZ2 (2.6%) in a fertile/normozoospermic and in an obstructive azoospermic man. CONCLUSION(S) AZFc subdeletions do not seem to cause severe impairment of spermatogenesis. Moreover, gr/gr-DAZ1/DAZ2 subdeletions do not appear to affect fertility in Chilean men.
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Affiliation(s)
- María C Lardone
- Institute of Maternal and Child Research, School of Medicine, University of Chile, Santiago, Chile
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Thomas DC, Haile RW, Duggan D. Recent developments in genomewide association scans: a workshop summary and review. Am J Hum Genet 2005; 77:337-45. [PMID: 16080110 PMCID: PMC1226200 DOI: 10.1086/432962] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [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: 06/14/2005] [Accepted: 06/20/2005] [Indexed: 01/18/2023] Open
Abstract
With the imminent availability of ultra-high-volume genotyping platforms (on the order of 100,000-1,000,000 genotypes per sample) at a manageable cost, there is growing interest in the possibility of conducting genomewide association studies for a variety of diseases but, so far, little consensus on methods to design and analyze them. In April 2005, an international group of >100 investigators convened at the University of Southern California over the course of 2 days to compare notes on planned or ongoing studies and to debate alternative technologies, study designs, and statistical methods. This report summarizes these discussions in the context of the relevant literature. A broad consensus emerged that the time was now ripe for launching such studies, and several common themes were identified--most notably the considerable efficiency gains of multistage sampling design, specifically those made by testing only a portion of the subjects with a high-density genomewide technology, followed by testing additional subjects and/or additional SNPs at regions identified by this initial scan.
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Affiliation(s)
- Duncan C Thomas
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089-9011, USA.
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