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De Oliveira TC, Secolin R, Lopes-Cendes I. A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations. Front Genet 2023; 14:1091269. [PMID: 36741309 PMCID: PMC9893294 DOI: 10.3389/fgene.2023.1091269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.
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Affiliation(s)
- Thais C. De Oliveira
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Rodrigo Secolin
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil,*Correspondence: Iscia Lopes-Cendes,
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Suárez D, Cruz R, Torres M, Mogollón F, Moncada J, Carracedo A, Usaquén W. Ancestry analysis using autosomal SNPs in northern South America, reveals interpretation differences between an AIM panel and an identification panel. Forensic Sci Int 2021; 326:110934. [PMID: 34404021 DOI: 10.1016/j.forsciint.2021.110934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/14/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022]
Abstract
Current human populations are studied to elucidate their ancestry composition and to obtain reference values for an array of genetic markers for forensic practice. This study compared the 79 ancestry informative markers (AIMs) panel with the SNPforID 52plex set used in forensic identification, using samples belonging to Continental Caribbean populations from Colombia with a high percentage of locals self-determined as Native American descendants. The results show a bias in the individual estimation made with the identification markers, which disregards the Native American ancestry component and overestimates the African ancestry component. Also, the analysis made with the Bayesian Classification Algorithm shows better likelihoods for individual assignment with AIMs than with SNPforID 52plex.
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Affiliation(s)
- Dayana Suárez
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia.
| | - Raquel Cruz
- CIBERER, Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - María Torres
- Galician Public Foundation of Genomic Medicine (SERGAS)-CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Fernanda Mogollón
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia
| | - Julie Moncada
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia
| | - Angel Carracedo
- CIBERER, Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Spain; Galician Public Foundation of Genomic Medicine (SERGAS)-CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain; Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - William Usaquén
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia.
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Yang TW, Li YH, Chou CF, Lai FP, Chien YH, Yin HI, Lee TT, Hwa HL. DNA mixture interpretation using linear regression and neural networks on massively parallel sequencing data of single nucleotide polymorphisms. AUST J FORENSIC SCI 2021. [DOI: 10.1080/00450618.2020.1807050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Ta-Wei Yang
- Graduate Institute of Networking and Multimedia, National Taiwan University, Taipei, Taiwan
| | - Yi-Hao Li
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Cheng-Fu Chou
- Graduate Institute of Networking and Multimedia, National Taiwan University, Taipei, Taiwan
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Fei-Pei Lai
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsiang-I Yin
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tsui-Ting Lee
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsiao-Lin Hwa
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
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Gomez-Lopera N, Alfaro JM, Leal SM, Pineda-Trujillo N. Type 1 diabetes loci display a variety of native American and African ancestries in diseased individuals from Northwest Colombia. World J Diabetes 2019; 10:534-545. [PMID: 31798789 PMCID: PMC6885725 DOI: 10.4239/wjd.v10.i11.534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) is a complex disease with a higher incidence in Europeans than other populations. The Colombians Living in Medellin (CLM) is admixed with ancestry contributions from Europeans, Native Americans (NAT) and Africans (AFR).
AIM Our aim was to analyze the genetic admixture component at candidate T1D loci in Colombian individuals with the disease.
METHODS Seventy-four ancestry informative markers (AIMs), which tagged 41 T1D candidate loci/genes, were tested by studying a cohort of 200 Northwest Colombia diseased individuals. T1D status was classified by testing for glutamic acid decarboxylase (GAD-65 kDa) and protein tyrosine-like antigen-2 auto-antibodies in serum samples. Candidate loci/genes included HLA, INS, PTPN22, CTLA4, IL2RA, SUMO4, CLEC16A, IFIH1, EFR3B, IL7R, NRP1 and RNASEH1, amongst others. The 1,000 genome database was used to analyze data from 94 individuals corresponding to the reference CLM. As the data did not comply with a normal distribution, medians were compared between groups using the Mann-Whitney U-test.
RESULTS Both T1D patients and individuals from CLM displayed mainly European ancestry (61.58 vs 62.06) followed by Native American (27.34 vs 27.46) and to a lesser extent the AFR ancestry (10.28 vs 10.65) components. However, compared to CLM, ancestry of T1D patients displayed a decrease of NAT ancestry at gene EFR3B (24.30 vs 37.10) and an increase at genes IFIH1 (32.07 vs 14.99) and IL7R (52.18 vs 39.18). Also, for gene NRP1 (36.67 vs 0.003), we observed a non-AFR contribution (attributed to NAT). Autoimmune patients (positive for any of two auto-antibodies) displayed lower NAT ancestry than idiopathic patients at the MHC region (20.36 vs 31.88). Also, late onset patients presented with greater AFR ancestry than early onset patients at gene IL7R (19.96 vs 6.17). An association analysis showed that, even after adjusting for admixture, an association exists for at least seven such AIMs, with the strongest findings on chromosomes 5 and 10 (gene IL7R, P = 5.56 × 10-6 and gene NRP1, P = 8.70 × 10-19, respectively).
CONCLUSION Although Colombian T1D patients have globally presented with higher European admixture, specific T1D loci have displayed varying levels of Native American and AFR ancestries in diseased individuals.
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Affiliation(s)
- Natalia Gomez-Lopera
- Grupo Mapeo Genetico, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín 050010470, Colombia
| | - Juan M Alfaro
- Grupo Mapeo Genetico, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín 050010470, Colombia
- Sección de Endocrinología Pediátrica, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín 050010470, Colombia
| | - Suzanne M Leal
- Center for Statistical Genetics, Columbia University, New York, NY 10032, United States
| | - Nicolas Pineda-Trujillo
- Grupo Mapeo Genetico, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín 050010470, Colombia
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Tobón-Arroyave SI, Jiménez-Arbeláez GA, Alvarado-Gómez VA, Isaza-Guzmán DM, Flórez-Moreno GA, Pérez-Cano MI. Association analysis between rs6184 and rs6180 polymorphisms of growth hormone receptor gene regarding skeletal-facial profile in a Colombian population. Eur J Orthod 2019; 40:378-386. [PMID: 29059297 DOI: 10.1093/ejo/cjx070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background/Objective There is strong evidence that genetic factors may affect the craniofacial morphology. This study aimed to examine the association between the rs6184 and rs6180 polymorphic variants of the growth hormone receptor (GHR) gene and skeletal-facial profile in a Colombian population. Subjects/Methods Saliva samples from 306 individuals ranging in age from 15 to 53 (mean 24.33) years were collected. Cephalometric parameters were used to categorize the participants as Class I, Class II, or Class III skeletal-facial profile. The polymerase chain reaction-restriction fragment length polymorphism method was used to identify genotypes of the rs6184 and rs6180 single nucleotide polymorphisms (SNPs). The association of polymorphisms with the skeletal-facial profile was assessed separately and adjusted for confounding using a multivariate binary logistic regression model, alongside with analysis of linkage disequilibrium and haplotype associations. Results Although individuals carrying the CA genotype of the rs6184 SNP showed both significantly decreased values for ANB angle and increased measures concerning mandibular body length and mandibular length, no significant differences amongst genotype groups of rs6180 SNP were observed. Moreover, chi-square test and logistic regression analysis revealed that the CA genotype of rs6184 SNP and the A-A haplotype were highly associated with Class III skeletal-facial profile. Conclusions Although these results do not support that rs6180 SNP could be identified as a predictor for skeletal-facial profile, they suggest that the allele A of rs6184 SNP alone or in combination with other SNPs in the GHR gene yields significant horizontal and longitudinal variations of the mandibular morphology and might be a strong/independent prognostic indicator for Class III skeletal-facial profile in the present population.
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Affiliation(s)
- Sergio Iván Tobón-Arroyave
- POPCAD Research Group, Laboratory of Immunodetection and Bioanalysis, Faculty of Dentistry, University of Antioquia. Medellín, Colombia
| | - Gustavo Adolfo Jiménez-Arbeláez
- POPCAD Research Group, Laboratory of Immunodetection and Bioanalysis, Faculty of Dentistry, University of Antioquia. Medellín, Colombia
| | - Viviana Andrea Alvarado-Gómez
- POPCAD Research Group, Laboratory of Immunodetection and Bioanalysis, Faculty of Dentistry, University of Antioquia. Medellín, Colombia
| | - Diana María Isaza-Guzmán
- POPCAD Research Group, Laboratory of Immunodetection and Bioanalysis, Faculty of Dentistry, University of Antioquia. Medellín, Colombia
| | - Gloria Amparo Flórez-Moreno
- POPCAD Research Group, Laboratory of Immunodetection and Bioanalysis, Faculty of Dentistry, University of Antioquia. Medellín, Colombia
| | - María Isabel Pérez-Cano
- POPCAD Research Group, Laboratory of Immunodetection and Bioanalysis, Faculty of Dentistry, University of Antioquia. Medellín, Colombia
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Gontijo CC, Mendes FM, Santos CA, Klautau-Guimarães MDN, Lareu MV, Carracedo Á, Phillips C, Oliveira SF. Ancestry analysis in rural Brazilian populations of African descent. Forensic Sci Int Genet 2018; 36:160-166. [DOI: 10.1016/j.fsigen.2018.06.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
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Yousefi S, Abbassi-Daloii T, Kraaijenbrink T, Vermaat M, Mei H, van 't Hof P, van Iterson M, Zhernakova DV, Claringbould A, Franke L, 't Hart LM, Slieker RC, van der Heijden A, de Knijff P, 't Hoen PAC. A SNP panel for identification of DNA and RNA specimens. BMC Genomics 2018; 19:90. [PMID: 29370748 PMCID: PMC5785835 DOI: 10.1186/s12864-018-4482-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND SNP panels that uniquely identify an individual are useful for genetic and forensic research. Previously recommended SNP panels are based on DNA profiles and mostly contain intragenic SNPs. With the increasing interest in RNA expression profiles, we aimed for establishing a SNP panel for both DNA and RNA-based genotyping. RESULTS To determine a small set of SNPs with maximally discriminative power, genotype calls were obtained from DNA and blood-derived RNA sequencing data belonging to healthy, geographically dispersed, Dutch individuals. SNPs were selected based on different criteria like genotype call rate, minor allele frequency, Hardy-Weinberg equilibrium and linkage disequilibrium. A panel of 50 SNPs was sufficient to identify an individual uniquely: the probability of identity was 6.9 × 10- 20 when assuming no family relations and 1.2 × 10- 10 when accounting for the presence of full sibs. The ability of the SNP panel to uniquely identify individuals on DNA and RNA level was validated in an independent population dataset. The panel is applicable to individuals from European descent, with slightly lower power in non-Europeans. Whereas most of the genes containing the 50 SNPs are expressed in various tissues, our SNP panel needs optimization for other tissues than blood. CONCLUSIONS This first DNA/RNA SNP panel will be useful to identify sample mix-ups in biomedical research and for assigning DNA and RNA stains in crime scenes to unique individuals.
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Affiliation(s)
- Soheil Yousefi
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Tooba Abbassi-Daloii
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Thirsa Kraaijenbrink
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Martijn Vermaat
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter van 't Hof
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Maarten van Iterson
- Molecular Epidemiology Section, Leiden University Medical Center, Leiden, The Netherlands
| | - Daria V Zhernakova
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Annique Claringbould
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Leen M 't Hart
- Molecular Epidemiology Section, Leiden University Medical Center, Leiden, The Netherlands.,Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Roderick C Slieker
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands.,Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, The Netherlands
| | - Amber van der Heijden
- Department of Epidemiology and Biostatistics, VU Medical Center, Amsterdam, The Netherlands.,Department of General Practice and Elderly Care Medicine, VU Medical Center, Amsterdam, The Netherlands
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | | | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands. .,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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Vanegas D, Triviño L, Galindo C, Franco L, Salguero G, Camacho B, Perdomo-Arciniegas AM. A new strategy for umbilical cord blood collection developed at the first Colombian public cord blood bank increases total nucleated cell content. Transfusion 2017; 57:2225-2233. [PMID: 28653354 DOI: 10.1111/trf.14190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/05/2017] [Accepted: 05/06/2017] [Indexed: 12/16/2023]
Abstract
BACKGROUND The total nucleated cell dosage of umbilical cord blood (UCB) is an important factor in determining successful allogeneic hematopoietic stem cell transplantation after a minimum human leukocyte antigen donor-recipient match. The northern South American population is in need of a new-generation cord blood bank that cryopreserves only units with high total nucleated cell content, thereby increasing the likelihood of use. Colombia set up a public cord blood bank in 2014; and, as a result of its research for improving high total nucleated cell content, a new strategy for UCB collection was developed. STUDY DESIGN AND METHODS Data from 2933 collected and 759 cryopreserved cord blood units between 2014 and 2015 were analyzed. The correlation of donor and collection variables with cellularity was evaluated. Moreover, blood volume, cell content, CD34+ count, clonogenic capacity, and microbial contamination were assessed comparing the new method, which combines in utero and ex utero techniques, with the conventional strategies. RESULTS Multivariate analysis confirmed a correlation between neonatal birth weight and cell content. The new collection method increased total nucleated cell content in approximately 26% and did not alter pre-cryopreservation and post-thaw cell recovery, viability, or clonogenic ability. Furthermore, it showed a remarkably low microbial contamination rate (1.2%). CONCLUSION The strategy for UCB collection developed at the first Colombian public cord blood bank increases total nucleated cell content and does not affect unit quality. The existence of this bank is a remarkable breakthrough for Latin-American patients in need of this kind of transplantation.
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Affiliation(s)
| | | | | | | | - Gustavo Salguero
- Cell Therapy Unit, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, Bogotá Distrito Capital, Colombia
| | - Bernardo Camacho
- Cord Blood Bank
- Cell Therapy Unit, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, Bogotá Distrito Capital, Colombia
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Genetic characterization of an X-STR decaplex system in the State of Mato Grosso, Brazil: distribution, forensic efficiency and population structure. Int J Legal Med 2017; 131:1523-1530. [PMID: 28405752 DOI: 10.1007/s00414-017-1578-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 03/17/2017] [Indexed: 10/19/2022]
Abstract
Studies with X-STR loci show population genetic substructure, which makes necessary the characterization of such markers in the different geographical and/or ethnic populations. Therefore, this study assessed the distribution and forensic efficiency of an X-STR decaplex system in the population of the State of Mato Grosso, as well as analysed the population structure of this State based on the aforementioned system. All X-STR markers were in Hardy-Weinberg equilibrium and linkage equilibrium, and the DXS6809 was the most informative marker. The power of discrimination value in females and males was 0.99999999995 and 0.9999994, respectively. Analysis of molecular variance indicated 1.10% (p < 0.00001) of heterogeneity among Europeans, Africans, Brazilians and other Latin Americans, and in relation to such groups, the population of the State of Mato Grosso showed lower genetic variation when compared with the Brazilian group (-0.10%, p = 0.67327). The genetic distance analysis showed lower values of F ST (0.0004 ≤ F ST ≤ 0.00331), with non-significant p value (p > 0.00024), between the populations of Mato Grosso and Mato Grosso do Sul, Paraná and the Southeast region of Brazil (except for one sample of Rio de Janeiro). F ST values with significant p values (p ≤ 0.00024) were obtained between the population of Mato Grosso and Iberian, African and some Latin American populations. The X-STR decaplex system proved to be extremely useful in the population of the State of Mato Grosso, and the data obtained does not show the need for a specific forensic database for this State in relation to the Brazilian populations compared in this study, except for population of Rio de Janeiro.
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Tobón-Arroyave SI, Isaza-Guzmán DM, Pineda-Trujillo N. Association Study of Vitamin D Receptor (VDR) - Related Genetic Polymorphisms and their Haplotypes with Chronic Periodontitis in Colombian Population. J Clin Diagn Res 2017; 11:ZC60-ZC66. [PMID: 28384983 DOI: 10.7860/jcdr/2017/23967.9451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/19/2016] [Indexed: 11/24/2022]
Abstract
INTRODUCTION There is strong evidence that both genetic and environmental factors may affect the periodontal clinical status. However, epidemiological evidence on the association between Vitamin D Receptor (VDR) polymorphisms and Chronic Periodontitis (CP) has been inconsistent. AIM The focus of this study was to identify if a possible association between VDR Single-Nucleotide Polymorphisms (SNPs) may be implicated in the aetiopathogenesis of CP in Colombian population. MATERIALS AND METHODS One hundred and ten CP patients and 50 Healthy Controls (HC) were recruited. Periodontal status was assessed based on probing depth, clinical attachment level, extent, and severity of periodontal breakdown. The polymerase chain reaction-restriction fragment length polymorphism method was used to identify the VDR rs7975232, rs1544410, rs2228570, and rs731236 SNPs from saliva samples. Odds Ratios (ORs) along with their 95% Confidence Intervals (CIs) were computed to compare the distribution of genotypes/alleles between HC and CP patients, alongside with analysis of Linkage Disequilibrium (LD) and haplotype associations between SNPs. Also, an analysis of the interaction between genetic findings and those significant demographic factors was performed for all SNPs. RESULTS There was no association neither between the different genotypes/allele frequencies nor haplotypes and CP. Similarly, no significant differences in extent or severity amongst genotype/allele groups were observed. Even so, interaction analysis revealed significant synergistic interactions between each SNP and age associated with the disease status. CONCLUSION Although these results do not support that VDR SNPs could be identified as independent risk predictor variables for CP in the Colombian population, synergistic biological interactive effects of all these SNPs related to age might play a significant role in the pathogenic pathways of CP.
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Affiliation(s)
- Sergio Iván Tobón-Arroyave
- Professor, Laboratory of Immunodetection and Bioanalysis, Faculty of Dentistry, University of Antioquia , Medellín, Antioquia, Colombia
| | - Diana María Isaza-Guzmán
- Professor, Laboratory of Immunodetection and Bioanalysis, Faculty of Dentistry, University of Antioquia , Medellín, Antioquia, Colombia
| | - Nicolás Pineda-Trujillo
- Professor, Gene Mapping Research Group, Faculty of Medicine, University of Antioquia , Medellín, Antioquia, Colombia
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Sanabria-Salas MC, Hernández-Suárez G, Umaña-Pérez A, Rawlik K, Tenesa A, Serrano-López ML, Sánchez de Gómez M, Rojas MP, Bravo LE, Albis R, Plata JL, Green H, Borgovan T, Li L, Majumdar S, Garai J, Lee E, Ashktorab H, Brim H, Li L, Margolin D, Fejerman L, Zabaleta J. IL1B-CGTC haplotype is associated with colorectal cancer in admixed individuals with increased African ancestry. Sci Rep 2017; 7:41920. [PMID: 28157220 PMCID: PMC5291207 DOI: 10.1038/srep41920] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 01/03/2017] [Indexed: 02/07/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) in cytokine genes can affect gene expression and thereby modulate inflammation and carcinogenesis. However, the data on the association between SNPs in the interleukin 1 beta gene (IL1B) and colorectal cancer (CRC) are conflicting. We found an association between a 4-SNP haplotype block of the IL1B (-3737C/-1464G/-511T/-31C) and CRC risk, and this association was exclusively observed in individuals with a higher proportion of African ancestry, such as individuals from the Coastal Colombian region (odds ratio, OR 2.06; 95% CI 1.31–3.25; p < 0.01). Moreover, a significant interaction between this CRC risk haplotype and local African ancestry dosage was identified in locus 2q14 (p = 0.03). We conclude that Colombian individuals with high African ancestry proportions at locus 2q14 harbour more IL1B-CGTC copies and are consequently at an increased risk of CRC. This haplotype has been previously found to increase the IL1B promoter activity and is the most frequent haplotype in African Americans. Despite of limitations in the number of samples and the lack of functional analysis to examine the effect of these haplotypes on CRC cell lines, our results suggest that inflammation and ethnicity play a major role in the modulation of CRC risk.
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Affiliation(s)
- María Carolina Sanabria-Salas
- Subdirección de Investigaciones, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia.,Departamento de Química, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Gustavo Hernández-Suárez
- Subdirección de Investigaciones, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia
| | - Adriana Umaña-Pérez
- Departamento de Química, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Konrad Rawlik
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, UK
| | - Albert Tenesa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, UK.,MRC-Human Genetics Unit, University of Edinburgh, UK
| | - Martha Lucía Serrano-López
- Subdirección de Investigaciones, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia.,Departamento de Química, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | | | - Martha Patricia Rojas
- Subdirección de Investigaciones, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia
| | | | - Rosario Albis
- Servicio de Gastroenterología, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia
| | | | | | | | - Li Li
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, US
| | - Sumana Majumdar
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, US
| | - Jone Garai
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, US
| | - Edward Lee
- Department of Pathology &Cancer Center, Howard University College of Medicine, Washington, D.C., US
| | - Hassan Ashktorab
- Department of Pathology &Cancer Center, Howard University College of Medicine, Washington, D.C., US
| | - Hassan Brim
- Department of Pathology &Cancer Center, Howard University College of Medicine, Washington, D.C., US
| | - Li Li
- Ochsner Clinic Foundation, New Orleans, LA, US
| | | | - Laura Fejerman
- Department of Medicine, Division of General Internal Medicine, Institute for Human Genetics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, US
| | - Jovanny Zabaleta
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, US.,Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, LA, US
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12
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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] [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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13
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Muñoz AM, Velásquez CM, Bedoya G. Cardio-metabolic parameters are associated with genetic admixture estimates in a pediatric population from Colombia. BMC Genet 2016; 17:93. [PMID: 27350247 PMCID: PMC4924275 DOI: 10.1186/s12863-016-0402-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 06/17/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND There are different genetic patterns for cardio-metabolic parameters among different populations. Additionally, it has been found that ancestral genetic components (the proportion of Amerindian, European and African) in admixed Latin American populations influence an individual's susceptibility to cardio-metabolic disorders. The aim of this study was to evaluate the effect of ancestral genetic composition on a series of cardio-metabolic risk factors in a young admixed population from Colombia. RESULTS In a sample of 853 Colombian youth, 10 to 18 years old, the mean European contribution was 66.6 % (range: 41-82 %), the mean African contribution was 14 % (range: 4-48 %), and the mean Amerindian contribution was 19.4 % (range: 10-35 %) using a panel of 40 autosomal ancestry-informative markers (AIMs). We assessed the degree of association between ancestral African, Amerindian and European genetic components and measures of body mass index, waist circumference, fasting glucose, fasting insulin, insulin resistance, triglycerides, high-density lipoprotein, and systolic and diastolic blood pressure. Two of the nine measures assessed presented a nominal significant association with ancestral components after adjusting for confounding variables: triglyceride levels were associated with the Amerindian component (OR = 1.06, 98.3 % CI = 1.01-1.11, P = 0.002) and systolic blood pressure was associated with the European component (OR = 0.93, 98.3 % CI = 0.87 to 0.99, P = 0.008) and the African component (OR = 1.07, CI = 1.01-1.14 P = 0.008), although it was not significant following a global Bonferroni correction. Additionally, insulin levels and insulin resistance showed associations with the African component. CONCLUSIONS Our findings support the idea that an Amerindian ancestral component may act as a risk factor for high triglyceride levels. In addition, an African ancestral component confers a risk for high systolic blood pressure, and a European ancestry serves as a protective factor for this condition in a young admixed population from Colombia. However, these results should be confirmed in a larger population.
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Affiliation(s)
- Angélica M Muñoz
- Research Group on Food and Human Nutrition, Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia. .,Laboratorio 413, Sede de Investigación Universitaria (SIU), Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia.
| | - Claudia M Velásquez
- Research Group on Food and Human Nutrition, Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia
| | - Gabriel Bedoya
- Research Group on Molecular Genetic (GENMOL), Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia
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14
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Determination of NLRP3 (rs4612666) and IL-1B (rs1143634) genetic polymorphisms in periodontally diseased and healthy subjects. Arch Oral Biol 2016; 65:44-51. [DOI: 10.1016/j.archoralbio.2016.01.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 12/26/2015] [Accepted: 01/24/2016] [Indexed: 01/01/2023]
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15
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Ramos BRDA, D'Elia MPB, Amador MAT, Santos NPC, Santos SEB, da Cruz Castelli E, Witkin SS, Miot HA, Miot LDB, da Silva MG. Neither self-reported ethnicity nor declared family origin are reliable indicators of genomic ancestry. Genetica 2016; 144:259-65. [PMID: 26984822 DOI: 10.1007/s10709-016-9894-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/13/2016] [Indexed: 12/11/2022]
Abstract
Ancestry information can be useful in investigations of diseases with a genetic or infectious background. As the Brazilian population is highly admixed physical traits tend to be poor indicators of ancestry. The assessment of ancestry by ancestry informative markers (AIMs) can exclude the subjectivity of self-declared ethnicity and reported family origin. We aimed to evaluate the reliability of self-reported ethnicity or reported family origin as indicators of genomic ancestry in a female population from the Southeast of Brazil. Two cohorts were included: 404 women asked to self-report their ethnicity (Pop1) and 234 women asked to report their family's origin (Pop2). Identification of AIMs was performed using a panel of 61 markers and results were plotted against parental populations-Amerindian, Western European and Sub-Saharan African-using Structure v2.3.4. In Pop1 57.4 % of women self-reported as white, 34.6 % as brown and 8.0 % as black. Median global European, Amerindian and African contributions were 66.8, 12.6 and 16.6 %. In Pop2, 66.4 % of women declared European origin, 23.9 % African origin and 26.9 % Amerindian. Median global European, Amerindian and African contributions were 80.8, 7.3 and 7.6 %, respectively. Only 31.0 and 21.0 % of the global variation in African and European contributions, respectively, could be explained by self-reported ethnicity and reported family origin only accounted for 20.0 and 5.0 % of the variations observed in African and European ancestries, respectively. Amerindian ancestry did not influence self-reported ethnicity or declared family origin. Neither self-reported ethnicity nor declared family origin are reliable indicators of genomic ancestry in these Brazilian populations.
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Affiliation(s)
- Bruna Ribeiro de Andrade Ramos
- Department of Pathology, Botucatu Medical School, São Paulo State University - UNESP, Distrito de Rubião Júnior, Botucatu, São Paulo, 18618-970, Brazil
| | - Maria Paula Barbieri D'Elia
- Depatment of Dermatology and Radiotherapy, Botucatu Medical School, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | | | | | | | - Erick da Cruz Castelli
- Department of Pathology, Botucatu Medical School, São Paulo State University - UNESP, Distrito de Rubião Júnior, Botucatu, São Paulo, 18618-970, Brazil
| | - Steven S Witkin
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Hélio Amante Miot
- Depatment of Dermatology and Radiotherapy, Botucatu Medical School, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Luciane Donida Bartoli Miot
- Depatment of Dermatology and Radiotherapy, Botucatu Medical School, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Márcia Guimarães da Silva
- Department of Pathology, Botucatu Medical School, São Paulo State University - UNESP, Distrito de Rubião Júnior, Botucatu, São Paulo, 18618-970, Brazil.
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16
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Pardo-Seco J, Heinz T, Taboada-Echalar P, Martinón-Torres F, Salas A. Mapping the genomic mosaic of two 'Afro-Bolivians' from the isolated Yungas valleys. BMC Genomics 2016; 17:207. [PMID: 26956021 PMCID: PMC4784306 DOI: 10.1186/s12864-016-2520-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 02/24/2016] [Indexed: 12/13/2022] Open
Abstract
Background Unraveling the ancestry of ‘Afro-American’ communities is hampered by the complex demographic processes that took place during the Transatlantic Slave Trade (TAST) and the (post-)colonization periods. ‘Afro-Bolivians’ from the subtropical Yungas valleys constitute small and isolated communities that live surrounded by the predominant Native American community of Bolivia. By genotyping >580,000 SNPs in two ‘Afro-Bolivians’, and comparing these genomic profiles with data compiled from more than 57 African groups and other reference ancestral populations (n = 1,161 in total), we aimed to disentangle the complex admixture processes undergone by ‘Afro-Bolivians’. Results The data indicate that these two genomes constitute a complex mosaic of ancestries that is approximately 80 % of recent African origin; the remaining ~20 % being European and Native American. West-Central Africa contributed most of the African ancestry to ‘Afro-Bolivians’, and this component is related to populations living along the Atlantic coast (i.e. Senegal, Ghana, Nigeria). Using tract length distribution of genomic segments attributable to distinct ancestries, we could date the time of admixture in about 400 years ago. This time coincides with the maximum importation of slaves to Bolivia to compensate the diminishing indigenous labor force needed for the development of the National Mint of Potosí. Conclusions Overall, the data indicate that the genome of ‘Afro-Bolivians’ was shaped by a complex process of admixture occurring in America among individuals originating in different West-Central African populations; their genomic mosaics received additional contributions of Europeans and local Native Americans (e.g. Aymaras). Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2520-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- 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, Calle San Francisco s/n, C.P. 15872, Galicia, Spain. .,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain.
| | - Tanja Heinz
- 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, Calle San Francisco s/n, C.P. 15872, Galicia, Spain.
| | - Patricia Taboada-Echalar
- 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, Calle San Francisco s/n, C.P. 15872, Galicia, Spain.
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), 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, Calle San Francisco s/n, C.P. 15872, Galicia, Spain. .,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain.
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17
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Genotyping of 75 SNPs using arrays for individual identification in five population groups. Int J Legal Med 2015; 130:81-9. [DOI: 10.1007/s00414-015-1250-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/12/2015] [Indexed: 10/23/2022]
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18
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Edelmann J, Kohl M, Dressler J, Hoffmann A. X-chromosomal 21-indel marker panel in German and Baltic populations. Int J Legal Med 2015; 130:357-60. [PMID: 26164591 DOI: 10.1007/s00414-015-1221-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/22/2015] [Indexed: 01/08/2023]
Abstract
In order to verify specific biallelic X-indels and their characteristic properties in distinct populations, one German and three Baltic population groups (Estonia, Latvia, and Lithuania) have been analyzed by a short amplicon method, which also enables detection of degraded DNA samples. To combine 21 indels in a single multiplex PCR, all products were arranged according to their expected amplicon length (~40-160 bp) on the basis of three different fluorochromes. Separation of PCR products was carried out in a single capillary electrophoresis. Data evaluating was performed including five further indel markers which have already been tested in identical samples, resulting in altogether 26 markers. The majority of the genetic material showed combinations of insertion elements (L-fragments). Combinations of deletion elements (S-fragments) in contrast occurred with significant lower ratios. Hardy-Weinberg equilibrium (HWE) was observed for all markers except for MID1361 and MID329. This was attributed to an insufficient number of samples. For two known linkage groups within the 26-indel set (MID357-MID356 and MID3690-MID3719-MID2089), haplotype data were determined. A pairwise comparison of German and Baltic allele frequencies did not show significant deviation. This result indicates a possible genetic association between all four population groups. The calculated biostatistical parameters show high forensic efficiency for this set of indel markers. In a segregation analysis investigating 194 meiosis, no mutations have been detected regarding expected transmission patterns.
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Affiliation(s)
- Jeanett Edelmann
- Institute of Legal Medicine, University of Leipzig, Leipzig, Germany.
| | - Michael Kohl
- Institute of Legal Medicine, University of Leipzig, Leipzig, Germany
| | - Jan Dressler
- Institute of Legal Medicine, University of Leipzig, Leipzig, Germany
| | - Andre Hoffmann
- Institute of Legal Medicine, University of Leipzig, Leipzig, Germany
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19
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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] [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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20
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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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21
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Vullo C, Gomes V, Romanini C, Oliveira AM, Rocabado O, Aquino J, Amorim A, Gusmão L. Association between Y haplogroups and autosomal AIMs reveals intra-population substructure in Bolivian populations. Int J Legal Med 2014; 129:673-80. [PMID: 24878616 DOI: 10.1007/s00414-014-1025-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 05/15/2014] [Indexed: 12/24/2022]
Abstract
For the correct evaluation of the weight of genetic evidence in a forensic context, databases must reflect the structure of the population, with all possible groups being represented. Countries with a recent history of admixture between strongly differentiated populations are usually highly heterogeneous and sub-structured. Bolivia is one of these countries, with a high diversity of ethnic groups and different levels of admixture (among Native Americans, Europeans and Africans) across the territory. For a better characterization of the male lineages in Bolivia, 17 Y-STR and 42 Y-SNP loci were genotyped in samples from La Paz and Chuquisaca. Only European and Native American Y-haplogroups were detected, and no sub-Saharan African chromosomes were found. Significant differences were observed between the two samples, with a higher frequency of European lineages in Chuquisaca than in La Paz. A sample belonging to haplogroup Q1a3a1a1-M19 was detected in La Paz, in a haplotype background different from those previously found in Argentina. This result supports an old M19 North-south dispersion in South America, possibly via two routes. When comparing the ancestry of each individual assessed through his Y chromosome with the one estimated using autosomal AIMs, (a) increased European ancestry in individuals with European Y chromosomes and (b) higher Native American ancestry in the carriers of Native American Y-haplogroups were observed, revealing an association between autosomal and Y-chromosomal markers. The results of this study demonstrate that a sub-structure does exist in Bolivia at both inter- and intrapopulation levels, a fact which must be taken into account in the evaluation of forensic genetic evidence.
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Affiliation(s)
- Carlos Vullo
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team (EAAF), Córdoba, Argentina
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22
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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] [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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