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Pedroza Matute S, Iyavoo S. Applications and Performance of Precision ID GlobalFiler NGS STR, Identity, and Ancestry Panels in Forensic Genetics. Genes (Basel) 2024; 15:1133. [PMID: 39336724 PMCID: PMC11431077 DOI: 10.3390/genes15091133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 08/19/2024] [Accepted: 08/23/2024] [Indexed: 09/30/2024] Open
Abstract
Short Tandem Repeat (STR) testing via capillary electrophoresis is undoubtedly the most popular forensic genetic testing method. However, its low multiplexing capabilities and limited performance with challenging samples are among the factors pushing scientists towards new technologies. Next-generation sequencing (NGS) methods overcome some of these limitations while also enabling the testing of Single-Nucleotide Polymorphisms (SNPs). Nonetheless, these methods are still under optimization, and their adoption into practice is limited. Among the available kits, Thermo Fisher Scientific (Waltham, MA, USA) produces three Precision ID Panels: GlobalFiler NGS STR, Identity, and Ancestry. A clear review of these kits, providing information useful for the promotion of their use, is, however, lacking. To close the gap, a literature review was performed to investigate the popularity, applications, and performance of these kits. Following the PRISMA guidelines, 89 publications produced since 2015 were identified. China was the most active country in the field, and the Identity Panel was the most researched. All kits appeared robust and useful for low-quality and low-quantity samples, while performance with mixtures varied. The need for more population data was highlighted, as well as further research surrounding variables affecting the quality of the sequencing results.
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Affiliation(s)
- Sharlize Pedroza Matute
- School of Natural Sciences, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, UK
- AttoGroup Limited, Scottow Enterprise Park, Badersfield, Norwich NR10 5FB, UK
| | - Sasitaran Iyavoo
- School of Natural Sciences, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, UK
- AttoGroup Limited, Scottow Enterprise Park, Badersfield, Norwich NR10 5FB, UK
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Chávez-Vélez E, Álvarez-Nava F, Torres-Vinueza A, Balarezo-Díaz T, Pilataxi K, Acosta-López C, Peña IZ, Narváez K. Single nucleotide variants in the CCL2, OAS1 and DPP9 genes and their association with the severity of COVID-19 in an Ecuadorian population. Front Cell Infect Microbiol 2024; 14:1322882. [PMID: 38694517 PMCID: PMC11061356 DOI: 10.3389/fcimb.2024.1322882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/15/2024] [Indexed: 05/04/2024] Open
Abstract
COVID-19 has a broad clinical spectrum, ranging from asymptomatic-mild form to severe phenotype. The severity of COVID-19 is a complex trait influenced by various genetic and environmental factors. Ethnic differences have been observed in relation to COVID-19 severity during the pandemic. It is currently unknown whether genetic variations may contribute to the increased risk of severity observed in Latin-American individuals The aim of this study is to investigate the potential correlation between gene variants at CCL2, OAS1, and DPP9 genes and the severity of COVID-19 in a population from Quito, Ecuador. This observational case-control study was conducted at the Carrera de Biologia from the Universidad Central del Ecuador and the Hospital Quito Sur of the Instituto Ecuatoriano de Seguridad Social (Quito-SUR-IESS), Quito, Ecuador. Genotyping for gene variants at rs1024611 (A>G), rs10774671 (A>G), and rs10406145 (G>C) of CCL2, OAS1, and DPP9 genes was performed on 100 COVID-19 patients (43 with severe form and 57 asymptomatic-mild) using RFLP-PCR. The genotype distribution of all SNVs throughout the entire sample of 100 individuals showed Hardy Weinberg equilibrium (P=0.53, 0.35, and 0.4 for CCL2, OAS1, and DPP9, respectively). The HWE test did not find any statistically significant difference in genotype distribution between the study and control groups for any of the three SNVs. The multivariable logistic regression analysis showed that individuals with the GG of the CCL2 rs1024611 gene variant had an increased association with the severe COVID-19 phenotype in a recessive model (P = 0.0003, OR = 6.43, 95% CI 2.19-18.89) and for the OAS1 rs10774671 gene variant, the log-additive model showed a significant association with the severe phenotype of COVID-19 (P=0.0084, OR=3.85, 95% CI 1.33-11.12). Analysis of haplotype frequencies revealed that the coexistence of GAG at CCL2, OAS1, and DPP9 variants, respectively, in the same individual increased the presence of the severe COVID-19 phenotype (OR=2.273, 95% CI: 1.271-4.068, P=0.005305). The findings of the current study suggests that the ethnic background affects the allele and genotype frequencies of genes associated with the severity of COVID-19. The experience with COVID-19 has provided an opportunity to identify an ethnicity-based approach to recognize genetically high-risk individuals in different populations for emerging diseases.
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Affiliation(s)
- Erik Chávez-Vélez
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Francisco Álvarez-Nava
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Alisson Torres-Vinueza
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Thalía Balarezo-Díaz
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Kathya Pilataxi
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Camila Acosta-López
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Ivonne Z. Peña
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
| | - Katherin Narváez
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
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Köksal Z, Meyer OL, Andersen JD, Gusmão L, Mogensen HS, Pereira V, Børsting C. Pitfalls and challenges with population assignments of individuals from admixed populations: Applying Genogeographer on Brazilian individuals. Forensic Sci Int Genet 2023; 67:102934. [PMID: 37713981 DOI: 10.1016/j.fsigen.2023.102934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/06/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
The assignment of individuals to a population can be of importance for the identification of mass disaster victims or criminal offenders in the field of forensic genetics. This assignment is based on biostatistical methods that process data of ancestry informative markers (AIMs), which are selected based on large allele frequency differences between the populations of interest. However, population assignments of individuals with an admixed genetic background are challenging. Admixed individuals are genetic mosaics of chromosomal segments from the parental populations, which may lead to ambiguous or no population assignment. This is problematic since admixture events are a substantial part of human history. In this study, we present challenges of interpreting the evidential weight of population assignments. We used Genogeographer for likelihood ratio (LR) calculations and Brazilians as examples of admixed individuals. Brazilians are a very heterogenous population representing a three-way admixture between Native Americans, Europeans, and Africans. Ancestry informative markers were typed in a total of 589 individuals from Brazil using the Precision ID Ancestry Panel. The Brazilians were assigned to six metapopulations (East Asia, Europe, Middle East, North Africa, South-Central Asia, Sub-Saharan Africa) defined in the Genogeographer software and LRs were calculated if the AIM profile was not an outlier in all metapopulations and simulated two-way (1:1) admixtures of the six metapopulations. Population assignments failed for 55% of the samples. These samples had significantly higher genetic contributions from East Asia, South-Central Asia and Sub-Saharan Africa, and significantly lower genetic contributions from Europe. Most of the individuals with population assignments were assigned to the metapopulations of Middle East (58%) or North Africa (36%), followed by Europe (4%), South-Central Asia (1%), and Sub-Saharan Africa (1%). For 8% of the samples, population assignments were only possible when assignments to simulated two-way (1:1) admixtures of the six metapopulations were considered. Most of these individuals were assigned to two-way admixtures of North Africa, South-Central Asia, or Sub-Saharan Africa. Relatively low median likelihood ratios (LRs<1000) were observed when comparing population likelihoods for Europe, Middle East, North Africa, South-Central Asia, or simulated 1:1 admixtures of these metapopulations. Comparisons including East Asian or Sub-Saharan African populations resulted in larger median LRs (LR>1010). The results suggested that the Precision ID Ancestry Panel provided too little information and that additional markers specifically selected for sub-continental differentiation may be required for accurate population assignment of admixed individuals. Furthermore, a Genogeographer database with additional populations including admixed populations would be advantageous for interpretation of admixed AIM profiles. It would likely increase the number of population assignments and illustrate alternatives to the most likely population, which would be valuable information for the case officer when writing the case report.
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Affiliation(s)
- Zehra Köksal
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Olivia Luxford Meyer
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Helle Smidt Mogensen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Wen Y, Liu J, Su Y, Chen X, Hou Y, Liao L, Wang Z. Forensic biogeographical ancestry inference: recent insights and current trends. Genes Genomics 2023; 45:1229-1238. [PMID: 37081293 DOI: 10.1007/s13258-023-01387-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/01/2023] [Indexed: 04/22/2023]
Abstract
BACKGROUND As a powerful complement to the paradigmatic DNA profiling strategy, biogeographical ancestry inference (BGAI) plays a significant part in human forensic investigation especially when a database hit or eyewitness testimony are not available. It indicates one's biogeographical profile based on known population-specific genetic variations, and thus is crucial for guiding authority investigations to find unknown individuals. Forensic biogeographical ancestry testing exploits much of the recent advances in the understanding of human genomic variation and improving of molecular biology. OBJECTIVE In this review, recent development of prospective ancestry informative markers (AIMs) and the statistical approaches of inferring biogeographic ancestry from AIMs are elucidated and discussed. METHODS We highlight the research progress of three potential AIMs (i.e., single nucleotide polymorphisms, microhaplotypes, and Y or mtDNA uniparental markers) and discuss the prospects and challenges of two methods that are commonly used in BGAI. CONCLUSION While BGAI for forensic purposes has been thriving in recent years, important challenges, such as ethics and responsibilities, data completeness, and ununified standards for evaluation, remain for the use of biogeographical ancestry information in human forensic investigations. To address these issues and fully realize the value of BGAI in forensic investigation, efforts should be made not only by labs/institutions around the world independently, but also by inter-lab/institution collaborations.
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Affiliation(s)
- Yufeng Wen
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital Sichuan University, Chengdu, 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Linchuan Liao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Zheng Wang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, China.
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
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Atarihuana S, Gallardo-Condor J, López-Cortés A, Jimenes-Vargas K, Burgos G, Karina-Zambrano A, Flores-Espinoza R, Coral M, Cabrera-Andrade A. Genetic basis and spatial distribution of glucose-6-phosphate dehydrogenase deficiency in ecuadorian ethnic groups: a malaria perspective. Malar J 2023; 22:283. [PMID: 37752491 PMCID: PMC10521485 DOI: 10.1186/s12936-023-04716-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Glucose-6-phosphate dehydrogenase deficiency (G6PDd) is an X-linked disorder affecting over 400 million people worldwide. Individuals with molecular variants associated with reduced enzymatic activity are susceptible to oxidative stress in red blood cells, thereby increasing the risk of pathophysiological conditions and toxicity to anti-malarial treatments. Globally, the prevalence of G6PDd varies among populations. Accordingly, this study aims to characterize G6PDd distribution within the Ecuadorian population and to describe the spatial distribution of reported malaria cases. METHODS Molecular variants associated with G6PDd were genotyped in 581 individuals from Afro-Ecuadorian, Indigenous, Mestizo, and Montubio ethnic groups. Additionally, spatial analysis was conducted to identify significant malaria clusters with high incidence rates across Ecuador, using data collected from 2010 to 2021. RESULTS The A- c.202G > A and A- c.968T > C variants underpin the genetic basis of G6PDd in the studied population. The overall prevalence of G6PDd was 4.6% in the entire population. However, this frequency increased to 19.2% among Afro-Ecuadorian people. Spatial analysis revealed 12 malaria clusters, primarily located in the north of the country and its Amazon region, with relative risks of infection of 2.02 to 87.88. CONCLUSIONS The findings of this study hold significant implications for public health interventions, treatment strategies, and targeted efforts to mitigate the burden of malaria in Ecuador. The high prevalence of G6PDd among Afro-Ecuadorian groups in the northern endemic areas necessitates the development of comprehensive malaria eradication strategies tailored to this geographical region.
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Affiliation(s)
- Sebastián Atarihuana
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | | | - Andrés López-Cortés
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Karina Jimenes-Vargas
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
- Department of Computer Science and Information Technologies, Computer Science Faculty, CITIC, RNASA Group, University of A Coruña, A Coruña, Spain
| | - Germán Burgos
- One Health Research Group, Facultad de Medicina, Universidad de las Américas, Quito, Ecuador
- Grupo de Medicina Xenómica, Instituto de Ciencias Forenses, Universidad de Santiago de Compostela, A Coruña, Spain
| | - Ana Karina-Zambrano
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Rodrigo Flores-Espinoza
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marco Coral
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
- Carrera de Medicina Veterinaria, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito, Ecuador
| | - Alejandro Cabrera-Andrade
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador.
- Escuela de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito, Ecuador.
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Corach D, Caputo M. Social injustice unveiled by genetic analysis: Argentina as a case study. Am J Hum Biol 2023; 35:e23820. [PMID: 36256489 DOI: 10.1002/ajhb.23820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 09/09/2022] [Accepted: 10/01/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The population of the American countries is genetically heterogeneous, whose genesis result from of recent admixture events. In this process, the transoceanic European component displaced the original inhabitants of the continent. AIM To investigate whether socially differentiated cohorts exhibit underlying ancestry components within an urban admixed population, two cohorts of individuals inhabiting Argentina were studied. One cohort included genetically unrelated individuals involved in voluntary paternity testing while the other included sexual or blood-crime suspects. MATERIALS & METHODS We analyzed over 2500 unrelated individuals: four Native American maternal lineage mtDNA markers in 1024 samples, five Y chromosome haplogroups in 658 male samples, 24 autosomal ancestry informative markers (AIMs) in 205 samples, and 15 autosomal short tandem repeats (STRs) in 1557 samples; countrywide and divided by regions. RESULTS While our results confirm a tricontinental ethnic contribution to both cohorts, their proportions showed statistically significant differences, with a higher proportion of Native American ancestry in the cohort linked to violent crimes compared to those in paternity testing. This hallmark was observed with all the marker sets used and at various levels of analysis. DISCUSSION Since paternity tests are costly, socio-economic differences might help to interpret our observations. The effect of discrimination against descendants of Native American minorities, and exposure to violent social environments, might link marginal groups to criminality. CONCLUSION Our findings underscore the relevance of proper social management since only by improving living conditions, reducing discrimination, promoting education, and providing job opportunities will it be possible to attain equality in a heterogeneous society. Genetic markers proved to be highly informative in unveiling unexpected social differences.
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Affiliation(s)
- Daniel Corach
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Universidad de Buenos Aires, Buenos Aires, Argentina.,CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Mariela Caputo
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Universidad de Buenos Aires, Buenos Aires, Argentina.,CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
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Felkl AB, Avila E, Gastaldo AZ, Lindholz CG, Dorn M, Alho CS. Ancestry resolution of South Brazilians by forensic 165 ancestry-informative SNPs panel. Forensic Sci Int Genet 2023; 64:102838. [PMID: 36736201 DOI: 10.1016/j.fsigen.2023.102838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/15/2023] [Accepted: 01/22/2023] [Indexed: 01/24/2023]
Abstract
Forensic DNA phenotyping (FDP) includes biogeographic ancestry (BGA) inference and externally visible characteristics (EVCs) prediction directly from an evidential DNA sample as alternatives to provide valuable intelligence when conventional DNA profiling fails to achieve identification. In this context, the application of Massively Parallel Sequencing (MPS) methodologies, which enables simultaneous typing of multiple samples and hundreds of forensic markers, has been gradually implemented in forensic genetic casework. The Precision ID Ancestry Panel (Thermo Fisher Scientific, Waltham, USA) is a forensic multiplex assay consisting of 165 autosomal SNPs designed to provide biogeographic ancestry information. In this work, a sample of 250 individuals from Rio Grande do Sul (RS) State, southern Brazil, apportioned into four main population groups (African-, European-, Amerindian-, and Admixed-derived Gauchos), was evaluated with this panel, to assess the feasibility of this approach in a highly heterogeneous population. Forensic descriptive parameters estimated for each population group revealed that this panel has enough polymorphic and informative SNPs to be used as a supplementary instrument in forensic individual identification and kinship testing regardless of ethnicity. No statistically significant deviation from Hardy-Weinberg equilibrium was observed after Bonferroni correction. However, seven loci pairs displayed linkage disequilibrium in pairwise LD testing (p < 3.70 × 10-6). Interpopulation comparisons by FST analysis, MDS plot, and STRUCTURE analysis among the four RS population groups apart and along with 89 reference worldwide populations demonstrated that Admixed- and African-derived Gauchos present the highest levels of admixture and population stratification, whereas European- and Amerindian-derived exhibit a more homogeneous genetic conformation.
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Affiliation(s)
- Aline Brugnera Felkl
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil.
| | - Eduardo Avila
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Technical Scientific Section, Federal Police Department in Rio Grande do Sul State, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - André Zoratto Gastaldo
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - Catieli Gobetti Lindholz
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Márcio Dorn
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil; Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Clarice Sampaio Alho
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
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Cao Y, Zhu Q, Huang Y, Li X, Wei Y, Wang H, Zhang J. An efficient ancestry informative SNPs panel for further discriminating East Asian populations. Electrophoresis 2022; 43:1774-1783. [PMID: 35749689 DOI: 10.1002/elps.202100349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 05/19/2022] [Accepted: 06/17/2022] [Indexed: 11/07/2022]
Abstract
In forensic genetics, the use of ancestry informative single-nucleotide polymorphisms (AISNPs) panels can narrow the direction of the investigation by estimating an individual's biogeographic ancestry. However, distinguishing subgroups within continental regions requires more specific panels. In this study, we screened 19 AISNPs from the 1000 Genomes Project (1KG) based on their FST values to distinguish target populations in East Asia and obtained genotypes through SNaPshot. The 19 AISNPs could divide the global population of the 1KG into five clusters and could further divide the East Asian population into four clusters: Japanese, Han Chinese, Dai Chinese, and Kinh in Ho Chi Minh City of Vietnam. In summary, the 19-AISNP panel may serve as a useful and cost-effective tool for forensic ancestry inference in East Asian populations at a finer scale.
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Affiliation(s)
- Yueyan Cao
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Qiang Zhu
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Yuguo Huang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Xi Li
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Yifan Wei
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Haoyu Wang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Ji Zhang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
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Farinango C, Gallardo-Cóndor J, Freire-Paspuel B, Flores-Espinoza R, Jaramillo-Koupermann G, López-Cortés A, Burgos G, Tejera E, Cabrera-Andrade A. Genetic Variations of the DPYD Gene and Its Relationship with Ancestry Proportions in Different Ecuadorian Trihybrid Populations. J Pers Med 2022; 12:jpm12060950. [PMID: 35743735 PMCID: PMC9225136 DOI: 10.3390/jpm12060950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 11/16/2022] Open
Abstract
Dihydropyrimidine dehydrogenase is one of the main pharmacological metabolizers of fluoropyrimidines, a group of drugs widely used in clinical oncology. Around 20 to 30% of patients treated with fluoropyrimidines experience severe toxicity caused by a partial or total decrease in enzymatic activity. This decrease is due to molecular variants in the DPYD gene. Their prevalence and allelic frequencies vary considerably worldwide, so their description in heterogeneous groups such as the Ecuadorian population will allow for the description of pharmacogenetic variants and proper characterization of this population. Thus, we genotyped all the molecular variants with a predictive value for DPYD in a total of 410 Ecuadorian individuals belonging to Mestizo, Afro-Ecuadorian, and Indigenous ethnic groups. Moreover, we developed a genetic ancestry analysis using 46 autosomal ancestry informative markers. We determined 20 genetic variations in 5 amplified regions, including 3 novel single nucleotide variants. The allele frequencies for DPYD variants c.1627G>A (*5, rs1801159), c.1129-15T>C (rs56293913), c.1218G>A (rs61622928), rs1337752, rs141050810, rs2786783, rs2811178, and g.97450142G>A (chr1, GRCh38.p13) are significantly related to Native American and African ancestry proportions. In addition, the FST calculated from these variants demonstrates the closeness between Indigenous and Mestizo populations, and evidences genetic divergence between Afro-Ecuadorian groups when compared with Mestizo and Indigenous ethnic groups. In conclusion, the genetic variability in the DPYD gene is related to the genetic component of ancestral populations in different Ecuadorian ethnic groups. The absence and low frequency of variants with predictive value for fluoropyrimidine toxicity such as DPYD *2A, HapB3, and c.2846A>T (prevalent in populations with European ancestry) is consistent with the genetic background found.
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Affiliation(s)
- Camila Farinango
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito 170125, Ecuador; (C.F.); (J.G.-C.); (E.T.)
| | - Jennifer Gallardo-Cóndor
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito 170125, Ecuador; (C.F.); (J.G.-C.); (E.T.)
| | - Byron Freire-Paspuel
- Laboratorios de Investigación, Universidad de Las Américas, Quito 170125, Ecuador; (B.F.-P.); (R.F.-E.)
- Vall d’Hebron Research Institute, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
| | - Rodrigo Flores-Espinoza
- Laboratorios de Investigación, Universidad de Las Américas, Quito 170125, Ecuador; (B.F.-P.); (R.F.-E.)
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-013, Brazil
| | - Gabriela Jaramillo-Koupermann
- Laboratorio de Biología Molecular, Subproceso de Anatomía Patológica, Hospital de Especialidades Eugenio Espejo, Quito 170403, Ecuador;
| | - Andrés López-Cortés
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito 170125, Ecuador; (A.L.-C.); (G.B.)
- Programa de Investigación en Salud Global, Facultad de Ciencias de la Salud, Universidad Internacional SEK, Quito 170302, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28001 Madrid, Spain
| | - Germán Burgos
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito 170125, Ecuador; (A.L.-C.); (G.B.)
| | - Eduardo Tejera
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito 170125, Ecuador; (C.F.); (J.G.-C.); (E.T.)
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito 170125, Ecuador
| | - Alejandro Cabrera-Andrade
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito 170125, Ecuador
- Carrera de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito 170125, Ecuador
- Correspondence:
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10
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Ortiz-Prado E, Encalada S, Mosquera J, Simbaña-Rivera K, Gomez-Barreno L, Duta D, Ochoa I, Izquierdo-Condoy JS, Vasconez E, Burgos G, Calvopiña M, Viscor G. A comparative analysis of lung function and spirometry parameters in genotype-controlled natives living at low and high altitude. BMC Pulm Med 2022; 22:100. [PMID: 35313848 PMCID: PMC8939107 DOI: 10.1186/s12890-022-01889-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/25/2022] [Indexed: 12/15/2022] Open
Abstract
Background The reference values for lung function are associated to anatomical and lung morphology parameters, but anthropometry it is not the only influencing factor: altitude and genetics are two important agents affecting respiratory physiology. Altitude and its influence on respiratory function has been studied independently of genetics, considering early and long-term acclimatization. Objective The objective of this study is to evaluate lung function through a spirometry study in autochthonous Kichwas permanently living at low and high-altitude. Methodology A cross-sectional study of spirometry differences between genetically matched lowland Kichwas from Limoncocha (230 m) at Amazonian basin and high-altitude Kichwas from Oyacachi (3180 m) in Andean highlands. The sample size estimates permitted to recruited 118 patients (40 men and 78 women) from Limoncocha and 95 (39 men and 56 women) from Oyacachi. Chi-square method was used to analyze association or independence of categorical variables, while Student’s t test was applied to comparison of means within quantitative variables. ANOVA, or in the case that the variables didn’t meet the criteria of normality, Kruskal Wallis test were used to compare more than two groups. Results The FVC and the FEV1 were significantly greater among highlanders than lowlanders (p value < 0.001), with a proportion difference of 15.2% for men and 8.5% for women. The FEV1/FVC was significantly higher among lowlanders than highlanders for men and women. A restrictive pattern was found in 12.9% of the participants. Conclusion Residents of Oyacachi had greater FVC and FEV1 than their peers from Limoncocha, a finding physiologically plausible according to published literature. Lung size and greater ventilatory capacities could be an adaptive mechanism developed by the highlander in response to hypoxia. Our results support the fact that this difference in FVC and FEV1 is a compensatory mechanism towards lower barometric and alveolar partial pressure of oxygen pressure.
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Affiliation(s)
- Esteban Ortiz-Prado
- One Health Research Group, Faculty of Medicine, Universidad de las Américas, Calle de los Colimes y Avenida De los Granados, 170137, Quito, Ecuador. .,Department of Cell Biology, Physiology and Immunology, Universidad de Barcelona, Barcelona, Spain.
| | - Sebastián Encalada
- One Health Research Group, Faculty of Medicine, Universidad de las Américas, Calle de los Colimes y Avenida De los Granados, 170137, Quito, Ecuador
| | - Johanna Mosquera
- One Health Research Group, Faculty of Medicine, Universidad de las Américas, Calle de los Colimes y Avenida De los Granados, 170137, Quito, Ecuador
| | - Katherine Simbaña-Rivera
- One Health Research Group, Faculty of Medicine, Universidad de las Américas, Calle de los Colimes y Avenida De los Granados, 170137, Quito, Ecuador
| | - Lenin Gomez-Barreno
- One Health Research Group, Faculty of Medicine, Universidad de las Américas, Calle de los Colimes y Avenida De los Granados, 170137, Quito, Ecuador
| | - Diego Duta
- Limoncocha Community Health Unit, Limoncocha, Ecuador
| | - Israel Ochoa
- Oyacachi Community Health Unit, Oyacachi, Ecuador
| | - Juan S Izquierdo-Condoy
- One Health Research Group, Faculty of Medicine, Universidad de las Américas, Calle de los Colimes y Avenida De los Granados, 170137, Quito, Ecuador
| | - Eduardo Vasconez
- One Health Research Group, Faculty of Medicine, Universidad de las Américas, Calle de los Colimes y Avenida De los Granados, 170137, Quito, Ecuador
| | - German Burgos
- Faculty of Medicine, Universidad de las Américas, Quito, Ecuador
| | - Manuel Calvopiña
- One Health Research Group, Faculty of Medicine, Universidad de las Américas, Calle de los Colimes y Avenida De los Granados, 170137, Quito, Ecuador
| | - Ginés Viscor
- Department of Cell Biology, Physiology and Immunology, Universidad de Barcelona, Barcelona, Spain
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11
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Feltes BC, Vieira IA, Parraga-Alava J, Meza J, Portmann E, Terán L, Dorn M. Feature selection reveal peripheral blood parameter's changes between COVID-19 infections patients from Brazil and Ecuador. INFECTION, GENETICS AND EVOLUTION 2022; 98:105228. [PMID: 35104680 PMCID: PMC8800568 DOI: 10.1016/j.meegid.2022.105228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/23/2022] [Indexed: 11/29/2022]
Abstract
The investigation of conventional complete blood-count (CBC) data for classifying the SARS-CoV-2 infection status became a topic of interest, particularly as a complementary laboratory tool in developing and third-world countries that financially struggled to test their population. Although hematological parameters in COVID-19-affected individuals from Asian and USA populations are available, there are no descriptions of comparative analyses of CBC findings between COVID-19 positive and negative cases from Latin American countries. In this sense, machine learning techniques have been employed to examine CBC data and aid in screening patients suspected of SARS-CoV-2 infection. In this work, we used machine learning to compare CBC data between two highly genetically distinguished Latin American countries: Brazil and Ecuador. We notice a clear distribution pattern of positive and negative cases between the two countries. Interestingly, almost all red blood cell count parameters were divergent. For males, neutrophils and lymphocytes are distinct between Brazil and Ecuador, while eosinophils are distinguished for females. Finally, neutrophils, lymphocytes, and monocytes displayed a particular distribution for both genders. Therefore, our findings demonstrate that the same set of CBC features relevant to one population is unlikely to apply to another. This is the first study to compare CBC data from two genetically distinct Latin American countries.
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Affiliation(s)
- Bruno César Feltes
- Department of Genetics, Institute of Bioscience, and Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Igor Araújo Vieira
- Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Jorge Parraga-Alava
- Facultad de Ciencias Informaticas, Universidad Técnica de Manabí, Portoviejo, Manabí, Ecuador
| | - Jaime Meza
- Facultad de Ciencias Informaticas, Universidad Técnica de Manabí, Portoviejo, Manabí, Ecuador
| | - Edy Portmann
- Human-IST Institute, University of Fribourg, Fribourg, Switzerland
| | - Luis Terán
- Human-IST Institute, University of Fribourg, Fribourg, Switzerland
| | - Márcio Dorn
- Institute of Informatics, Center of Biotechnology, Federal University of Rio Grande do Sul, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil.
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12
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Ortiz-Prado E, Portilla D, Mosquera-Moscoso J, Simbaña-Rivera K, Duta D, Ochoa I, Burgos G, Izquierdo-Condoy JS, Vásconez E, Calvopiña M, Viscor G. Hematological Parameters, Lipid Profile, and Cardiovascular Risk Analysis Among Genotype-Controlled Indigenous Kiwcha Men and Women Living at Low and High Altitudes. Front Physiol 2021; 12:749006. [PMID: 34759840 PMCID: PMC8573321 DOI: 10.3389/fphys.2021.749006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/21/2021] [Indexed: 01/29/2023] Open
Abstract
Introduction: Human adaptation to high altitude is due to characteristic adjustments at every physiological level. Differences in lipid profile and cardiovascular risk factors in altitude dwellers have been previously explored. Nevertheless, there are no reports available on genotype-controlled matches among different altitude-adapted indigenous populations. Objective: To explore the possible differences in plasma lipid profile and cardiovascular risk among autochthonous Kiwcha people inhabitants of low and high-altitude locations. Methodology: A cross-sectional analysis of plasmatic lipid profiles and cardiovascular risk factors in lowland Kiwchas from Limoncocha (230 m) and high-altitude Kiwchas from Oyacachi (3,800 m). Results: In the low altitude group, 66% were women (n = 78) and 34% (n = 40) were men, whereas in the high altitude group, 59% (n = 56) were women and 41% (n = 41%) were men. We found the proportion of overweight and obese individuals to be higher among low altitude dwellers (p < 0.05). Red blood cells (RBCs), hemoglobin concentration, and SpO2% were higher among high altitude dwellers and the erythrocyte size was found to be smaller at high altitude. The group located at low altitude also showed lower levels of plasma cholesterol, low-density lipoprotein (LDL), and high-density lipoprotein (HDL), but most of these differences are not influenced by gender or elevation. Conclusions: Living at an altitude elicits well-known adaptive physiological changes such as erythrocyte count, hemoglobin concentration, hematocrit level, and serum glucose level. We also report clinical differences in the plasma lipid profile, with higher levels of cholesterol, HDL, and LDL in inhabitants of the Andes Mountain vs. their Amazonian basin peers. Despite this, we did not find significant differences in cardiovascular risk.
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Affiliation(s)
- Esteban Ortiz-Prado
- One Health Research Group, Faculty of Medicine, Universidad de las Americas, Quito, Ecuador.,Department of Cell Biology, Physiology and Immunology, Universidad de Barcelona, Barcelona, Spain
| | - David Portilla
- One Health Research Group, Faculty of Medicine, Universidad de las Americas, Quito, Ecuador
| | | | | | - Diego Duta
- General Ward, Limoncocha Community Health Unit, Limoncocha, Ecuador
| | - Israel Ochoa
- General Ward, Oyacachi Community Health Unit, Oyacachi, Ecuador
| | - German Burgos
- Faculty of Medicine, Universidad de Las Americas, Quito, Ecuador
| | | | - Eduardo Vásconez
- One Health Research Group, Faculty of Medicine, Universidad de las Americas, Quito, Ecuador
| | - Manuel Calvopiña
- One Health Research Group, Faculty of Medicine, Universidad de las Americas, Quito, Ecuador
| | - Ginés Viscor
- Department of Cell Biology, Physiology and Immunology, Universidad de Barcelona, Barcelona, Spain
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13
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Nagar SD, Conley AB, Chande AT, Rishishwar L, Sharma S, Mariño-Ramírez L, Aguinaga-Romero G, González-Andrade F, Jordan IK. Genetic ancestry and ethnic identity in Ecuador. HGG ADVANCES 2021; 2:100050. [PMID: 35047841 PMCID: PMC8756502 DOI: 10.1016/j.xhgg.2021.100050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 08/09/2021] [Indexed: 02/05/2023] Open
Abstract
We investigated the ancestral origins of four Ecuadorian ethnic groups-Afro-Ecuadorian, Mestizo, Montubio, and the Indigenous Tsáchila-in an effort to gain insight on the relationship between ancestry, culture, and the formation of ethnic identities in Latin America. The observed patterns of genetic ancestry are largely concordant with ethnic identities and historical records of conquest and colonization in Ecuador. Nevertheless, a number of exceptional findings highlight the complex relationship between genetic ancestry and ethnicity in Ecuador. Afro-Ecuadorians show far less African ancestry, and the highest levels of Native American ancestry, seen for any Afro-descendant population in the Americas. Mestizos in Ecuador show high levels of Native American ancestry, with substantially less European ancestry, despite the relatively low Indigenous population in the country. The recently recognized Montubio ethnic group is highly admixed, with substantial contributions from all three continental ancestries. The Tsáchila show two distinct ancestry subgroups, with most individuals showing almost exclusively Native American ancestry and a smaller group showing a Mestizo characteristic pattern. Considered together with historical data and sociological studies, our results indicate the extent to which ancestry and culture interact, often in unexpected ways, to shape ethnic identity in Ecuador.
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Affiliation(s)
- Shashwat Deepali Nagar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Andrew B Conley
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, USA.,National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Aroon T Chande
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Lavanya Rishishwar
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, USA.,National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Shivam Sharma
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Leonardo Mariño-Ramírez
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | | | | | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, USA
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14
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Flores-Espinoza R, Paz-Cruz E, Ruiz-Pozo VA, Lopez-Carrera M, Cabrera-Andrade A, Gusmão L, Burgos G. Investigating genetic diversity in admixed populations from Ecuador. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:109-119. [PMID: 34169504 DOI: 10.1002/ajpa.24341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/21/2021] [Accepted: 05/23/2021] [Indexed: 11/10/2022]
Abstract
OBJECTIVES According to demographic history, Ecuador has experienced shifts in its Native American populations caused by European colonization and the African slave trade. The continuous admixture events among Europeans, Native Americans, and Africans occurred differently in each region of the country, producing a stratified population. Thus, the aim of this study was to investigate the level of genetic substructure in the Ecuadorian Mestizo population. MATERIALS AND METHODS A total of 377 male and 209 female samples were genotyped for two sets of X-chromosomal markers (32 X-Indels and 12 X-STRs). Population analyses performed included Hardy-Weinberg equilibrium tests, LD analysis, PCA, pairwise FST s, and AMOVA. RESULTS Significant levels of LD were observed between markers separated by distances of less than 1 cM, as well as between markers separated by distances varying from 10.891 to 163.53 cM. Among Ecuadorian regions, Amazonia showed the highest average R2 value. DISCUSSION When X-chromosomal and autosomal differentiation values were compared, a sex-biased admixture between European men and Native American and African women was revealed, as well as between African men and Native American women. Moreover, a distinct Native American ancestry was discernible in the Amazonian population, in addition to sex-biased gene flow between Amazonia and the Andes and Pacific coast regions. Overall, these results underline the importance of integrating X chromosome information to achieve a more comprehensive view of the genetic and demographic histories of South American admixed populations.
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Affiliation(s)
- Rodrigo Flores-Espinoza
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Laboratorios de Investigación, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Elius Paz-Cruz
- Laboratorio de ADN, Fiscalía General del Estado, Quito, Ecuador
| | | | | | - Alejandro Cabrera-Andrade
- Grupo de Bio-Quimioinformática, Universidad de Las Américas (UDLA), Quito, Ecuador.,Carrera de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Leonor Gusmão
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - German Burgos
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de Las Américas (UDLA), Quito, Ecuador.,Grupo de Medicina Xenómica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
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15
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Maternal and Perinatal Factors Associated With Twin Pregnancies in Ecuador. Twin Res Hum Genet 2021; 24:133-139. [PMID: 33752776 DOI: 10.1017/thg.2021.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
There are few studies on twins in Ecuador and Latin America. It requires a better understanding of perinatal conditions, especially from an ethnic perspective. This work aims to assess perinatal factors related to twin pregnancy in Ecuadorian Mestizo individuals. We performed an epidemiological, observational and cross-sectional study at the Hospital San Francisco and Hospital Nueva Aurora in Quito, Ecuador, from November 2019 to January 2020. It included 203 newborns from twin pregnancies, including mothers with and without pathological history. The average gestational age was 31 weeks, and the APGAR score at first minute was 6.86, with significant differences. Regarding the metabolic balance, the mean pH was 6.14; and bicarbonate was 11.57, with significant differences. Twins had intrauterine growth restriction in 6.9% of cases, with significant differences (p = .003); 81.4% required supplemental oxygen, with significant differences (p = .002); 93% required noninvasive mechanical ventilation (NIMV), with significant differences (p = . 003); 93% required inotropic and sedation, with substantial differences; 69% required antibiotics (≥21 days), with significant differences (p = .014); and 17.2% needed between 8 to 14 days of hospitalization, and 51% more than 28 days, with significant differences. The studied mothers' demographic profile was mostly Mestizos, with an average age of 32 years, and 93% had a poverty status. Most of the twins were diamniotic monochorial and were discordant twins. It found jaundice, premature anemia and sepsis in 100% of twins and hyaline membrane disease in 89.66% of twins. Twins of women with relevant prenatal care had more premature births (30.4 ± 2.6 weeks), more acid-base imbalance, APGAR at ≥7 min in 90% of cases, and patent ductus arteriosus in all. There was also a greater need for double intensive phototherapy than twins of healthy women.
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16
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Massively parallel sequencing of 165 ancestry-informative SNPs and forensic biogeographical ancestry inference in three southern Chinese Sinitic/Tai-Kadai populations. Forensic Sci Int Genet 2021; 52:102475. [PMID: 33561661 DOI: 10.1016/j.fsigen.2021.102475] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 12/06/2020] [Accepted: 01/20/2021] [Indexed: 01/01/2023]
Abstract
Ancestry informative markers (AIMs), which are distributed throughout the human genome, harbor significant allele frequency differences among diverse ethnic groups. The use of sets of AIMs to reconstruct population history and genetic relationships is attracting interest in the forensic community, because biogeographic ancestry information for a casework sample can potentially be predicted and used to guide the investigative process. However, subpopulation ancestry inference within East Asia remains in its infancy due to a lack of population reference data collection and incomplete validation work on newly developed or commercial AIM sets. In the present study, 316 Chinese persons, including 85 Sinitic-speaking Haikou Han, 120 Qiongzhong Hlai and 111 Daozhen Gelao individuals belonging to Tai-Kadai-speaking populations, were analyzed using the Precision ID Ancestry Panel (165 AISNPs). Combined with our previous 165-AISNP data (375 individuals from 6 populations), the 1000 Genomes Project and forensic literature, comprehensive population genetic comparisons and ancestry inference were further performed via ADMIXTURE, TreeMix, PCA, f-statistics and N-J tree. Although several nonpolymorphic loci were identified in the three southern Chinese populations, the forensic parameters of this ancestry inference panel were better than those for the 23 STR-based Huaxia Platinum System, which is suitable for use as a robust tool in forensic individual identification and parentage testing. The results based on the ancestry assignment and admixture proportion evaluation revealed that this panel could be used successfully to assign individuals at a continental scale but also possessed obvious limitations in discriminatory power in intercontinental individuals, especially for European-Asian admixed Uyghurs or in populations lacking reference databases. Population genetic analyses further revealed five continental population clusters and three East Asian-focused population subgroups, which is consistent with linguistic affiliations. Ancestry composition and multiple phylogenetic analysis further demonstrated that the geographically isolated Qiongzhong Hlai harbored a close phylogenetic relationship with Austronesian speakers and possessed a homogenous Tai-Kadai-dominant ancestry, which could be used as the ancestral source proxy in population history reconstruction of Tai-Kadai-speaking populations and as one of the representatives for forensic database establishment. In summary, more population-specific AIM sets focused on East Asian subpopulations, comprehensive algorithms and high-coverage population reference data should be developed and validated in the next step.
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17
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Truelsen D, Pereira V, Phillips C, Morling N, Børsting C. Evaluation of a custom GeneRead™ massively parallel sequencing assay with 210 ancestry informative SNPs using the Ion S5™ and MiSeq platforms. Forensic Sci Int Genet 2020; 50:102411. [PMID: 33176271 DOI: 10.1016/j.fsigen.2020.102411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 01/20/2023]
Abstract
A custom GeneRead DNAseq SNP panel with 210 markers was evaluated using the Ion S5 and MiSeq sequencing platforms. Sensitivity, PCR cycle number, and the use of half volume of reagents for target enrichment and library preparation were tested. Furthermore, genotype concordance between results obtained with the different sequencing platforms and with known profiles generated using other sequencing assays was analysed. The GeneRead DNASeq SNP assay gave reproducible results with an input of 200 pg DNA on both platforms. A total of 204 loci were successfully sequenced. Three loci failed completely in the PCR amplification, and three additional loci displayed frequent locus drop-outs due to low read depth or high heterozygote imbalance. Overall, the read depth across the loci was more well-balanced with the MiSeq, while the heterozygote balance was less variable with the Ion S5. Noise levels were low on both platforms (median< 0.2 %). Two simple criteria for genotyping were applied: A minimum threshold of 45 reads and an acceptable heterozygote balance range of 0.3-3.0. Complete concordance between platforms was observed except for three genotypes in one of the poorly performing loci, rs1470637. This locus had relatively low read depths on both platforms, skewed heterozygote balance, and frequent locus drop-outs. There was also full genotype concordance between the results from the GeneRead assay and known profiles generated with the QIAseq and Ion AmpliSeq assays. The few discordant results were either due to locus drop-outs in the poorly performing loci or allele drop-outs in the QIAseq assay. Profiles with a minimum of 179 SNPs were obtained from four challenging case work samples (blood swabs, bone, or blood from a corpse). Overall, the GeneRead DNASeq assay showed considerable potential and could provide a reliable method for SNP genotyping in cases involving identification of individuals, prediction of phenotypic traits, and ancestry inference.
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Affiliation(s)
- Ditte Truelsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Chris Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark; Department of Mathematical Sciences, Aalborg University, DK-9220 Aalborg East, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
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18
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Pereira V, Santangelo R, Børsting C, Tvedebrink T, Almeida APF, Carvalho EF, Morling N, Gusmão L. Evaluation of the Precision of Ancestry Inferences in South American Admixed Populations. Front Genet 2020; 11:966. [PMID: 32973885 PMCID: PMC7472784 DOI: 10.3389/fgene.2020.00966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/31/2020] [Indexed: 11/13/2022] Open
Abstract
Ancestry informative markers (AIMs) are used in forensic genetics to infer biogeographical ancestry (BGA) of individuals and may also have a prominent role in future police and identification investigations. In the last few years, many studies have been published reporting new AIM sets. These sets include markers (usually around 100 or less) selected with different purposes and different population resolutions. Regardless of the ability of these sets to separate populations from different continents or regions, the uncertainty associated with the estimates provided by these panels and their capacity to accurately report the different ancestral contributions in individuals of admixed populations has rarely been investigated. This issue is addressed in this study by evaluating different AIM sets. Ancestry inference was carried out in admixed South American populations, both at population and individual levels. The results of ancestry inferences using AIM sets with different numbers of markers among admixed reference populations were compared. To evaluate the performance of the different ancestry panels at the individual level, expected and observed estimates among families and their offspring were compared, considering that (1) the apportionment of ancestry in the offspring should be closer to the average ancestry of the parents, and (2) full siblings should present similar ancestry values. The results obtained illustrate the importance of having a good balance/compromise between not only the number of markers and their ability to differentiate ancestral populations, but also a balanced differentiation among reference groups, to obtain more precise values of genetic ancestry. This work also highlights the importance of estimating errors associated with the use of a limited number of markers. We demonstrate that although these errors have a moderate effect at the population level, they may have an important impact at the individual level. Considering that many AIM-sets are being described for inferences at the individual level and not at the population level, e.g., in association studies or the determination of a suspect's BGA, the results of this work point to the need of a more careful evaluation of the uncertainty associated with the ancestry estimates in admixed populations, when small AIM-sets are used.
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Affiliation(s)
- Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Roberta Santangelo
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Tvedebrink
- Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark
| | - Ana Paula F Almeida
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elizeu F Carvalho
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto de Investigação e Inovação em Saúde, i3S, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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19
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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] [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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20
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Pregnancy in adolescence and adverse neonatal outcomes in Ecuadorian mestizo newborns. Pediatr Neonatol 2020; 61:216-223. [PMID: 31839422 DOI: 10.1016/j.pedneo.2019.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/22/2019] [Accepted: 11/08/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND To establish the association between pregnancy in early and middle adolescence and adverse neonatal outcomes in Ecuadorian mestizo newborns. METHODS Study design: epidemiological, observational/descriptive, and cross-sectional. SETTINGS Gynecological and Obstetric Hospital Isidro Ayora at Quito, Ecuador, from July to October of 2018. PARTICIPANTS this study included 303 newborns and their mothers, 101 children of adolescent mothers between 14 and 16 years old, 101 adolescents between the ages of 17 and 19, and 101 infants born to adult mothers between 20 and 34 years of age. RESULTS There is no statistically significant association between maternal age, gestation time, neonatal morbidity and APGAR at 5 min. Neonatal morbidity is higher in adolescent mothers residing in rural areas and in these who had fewer than five prenatal check-ups. In the case of mothers with a pathological history, regardless of the area in which they resided, the highest percentages were recorded in the case of mothers of 24-30 years with five or more prenatal appointments, and in adolescent mothers from 14 to 19 years of age with fewer than five prenatal appointments. Indeed, the greater the number of prenatal evaluations the higher the percentage of pathological findings. There is a close relationship between the age of the mother and the number of prenatal check-ups performed during pregnancy. CONCLUSION Teenage mothers have a higher percentage of neonatal morbidity in deliveries with gestational age equal to or greater than 37 weeks of gestation and AGPAR 8 and 9 at 5 min. In addition, there were a higher percentage of cases of respiratory failure and sepsis in newborns, especially when fewer than five prenatal examinations were performed. The highest percentage of identified prenatal pathological antecedents occurred in the group of mothers from 20 to 34 years old who attended more than five prenatal controls. Young pregnant women go less frequently to prenatal appointments, particularly in rural areas, and their newborns have a higher percentage of respiratory failure and sepsis.
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21
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Next generation sequencing of a set of ancestry-informative SNPs: ancestry assignment of three continental populations and estimating ancestry composition for Mongolians. Mol Genet Genomics 2020; 295:1027-1038. [PMID: 32206883 DOI: 10.1007/s00438-020-01660-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/27/2020] [Indexed: 12/31/2022]
Abstract
When traditional short tandem repeat profiling fails to provide valuable information to arrest the criminal, forensic ancestry inference of the biological samples left at the crime scene will probably offer investigative leads and facilitate the investigation process of the case. That is why there are consistent efforts in developing panels for ancestry inference in forensic science. Presently, a 30-plex next generation sequencing-based assay was exploited in this study by assembling well-differentiated single nucleotide polymorphisms for ancestry assignment of unknown individuals from three continental populations (African, European and East Asian). And meanwhile, relatively balanced population-specific differentiation values were maintained to avoid the over-estimation or under-estimation of co-ancestry proportions in individuals with admixed ancestry. The principal component analysis and STRUCTURE analysis of reference populations, test populations and the studied Mongolian group indicated that the novel assay was efficient enough to determine the ancestry origin of an unknown individual from the three continental populations. Besides, ancestry membership proportion estimations for the Mongolian group revealed that a large fraction of the ancestry was contributed by East Asian genetic component (approximately 83.9%), followed by European (approximately 12.6%) and African genetic components (approximately 3.5%), respectively. And next generation sequencing technology applied in this study offers possibility to incorporate more single nucleotide polymorphisms for individual identification and phenotype prediction into the same assay to provide as many as possible investigative clues in the future.
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22
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Xie T, Shen C, Liu C, Fang Y, Guo Y, Lan Q, Wang L, Ge J, Zhou Y, Wen S, Yang Q, Zhu B. Ancestry inference and admixture component estimations of Chinese Kazak group based on 165 AIM-SNPs via NGS platform. J Hum Genet 2020; 65:461-468. [DOI: 10.1038/s10038-020-0725-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022]
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González-Andrade F. High Altitude as a Cause of Congenital Heart Defects: A Medical Hypothesis Rediscovered in Ecuador. High Alt Med Biol 2020; 21:126-134. [PMID: 31976751 DOI: 10.1089/ham.2019.0110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: There are ∼83 million people living at high altitude (>2500 m) worldwide who endure chronic hypoxia conditions. This article aims to analyze the relationship between high altitude, identified in several cities in Ecuador, and the prevalence of congenital heart disease (CHD). Methods: Set in Ecuador, this epidemiological observational cross-sectional study analyzes data over a range of 18 years (from 2000 to 2017), including 34,904 reported cases of CHD, with a mean of 1939 cases per year. Results: The mean prevalence rate of CHD found is 70.6 per 10,000 live newborns. A K-means analysis resulted in three clusters. Cluster 1 shows the lowest altitude and prevalence of CHD, with an average of 2619 m and 63.02 cases per 10,000 live newborns. Cluster 2 presents the second highest altitude and prevalence of CHD, with an average of 2909 m and 72.04 cases per 10,000 live newborns. Cluster 3 shows the highest values of altitude and prevalence of CHD, with an average of 3176 m and 86.62 cases per 10,000 live newborns. Pearson's coefficient is 0.979, so the correlation between the variables is positive. An altitude ranging from 2500 to 2750 m relates to a prevalence of CHD of ≤71 cases per 10,000 live newborns. An altitude ranging from 2751 to 3000 m relates to a prevalence of CHD of >71 and <89 cases per 10,000 live newborns. An altitude ranging between 3001 and 3264 m relates to a prevalence of CHD of ≥89 cases per 10,000 live newborns. Conclusions: The findings show that high altitude (>2500 m), ethnicity (Native American), rural locations, and limited access to health care are factors that influence and increase the prevalence rate of CHD. A correlation coefficient of 0.914 shows the direct relationship between high altitude and prevalence rates of CHD. For each year elapsed, the prevalence of CHD increased by 3.33 cases per 10,000 live newborns.
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Affiliation(s)
- Fabricio González-Andrade
- Unidad de Medicina Traslacional, Facultad de Ciencias Médicas, Universidad Central del Ecuador, Quito, Ecuador.,Colegio Ciencias de la Salud, Universidad San Francisco de Quito USFQ, Quito, Ecuador
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24
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Espinosa-Herrera F, Espín E, Tito-Álvarez AM, Beltrán LJ, Gómez-Correa D, Burgos G, Llamos A, Zurita C, Rojas S, Dueñas-Espín I, Cueva-Ludeña K, Salazar-Vega J, Pinto-Basto J. A report of congenital adrenal hyperplasia due to 17α-hydroxylase deficiency in two 46,XX sisters. Gynecol Endocrinol 2020; 36:24-29. [PMID: 31464148 DOI: 10.1080/09513590.2019.1650342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Congenital adrenal hyperplasia (CAH) is a group of rare orphan disorders caused by mutations in seven different enzymes that impair cortisol biosynthesis. The 17α-hydroxylase deficiency (17OHD) is one of the less common forms of CAH, corresponding to approximately 1% of the cases, with an estimated annual incidence of 1 in 50,000 newborns. Cases description - two phenotypically female Ecuadorian sisters, both with primary amenorrhea, absence of secondary sexual characteristics, and osteoporosis. High blood pressure was present in the older sister. Hypergonadotropic hypogonadism profile was observed: decreased cortisol and dehydroepiandrosterone sulfate (DHEAS), increased adrenocorticotropic hormone (ACTH) and normal levels of 17-hydroxyprogesterone, extremely high deoxycorticosterone (DOC) levels, and a tomography showed bilateral adrenal hyperplasia in both sisters. Consanguinity was evident in their ancestors. Furthermore, in the exon 7, the variant c.1216T > C, p.Trp406Arg was detected in homozygosis in the CYP17A1 gene of both sisters. We report a homozygous missense mutation in the CYP17A1 gene causing 17OHD in two sisters from Loja, Ecuador. According to the authors, this is the first time such deficiency and mutation are described in two members of the same family in Ecuador.
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Affiliation(s)
- Fernando Espinosa-Herrera
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de las Américas (UDLA), Quito, Ecuador
- Sociedad Ecuatoriana de Medicina Familiar (SEMF), Hospital Vozandes Quito, Quito, Ecuador
| | - Estefanía Espín
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de las Américas (UDLA), Quito, Ecuador
| | - Ana M Tito-Álvarez
- Escuela de Enfermería, Facultad de Ciencias de la Salud, Universidad de las Américas (UDLA), Quito, Ecuador
| | - Leonardo-J Beltrán
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de las Américas (UDLA), Quito, Ecuador
| | - Diego Gómez-Correa
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de las Américas (UDLA), Quito, Ecuador
| | - German Burgos
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de las Américas (UDLA), Quito, Ecuador
| | - Arianne Llamos
- Facultad de Ciencias Médicas, de la Salud y de La Vida, Escuela de Odontología, Universidad Internacional del Ecuador (UIDE), Quito, Ecuador
| | - Camilo Zurita
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Cátedra de Inmunología, Facultad de Medicina, Universidad Central del Ecuador (UCE), Quito, Ecuador
| | - Samantha Rojas
- Hospital Isidro Ayora de Loja, Ministerio de Salud Pública del Ecuador, Quito, Ecuador
| | - Iván Dueñas-Espín
- Instituto de Salud Pública, Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Kenny Cueva-Ludeña
- Hospital General Docente de Calderón, Ministerio de Salud Pública del Ecuador, Quito, Ecuador
| | - Jorge Salazar-Vega
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de las Américas (UDLA), Quito, Ecuador
- Hospital Eugenio Espejo, Ministerio de Salud Pública del Ecuador, Quito, Ecuador
| | - Jorge Pinto-Basto
- Molecular Diagnostics and Clinical Genomics Laboratories, CGC Genetics, Porto, Portugal
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Genetic relationships of European, Mediterranean, and SW Asian populations using a panel of 55 AISNPs. Eur J Hum Genet 2019; 27:1885-1893. [PMID: 31285530 PMCID: PMC6871633 DOI: 10.1038/s41431-019-0466-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 04/05/2019] [Accepted: 06/25/2019] [Indexed: 11/08/2022] Open
Abstract
The set of 55 ancestry informative SNPs (AISNPs) originally developed by the Kidd Lab has been studied on a large number of populations and continues to be applied to new population samples. The existing reference database of population samples allows the relationships of new population samples to be inferred on a global level. Analyses show that these autosomal markers constitute one of the better panels of AISNPs. Continuing to build this reference database enhances its value. Because more than half of the 25 ethnic groups recently studied with these AISNPs are from Southwest Asia and the Mediterranean region, we present here various analyses focused on populations from these regions along with selected reference populations from nearby regions where genotype data are available. Many of these ethnic groups have not been previously studied for forensic markers. Data on populations from other world regions have also been added to the database but are not included in these focused analyses. The new population samples added to ALFRED and FROG-kb increase the total to 164 population samples that have been studied for all 55 AISNPs.
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26
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Qu S, Zhu J, Wang Y, Yin L, Lv M, Wang L, Jian H, Tan Y, Zhang R, Liu Y, Li F, Huang S, Liang W, Zhang L. Establishing a second-tier panel of 18 ancestry informative markers to improve ancestry distinctions among Asian populations. Forensic Sci Int Genet 2019; 41:159-167. [DOI: 10.1016/j.fsigen.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 11/16/2022]
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27
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The three-hybrid genetic composition of an Ecuadorian population using AIMs-InDels compared with autosomes, mitochondrial DNA and Y chromosome data. Sci Rep 2019; 9:9247. [PMID: 31239502 PMCID: PMC6592923 DOI: 10.1038/s41598-019-45723-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/04/2019] [Indexed: 11/08/2022] Open
Abstract
The history of Ecuador was marked by the arrival of Europeans with Africans, resulting in the mixture of Native Americans with Africans and Europeans. The present study contributes to the knowledge of the Ecuadorian mestizo population by offering information about ancestry and ethnic heterogeneity. Forty-six AIM-InDels (Ancestry Informative Insertion/Deletion Markers) were used to obtain information on 240 Ecuadorian individuals from three regions (Amazonia, the Highlands, and the Coast). As a result, the population involved a significant contribution from Native Americans (values up to 51%), followed by Europeans (values up to 33%) and Africans (values up to 13%). Furthermore, we compared the data obtained with nine previously reported scientific articles on autosomal, mitochondrial DNA and Y chromosomes. The admixture results correspond to Ecuador's historical background and vary slightly between regions.
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28
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Mass spectrometry-based SNP genotyping as a potential tool for ancestry inference and human identification in Chinese Han and Uygur populations. Sci Justice 2019; 59:228-233. [DOI: 10.1016/j.scijus.2019.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/27/2018] [Accepted: 01/27/2019] [Indexed: 01/04/2023]
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Luna J, Preux PM, Logroscino G, Erazo D, Del Brutto OH, Boumediene F, Couratier P, Marin B. Amyotrophic lateral sclerosis mortality rates among ethnic groups in a predominant admixed population in Latin America: a population-based study in Ecuador. Amyotroph Lateral Scler Frontotemporal Degener 2019; 20:404-412. [DOI: 10.1080/21678421.2019.1587632] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jaime Luna
- INSERM, U1094, Tropical Neuroepidemiology, Limoges, France,
- University Limoges, UMR_S 1094, Tropical Neuroepidemiology, Institute of Neuroepidemiology and Tropical Neurology, Limoges, France,
| | - Pierre-Marie Preux
- INSERM, U1094, Tropical Neuroepidemiology, Limoges, France,
- University Limoges, UMR_S 1094, Tropical Neuroepidemiology, Institute of Neuroepidemiology and Tropical Neurology, Limoges, France,
- CHU Limoges, Centre d’Epidémiologie de Biostatistique et de Méthodologie de la Recherche, Limoges, France,
| | - Giancarlo Logroscino
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy,
- Department of Clinical Research in Neurology, Unit of Neurodegenerative Diseases, University of Bari Aldo Moro at ‘‘Pia Fondazione Cardinale G. Panico’’, Tricase, Italy,
| | - Daniells Erazo
- INSERM, U1094, Tropical Neuroepidemiology, Limoges, France,
- University Limoges, UMR_S 1094, Tropical Neuroepidemiology, Institute of Neuroepidemiology and Tropical Neurology, Limoges, France,
| | | | - Farid Boumediene
- INSERM, U1094, Tropical Neuroepidemiology, Limoges, France,
- University Limoges, UMR_S 1094, Tropical Neuroepidemiology, Institute of Neuroepidemiology and Tropical Neurology, Limoges, France,
| | - Philippe Couratier
- INSERM, U1094, Tropical Neuroepidemiology, Limoges, France,
- CHU Limoges, Service de Neurologie, Centre expert ALS, Limoges, France
| | - Benoit Marin
- INSERM, U1094, Tropical Neuroepidemiology, Limoges, France,
- University Limoges, UMR_S 1094, Tropical Neuroepidemiology, Institute of Neuroepidemiology and Tropical Neurology, Limoges, France,
- CHU Limoges, Centre d’Epidémiologie de Biostatistique et de Méthodologie de la Recherche, Limoges, France,
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30
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Angiographic Features of Intracranial Aneurysms in Ecuador. J Stroke Cerebrovasc Dis 2019; 28:761-767. [DOI: 10.1016/j.jstrokecerebrovasdis.2018.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/08/2018] [Accepted: 11/14/2018] [Indexed: 11/22/2022] Open
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31
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Standardized clinical criteria and sweat test combined as a tool to diagnose Cystic Fibrosis. Heliyon 2018; 4:e01050. [PMID: 30582056 PMCID: PMC6299035 DOI: 10.1016/j.heliyon.2018.e01050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/29/2018] [Accepted: 12/11/2018] [Indexed: 11/23/2022] Open
Abstract
Context CF is under-diagnosed in Ecuador; one out of every 11,252 live births born in Ecuador could have CF. Aim To analyze the clinical findings, based on previously established criteria, with the results of the sweat test, in circumstances where we do not have the routine molecular study. Methods Epidemiological, observational, analytic, cross-sectional study. It analyzed 180 patients clinically suspected of CF. Inclusion criteria: children of both sexes older than 30 days and younger than 12 years, who meet at least three clinical criteria suggestive for CF, outpatient and referred by a specialist physician who made a preliminary diagnosis. This is a pilot study. Results The combination of criteria pneumonia, chronic cough and chronic obstructive bronchial syndrome is the most frequent, with not a significant relationship with a positive sweat test. On the contrary, a significant relationship was found between the clinical combinations of pneumonia with cough and rhinosinusitis; pneumonia with cough; presence of Pseudomonas aeruginosa; and pneumonia with digital cough and clubbing, so it is recommended to perform the test in all these associations. The most frequent clinical criterion for the reference and performance of the electrolyte test in sweat is pneumonia to repeat for two or more episodes. Conclusion Clinical combinations of pneumonia with cough and rhinosinusitis; pneumonia with cough; presence of Pseudomonas aeruginosa; and pneumonia with digital cough and clubbing are pathognomonic for CF and indication for the sweat test. The predictive performance in CF diagnosis, defined as compatible clinical presence plus high values of chloride in sweat test, was 91.1%.
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32
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Das R, Upadhyai P. An Ancestry Informative Marker Set Which Recapitulates the Known Fine Structure of Populations in South Asia. Genome Biol Evol 2018; 10:2408-2416. [PMID: 30184103 PMCID: PMC6143162 DOI: 10.1093/gbe/evy182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2018] [Indexed: 12/16/2022] Open
Abstract
The inference of genomic ancestry using ancestry informative markers (AIMs) can be useful for a range of studies in evolutionary genetics, biomedical research, and forensic analyses. However, the determination of AIMs for highly admixed populations with complex ancestries has remained a formidable challenge. Given the immense genetic heterogeneity and unique population structure of the Indian subcontinent, here we sought to derive AIMs that would yield a cohesive and faithful understanding of South Asian genetic origins. To discern the most optimal strategy for extracting AIMs for South Asians we compared three commonly used AIMs-determining methods namely, Infocalc, FST, and Smart Principal Component Analysis with ADMIXTURE, using previously published whole genome data from the Indian subcontinent. Our findings suggest that the Infocalc approach is likely most suitable for delineation of South Asian AIMs. In particular, Infocalc-2,000 (N = 2,000) appeared as the most informative South Asian AIMs panel that recapitulated the finer structure within South Asian genomes with high degree of sensitivity and precision, whereas a negative control with an equivalent number of randomly selected markers when used to interrogate the South Asian populations, failed to do so. We discuss the utility of all approaches under evaluation for AIMs derivation and interpreting South Asian genomic ancestries. Notably, this is the first report of an AIMs panel for South Asian ancestry inference. Overall these findings may aid in developing cost-effective resources for large-scale demographic analyses and foster expansion of our knowledge of human origins and disease, in the South Asian context.
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Affiliation(s)
- Ranajit Das
- Manipal Centre for Natural Sciences (MCNS), Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
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Jin S, Chase M, Henry M, Alderson G, Morrow JM, Malik S, Ballard D, McGrory J, Fernandopulle N, Millman J, Laird J. Implementing a biogeographic ancestry inference service for forensic casework. Electrophoresis 2018; 39:2757-2765. [PMID: 30125362 DOI: 10.1002/elps.201800171] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 01/12/2023]
Abstract
The Centre of Forensic Sciences has validated the Precision ID Ancestry Panel on the Ion S5™ Massively Parallel Sequencing instrument for use in forensic casework. The focus of this paper is the development of reporting guidelines for implementation of the biogeographic ancestry inference service based on the Admixture Prediction results produced using the Torrent Suite™ Software (Thermo Fisher Scientific). The Admixture Prediction algorithm estimates the genetic ancestry of a sample using seven root populations (Europe, East Asia, Oceania, America, Africa, South Asia, and Southwest Asia). For individuals that declared a single ancestry, there was a high correlation between the declared ancestry and the ancestry predicted by the algorithm. However, some individuals with declared ancestries of Southern Europe, Southwest Asia, South Asia and Horn of Africa had Admixture Predictions that were composed of two or more root populations at 20% or greater. For individuals with known admixed ancestry, the major component of their declaration was included in their results in all but one case. Based on these results, reporting guidelines were developed and subsequently evaluated using the Admixture Predictions of additional samples. This paper discusses the development and evaluation of these reporting guidelines, along with an implementation plan for forensic casework.
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Affiliation(s)
- Soulbee Jin
- Centre of Forensic Sciences, Toronto, Canada
| | | | | | | | | | - Sobia Malik
- Centre of Forensic Sciences, Toronto, Canada
| | | | | | | | | | - Jack Laird
- Centre of Forensic Sciences, Toronto, Canada
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34
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Vlachos NT, Meiklejohn KA, Robertson JM. An automated independent workflow for the analysis of massively parallel sequence data from forensic SNP assays. Electrophoresis 2018; 39:2752-2756. [PMID: 30010201 DOI: 10.1002/elps.201800085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/15/2018] [Accepted: 07/01/2018] [Indexed: 12/30/2022]
Abstract
Illumina and Thermo Fisher Scientific have developed assays that permit the sequencing of forensically relevant single nucleotide polymorphisms (SNPs), along with software to determine the associated genotypes. Currently there is no method to either independently confirm the genotypes determined using the manufacturer's software, or to compare genotypes and quality metrics among samples processed using both platforms. This paper outlines an automated workflow developed in CLC Genomics Workbench that permits accurate, fast and independent analysis of SNP sequence data from either platform. To facilitate the straightforward comparison of genotypes generated from both the manufacturer's software and the independent CLC analysis, a Python script was written. Data for a total of 323 forensically relevant ancestry, identity and phenotypic SNPs can be analyzed, and the resulting genotypes, coverage, quality flags and major allele frequencies are easily compared across samples and platforms.
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Affiliation(s)
- Nicholas T Vlachos
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, VA, USA
| | - Kelly A Meiklejohn
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, VA, USA.,Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - James M Robertson
- Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation Laboratory Division, Quantico, VA, USA
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35
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Choudhury A, Aron S, Sengupta D, Hazelhurst S, Ramsay M. African genetic diversity provides novel insights into evolutionary history and local adaptations. Hum Mol Genet 2018; 27:R209-R218. [PMID: 29741686 PMCID: PMC6061870 DOI: 10.1093/hmg/ddy161] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 12/22/2022] Open
Abstract
Genetic variation and susceptibility to disease are shaped by human demographic history and adaptation. We can now study the genomes of extant Africans and uncover traces of population migration, admixture, assimilation and selection by applying sophisticated computational algorithms. There are four major ethnolinguistic divisions among present day Africans: Hunter-gatherer populations in southern and central Africa; Nilo-Saharan speakers from north and northeast Africa; Afro-Asiatic speakers from north and east Africa; and Niger-Congo speakers who are the predominant ethnolinguistic group spread across most of sub-Saharan Africa. The enormous ethnolinguistic diversity in sub-Saharan African populations is largely paralleled by extensive genetic diversity and until a decade ago, little was known about detailed origins and divergence of these groups. Results from large-scale population genetic studies, and more recently whole genome sequence data, are unravelling the critical role of events like migration and admixture and environmental factors including diet, infectious diseases and climatic conditions in shaping current population diversity. It is now possible to start providing quantitative estimates of divergence times, population size and dynamic processes that have affected populations and their genetic risk for disease. Finally, the availability of ancient genomes from Africa provides historical insights of unprecedented depth. In this review, we highlight some key interpretations that have emerged from recent African genome studies.
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Affiliation(s)
- Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shaun Aron
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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36
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He G, Wang Z, Wang M, Luo T, Liu J, Zhou Y, Gao B, Hou Y. Forensic ancestry analysis in two Chinese minority populations using massively parallel sequencing of 165 ancestry-informative SNPs. Electrophoresis 2018; 39:2732-2742. [PMID: 29869338 DOI: 10.1002/elps.201800019] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 04/28/2018] [Accepted: 05/21/2018] [Indexed: 11/08/2022]
Abstract
Ancestry inference based on SNPs with marked allele frequency differences in diverse populations (called ancestry-informative SNP (AISNP)) is rapidly developed with the technology advancements of massively parallel sequencing. Despite the decade of exploration and broad public interest in the peopling of East-Asians, the genetic landscape of Chinese Silk Road populations based on the AISNPs is still little known. In this work, 206 unrelated individuals from Chinese Uyghur and Hui populations were firstly genotyped by 165 AISNPs (The Precision ID Ancestry Panel) using the Ion Torrent Personal Genome Machine system. The ethnic origin of two investigated populations and population structures and genetic relationships were subsequently investigated. The 165 AISNPs panel not only can differentiate Uyghur and Hui populations but also has potential applications in individual identification. Comprehensive population comparisons and admixture estimates demonstrated a predominantly higher European-related ancestry (36.30%) in Uyghurs than Huis (3.66%). Overall, the Precision ID Ancestry Panel can provide good resolution at the intercontinental level, but has limitations on the genetic homogeneous populations, such as the Hui and Han. Additional population-specific AISNPs remain necessary to get better-scale resolution within geographically proximate populations in East Asia.
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Affiliation(s)
- Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Tao Luo
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - You Zhou
- Kumul Public Security Bureau, Xinjiang Uygur Autonomous Region, P. R. China
| | - Bo Gao
- Yili Public Security Bureau, Xinjiang Uygur Autonomous Region, P. R. China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
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37
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Massively parallel sequencing of 165 ancestry informative SNPs in two Chinese Tibetan-Burmese minority ethnicities. Forensic Sci Int Genet 2018; 34:141-147. [PMID: 29477877 DOI: 10.1016/j.fsigen.2018.02.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/03/2018] [Accepted: 02/08/2018] [Indexed: 11/21/2022]
Abstract
The Tibeto-Burman language, one subfamily of the Sino-Tibetan languages, is spoken by over 60 million people all over East Asia. Yet the ethnic origin and genetic architecture of Tibeto-Burman speaking populations remain largely unexplored. In the present study, 169 Chinese individuals from Tibeto-Burman speaking populations (two ethnic groups: Tibetan and Yi) in four different geographic regions in western China were analyzed using the Precision ID Ancestry Panel (165 AISNPs) and the Ion PGM System. The performance and corresponding forensic statistical parameters of this AISNPs panel were investigated. Comprehensive population genetic comparisons (143 populations based on Kidd' SNPs, 92 populations on the basis of Seldin' SNPs and 31 populations based on the Precision ID Ancestry Panel) and ancestry inference were further performed. Sequencing performance demonstrated that the Precision ID Ancestry Panel is effective and robust. Forensic characteristics suggested that this panel not only can be used for ancestry estimation of Tibeto-Burman populations but also for individual identification. Tibetan and Yi shared a common genetic ancestry origin but experienced the complex history of gene flow, local adaptation, and isolation, and constructed the specific genetic landscape of human genetic diversity of Highlander and Lowlander populations. Tibetan-Burman populations and other East Asian populations showed sufficient genetic difference and could be distinguished into three distinct groups. Furthermore, analysis of population structure revealed that significant genetic difference was existed inter-continent populations and strong genetic affinity was observed within-continent populations. Additional population-specific AISNPs and a relatively more comprehensive database with sufficient reference population data remain necessary to get better-scale resolution within a geographically proximate populations in East Asia.
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38
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Brandini S, Bergamaschi P, Cerna MF, Gandini F, Bastaroli F, Bertolini E, Cereda C, Ferretti L, Gómez-Carballa A, Battaglia V, Salas A, Semino O, Achilli A, Olivieri A, Torroni A. The Paleo-Indian Entry into South America According to Mitogenomes. Mol Biol Evol 2018; 35:299-311. [PMID: 29099937 PMCID: PMC5850732 DOI: 10.1093/molbev/msx267] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Recent and compelling archaeological evidence attests to human presence ∼14.5 ka at multiple sites in South America and a very early exploitation of extreme high-altitude Andean environments. Considering that, according to genetic evidence, human entry into North America from Beringia most likely occurred ∼16 ka, these archeological findings would imply an extremely rapid spread along the double continent. To shed light on this issue from a genetic perspective, we first completely sequenced 217 novel modern mitogenomes of Native American ancestry from the northwestern area of South America (Ecuador and Peru); we then evaluated them phylogenetically together with other available mitogenomes (430 samples, both modern and ancient) from the same geographic area and, finally, with all closely related mitogenomes from the entire double continent. We detected a large number (N = 48) of novel subhaplogroups, often branching into further subclades, belonging to two classes: those that arose in South America early after its peopling and those that instead originated in North or Central America and reached South America with the first settlers. Coalescence age estimates for these subhaplogroups provide time boundaries indicating that early Paleo-Indians probably moved from North America to the area corresponding to modern Ecuador and Peru over the short time frame of ∼1.5 ka comprised between 16.0 and 14.6 ka.
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Affiliation(s)
- Stefania Brandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Paola Bergamaschi
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Servizio di Immunoematologia e Medicina Trasfusionale, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marco Fernando Cerna
- Biotechnology Laboratory, Salesian Polytechnic University of Ecuador, Quito, Ecuador
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | | | - Emilie Bertolini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, National Neurological Institute C. Mondino, Pavia, Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alberto Gómez-Carballa
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Unidade de Xenética, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Galicia, Spain
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, Galicia, Spain
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Antonio Salas
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Unidade de Xenética, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Galicia, Spain
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
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