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Barahona-Correa JE, Herrera-Leaño NM, Bernal-Macías S, Fernández-Ávila DG. Prevalence of axial spondyloarthritis in Colombia: data from the National Health Registry 2017-2021. Clin Rheumatol 2024; 43:49-57. [PMID: 37953369 PMCID: PMC10774146 DOI: 10.1007/s10067-023-06799-y] [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: 06/05/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023]
Abstract
INTRODUCTION Registries allow ascertaining the epidemiology of chronic diseases such as axial spondyloarthritis (axSpA). The Colombian Ministry of Health has implemented a National Health Registry (SISPRO) that collects data from each medical contact in the system, which provides close to universal coverage (around 98%). OBJECTIVE To establish the 5-year prevalence of axSpA in Colombia, and to describe its demographics, using data from January 1st, 2017, to December 31st, 2021. METHODS We performed an observational, cross-sectional study using the International Statistical Classification of Diseases and Related Health Problems as search terms related to ax-SpA, based on SISPRO data. We estimated the prevalence using three approaches: (1) ankylosing spondylitis (AS) diagnoses; (2) diagnoses compatible with axSpA; and (3) diagnoses compatible with axSpA, including sacroiliitis. We calculated prevalence per 100,000 inhabitants. RESULTS Based on our three approaches, patients with a primary diagnosis compatible with ax-SpA ranged between 12,684 and 117,648, with an estimated 5-year adjusted prevalence between 26.3 and 244 cases per 100,000 inhabitants (0.03-0.2%). The male-to-female ratio ranged between 1.2:1 and 0.4:1, which was markedly skewed towards a higher prevalence in women when we included the code for sacroiliitis. We found the highest frequency of cases in the 50-54 years group. A differential prevalence was observed between different regions in our country, particularly in regions known to have European ancestors. CONCLUSION This is the first study that describes demographic characteristics of ax-SpA in Colombia and offers valuable information for stakeholders. Key Points • Using the official country-level health database, the prevalence of axSpA in Colombia ranges between 26.3 and 244 cases per 100,000 inhabitants (0.03% - 0.2%) • The prevalence of axSpA peaked among the 50-54 years patient group, suggesting an increased survival • Nations with a substantial admixture, such as Colombia, may present a differential prevalence of axSpA among regions within the country • Including the ICD-10 code for sacroiliitis (M46.1) in epidemiological studies probably overestimates the frequency of axSpA.
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Affiliation(s)
- Julián E Barahona-Correa
- Department of Internal Medicine, Hospital Universitario San Ignacio, Bogota, Colombia.
- Division of Rheumatology, Hospital Universitario San Ignacio, Bogota, Colombia.
- School of Medicine, Pontificia Universidad Javeriana, Bogota, Colombia.
| | - Nancy M Herrera-Leaño
- Department of Internal Medicine, Hospital Universitario San Ignacio, Bogota, Colombia
- School of Medicine, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Santiago Bernal-Macías
- Department of Internal Medicine, Hospital Universitario San Ignacio, Bogota, Colombia
- Division of Rheumatology, Hospital Universitario San Ignacio, Bogota, Colombia
- School of Medicine, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Daniel G Fernández-Ávila
- Department of Internal Medicine, Hospital Universitario San Ignacio, Bogota, Colombia
- Division of Rheumatology, Hospital Universitario San Ignacio, Bogota, Colombia
- School of Medicine, Pontificia Universidad Javeriana, Bogota, Colombia
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Cotter DJ, Webster TH, Wilson MA. Genomic and demographic processes differentially influence genetic variation across the human X chromosome. PLoS One 2023; 18:e0287609. [PMID: 37910456 PMCID: PMC10619814 DOI: 10.1371/journal.pone.0287609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/08/2023] [Indexed: 11/03/2023] Open
Abstract
Many forces influence genetic variation across the genome including mutation, recombination, selection, and demography. Increased mutation and recombination both lead to increases in genetic diversity in a region-specific manner, while complex demographic patterns shape patterns of diversity on a more global scale. While these processes act across the entire genome, the X chromosome is particularly interesting because it contains several distinct regions that are subject to different combinations and strengths of these forces: the pseudoautosomal regions (PARs) and the X-transposed region (XTR). The X chromosome thus can serve as a unique model for studying how genetic and demographic forces act in different contexts to shape patterns of observed variation. We therefore sought to explore diversity, divergence, and linkage disequilibrium in each region of the X chromosome using genomic data from 26 human populations. Across populations, we find that both diversity and substitution rate are consistently elevated in PAR1 and the XTR compared to the rest of the X chromosome. In contrast, linkage disequilibrium is lowest in PAR1, consistent with the high recombination rate in this region, and highest in the region of the X chromosome that does not recombine in males. However, linkage disequilibrium in the XTR is intermediate between PAR1 and the autosomes, and much lower than the non-recombining X. Finally, in addition to these global patterns, we also observed variation in ratios of X versus autosomal diversity consistent with population-specific evolutionary history as well. While our results were generally consistent with previous work, two unexpected observations emerged. First, our results suggest that the XTR does not behave like the rest of the recombining X and may need to be evaluated separately in future studies. Second, the different regions of the X chromosome appear to exhibit unique patterns of linked selection across different human populations. Together, our results highlight profound regional differences across the X chromosome, simultaneously making it an ideal system for exploring the action of evolutionary forces as well as necessitating its careful consideration and treatment in genomic analyses.
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Affiliation(s)
- Daniel J. Cotter
- Department of Genetics, Stanford University, Stanford, CA, United States of America
| | - Timothy H. Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT, United States of America
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
- Center for Evolution and Medicine, Biodesign Institute, Arizona State University, Tempe, AZ, United States of America
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Ayala NM, Genetti M, Corbett-Detig R. Inferring multi-locus selection in admixed populations. PLoS Genet 2023; 19:e1011062. [PMID: 38015992 PMCID: PMC10707604 DOI: 10.1371/journal.pgen.1011062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 12/08/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023] Open
Abstract
Admixture, the exchange of genetic information between distinct source populations, is thought to be a major source of adaptive genetic variation. Unlike mutation events, which periodically generate single alleles, admixture can introduce many selected alleles simultaneously. As such, the effects of linkage between selected alleles may be especially pronounced in admixed populations. However, existing tools for identifying selected mutations within admixed populations only account for selection at a single site, overlooking phenomena such as linkage among proximal selected alleles. Here, we develop and extensively validate a method for identifying and quantifying the individual effects of multiple linked selected sites on a chromosome in admixed populations. Our approach numerically calculates the expected local ancestry landscape in an admixed population for a given multi-locus selection model, and then maximizes the likelihood of the model. After applying this method to admixed populations of Drosophila melanogaster and Passer italiae, we found that the impacts between linked sites may be an important contributor to natural selection in admixed populations. Furthermore, for the situations we considered, the selection coefficients and number of selected sites are overestimated in analyses that do not consider the effects of linkage among selected sites. Our results imply that linkage among selected sites may be an important evolutionary force in admixed populations. This tool provides a powerful generalized method to investigate these crucial phenomena in diverse populations.
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Affiliation(s)
- Nicolas M. Ayala
- Genomics Institute, University of California, Santa Cruz; Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California, Santa Cruz; Santa Cruz, California, United States of America
| | - Maximilian Genetti
- Genomics Institute, University of California, Santa Cruz; Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California, Santa Cruz; Santa Cruz, California, United States of America
| | - Russell Corbett-Detig
- Genomics Institute, University of California, Santa Cruz; Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California, Santa Cruz; Santa Cruz, California, United States of America
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Adkins-Jackson PB, Kraal AZ, Hill-Jarrett TG, George KM, Deters KD, Besser LM, Avila-Rieger JF, Turney I, Manly JJ. Riding the merry-go-round of racial disparities in ADRD research. Alzheimers Dement 2023; 19:4735-4742. [PMID: 37394968 DOI: 10.1002/alz.13359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023]
Abstract
INTRODUCTION With the rapid expansion of the aging population, the burden of Alzheimer's disease related dementias (ADRD) is anticipated to increase in racialized and minoritized groups who are at disproportionately higher risk. To date, research emphasis has been on further characterizing the existence of racial disparities in ADRD through comparisons to groups racialized as White that are assumed to be normative. Much of the literature on this comparison insinuates that racialized and minoritized groups experience poorer outcomes due to genetics, culture, and/or health behaviors. METHODS This perspective shines a light on a category of ADRD research that employs ahistorical methodological approaches to describe racial disparities in ADRD that puts us on a merry-go-round of research with no benefits to society. METHODS This commentary provides historical context for the use of race in ADRD research and justification for the study of structural racism. The commentary concludes with recommendations to guide future research.
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Affiliation(s)
- Paris B Adkins-Jackson
- Departments of Epidemiology & Sociomedical Sciences, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - A Zarina Kraal
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Tanisha G Hill-Jarrett
- Department of Neurology, Memory and Aging Center, University of California San Francisco, San Francisco, California, USA
| | - Kristen M George
- Department of Public Health Sciences, University of California Davis School of Medicine, Davis, California, USA
| | - Kacie D Deters
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California, USA
| | - Lilah M Besser
- Comprehensive Center for Brain Health, University of Miami Miller School of Medicine, Boca Raton, Florida, USA
| | - Justina F Avila-Rieger
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Indira Turney
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Jennifer J Manly
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
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Hamid I, Korunes KL, Schrider DR, Goldberg A. Localizing Post-Admixture Adaptive Variants with Object Detection on Ancestry-Painted Chromosomes. Mol Biol Evol 2023; 40:msad074. [PMID: 36947126 PMCID: PMC10116606 DOI: 10.1093/molbev/msad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 03/23/2023] Open
Abstract
Gene flow between previously differentiated populations during the founding of an admixed or hybrid population has the potential to introduce adaptive alleles into the new population. If the adaptive allele is common in one source population, but not the other, then as the adaptive allele rises in frequency in the admixed population, genetic ancestry from the source containing the adaptive allele will increase nearby as well. Patterns of genetic ancestry have therefore been used to identify post-admixture positive selection in humans and other animals, including examples in immunity, metabolism, and animal coloration. A common method identifies regions of the genome that have local ancestry "outliers" compared with the distribution across the rest of the genome, considering each locus independently. However, we lack theoretical models for expected distributions of ancestry under various demographic scenarios, resulting in potential false positives and false negatives. Further, ancestry patterns between distant sites are often not independent. As a result, current methods tend to infer wide genomic regions containing many genes as under selection, limiting biological interpretation. Instead, we develop a deep learning object detection method applied to images generated from local ancestry-painted genomes. This approach preserves information from the surrounding genomic context and avoids potential pitfalls of user-defined summary statistics. We find the method is robust to a variety of demographic misspecifications using simulated data. Applied to human genotype data from Cabo Verde, we localize a known adaptive locus to a single narrow region compared with multiple or long windows obtained using two other ancestry-based methods.
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Affiliation(s)
- Iman Hamid
- Department of Evolutionary Anthropology, Duke University, Durham, NC
| | | | - Daniel R Schrider
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, NC
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Montero-Ovalle W, Sanabria-Salas MC, Mesa-López de Mesa J, Varela-Ramírez R, Segura-Moreno YY, Sánchez-Villalobos SA, Nuñez-Lemus M, Serrano ML. Determination of TMPRSS2-ERG, SPOP, FOXA1, and IDH1 prostate cancer molecular subtypes in Colombian patients and their possible implications for prognosis. Cell Biol Int 2023; 47:1017-1030. [PMID: 36740223 DOI: 10.1002/cbin.12000] [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: 08/17/2022] [Revised: 11/30/2022] [Accepted: 01/21/2023] [Indexed: 02/07/2023]
Abstract
Prostate cancer (PCa) is one of cancer with of the highest incidence and mortality worldwide. Current disease prognostic markers do not differentiate aggressive from indolent PCa with sufficient certainty, and characterization by molecular subtypes has been sought to allow a better classification. TMPRSS2-ERG, SPOP, FOXA1, and IDH1 molecular subtypes have been described, but the association of these subtypes with prognosis in PCa is unclear; their frequency in Colombian patients is also unknown. Formalin-fixed and paraffin-embedded samples of radical prostatectomy from 112 patients with PCa were used. The TMPRSS2-ERG subtype was assessed with fluorescent in situ hybridization. The mutations in SPOP, FOXA1, and IDH1 in hot-spot regions were evaluated using Sanger sequencing. Fusion was detected in 71 patients (63.4%). No statistically significant differences were found between the state of fusion and the variables analyzed. In the 41 fusion-negative cases (36.6%), two patients (4.9%) had missense mutations in SPOP (p.F102C and p.F133L), representing a 1.8% of the overall cohort. The low frequency of this subtype in Colombians could be explained by the reported variability in the frequency of these mutations according to the population (5%-20%). No mutations were found in FOXA1 in the cases analyzed. The synonym SNP rs11554137 IDH1105GGT was found in tumor tissue but not in the normal tissue in one case. A larger cohort of Colombian PCa patients is needed for future studies to validate these findings and gain a better understanding of the molecular profile of this cancer in our population and if there are any differences by Colombian regions.
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Affiliation(s)
- Wendy Montero-Ovalle
- Cancer Biology Research Group, Instituto Nacional de Cancerología, Bogotá, Colombia.,Department of Chemistry, Faculty of Sciences, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | | | - Rodolfo Varela-Ramírez
- Department of Oncological Urology, Instituto Nacional de Cancerología, Bogotá, Colombia.,Department of Surgery, Faculty of Medicine Universidad Nacional de Colombia, Bogotá, Colombia
| | | | | | - Marcela Nuñez-Lemus
- Research Support and Monitoring Group, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Martha L Serrano
- Cancer Biology Research Group, Instituto Nacional de Cancerología, Bogotá, Colombia.,Department of Chemistry, Faculty of Sciences, Universidad Nacional de Colombia, Bogotá, Colombia
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Sleep problems in low income, urban pediatric populations living at different altitudes in Colombia. Sleep Med 2022; 100:64-70. [PMID: 36027664 DOI: 10.1016/j.sleep.2022.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To determine the frequency of sleep problems in low-income, urban pediatric populations in cities at different altitudes in Colombia. METHODS A descriptive, cross-sectional population-based observational study was conducted in children aged between 2 and 12 years in the low income, urban areas of three cities in Colombia (Santa Marta, Bucaramanga, and Bogotá) located at 15, 959, and 2640 m above sea level, respectively. Sociodemographic data were collected, and the Spanish version of the Pediatric Sleep Questionnaire was used. RESULTS 1989 children were surveyed, distributed as follows: Santa Marta (32.0%), Bucaramanga (33.4%), and Bogotá (34.6%). The overall prevalence of sleep problems was 39.0%. Children from Santa Marta had the highest frequency of parasomnias (58.0%); those from Bucaramanga had the highest frequency of attention deficit symptoms (4.0%) and apneic pauses witnessed by parents or caregivers (5.7%). Finally, Bogotá, the only high-altitude location, had the highest frequency of sleep disordered breathing (17.2%). CONCLUSIONS The study found a high frequency of sleep problems in the pediatric population, especially at higher altitudes when compared to lower altitude settings. Sleep disorders warrant early detection and timely therapeutic intervention.
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Oriol Sabat B, Mas Montserrat D, Giro-i-Nieto X, Ioannidis AG. SALAI-Net: species-agnostic local ancestry inference network. Bioinformatics 2022; 38:ii27-ii33. [PMID: 36124792 PMCID: PMC9486591 DOI: 10.1093/bioinformatics/btac464] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION Local ancestry inference (LAI) is the high resolution prediction of ancestry labels along a DNA sequence. LAI is important in the study of human history and migrations, and it is beginning to play a role in precision medicine applications including ancestry-adjusted genome-wide association studies (GWASs) and polygenic risk scores (PRSs). Existing LAI models do not generalize well between species, chromosomes or even ancestry groups, requiring re-training for each different setting. Furthermore, such methods can lack interpretability, which is an important element in each of these applications. RESULTS We present SALAI-Net, a portable statistical LAI method that can be applied on any set of species and ancestries (species-agnostic), requiring only haplotype data and no other biological parameters. Inspired by identity by descent methods, SALAI-Net estimates population labels for each segment of DNA by performing a reference matching approach, which leads to an interpretable and fast technique. We benchmark our models on whole-genome data of humans and we test these models' ability to generalize to dog breeds when trained on human data. SALAI-Net outperforms previous methods in terms of balanced accuracy, while generalizing between different settings, species and datasets. Moreover, it is up to two orders of magnitude faster and uses considerably less RAM memory than competing methods. AVAILABILITY AND IMPLEMENTATION We provide an open source implementation and links to publicly available data at github.com/AI-sandbox/SALAI-Net. Data is publicly available as follows: https://www.internationalgenome.org (1000 Genomes), https://www.simonsfoundation.org/simons-genome-diversity-project (Simons Genome Diversity Project), https://www.sanger.ac.uk/resources/downloads/human/hapmap3.html (HapMap), ftp://ngs.sanger.ac.uk/production/hgdp/hgdp_wgs.20190516 (Human Genome Diversity Project) and https://www.ncbi.nlm.nih.gov/bioproject/PRJNA448733 (Canid genomes). SUPPLEMENTARY INFORMATION Supplementary data are available from Bioinformatics online.
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Affiliation(s)
- Benet Oriol Sabat
- Department of Signal Theory and Communications, Universitat Politecnica de Catalunya, Barcelona 08034, Spain
- Department of Biomedical Data Science, Stanford Medical School
| | | | - Xavier Giro-i-Nieto
- Department of Signal Theory and Communications, Universitat Politecnica de Catalunya, Barcelona 08034, Spain
| | - Alexander G Ioannidis
- Department of Biomedical Data Science, Stanford Medical School
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
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Killer-Cell Immunoglobulin-like Receptor Diversity in an Admixed South American Population. Cells 2022; 11:cells11182776. [PMID: 36139351 PMCID: PMC9496851 DOI: 10.3390/cells11182776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Natural Killer (NK) cells are innate immune cells that mediate antiviral and antitumor responses. NK cell activation and induction of effector functions are tightly regulated by the integration of activating and inhibitory receptors such as killer immunoglobulin-like receptors (KIR). KIR genes are characterized by a high degree of diversity due to presence or absence, gene copy number and allelic polymorphism. The aim of this study was to establish the distribution of KIR genes and genotypes, to infer the most common haplotypes in an admixed Colombian population and to compare these KIR gene frequencies with some Central and South American populations and worldwide. A total of 161 individuals from Medellin, Colombia were included in the study. Genomic DNA was used for KIR and HLA genotyping. We analyzed only KIR gene-content (presence or absence) based on PCR-SSO. The KIR genotype, most common haplotypes and combinations of KIR and HLA ligands frequencies were estimated according to the presence or absence of KIR and HLA genes. Dendrograms, principal component (PC) analysis and Heatmap analysis based on genetic distance were constructed to compare KIR gene frequencies among Central and South American, worldwide and Amerindian populations. The 16 KIR genes analyzed were distributed in 37 different genotypes and the 7 most frequent KIR inferred haplotypes. Importantly, we found three new genotypes not previously reported in any other ethnic group. Our genetic distance, PC and Heatmap analysis revealed marked differences in the distribution of KIR gene frequencies in the Medellin population compared to worldwide populations. These differences occurred mainly in the activating KIR isoforms, which are more frequent in our population, particularly KIR3DS1. Finally, we observed unique structural patterns of genotypes, which evidences the potential diversity and variability of this gene family in our population, and the need for exhaustive genetic studies to expand our understanding of the KIR gene complex in Colombian populations.
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Collen EJ, Johar AS, Teixeira JC, Llamas B. The immunogenetic impact of European colonization in the Americas. Front Genet 2022; 13:918227. [PMID: 35991555 PMCID: PMC9388791 DOI: 10.3389/fgene.2022.918227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
The introduction of pathogens originating from Eurasia into the Americas during early European contact has been associated with high mortality rates among Indigenous peoples, likely contributing to their historical and precipitous population decline. However, the biological impacts of imported infectious diseases and resulting epidemics, especially in terms of pathogenic effects on the Indigenous immunity, remain poorly understood and highly contentious to this day. Here, we examine multidisciplinary evidence underpinning colonization-related immune genetic change, providing contextualization from anthropological studies, paleomicrobiological evidence of contrasting host-pathogen coevolutionary histories, and the timings of disease emergence. We further summarize current studies examining genetic signals reflecting post-contact Indigenous population bottlenecks, admixture with European and other populations, and the putative effects of natural selection, with a focus on ancient DNA studies and immunity-related findings. Considering current genetic evidence, together with a population genetics theoretical approach, we show that post-contact Indigenous immune adaptation, possibly influenced by selection exerted by introduced pathogens, is highly complex and likely to be affected by multifactorial causes. Disentangling putative adaptive signals from those of genetic drift thus remains a significant challenge, highlighting the need for the implementation of population genetic approaches that model the short time spans and complex demographic histories under consideration. This review adds to current understandings of post-contact immunity evolution in Indigenous peoples of America, with important implications for bettering our understanding of human adaptation in the face of emerging infectious diseases.
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Affiliation(s)
- Evelyn Jane Collen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- *Correspondence: Evelyn Jane Collen, ; Bastien Llamas,
| | - Angad Singh Johar
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Culture History and Language, The Australian National University, Canberra, ACT, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia
- Telethon Kids Institute, Indigenous Genomics Research Group, Adelaide, SA, Australia
- *Correspondence: Evelyn Jane Collen, ; Bastien Llamas,
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Angulo-Aguado M, Corredor-Orlandelli D, Carrillo-Martínez JC, Gonzalez-Cornejo M, Pineda-Mateus E, Rojas C, Triana-Fonseca P, Contreras Bravo NC, Morel A, Parra Abaunza K, Restrepo CM, Fonseca-Mendoza DJ, Ortega-Recalde O. Association Between the LZTFL1 rs11385942 Polymorphism and COVID-19 Severity in Colombian Population. Front Med (Lausanne) 2022; 9:910098. [PMID: 35795626 PMCID: PMC9251207 DOI: 10.3389/fmed.2022.910098] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/26/2022] [Indexed: 01/08/2023] Open
Abstract
Genetic and non-genetic factors are responsible for the high interindividual variability in the response to SARS-CoV-2. Although numerous genetic polymorphisms have been identified as risk factors for severe COVID-19, these remain understudied in Latin-American populations. This study evaluated the association of non-genetic factors and three polymorphisms: ACE rs4646994, ACE2 rs2285666, and LZTFL1 rs11385942, with COVID severity and long-term symptoms by using a case-control design. The control group was composed of asymptomatic/mild cases (n = 61) recruited from a private laboratory, while the case group was composed of severe/critical patients (n = 63) hospitalized in the Hospital Universitario Mayor-Méderi, both institutions located in Bogotá, Colombia. Clinical follow up and exhaustive revision of medical records allowed us to assess non-genetic factors. Genotypification of the polymorphism of interest was performed by amplicon size analysis and Sanger sequencing. In agreement with previous reports, we found a statistically significant association between age, male sex, and comorbidities, such as hypertension and type 2 diabetes mellitus (T2DM), and worst outcomes. We identified the polymorphism LZTFL1 rs11385942 as an important risk factor for hospitalization (p < 0.01; OR = 5.73; 95% CI = 1.2–26.5, under the allelic test). Furthermore, long-term symptoms were common among the studied population and associated with disease severity. No association between the polymorphisms examined and long-term symptoms was found. Comparison of allelic frequencies with other populations revealed significant differences for the three polymorphisms investigated. Finally, we used the statistically significant genetic and non-genetic variables to develop a predictive logistic regression model, which was implemented in a Shiny web application. Model discrimination was assessed using the area under the receiver operating characteristic curve (AUC = 0.86; 95% confidence interval 0.79–0.93). These results suggest that LZTFL1 rs11385942 may be a potential biomarker for COVID-19 severity in addition to conventional non-genetic risk factors. A better understanding of the impact of these genetic risk factors may be useful to prioritize high-risk individuals and decrease the morbimortality caused by SARS-CoV2 and future pandemics.
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Affiliation(s)
- Mariana Angulo-Aguado
- Center for Research in Genetics and Genomics – CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - David Corredor-Orlandelli
- Center for Research in Genetics and Genomics – CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Juan Camilo Carrillo-Martínez
- Center for Research in Genetics and Genomics – CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Mónica Gonzalez-Cornejo
- Center for Research in Genetics and Genomics – CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Eliana Pineda-Mateus
- Center for Research in Genetics and Genomics – CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Carolina Rojas
- Center for Research in Genetics and Genomics – CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Paula Triana-Fonseca
- Department of Molecular Diagnosis, Genética Molecular de Colombia SAS, Bogotá, Colombia
| | - Nora Constanza Contreras Bravo
- Center for Research in Genetics and Genomics – CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Adrien Morel
- Center for Research in Genetics and Genomics – CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | | | - Carlos M. Restrepo
- Center for Research in Genetics and Genomics – CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Dora Janeth Fonseca-Mendoza
- Center for Research in Genetics and Genomics – CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
- Dora Janeth Fonseca-Mendoza
| | - Oscar Ortega-Recalde
- Center for Research in Genetics and Genomics – CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
- *Correspondence: Oscar Ortega-Recalde
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12
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Kotlík P, Marková S, Horníková M, Escalante MA, Searle JB. The Bank Vole (Clethrionomys glareolus) as a Model System for Adaptive Phylogeography in the European Theater. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.866605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The legacy of climatic changes during the Pleistocene glaciations allows inferences to be made about the patterns and processes associated with range expansion/colonization, including evolutionary adaptation. With the increasing availability of population genomic data, we have the opportunity to examine these questions in detail and in a variety of non-traditional model species. As an exemplar, here we review more than two decades of work by our group and others that illustrate the potential of a single “non-model model” mammal species - the bank vole (Clethrionomys glareolus), which is particularly well suited to illustrate the complexities that may be associated with range expansion and the power of genomics (and other datasets) to uncover them. We first summarize early phylogeographic work using mitochondrial DNA and then describe new phylogeographic insights gained from population genomic analysis of genome-wide SNP data to highlight the bank vole as one of the most compelling examples of a forest mammal, that survived in cryptic extra-Mediterranean (“northern”) glacial refugia in Europe, and as one of the species in which substantial replacement and mixing of lineages originating from different refugia occurred during end-glacial colonization. Our studies of bank vole hemoglobin structure and function, as well as our recent ecological niche modeling study examining differences among bank vole lineages, led us to develop the idea of “adaptive phylogeography.” This is what we call the study of the role of adaptive differences among populations in shaping phylogeographic patterns. Adaptive phylogeography provides a link between past population history and adaptation that can ultimately help predict the potential of future species responses to climate change. Because the bank vole is part of a community of organisms whose range has repeatedly contracted and then expanded in the past, what we learn from the bank vole will be useful for our understanding of a broad range of species.
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13
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Mendoza-Revilla J, Chacón-Duque JC, Fuentes-Guajardo M, Ormond L, Wang K, Hurtado M, Villegas V, Granja V, Acuña-Alonzo V, Jaramillo C, Arias W, Barquera R, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Badillo Rivera KM, Nieves-Colón MA, Gignoux CR, Wojcik GL, Moreno-Estrada A, Hünemeier T, Ramallo V, Schuler-Faccini L, Gonzalez-José R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Balding D, Fumagalli M, Adhikari K, Ruiz-Linares A, Hellenthal G. Disentangling Signatures of Selection Before and After European Colonization in Latin Americans. Mol Biol Evol 2022; 39:6565306. [PMID: 35460423 PMCID: PMC9034689 DOI: 10.1093/molbev/msac076] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.
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Affiliation(s)
- Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Louise Ormond
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom
| | - Ke Wang
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,National School of Anthropology and History, Mexico City, Mexico
| | | | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | | | - Maria A Nieves-Colón
- Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Christopher R Gignoux
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Genevieve L Wojcik
- Bloomberg School of Public Health, John Hopkins University, Baltimore, MD, USA
| | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Tábita Hünemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | | | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | | | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, Australia
| | - Matteo Fumagalli
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China.,Aix-Marseille Université, CNRS, EFS, ADES, Marseille, France
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom
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14
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Cuadros-Espinoza S, Laval G, Quintana-Murci L, Patin E. The genomic signatures of natural selection in admixed human populations. Am J Hum Genet 2022; 109:710-726. [PMID: 35259336 DOI: 10.1016/j.ajhg.2022.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
Admixture has been a pervasive phenomenon in human history, extensively shaping the patterns of population genetic diversity. There is increasing evidence to suggest that admixture can also facilitate genetic adaptation to local environments, i.e., admixed populations acquire beneficial mutations from source populations, a process that we refer to as "adaptive admixture." However, the role of adaptive admixture in human evolution and the power to detect it remain poorly characterized. Here, we use extensive computer simulations to evaluate the power of several neutrality statistics to detect natural selection in the admixed population, assuming multiple admixture scenarios. We show that statistics based on admixture proportions, Fadm and LAD, show high power to detect mutations that are beneficial in the admixed population, whereas other statistics, including iHS and FST, falsely detect neutral mutations that have been selected in the source populations only. By combining Fadm and LAD into a single, powerful statistic, we scanned the genomes of 15 worldwide, admixed populations for signatures of adaptive admixture. We confirm that lactase persistence and resistance to malaria have been under adaptive admixture in West Africans and in Malagasy, North Africans, and South Asians, respectively. Our approach also uncovers other cases of adaptive admixture, including APOL1 in Fulani nomads and PKN2 in East Indonesians, involved in resistance to infection and metabolism, respectively. Collectively, our study provides evidence that adaptive admixture has occurred in human populations whose genetic history is characterized by periods of isolation and spatial expansions resulting in increased gene flow.
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15
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Acosta-Uribe J, Aguillón D, Cochran JN, Giraldo M, Madrigal L, Killingsworth BW, Singhal R, Labib S, Alzate D, Velilla L, Moreno S, García GP, Saldarriaga A, Piedrahita F, Hincapié L, López HE, Perumal N, Morelo L, Vallejo D, Solano JM, Reiman EM, Surace EI, Itzcovich T, Allegri R, Sánchez-Valle R, Villegas-Lanau A, White CL, Matallana D, Myers RM, Browning SR, Lopera F, Kosik KS. A neurodegenerative disease landscape of rare mutations in Colombia due to founder effects. Genome Med 2022; 14:27. [PMID: 35260199 PMCID: PMC8902761 DOI: 10.1186/s13073-022-01035-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 02/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Colombian population, as well as those in other Latin American regions, arose from a recent tri-continental admixture among Native Americans, Spanish invaders, and enslaved Africans, all of whom passed through a population bottleneck due to widespread infectious diseases that left small isolated local settlements. As a result, the current population reflects multiple founder effects derived from diverse ancestries. METHODS We characterized the role of admixture and founder effects on the origination of the mutational landscape that led to neurodegenerative disorders under these historical circumstances. Genomes from 900 Colombian individuals with Alzheimer's disease (AD) [n = 376], frontotemporal lobar degeneration-motor neuron disease continuum (FTLD-MND) [n = 197], early-onset dementia not otherwise specified (EOD) [n = 73], and healthy participants [n = 254] were analyzed. We examined their global and local ancestry proportions and screened this cohort for deleterious variants in disease-causing and risk-conferring genes. RESULTS We identified 21 pathogenic variants in AD-FTLD related genes, and PSEN1 harbored the majority (11 pathogenic variants). Variants were identified from all three continental ancestries. TREM2 heterozygous and homozygous variants were the most common among AD risk genes (102 carriers), a point of interest because the disease risk conferred by these variants differed according to ancestry. Several gene variants that have a known association with MND in European populations had FTLD phenotypes on a Native American haplotype. Consistent with founder effects, identity by descent among carriers of the same variant was frequent. CONCLUSIONS Colombian demography with multiple mini-bottlenecks probably enhanced the detection of founder events and left a proportionally higher frequency of rare variants derived from the ancestral populations. These findings demonstrate the role of genomically defined ancestry in phenotypic disease expression, a phenotypic range of different rare mutations in the same gene, and further emphasize the importance of inclusiveness in genetic studies.
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Affiliation(s)
- Juliana Acosta-Uribe
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - David Aguillón
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | | | - Margarita Giraldo
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
- Instituto Neurológico de Colombia (INDEC), Medellín, Colombia
| | - Lucía Madrigal
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Bradley W Killingsworth
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Rijul Singhal
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Sarah Labib
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Diana Alzate
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Lina Velilla
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Sonia Moreno
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Gloria P García
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Amanda Saldarriaga
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Francisco Piedrahita
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Liliana Hincapié
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Hugo E López
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Nithesh Perumal
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Leonilde Morelo
- Department of Internal Medicine, School of Medicine, Universidad del Sinú, Montería, Colombia
| | - Dionis Vallejo
- Department of Neurology, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Juan Marcos Solano
- Department of Neurology, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | | | - Ezequiel I Surace
- Laboratorio de Enfermedades Neurodegenerativas (Fleni-CONICET), Buenos Aires, Argentina
| | - Tatiana Itzcovich
- Laboratorio de Enfermedades Neurodegenerativas (Fleni-CONICET), Buenos Aires, Argentina
| | - Ricardo Allegri
- Centro de Memoria y Envejecimiento (Fleni-CONICET), Buenos Aires, Argentina
| | - Raquel Sánchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
| | - Andrés Villegas-Lanau
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Charles L White
- Neuropathology Section, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Diana Matallana
- Instituto de Envejecimiento, Department of Psychiatry, School of Medicine, Pontifical Xaverian University, Bogotá, Colombia
- Department of Mental Health, Hospital Universitario Santa Fe de Bogotá, Bogotá, Colombia
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia.
| | - Kenneth S Kosik
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.
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16
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Chande AT, Nagar SD, Rishishwar L, Mariño-Ramírez L, Medina-Rivas MA, Valderrama-Aguirre AE, Jordan IK, Gallo JE. The Impact of Ethnicity and Genetic Ancestry on Disease Prevalence and Risk in Colombia. Front Genet 2021; 12:690366. [PMID: 34650589 PMCID: PMC8507149 DOI: 10.3389/fgene.2021.690366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
Currently, the vast majority of genomic research cohorts are made up of participants with European ancestry. Genomic medicine will only reach its full potential when genomic studies become more broadly representative of global populations. We are working to support the establishment of genomic medicine in developing countries in Latin America via studies of ethnically and ancestrally diverse Colombian populations. The goal of this study was to analyze the effect of ethnicity and genetic ancestry on observed disease prevalence and predicted disease risk in Colombia. Population distributions of Colombia's three major ethnic groups - Mestizo, Afro-Colombian, and Indigenous - were compared to disease prevalence and socioeconomic indicators. Indigenous and Mestizo ethnicity show the highest correlations with disease prevalence, whereas the effect of Afro-Colombian ethnicity is substantially lower. Mestizo ethnicity is mostly negatively correlated with six high-impact health conditions and positively correlated with seven of eight common cancers; Indigenous ethnicity shows the opposite effect. Malaria prevalence in particular is strongly correlated with ethnicity. Disease prevalence co-varies across geographic regions, consistent with the regional distribution of ethnic groups. Ethnicity is also correlated with regional variation in human development, partially explaining the observed differences in disease prevalence. Patterns of genetic ancestry and admixture for a cohort of 624 individuals from Medellín were compared to disease risk inferred via polygenic risk scores (PRS). African genetic ancestry is most strongly correlated with predicted disease risk, whereas European and Native American ancestry show weaker effects. African ancestry is mostly positively correlated with disease risk, and European ancestry is mostly negatively correlated. The relationships between ethnicity and disease prevalence do not show an overall correspondence with the relationships between ancestry and disease risk. We discuss possible reasons for the divergent health effects of ethnicity and ancestry as well as the implication of our results for the development of precision medicine in Colombia.
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Affiliation(s)
- Aroon T Chande
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Shashwat Deepali Nagar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Lavanya Rishishwar
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Leonardo Mariño-Ramírez
- PanAmerican Bioinformatics Institute, Cali, Colombia.,National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, United States
| | - Miguel A Medina-Rivas
- Centro de Investigación en Biodiversidad y Hábitat, Universidad Tecnológica del Chocó, Quibdó, Colombia
| | - Augusto E Valderrama-Aguirre
- Biomedical Research Institute (COL0082529), Cali, Colombia.,Department of Biomedical Sciences, Universidad Santiago de Cali, Cali, Colombia.,Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
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17
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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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18
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Isshiki M, Naka I, Kimura R, Nishida N, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R, Ohashi J. Admixture with indigenous people helps local adaptation: admixture-enabled selection in Polynesians. BMC Ecol Evol 2021; 21:179. [PMID: 34551727 PMCID: PMC8456657 DOI: 10.1186/s12862-021-01900-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 08/25/2021] [Indexed: 01/08/2023] Open
Abstract
Background Homo sapiens have experienced admixture many times in the last few thousand years. To examine how admixture affects local adaptation, we investigated genomes of modern Polynesians, who are shaped through admixture between Austronesian-speaking people from Southeast Asia (Asian-related ancestors) and indigenous people in Near Oceania (Papuan-related ancestors). Methods In this study local ancestry was estimated across the genome in Polynesians (23 Tongan subjects) to find the candidate regions of admixture-enabled selection contributed by Papuan-related ancestors. Results The mean proportion of Papuan-related ancestry across the Polynesian genome was estimated as 24.6% (SD = 8.63%), and two genomic regions, the extended major histocompatibility complex (xMHC) region on chromosome 6 and the ATP-binding cassette transporter sub-family C member 11 (ABCC11) gene on chromosome 16, showed proportions of Papuan-related ancestry more than 5 SD greater than the mean (> 67.8%). The coalescent simulation under the assumption of selective neutrality suggested that such signals of Papuan-related ancestry enrichment were caused by positive selection after admixture (false discovery rate = 0.045). The ABCC11 harbors a nonsynonymous SNP, rs17822931, which affects apocrine secretory cell function. The approximate Bayesian computation indicated that, in Polynesian ancestors, a strong positive selection (s = 0.0217) acted on the ancestral allele of rs17822931 derived from Papuan-related ancestors. Conclusions Our results suggest that admixture with Papuan-related ancestors contributed to the rapid local adaptation of Polynesian ancestors. Considering frequent admixture events in human evolution history, the acceleration of local adaptation through admixture should be a common event in humans. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01900-y.
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Affiliation(s)
- Mariko Isshiki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0125, Japan
| | - Nao Nishida
- Genome Medical Science Project, Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, 272-8516, Japan
| | - Takuro Furusawa
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, 606-8501, Japan
| | - Kazumi Natsuhara
- Department of International Health and Nursing, Faculty of Nursing, Toho University, Tokyo, 143-0015, Japan
| | - Taro Yamauchi
- Faculty of Health Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Minato Nakazawa
- Graduate School of Health Sciences, Kobe University, Kobe, 654-0142, Japan
| | - Takafumi Ishida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Tsukasa Inaoka
- Department of Human Ecology, Faculty of Agriculture, Saga University, Saga, 840-8502, Japan
| | - Yasuhiro Matsumura
- Faculty of Health and Nutrition, Bunkyo University, Chigasaki, 253-8550, Japan
| | | | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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19
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Romero-Sánchez C, Hernández N, Chila-Moreno L, Jiménez K, Padilla D, Bello-Gualtero JM, Bautista-Molano W. HLA-B Allele, Genotype, and Haplotype Frequencies in a Group of Healthy Individuals in Colombia. J Clin Rheumatol 2021; 27:S148-S152. [PMID: 33790206 DOI: 10.1097/rhu.0000000000001671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The sequencing of alleles of the HLA-B, a human leukocyte antigen (HLA) class I gene, was established as the most polymorphic of chromosome 6 and of the entire human genome. In this locus, the HLA-B*27 allele is highly polymorphic and has clinical relevance. Literature about the subtypes and singular frequency of these alleles in Colombia's healthy population is scarce. OBJECTIVE The aim of this study was to establish the HLA-B allele, genotype, and haplotype frequencies in a healthy Colombian population and analyze their association with the sex and geographical distribution of the individuals studied. METHODS This is a nonexperimental and descriptive study. The data from whole-blood samples whose HLA genes were genotyped by protocol with the Luminex 100/200 xMAP technology were evaluated. HLA-B*27 positivity was confirmed by the new-generation sequencing technology. The associations between the HLA-B alleles and demographic variables were evaluated by χ2 and Fisher exact tests. RESULTS Twenty-seven HLA-B genotypes were identified in 255 individuals, with the highest frequencies for HLA-B*35 (44.7%), B*40 (19.6%), and B*44 (16.8%). Additionally, 89 HLA-B alleles were found; the most common were HLA-B*35:01 (6.7%) and B*40:02 (6.5%). Nine individuals tested positive for the HLA-B*27 allele with genotype and allele frequencies of 3.5% and 1.8%, respectively; the HLA-B*27:05:02 subtype predominated. CONCLUSIONS Here, we report the most common HLA-B allele, genotype, and haplotype frequencies in a healthy Colombian population group and analyzed their association with the sex and geographical distribution of the individuals studied. Results for the HLA-B*27 allele confirm racial mixing in Colombia with a high degree of Caucasian influence, as well as the repopulation of Colombia's central region, attributed to the migration phenomena. Results agree with data published in Colombia that was obtained from cord blood samples.
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Affiliation(s)
| | - Natalia Hernández
- Bacteriology Program, Faculty of Basic Sciences, Universidad Colegio Mayor de Cundinamarca, Bogotá
| | - Lorena Chila-Moreno
- Clinical Immunology Group, Hospital Militar Central, School of Medicine, Universidad Militar Nueva Granada
| | - Karen Jiménez
- Pediatric Rheumatology Program, Faculty of Medicine, Universidad El Bosque
| | - Diana Padilla
- Rheumatology Program, Faculty of Medicine Universidad de la Sabana, Universidad de La Sabana, Chia, Colombia
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20
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Casares-Marfil D, Guillen-Guio B, Lorenzo-Salazar JM, Rodríguez-Pérez H, Kerick M, Jaimes-Campos MA, Díaz ML, Estupiñán E, Echeverría LE, González CI, Martin J, Flores C, Acosta-Herrera M. Admixture mapping analysis reveals differential genetic ancestry associated with Chagas disease susceptibility in the Colombian population. Hum Mol Genet 2021; 30:2503-2512. [PMID: 34302177 PMCID: PMC8643504 DOI: 10.1093/hmg/ddab213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 01/02/2023] Open
Abstract
Chagas disease is an infection caused by the parasite Trypanosoma cruzi, endemic in Latino America. Leveraging the three-way admixture between Native American (AMR), European (EUR) and African (AFR) populations in Latin Americans, we aimed to better understand the genetic basis of Chagas disease by performing an admixture mapping study in a Colombian population. A two-stage study was conducted, and subjects were classified as seropositive and seronegative for T. cruzi. In stage 1, global and local ancestries were estimated using reference data from the 1000 Genomes Project (1KGP) and local ancestry associations were performed by logistic regression models. The AMR ancestry showed a protective association with Chagas disease within the Major Histocompatibility Complex region (OR = 0.74, 95%CI = 0.66-0.83, lowest p-value = 4.53x10-8). The fine mapping assessment on imputed genotypes combining data from stage 1 and 2 from an independent Colombian cohort, revealed nominally associated variants in high linkage disequilibrium with the top signal (rs2032134, OR = 0.93, 95%CI = 0.90-0.97, p-value = 3.54x10-4) in the previously associated locus. To assess ancestry-specific adaptive signals, a selective sweep scan in an AMR reference population from 1KGP together with an in silico functional analysis highlighted the Tripartite Motif family and the Human Leukocyte Antigen (HLA) genes, with crucial role in the immune response against pathogens. Furthermore, these analyses emphasized the macrophages, neutrophils, and eosinophils, as key players in the defense against T. cruzi. This first admixture mapping study in Chagas disease provided novel insights underlying the host immune response in the pathogenesis of this neglected disease.
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Affiliation(s)
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Martin Kerick
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Mayra A Jaimes-Campos
- Grupo de Inmunología y Epidemiología Molecular, Escuela de Microbiología, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Martha L Díaz
- Grupo de Inmunología y Epidemiología Molecular, Escuela de Microbiología, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Elkyn Estupiñán
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.,Grupo de Inmunología y Epidemiología Molecular, Escuela de Microbiología, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Luis E Echeverría
- Heart Failure and Heart Transplant Clinic, Fundación Cardiovascular de Colombia, Floridablanca, Colombia
| | - Clara I González
- Grupo de Inmunología y Epidemiología Molecular, Escuela de Microbiología, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Javier Martin
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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21
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Ongaro L, Mondal M, Flores R, Marnetto D, Molinaro L, Alarcón-Riquelme ME, Moreno-Estrada A, Mabunda N, Ventura M, Tambets K, Hellenthal G, Capelli C, Kivisild T, Metspalu M, Pagani L, Montinaro F. Continental-scale genomic analysis suggests shared post-admixture adaptation in the Americas. Hum Mol Genet 2021; 30:2123-2134. [PMID: 34196708 PMCID: PMC8561420 DOI: 10.1093/hmg/ddab177] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 01/05/2023] Open
Abstract
American populations are one of the most interesting examples of recently admixed groups, where ancestral components from three major continental human groups (Africans, Eurasians and Native Americans) have admixed within the last 15 generations. Recently, several genetic surveys focusing on thousands of individuals shed light on the geography, chronology and relevance of these events. However, even though gene flow could drive adaptive evolution, it is unclear whether and how natural selection acted on the resulting genetic variation in the Americas. In this study, we analysed the patterns of local ancestry of genomic fragments in genome-wide data for ~ 6000 admixed individuals from 10 American countries. In doing so, we identified regions characterized by a divergent ancestry profile (DAP), in which a significant over or under ancestral representation is evident. Our results highlighted a series of genomic regions with DAPs associated with immune system response and relevant medical traits, with the longest DAP region encompassing the human leukocyte antigen locus. Furthermore, we found that DAP regions are enriched in genes linked to cancer-related traits and autoimmune diseases. Then, analysing the biological impact of these regions, we showed that natural selection could have acted preferentially towards variants located in coding and non-coding transcripts and characterized by a high deleteriousness score. Taken together, our analyses suggest that shared patterns of post admixture adaptation occurred at a continental scale in the Americas, affecting more often functional and impactful genomic variants.
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Affiliation(s)
- Linda Ongaro
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Mayukh Mondal
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Rodrigo Flores
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Davide Marnetto
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Ludovica Molinaro
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Marta E Alarcón-Riquelme
- Department of Medical Genomics, GENYO. Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica, Av de la Ilustración 114, Parque Tecnológico de la Salud (PTS), 18016, Granada, Spain
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | - Nedio Mabunda
- Instituto Nacional de Saúde, Distrito de Marracuene, Estrada Nacional N°1, Província de Maputo, Maputo, 1120, Mozambique
| | - Mario Ventura
- Department of Biology-Genetics, University of Bari, Bari, 70126, Italy
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, UK.,Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Toomas Kivisild
- Department of Human Genetics, KU Leuven, Herestraat 49 - box 602, B-3000, Leuven, Belgium
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia.,Department of Biology, University of Padua, Padua, Italy
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia.,Department of Biology-Genetics, University of Bari, Bari, 70126, Italy
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22
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Chande AT, Rishishwar L, Ban D, Nagar SD, Conley AB, Rowell J, Valderrama-Aguirre AE, Medina-Rivas MA, Jordan IK. The Phenotypic Consequences of Genetic Divergence between Admixed Latin American Populations: Antioquia and Chocó, Colombia. Genome Biol Evol 2021; 12:1516-1527. [PMID: 32681795 PMCID: PMC7513793 DOI: 10.1093/gbe/evaa154] [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] [Accepted: 07/12/2020] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies have uncovered thousands of genetic variants that are associated with a wide variety of human traits. Knowledge of how trait-associated variants are distributed within and between populations can provide insight into the genetic basis of group-specific phenotypic differences, particularly for health-related traits. We analyzed the genetic divergence levels for 1) individual trait-associated variants and 2) collections of variants that function together to encode polygenic traits, between two neighboring populations in Colombia that have distinct demographic profiles: Antioquia (Mestizo) and Chocó (Afro-Colombian). Genetic ancestry analysis showed 62% European, 32% Native American, and 6% African ancestry for Antioquia compared with 76% African, 10% European, and 14% Native American ancestry for Chocó, consistent with demography and previous results. Ancestry differences can confound cross-population comparison of polygenic risk scores (PRS); however, we did not find any systematic bias in PRS distributions for the two populations studied here, and population-specific differences in PRS were, for the most part, small and symmetrically distributed around zero. Both genetic differentiation at individual trait-associated single nucleotide polymorphisms and population-specific PRS differences between Antioquia and Chocó largely reflected anthropometric phenotypic differences that can be readily observed between the populations along with reported disease prevalence differences. Cases where population-specific differences in genetic risk did not align with observed trait (disease) prevalence point to the importance of environmental contributions to phenotypic variance, for both infectious and complex, common disease. The results reported here are distributed via a web-based platform for searching trait-associated variants and PRS divergence levels at http://map.chocogen.com (last accessed August 12, 2020).
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Affiliation(s)
- Aroon T Chande
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Lavanya Rishishwar
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Dongjo Ban
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Shashwat D Nagar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Andrew B Conley
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Jessica Rowell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Augusto E Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia.,Biomedical Research Institute (COL0082529), Cali, Colombia.,Universidad Santiago de Cali, Colombia
| | - Miguel A Medina-Rivas
- PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia.,Centro de Investigación en Biodiversidad y Hábitat, Universidad Tecnológica del Chocó, Quibdó, Colombia
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
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23
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Horníková M, Marková S, Lanier HC, Searle JB, Kotlík P. A dynamic history of admixture from Mediterranean and Carpathian glacial refugia drives genomic diversity in the bank vole. Ecol Evol 2021; 11:8215-8225. [PMID: 34188881 PMCID: PMC8216894 DOI: 10.1002/ece3.7652] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/22/2021] [Indexed: 01/26/2023] Open
Abstract
Understanding the historical contributions of differing glacial refugia is key to evaluating the roles of microevolutionary forces, such as isolation, introgression, and selection in shaping genomic diversity in present-day populations. In Europe, where both Mediterranean and extra-Mediterranean (e.g., Carpathian) refugia of the bank vole (Clethrionomys glareolus) have been identified, mtDNA indicates that extra-Mediterranean refugia were the main source of colonization across the species range, while Mediterranean peninsulas harbor isolated, endemic lineages. Here, we critically evaluate this hypothesis using previously generated genomic data (>6,000 SNPs) for over 800 voles, focusing on genomic contributions to bank voles in central Europe, a key geographic area in considering range-wide colonization. The results provide clear evidence that both extra-Mediterranean (Carpathian) and Mediterranean (Spanish, Calabrian, and Balkan) refugia contributed to the ancestry and genomic diversity of bank vole populations across Europe. Few strong barriers to dispersal and frequent admixture events in central Europe have led to a prominent mid-latitude peak in genomic diversity. Although the genomic contribution of the centrally located Carpathian refugium predominates, populations in different parts of Europe have admixed origins from Mediterranean (28%-47%) and the Carpathian (53%-72%) sources. We suggest that the admixture from Mediterranean refugia may have provisioned adaptive southern alleles to more northern populations, facilitating the end-glacial spread of the admixed populations and contributing to increased bank vole diversity in central Europe. This study adds critical details to the complex end-glacial colonization history of this well-studied organism and underscores the importance of genomic data in phylogeographic interpretation.
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Affiliation(s)
- Michaela Horníková
- Laboratory of Molecular Ecology Institute of Animal Physiology and Genetics of the Czech Academy of Sciences Liběchov Czech Republic
- Department of Zoology, Faculty of Science Charles University Prague Czech Republic
| | - Silvia Marková
- Laboratory of Molecular Ecology Institute of Animal Physiology and Genetics of the Czech Academy of Sciences Liběchov Czech Republic
| | - Hayley C Lanier
- Department of Biology, Program in Ecology & Evolutionary Biology University of Oklahoma Norman OK USA
- Sam Noble Museum University of Oklahoma Norman OK USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology Institute of Animal Physiology and Genetics of the Czech Academy of Sciences Liběchov Czech Republic
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24
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Deng Z, Zhen J, Harrison GF, Zhang G, Chen R, Sun G, Yu Q, Nemat-Gorgani N, Guethlein LA, He L, Tang M, Gao X, Cai S, Palmer WH, Shortt JA, Gignoux CR, Carrington M, Zou H, Parham P, Hong W, Norman PJ. Adaptive Admixture of HLA Class I Allotypes Enhanced Genetically Determined Strength of Natural Killer Cells in East Asians. Mol Biol Evol 2021; 38:2582-2596. [PMID: 33616658 PMCID: PMC8136484 DOI: 10.1093/molbev/msab053] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Human natural killer (NK) cells are essential for controlling infection, cancer, and fetal development. NK cell functions are modulated by interactions between polymorphic inhibitory killer cell immunoglobulin-like receptors (KIR) and polymorphic HLA-A, -B, and -C ligands expressed on tissue cells. All HLA-C alleles encode a KIR ligand and contribute to reproduction and immunity. In contrast, only some HLA-A and -B alleles encode KIR ligands and they focus on immunity. By high-resolution analysis of KIR and HLA-A, -B, and -C genes, we show that the Chinese Southern Han (CHS) are significantly enriched for interactions between inhibitory KIR and HLA-A and -B. This enrichment has had substantial input through population admixture with neighboring populations, who contributed HLA class I haplotypes expressing the KIR ligands B*46:01 and B*58:01, which subsequently rose to high frequency by natural selection. Consequently, over 80% of Southern Han HLA haplotypes encode more than one KIR ligand. Complementing the high number of KIR ligands, the CHS KIR locus combines a high frequency of genes expressing potent inhibitory KIR, with a low frequency of those expressing activating KIR. The Southern Han centromeric KIR region encodes strong, conserved, inhibitory HLA-C-specific receptors, and the telomeric region provides a high number and diversity of inhibitory HLA-A and -B-specific receptors. In all these characteristics, the CHS represent other East Asians, whose NK cell repertoires are thus enhanced in quantity, diversity, and effector strength, likely augmenting resistance to endemic viral infections.
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Affiliation(s)
- Zhihui Deng
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Jianxin Zhen
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
- Central Laboratory, Shenzhen Baoan Women’s and Children’s Hospital, Shenzhen, Guangdong, P. R. China
| | - Genelle F Harrison
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Guobin Zhang
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Rui Chen
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Ge Sun
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Qiong Yu
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Liumei He
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Mingzhong Tang
- Clinical Laboratory, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, P. R. China
| | - Xiaojiang Gao
- Inflammatory Cell Dynamics Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Siqi Cai
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - William H Palmer
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Jonathan A Shortt
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Christopher R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD21702, and Ragon Institute of MGH, Cambridge, MA, USA
| | - Hongyan Zou
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wenxu Hong
- Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
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25
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Sengupta D, Choudhury A, Fortes-Lima C, Aron S, Whitelaw G, Bostoen K, Gunnink H, Chousou-Polydouri N, Delius P, Tollman S, Gómez-Olivé FX, Norris S, Mashinya F, Alberts M, Hazelhurst S, Schlebusch CM, Ramsay M. Genetic substructure and complex demographic history of South African Bantu speakers. Nat Commun 2021; 12:2080. [PMID: 33828095 PMCID: PMC8027885 DOI: 10.1038/s41467-021-22207-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 02/10/2021] [Indexed: 02/01/2023] Open
Abstract
South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ~400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.
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Affiliation(s)
- Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cesar Fortes-Lima
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Shaun Aron
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gavin Whitelaw
- KwaZulu-Natal Museum, Pietermaritzburg, South Africa
- School of Geography, Archaeology & Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa
| | - Koen Bostoen
- UGent Centre for Bantu Studies, Department of Languages and Cultures, Ghent University, Ghent, Belgium
| | - Hilde Gunnink
- UGent Centre for Bantu Studies, Department of Languages and Cultures, Ghent University, Ghent, Belgium
| | - Natalia Chousou-Polydouri
- Department of Comparative Linguistic Science and Center for the Interdisciplinary Study of Language Evolution, University of Zürich, Zürich, Switzerland
| | - Peter Delius
- Department of History, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shane Norris
- MRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Felistas Mashinya
- Department of Pathology and Medical Sciences; School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - Marianne Alberts
- Department of Pathology and Medical Sciences; School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Carina M Schlebusch
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- SciLifeLab, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, 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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26
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Soler AM, Piellusch BF, da Silveira L, Pedroso GA, López P, Savio E, Sonati MDF, da Luz J. Alpha thalassemia and alpha-MRE haplotypes in Uruguayan patients with microcytosis and hypochromia without anemia. Genet Mol Biol 2021; 44:e20200399. [PMID: 33769430 PMCID: PMC7995682 DOI: 10.1590/1678-4685-gmb-2020-0399] [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: 10/30/2020] [Accepted: 02/10/2021] [Indexed: 11/21/2022] Open
Abstract
Alpha thalassemia is the most common genetic disorder across the world, being the α-3.7 deletion the most frequent mutation. In order to analyze the spectrum and origin of alpha thalassemia mutations in Uruguay, we obtained a sample of 168 unrelated outpatients with normal hemoglobin levels with microcytosis and hypochromia from two cities: Montevideo and Salto. The presence of α-thalassemia mutations was investigated by gap-PCR, restriction endonucleases analysis and HBA2 and HBA1 genes sequencing, whereas the alpha-MRE haplotypes were investigated by sequencing. We found 55 individuals (32.7%) with α-thalassemia mutations, 51(30.4%) carrying the -α3.7 deletion, one with the -α4.2 deletion and three having the rare punctual mutation HBA2:c.-59C>T. Regarding alpha-MRE analysis, we observed a significant higher frequency of haplotype D, characteristic of African populations, in the sample with the -α3.7 deletion. These results show that α-thalassemia mutations are an important determinant of microcytosis and hypochromia in Uruguayan patients with microcytosis and hypochromia without anemia, mainly due to the -α3.7 deletion. The alpha-MRE haplotypes and the α-thalassemia mutations spectrum suggest a predominant, but not exclusive, African origin of these mutations in Uruguay.
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Affiliation(s)
- Ana María Soler
- Universidad de la República (UdelaR), Centro Universitario Regional (CENUR) Litoral Norte, Departamento de Ciencias Biológicas, Laboratorio de Genética Molecular Humana, Salto, Uruguay
| | - Bruna Facanali Piellusch
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patología Clínica, Campinas, SP, Brazil
| | - Lorena da Silveira
- Universidad de la República (UdelaR), Centro Universitario Regional (CENUR) Litoral Norte, Departamento de Ciencias Biológicas, Laboratorio de Genética Molecular Humana, Salto, Uruguay
| | - Gisele Audrei Pedroso
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patología Clínica, Campinas, SP, Brazil
| | - Pablo López
- Universidad de la República (UdelaR), Facultad de Medicina, Hospital de Clínicas Manuel Quintela, Departamento de Laboratorio de Patología Clínica, Montevideo, Uruguay
| | - Enrique Savio
- Administración de los Servicios de Salud del Estado (ASSE), Hospital Departamental de Salto, Servicio de Laboratorio Clínico, Salto, Uruguay
| | - María de Fatima Sonati
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patología Clínica, Campinas, SP, Brazil
| | - Julio da Luz
- Universidad de la República (UdelaR), Centro Universitario Regional (CENUR) Litoral Norte, Departamento de Ciencias Biológicas, Laboratorio de Genética Molecular Humana, Salto, Uruguay
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27
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Abstract
Throughout human history, large-scale migrations have facilitated the formation of populations with ancestry from multiple previously separated populations. This process leads to subsequent shuffling of genetic ancestry through recombination, producing variation in ancestry between populations, among individuals in a population, and along the genome within an individual. Recent methodological and empirical developments have elucidated the genomic signatures of this admixture process, bringing previously understudied admixed populations to the forefront of population and medical genetics. Under this theme, we present a collection of recent PLOS Genetics publications that exemplify recent progress in human genetic admixture studies, and we discuss potential areas for future work.
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Affiliation(s)
- Katharine L. Korunes
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
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28
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Hamid I, Korunes KL, Beleza S, Goldberg A. Rapid adaptation to malaria facilitated by admixture in the human population of Cabo Verde. eLife 2021; 10:e63177. [PMID: 33393457 PMCID: PMC7815310 DOI: 10.7554/elife.63177] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
Humans have undergone large migrations over the past hundreds to thousands of years, exposing ourselves to new environments and selective pressures. Yet, evidence of ongoing or recent selection in humans is difficult to detect. Many of these migrations also resulted in gene flow between previously separated populations. These recently admixed populations provide unique opportunities to study rapid evolution in humans. Developing methods based on distributions of local ancestry, we demonstrate that this sort of genetic exchange has facilitated detectable adaptation to a malaria parasite in the admixed population of Cabo Verde within the last ~20 generations. We estimate that the selection coefficient is approximately 0.08, one of the highest inferred in humans. Notably, we show that this strong selection at a single locus has likely affected patterns of ancestry genome-wide, potentially biasing demographic inference. Our study provides evidence of adaptation in a human population on historical timescales.
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Affiliation(s)
- Iman Hamid
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | | | - Sandra Beleza
- Department of Genetics and Genome Biology, University of LeicesterLeicesterUnited Kingdom
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
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29
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Mario-Vásquez JE, Naranjo-González CA, Montiel J, Zuluaga LM, Vásquez AM, Tobón-Castaño A, Bedoya G, Segura C. Association of variants in IL1B, TLR9, TREM1, IL10RA, and CD3G and Native American ancestry on malaria susceptibility in Colombian populations. INFECTION GENETICS AND EVOLUTION 2020; 87:104675. [PMID: 33316430 DOI: 10.1016/j.meegid.2020.104675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/19/2020] [Accepted: 12/09/2020] [Indexed: 12/24/2022]
Abstract
Host genetics is an influencing factor in the manifestation of infectious diseases. In this study, the association of mild malaria with 28 variants in 16 genes previously reported in other populations and/or close to ancestry-informative markers (AIMs) selected was evaluated in an admixed 736 Colombian population sample. Additionally, the effect of genetic ancestry on phenotype expression was explored. For this purpose, the ancestral genetic composition of Turbo and El Bagre was determined. A higher Native American ancestry trend was found in the population with lower malaria susceptibility [odds ratio (OR) = 0.416, 95% confidence interval (95% CI) = 0.234-0.740, P = 0.003]. Three AIMs presented significant associations with the disease phenotype (MID1752, MID921, and MID1586). The first two were associated with greater malaria susceptibility (D/D, OR = 2.23, 95% CI = 1.06-4.69, P = 0.032 and I/D-I/I, OR = 2.14, 95% CI = 1.18-3.87, P = 0.011, respectively), and the latter has a protective effect on the appearance of malaria (I/I, OR = 0.18, 95% CI = 0.08-0.40, P < 0.0001). After adjustment by age, sex, municipality, and genetic ancestry, genotype association analysis showed evidence of association with malaria susceptibility for variants in or near IL1B, TLR9, TREM1, IL10RA, and CD3G genes: rs1143629-IL1B (G/A-A/A, OR = 0.41, 95% CI = 0.21-0.78, P = 0.0051), rs352139-TLR9 (T/T, OR = 0.28, 95% CI = 0.11-0.72, P = 0.0053), rs352140-TLR9 (C/C, OR = 0.41, 95% CI = 0.20-0.87, P = 0.019), rs2234237-TREM1 (T/A-A/A, OR = 0.43, 95% CI = 0.23-0.79, P = 0.0056), rs4252246-IL10RA (C/A-A/A, OR = 2.11, 95% CI = 1.18-3.75, P = 0.01), and rs1561966-CD3G (A/A, OR = 0.20, 95% CI = 0.06-0.69, P = 0.0058). The results showed the participation of genes involved in immunological processes and suggested an effect of ancestral genetic composition over the traits analyzed. Compared to the paisa population (Antioquia), Turbo and El Bagre showed a strong decrease in European ancestry and an increase in African and Native American ancestries. Also, a novel association of two single nucleotide polymorphisms with malaria susceptibility was identified in this study.
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Affiliation(s)
- Jorge Eliécer Mario-Vásquez
- Grupo Genética Molecular (GENMOL), Universidad de Antioquia, Carrera 53 No. 61-30, Lab 430. Medellín, Colombia
| | | | - Jehidys Montiel
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Lina M Zuluaga
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Ana M Vásquez
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Alberto Tobón-Castaño
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Gabriel Bedoya
- Grupo Genética Molecular (GENMOL), Universidad de Antioquia, Carrera 53 No. 61-30, Lab 430. Medellín, Colombia
| | - Cesar Segura
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia.
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30
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Abstract
Canalization refers to the evolution of populations such that the number of individuals who deviate from the optimum trait, or experience disease, is minimized. In the presence of rapid cultural, environmental, or genetic change, the reverse process of decanalization may contribute to observed increases in disease prevalence. This review starts by defining relevant concepts, drawing distinctions between the canalization of populations and robustness of individuals. It then considers evidence pertaining to three continuous traits and six domains of disease. In each case, existing genetic evidence for genotype-by-environment interactions is insufficient to support a strong inference of decanalization, but we argue that the advent of genome-wide polygenic risk assessment now makes an empirical evaluation of the role of canalization in preventing disease possible. Finally, the contributions of both rare and common variants to congenital abnormality and adult onset disease are considered in light of a new kerplunk model of genetic effects.
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Affiliation(s)
- Greg Gibson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
| | - Kristine A Lacek
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
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31
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Minimal Erythema Dose: Correlation with Fitzpatrick Skin Type and Concordance Between Methods of Erythema Assessment in a Patient Sample in Colombia. ACTAS DERMO-SIFILIOGRAFICAS 2020. [DOI: 10.1016/j.adengl.2019.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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32
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Minimal Erythema Dose: Correlation with Fitzpatrick Skin Type and Concordance Between Methods of Erythema Assessment in a Patient Sample in Colombia. ACTAS DERMO-SIFILIOGRAFICAS 2020; 111:390-397. [PMID: 32408973 DOI: 10.1016/j.ad.2019.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/21/2019] [Accepted: 12/24/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND AND OBJECTIVE The minimal erythema dose (MED), an essential measurement in studies of skin photosensitivity, requires establishing MED values for specific populations, given genetic variation. Different ways to assess erythema are also relevant. We aimed to determine MED values in a sample of Colombian patients and correlations between MED and Fitzpatrick skin type. We also studied concordance correlation between MEDs and two alternative ways to assess erythema. PATIENTS AND METHODS Cross-sectional study of 113 individuals in Bogotá, Colombia. We used a solar simulator to measure UV-A radiation and combined UV-A and UV-B (UVA+UVB) radiation, o se podría suprimir este término porque UVA y UVB son términos conocidos for MED calculation. Narrowband UV-B (NBUVB) radiation was measured in a phototherapy cabin. Erythema was assessed visually and with a Mexameter MX 18 device. RESULTS The median MEDs of UVA+UVB radiation were 22mJ/cm2 for Fitzpatrick skin typesI andII, and 33 and 43mJ/cm2, respectively, for typesIII andIV. The MEDs of UV-A radiation were 22, 42, 86, and 100J/cm2 for typesI, II, III, andIV, respectively. The MEDs of NBUVB light were 390, 550, 770, and 885mJ/cm2 for the 4 skin types. The correlation between MEDs and skin types ranged from 0.5 to 0.69. Lin's concordance correlation coefficients between visual and Mexameter assessments of erythema were greater than 0.8 in all cases. CONCLUSION This study allowed us to understand MED values for UV-A, UVA+UVB, and NBUVB according to different skin types in the Colombian population. Concordance correlation coefficients between the different methods of erythema assessment were very good. Correlations between MEDs and skin types were moderate to good.
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33
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Lavalett L, Ortega H, Barrera LF. Human Alveolar and Splenic Macrophage Populations Display a Distinct Transcriptomic Response to Infection With Mycobacterium tuberculosis. Front Immunol 2020; 11:630. [PMID: 32373118 PMCID: PMC7186480 DOI: 10.3389/fimmu.2020.00630] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) infects alveolar macrophages (AMs), causing pulmonary tuberculosis (PTB), the most common form of the disease. Less frequently, Mtb is disseminated to many other organs and tissues, resulting in different extrapulmonary forms of TB. Nevertheless, very few studies have addressed the global mRNA response of human AMs, particularly from humans with the active form of the disease. Strikingly, almost no studies have addressed the response of human extrapulmonary macrophages to Mtb infection. In this pilot study, using microarray technology, we examined the transcriptomic ex vivo response of AMs from PTB patients (AMTBs) and AMs from control subjects (AMCTs) infected with two clinical isolates of Mtb. Furthermore, we also studied the infection response of human splenic macrophages (SMs) to Mtb isolates, as a model for extrapulmonary infection, and compared the transcriptomic response between AMs and SMs. Our results showed a striking difference in global mRNA profiles in response to infection between AMs and SMs, implicating a tissue-specific macrophage response to Mtb.
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Affiliation(s)
- Lelia Lavalett
- Grupo de Inmunología Celular e Inmunogenética, Facultad de Medicina, Instituto de Investigaciones Médicas, Universidad de Antioquia, Medellín, Colombia.,Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellín, Medellín, Colombia
| | - Hector Ortega
- Clínica Cardiovascular Santa María, Medellín, Colombia.,Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Luis F Barrera
- Grupo de Inmunología Celular e Inmunogenética, Facultad de Medicina, Instituto de Investigaciones Médicas, Universidad de Antioquia, Medellín, Colombia.,Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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34
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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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35
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Evolutionary and population (epi)genetics of immunity to infection. Hum Genet 2020; 139:723-732. [PMID: 32285198 DOI: 10.1007/s00439-020-02167-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/07/2020] [Indexed: 12/29/2022]
Abstract
Immune response is one of the functions that have been more strongly targeted by natural selection during human evolution. The evolutionary genetic dissection of the immune system has greatly helped to distinguish genes and functions that are essential, redundant or advantageous for human survival. It is also becoming increasingly clear that admixture between early Eurasians with now-extinct hominins such as Neanderthals or Denisovans, or admixture between modern human populations, can be beneficial for human adaptation to pathogen pressures. In this review, we discuss how the integration of population genetics with functional genomics in diverse human populations can inform about the changes in immune functions related to major lifestyle transitions (e.g., from hunting and gathering to farming), the action of natural selection to the evolution of the immune system, and the history of past epidemics. We also highlight the need of expanding the characterization of the immune system to a larger array of human populations-particularly neglected human groups historically exposed to different pathogen pressures-to fully capture the relative contribution of genetic, epigenetic, and environmental factors to immune response variation in humans.
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Harismendy O, Kim J, Xu X, Ohno-Machado L. Evaluating and sharing global genetic ancestry in biomedical datasets. J Am Med Inform Assoc 2020; 26:457-461. [PMID: 30869786 PMCID: PMC6433181 DOI: 10.1093/jamia/ocy194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/14/2018] [Accepted: 12/28/2018] [Indexed: 11/13/2022] Open
Abstract
Genetic ancestry is a critical co-factor to study phenotype-genotype associations using cohorts of human subjects. Most publicly available molecular datasets are, however, missing this information or only share self-reported race and ethnicity, representing a limitation to identify and repurpose datasets to investigate the contribution of ancestry to diseases and traits. We propose an analytical framework to enrich the metadata from publicly available cohorts with genetic ancestry information and a resulting diversity score at continental resolution, calculated directly from the data. We illustrate this framework using The Cancer Genome Atlas datasets searched through the DataMed Data Discovery Index. Data repositories and contributors can use this framework to provide genetic diversity measurements for controlled access datasets, minimizing the work involved in requesting a dataset that may ultimately prove inadequate for a researcher's purpose. With the increasing global scale of human genetics research, studies on disease risk and susceptibility would benefit greatly from the adequate estimation and sharing of genetic diversity in publicly available datasets following a framework such as the one presented.
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Affiliation(s)
- Olivier Harismendy
- Health Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA.,Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Jihoon Kim
- Health Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Xiaojun Xu
- Health Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Lucila Ohno-Machado
- Health Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA.,UC San Diego Health Department of Biomedical Informatics.,Health Services Research Division, San Diego Veterans Health Administration
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Norris ET, Rishishwar L, Chande AT, Conley AB, Ye K, Valderrama-Aguirre A, Jordan IK. Admixture-enabled selection for rapid adaptive evolution in the Americas. Genome Biol 2020; 21:29. [PMID: 32028992 PMCID: PMC7006128 DOI: 10.1186/s13059-020-1946-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/24/2020] [Indexed: 02/08/2023] Open
Abstract
Background Admixture occurs when previously isolated populations come together and exchange genetic material. We hypothesize that admixture can enable rapid adaptive evolution in human populations by introducing novel genetic variants (haplotypes) at intermediate frequencies, and we test this hypothesis through the analysis of whole genome sequences sampled from admixed Latin American populations in Colombia, Mexico, Peru, and Puerto Rico. Results Our screen for admixture-enabled selection relies on the identification of loci that contain more or less ancestry from a given source population than would be expected given the genome-wide ancestry frequencies. We employ a combined evidence approach to evaluate levels of ancestry enrichment at single loci across multiple populations and multiple loci that function together to encode polygenic traits. We find cross-population signals of African ancestry enrichment at the major histocompatibility locus on chromosome 6, consistent with admixture-enabled selection for enhanced adaptive immune response. Several of the human leukocyte antigen genes at this locus, such as HLA-A, HLA-DRB51, and HLA-DRB5, show independent evidence of positive selection prior to admixture, based on extended haplotype homozygosity in African populations. A number of traits related to inflammation, blood metabolites, and both the innate and adaptive immune system show evidence of admixture-enabled polygenic selection in Latin American populations. Conclusions The results reported here, considered together with the ubiquity of admixture in human evolution, suggest that admixture serves as a fundamental mechanism that drives rapid adaptive evolution in human populations.
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Affiliation(s)
- Emily T Norris
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, USA.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, USA.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Aroon T Chande
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, USA.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Andrew B Conley
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Kaixiong Ye
- Department of Genetics, University of Georgia, Athens, GA, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Biomedical Research Institute (COL0082529), Cali, Colombia.,Universidad Santiago de Cali, Cali, Colombia
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, USA. .,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, USA. .,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.
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Gomez-Lopera N, Alfaro JM, Leal SM, Pineda-Trujillo N. Type 1 diabetes loci display a variety of native American and African ancestries in diseased individuals from Northwest Colombia. World J Diabetes 2019; 10:534-545. [PMID: 31798789 PMCID: PMC6885725 DOI: 10.4239/wjd.v10.i11.534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) is a complex disease with a higher incidence in Europeans than other populations. The Colombians Living in Medellin (CLM) is admixed with ancestry contributions from Europeans, Native Americans (NAT) and Africans (AFR).
AIM Our aim was to analyze the genetic admixture component at candidate T1D loci in Colombian individuals with the disease.
METHODS Seventy-four ancestry informative markers (AIMs), which tagged 41 T1D candidate loci/genes, were tested by studying a cohort of 200 Northwest Colombia diseased individuals. T1D status was classified by testing for glutamic acid decarboxylase (GAD-65 kDa) and protein tyrosine-like antigen-2 auto-antibodies in serum samples. Candidate loci/genes included HLA, INS, PTPN22, CTLA4, IL2RA, SUMO4, CLEC16A, IFIH1, EFR3B, IL7R, NRP1 and RNASEH1, amongst others. The 1,000 genome database was used to analyze data from 94 individuals corresponding to the reference CLM. As the data did not comply with a normal distribution, medians were compared between groups using the Mann-Whitney U-test.
RESULTS Both T1D patients and individuals from CLM displayed mainly European ancestry (61.58 vs 62.06) followed by Native American (27.34 vs 27.46) and to a lesser extent the AFR ancestry (10.28 vs 10.65) components. However, compared to CLM, ancestry of T1D patients displayed a decrease of NAT ancestry at gene EFR3B (24.30 vs 37.10) and an increase at genes IFIH1 (32.07 vs 14.99) and IL7R (52.18 vs 39.18). Also, for gene NRP1 (36.67 vs 0.003), we observed a non-AFR contribution (attributed to NAT). Autoimmune patients (positive for any of two auto-antibodies) displayed lower NAT ancestry than idiopathic patients at the MHC region (20.36 vs 31.88). Also, late onset patients presented with greater AFR ancestry than early onset patients at gene IL7R (19.96 vs 6.17). An association analysis showed that, even after adjusting for admixture, an association exists for at least seven such AIMs, with the strongest findings on chromosomes 5 and 10 (gene IL7R, P = 5.56 × 10-6 and gene NRP1, P = 8.70 × 10-19, respectively).
CONCLUSION Although Colombian T1D patients have globally presented with higher European admixture, specific T1D loci have displayed varying levels of Native American and AFR ancestries in diseased individuals.
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Affiliation(s)
- Natalia Gomez-Lopera
- Grupo Mapeo Genetico, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín 050010470, Colombia
| | - Juan M Alfaro
- Grupo Mapeo Genetico, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín 050010470, Colombia
- Sección de Endocrinología Pediátrica, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín 050010470, Colombia
| | - Suzanne M Leal
- Center for Statistical Genetics, Columbia University, New York, NY 10032, United States
| | - Nicolas Pineda-Trujillo
- Grupo Mapeo Genetico, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellín 050010470, Colombia
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Jordan IK, Rishishwar L, Conley AB. Native American admixture recapitulates population-specific migration and settlement of the continental United States. PLoS Genet 2019; 15:e1008225. [PMID: 31545791 PMCID: PMC6756731 DOI: 10.1371/journal.pgen.1008225] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 05/31/2019] [Indexed: 11/19/2022] Open
Abstract
European and African descendants settled the continental US during the 17th-19th centuries, coming into contact with established Native American populations. The resulting admixture among these groups yielded a significant reservoir of Native American ancestry in the modern US population. We analyzed the patterns of Native American admixture seen for the three largest genetic ancestry groups in the US population: African descendants, Western European descendants, and Spanish descendants. The three groups show distinct Native American ancestry profiles, which are indicative of their historical patterns of migration and settlement across the country. Native American ancestry in the modern African descendant population does not coincide with local geography, instead forming a single group with origins in the southeastern US, consistent with the Great Migration of the early 20th century. Western European descendants show Native American ancestry that tracks their geographic origins across the US, indicative of ongoing contact during westward expansion, and Native American ancestry can resolve Spanish descendant individuals into distinct local groups formed by more recent migration from Mexico and Puerto Rico. We found an anomalous pattern of Native American ancestry from the US southwest, which most likely corresponds to the Nuevomexicano descendants of early Spanish settlers to the region. We addressed a number of controversies surrounding this population, including the extent of Sephardic Jewish ancestry. Nuevomexicanos are less admixed than nearby Mexican-American individuals, with more European and less Native American and African ancestry, and while they do show demonstrable Sephardic Jewish ancestry, the fraction is no greater than seen for other New World Spanish descendant populations.
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Affiliation(s)
- I. King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Lavanya Rishishwar
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Andrew B. Conley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
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40
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Genetic variability analysis in a population from Bogotá: Towards a haplotype map. ACTA ACUST UNITED AC 2019; 39:595-600. [PMID: 31584772 PMCID: PMC7357366 DOI: 10.7705/biomedica.4753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Indexed: 11/21/2022]
Abstract
Introducción. Los proyectos del mapa de haplotipos (HapMap) y de los 1.000 genomas han sido fundamentales para la compresión del componente genético de las enfermedades comunes y los fenotipos normales. Sin embargo, la variabilidad genética colombiana incluida en estos proyectos no es representativa del país. Objetivo. Contribuir al conocimiento de la variabilidad genética de la población colombiana a partir del estudio genómico de una muestra de individuos de Bogotá. Materiales y métodos. Se genotipificaron 2’372.784 marcadores genéticos de 32 individuos nacidos en Bogotá y de padres originarios de la misma ciudad utilizando la plataforma Illumina™. Los niveles de variabilidad genética se determinaron y se compararon con los datos disponibles de otras poblaciones del proyecto de los 1.000 genomas. Resultados. Los individuos analizados presentaron una variabilidad genética semejante a la de poblaciones con las que comparten ancestros. No obstante, a pesar de la poca diferenciación genética detectada en la población de Bogotá y en la de Medellín, el análisis de los componentes principales sugiere una composición genética diferente en las dos poblaciones. Conclusiones. El análisis genómico de la muestra de Bogotá permitió detectar similitudes y diferencias con otras poblaciones americanas. El aumento de tamaño de la muestra bogotana y la inclusión de muestras de otras regiones del país permitirán una mejor compresión de la variabilidad genética en Colombia, lo cual es fundamental para los estudios de salud humana, y la prevención y el tratamiento de enfermedades comunes en el país.
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Fernández-Ávila DG, Bernal-Macías S, Rincón-Riaño DN, Gutiérrez JM, Rosselli D. Prevalence of polymyalgia rheumatica in Colombia: data from the national health registry 2012–2016. Rheumatol Int 2019; 39:1631-1635. [PMID: 31327052 DOI: 10.1007/s00296-019-04387-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 07/16/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel G Fernández-Ávila
- Department of Internal Medicine, Rheumatology Unit, Hospital Universitario San Ignacio, Kra 7 No. 40-62, Bogotá, Colombia.
- Clinical Epidemiology and Biostatistics Department, Medical School, Pontificia Universidad Javeriana, Bogotá, Colombia.
| | - Santiago Bernal-Macías
- Department of Internal Medicine, Rheumatology Unit, Hospital Universitario San Ignacio, Kra 7 No. 40-62, Bogotá, Colombia
- Medicinal School, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Diana N Rincón-Riaño
- Rheumatology Service, Hospital Militar Central-Universidad Militar Nueva Granada, Bogotá, Colombia
| | - Juan M Gutiérrez
- Department of Internal Medicine, Rheumatology Unit, Hospital Universitario San Ignacio, Kra 7 No. 40-62, Bogotá, Colombia
- Medicinal School, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Diego Rosselli
- Clinical Epidemiology and Biostatistics Department, Medical School, Pontificia Universidad Javeriana, Bogotá, Colombia
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42
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Aristizabal-Duque R, Castiblanco E, Rodriguez I, Sossa-Briceño MP, Rodriguez-Martinez CE. Reference values for spirometric parameters in healthy children living in a Colombian city located at 2640 m altitude. Pediatr Pulmonol 2019; 54:886-893. [PMID: 30957980 DOI: 10.1002/ppul.24331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/06/2019] [Accepted: 03/24/2019] [Indexed: 11/07/2022]
Abstract
OBJECTIVES To identify the spirometric equations that are most appropriate for use in children and adolescents living in Bogota, Colombia after evaluating a set of relevant previously-developed equations, including the Global Lung Function Initiative (GLI) 2012 spirometry reference equations. METHODS Healthy children aged between 6 and 17 years that were attending two randomly-selected schools in Bogota were invited to participate in the study, from January 2017 to January 2018. All participants underwent spirometry, following the procedures recommended by the American Thoracic Society/European Respiratory Society (ATS/ERS) Task Force. To identify the model or group of models that best predict each spirometric parameter in our population, we performed extensive residuals analyses and constructed Bland-Altman plots. RESULTS Three hundred twenty-six spirometric tests (149 boys, 177 girls) formed the reference data set. Knudson and GLI-2012 spirometry reference equations proved to be the most accurate in predicting the majority of spirometry parameters in both sexes and both age groups, each providing the lowest median prediction error in the residual analyses or the narrowest limits of agreement in the Bland-Altman plots in approximately one-third of the spirometry parameters analyzed. CONCLUSION For the majority of spirometry parameters, we recommend the use of Knudson and GLI-2012 spirometry reference equations for evaluating the respiratory function of children living in Bogota, Colombia, a city located at an altitude of 2640 m. Future investigations should target additional spirometric equations from Latin American populations living at moderate to high altitude to improve the GLI-2012 equations.
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Affiliation(s)
| | - Edwin Castiblanco
- Department of Pediatric Pulmonology, School of Medicine, Universidad El Bosque, Bogota, Colombia
| | - Ingrid Rodriguez
- Department of Pediatric Pulmonology, School of Medicine, Universidad El Bosque, Bogota, Colombia
| | - Monica P Sossa-Briceño
- Department of Internal Medicine, School of Medicine, Universidad Nacional de Colombia, Bogota, Colombia
| | - Carlos E Rodriguez-Martinez
- Department of Pediatrics, School of Medicine, Universidad Nacional de Colombia, Bogota, Colombia.,Department of Pediatric Pulmonology and Pediatric Critical Care Medicine, School of Medicine, Universidad El Bosque, Bogota, Colombia
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43
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Norris ET, Rishishwar L, Wang L, Conley AB, Chande AT, Dabrowski AM, Valderrama-Aguirre A, Jordan IK. Assortative Mating on Ancestry-Variant Traits in Admixed Latin American Populations. Front Genet 2019; 10:359. [PMID: 31105740 PMCID: PMC6491930 DOI: 10.3389/fgene.2019.00359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 04/04/2019] [Indexed: 11/13/2022] Open
Abstract
Assortative mating is a universal feature of human societies, and individuals from ethnically diverse populations are known to mate assortatively based on similarities in genetic ancestry. However, little is currently known regarding the exact phenotypic cues, or their underlying genetic architecture, which inform ancestry-based assortative mating. We developed a novel approach, using genome-wide analysis of ancestry-specific haplotypes, to evaluate ancestry-based assortative mating on traits whose expression varies among the three continental population groups – African, European, and Native American – that admixed to form modern Latin American populations. Application of this method to genome sequences sampled from Colombia, Mexico, Peru, and Puerto Rico revealed widespread ancestry-based assortative mating. We discovered a number of anthropometric traits (body mass, height, and facial development) and neurological attributes (educational attainment and schizophrenia) that serve as phenotypic cues for ancestry-based assortative mating. Major histocompatibility complex (MHC) loci show population-specific patterns of both assortative and disassortative mating in Latin America. Ancestry-based assortative mating in the populations analyzed here appears to be driven primarily by African ancestry. This study serves as an example of how population genomic analyses can yield novel insights into human behavior.
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Affiliation(s)
- Emily T Norris
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Lu Wang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Andrew B Conley
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States
| | - Aroon T Chande
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Adam M Dabrowski
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | | | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
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44
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Nagar SD, Moreno AM, Norris ET, Rishishwar L, Conley AB, O'Neal KL, Vélez-Gómez S, Montes-Rodríguez C, Jaraba-Álvarez WV, Torres I, Medina-Rivas MA, Valderrama-Aguirre A, Jordan IK, Gallo JE. Population Pharmacogenomics for Precision Public Health in Colombia. Front Genet 2019; 10:241. [PMID: 30967898 PMCID: PMC6439339 DOI: 10.3389/fgene.2019.00241] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 03/04/2019] [Indexed: 11/13/2022] Open
Abstract
While genomic approaches to precision medicine hold great promise, they remain prohibitively expensive for developing countries. The precision public health paradigm, whereby healthcare decisions are made at the level of populations as opposed to individuals, provides one way for the genomics revolution to directly impact health outcomes in the developing world. Genomic approaches to precision public health require a deep understanding of local population genomics, which is still missing for many developing countries. We are investigating the population genomics of genetic variants that mediate drug response in an effort to inform healthcare decisions in Colombia. Our work focuses on two neighboring populations with distinct ancestry profiles: Antioquia and Chocó. Antioquia has primarily European genetic ancestry followed by Native American and African components, whereas Chocó shows mainly African ancestry with lower levels of Native American and European admixture. We performed a survey of the global distribution of pharmacogenomic variants followed by a more focused study of pharmacogenomic allele frequency differences between the two Colombian populations. Worldwide, we found pharmacogenomic variants to have both unusually high minor allele frequencies and high levels of population differentiation. A number of these pharmacogenomic variants also show anomalous effect allele frequencies within and between the two Colombian populations, and these differences were found to be associated with their distinct genetic ancestry profiles. For example, the C allele of the single nucleotide polymorphism (SNP) rs4149056 [Solute Carrier Organic Anion Transporter Family Member 1B1 (SLCO1B1)∗5], which is associated with an increased risk of toxicity to a commonly prescribed statin, is found at relatively high frequency in Antioquia and is associated with European ancestry. In addition to pharmacogenomic alleles related to increased toxicity risk, we also have evidence that alleles related to dosage and metabolism have large frequency differences between the two populations, which are associated with their specific ancestries. Using these findings, we have developed and validated an inexpensive allele-specific PCR assay to test for the presence of such population-enriched pharmacogenomic SNPs in Colombia. These results serve as an example of how population-centered approaches to pharmacogenomics can help to realize the promise of precision medicine in resource-limited settings.
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Affiliation(s)
- Shashwat Deepali Nagar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | | | - Emily T Norris
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Lavanya Rishishwar
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Andrew B Conley
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Kelly L O'Neal
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | | | | | | | | | - Miguel A Medina-Rivas
- PanAmerican Bioinformatics Institute, Cali, Colombia.,Centro de Investigación en Biodiversidad y Hábitat, Universidad Tecnológica del Chocó, Quibdó, Colombia
| | - Augusto Valderrama-Aguirre
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia.,Biomedical Research Institute, Cali, Colombia
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Juan Esteban Gallo
- PanAmerican Bioinformatics Institute, Cali, Colombia.,GenomaCES, Universidad CES, Medellín, Colombia
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45
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Human Immunology through the Lens of Evolutionary Genetics. Cell 2019; 177:184-199. [DOI: 10.1016/j.cell.2019.02.033] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 01/04/2023]
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46
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Ramirez Aguilar L, Acosta-Uribe J, Giraldo MM, Moreno S, Baena A, Alzate D, Cuastumal R, Aguillón D, Madrigal L, Saldarriaga A, Navarro A, Garcia GP, Aguirre-Acevedo DC, Geier EG, Cochran JN, Quiroz YT, Myers RM, Yokoyama JS, Kosik KS, Lopera F. Genetic origin of a large family with a novel PSEN1 mutation (Ile416Thr). Alzheimers Dement 2019; 15:709-719. [PMID: 30745123 DOI: 10.1016/j.jalz.2018.12.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 11/25/2022]
Abstract
INTRODUCTION A small percentage of Alzheimer's disease (AD) cases are caused by genetic mutations with autosomal dominant inheritance. We report a family with a novel variant in PSEN1. METHODS We performed clinical and genetic evaluation of 93 related individuals from a Colombian admixed population. 31 individuals had whole-genome sequencing. RESULTS Genetic analysis revealed a missense variant in PSEN1 (NM_000021.3: c.1247T>C p.Ile416Thr), which originated on an African haplotype and segregated with AD logarithm of the odds score of 6. Their clinical phenotype is similar to sporadic AD except for earlier age at onset: the mean age at onset for mild cognitive impairment was 47.6 years (standard deviation 5.83) and for dementia 51.6 years (standard deviation 5.03). DISCUSSION Ile416Thr is a novel pathogenic variant that causes AD in the sixth decade of life. The history of the region that included slave importation and admixtures within a confined geographic locale represents a "mini-population bottleneck" and subsequent emergence of a rare dominant mutation.
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Affiliation(s)
- Laura Ramirez Aguilar
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Juliana Acosta-Uribe
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia; Neuroscience Research Institute, University of California, Santa Barbara, CA, USA; Department of Molecular Cellular and Developmental Biology University of California, Santa Barbara, CA, USA
| | - Margarita M Giraldo
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Sonia Moreno
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Ana Baena
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Diana Alzate
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Rosario Cuastumal
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - David Aguillón
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Lucía Madrigal
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Amanda Saldarriaga
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Alexander Navarro
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Gloria P Garcia
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Daniel C Aguirre-Acevedo
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Ethan G Geier
- Department of Neurology, University of California, San Francisco, CA, USA
| | | | - Yakeel T Quiroz
- Departments of Psychiatry and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Kenneth S Kosik
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA; Department of Molecular Cellular and Developmental Biology University of California, Santa Barbara, CA, USA.
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Antioquia, Colombia
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Montalva N, Adhikari K, Liebert A, Mendoza-Revilla J, Flores SV, Mace R, Swallow DM. Adaptation to milking agropastoralism in Chilean goat herders and nutritional benefit of lactase persistence. Ann Hum Genet 2019; 83:11-22. [PMID: 30264486 PMCID: PMC6393766 DOI: 10.1111/ahg.12277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/05/2018] [Accepted: 07/06/2018] [Indexed: 12/31/2022]
Abstract
The genetic trait of lactase persistence (LP) evolved as an adaptation to milking pastoralism in the Old World and is a well-known example of positive natural selection in humans. However, the specific mechanisms conferring this selective advantage are unknown. To understand the relationship between milk drinking, LP, growth, reproduction, and survival, communities of the Coquimbo Region in Chile, with recent adoption of milking agropastoralism, were used as a model population. DNA samples and data on stature, reproduction, and diet were collected from 451 participants. Lactose tolerance tests were done on 41 of them. The European -13,910*T (rs4988235) was the only LP causative variant found, showing strong association (99.6%) with LP phenotype. Models of associations of inferred LP status and milk consumption, with fertility, mortality, height, and weight were adjusted with measures of ancestry and relatedness to control for population structure. Although we found no statistically significant effect of LP on fertility, a significant effect (P = 0.002) was observed of LP on body mass index (BMI) in males and of BMI on fertility (P = 0.003). These results fail to support a causal relationship between LP and fertility yet suggest the idea of a nutritional advantage of LP. Furthermore, the proportion of European ancestry around the genetic region of -13,910*T is significantly higher (P = 0.008) than the proportion of European ancestry genome-wide, providing evidence of recent positive selection since European-Amerindian admixture. This signature was absent in nonpastoralist Latin American populations, supporting the hypothesis of specific adaptation to milking agropastoralism in the Coquimbo communities.
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Affiliation(s)
- Nicolás Montalva
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom
- Department of Anthropology, Human Evolutionary Ecology Group, University College London, 14 Taviton St, London, WC1H 0BW, United Kingdom
- Departamento de Antropología, Facultad de Ciencias Sociales y Jurídicas, Universidad de Tarapacá, 384 Calle Cardenal Caro, Arica, Chile
| | - Kaustubh Adhikari
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom
- Department of Cell & Developmental Biology, University College London, Anatomy Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Anke Liebert
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Javier Mendoza-Revilla
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 430 Honorario Delgado, Lima 31, Perú
| | - Sergio V Flores
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, 1045 Av. Capitan Ignacio Carrera Pinto, Nunoa, 7800284, Chile
| | - Ruth Mace
- Department of Anthropology, Human Evolutionary Ecology Group, University College London, 14 Taviton St, London, WC1H 0BW, United Kingdom
| | - Dallas M Swallow
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom
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Norris ET, Wang L, Conley AB, Rishishwar L, Mariño-Ramírez L, Valderrama-Aguirre A, Jordan IK. Genetic ancestry, admixture and health determinants in Latin America. BMC Genomics 2018; 19:861. [PMID: 30537949 PMCID: PMC6288849 DOI: 10.1186/s12864-018-5195-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Modern Latin American populations were formed via genetic admixture among ancestral source populations from Africa, the Americas and Europe. We are interested in studying how combinations of genetic ancestry in admixed Latin American populations may impact genomic determinants of health and disease. For this study, we characterized the impact of ancestry and admixture on genetic variants that underlie health- and disease-related phenotypes in population genomic samples from Colombia, Mexico, Peru, and Puerto Rico. RESULTS We analyzed a total of 347 admixed Latin American genomes along with 1102 putative ancestral source genomes from Africans, Europeans, and Native Americans. We characterized the genetic ancestry, relatedness, and admixture patterns for each of the admixed Latin American genomes, finding a spectrum of ancestry proportions within and between populations. We then identified single nucleotide polymorphisms (SNPs) with anomalous ancestry-enrichment patterns, i.e. SNPs that exist in any given Latin American population at a higher frequency than expected based on the population's genetic ancestry profile. For this set of ancestry-enriched SNPs, we inspected their phenotypic impact on disease, metabolism, and the immune system. All four of the Latin American populations show ancestry-enrichment for a number of shared pathways, yielding evidence of similar selection pressures on these populations during their evolution. For example, all four populations show ancestry-enriched SNPs in multiple genes from immune system pathways, such as the cytokine receptor interaction, T cell receptor signaling, and antigen presentation pathways. We also found SNPs with excess African or European ancestry that are associated with ancestry-specific gene expression patterns and play crucial roles in the immune system and infectious disease responses. Genes from both the innate and adaptive immune system were found to be regulated by ancestry-enriched SNPs with population-specific regulatory effects. CONCLUSIONS Ancestry-enriched SNPs in Latin American populations have a substantial effect on health- and disease-related phenotypes. The concordant impact observed for same phenotypes across populations points to a process of adaptive introgression, whereby ancestry-enriched SNPs with specific functional utility appear to have been retained in modern populations by virtue of their effects on health and fitness.
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Affiliation(s)
- Emily T Norris
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory (ABiL), Atlanta, GA, USA
| | - Lu Wang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Andrew B Conley
- IHRC-Georgia Tech Applied Bioinformatics Laboratory (ABiL), Atlanta, GA, USA
| | - Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory (ABiL), Atlanta, GA, USA
| | - Leonardo Mariño-Ramírez
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Biomedical Research Institute, Faculty of Health, Universidad Libre-Seccional Cali, Cali, Valle del Cauca, Colombia
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA. .,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia. .,IHRC-Georgia Tech Applied Bioinformatics Laboratory (ABiL), Atlanta, GA, USA.
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Useche YM, Ribeiro-Alves M, Restrepo BN, Salgado DM, Narváez CF, Campo O, Avendaño E, Martínez C, Chacon-Duque JC, Bedoya G. Single-Nucleotide Polymorphisms in NOD1, RIPK2, MICB, PLCE1, TNF, and IKBKE Genes Associated with Symptomatic Dengue in Children from Colombia. Viral Immunol 2018; 31:613-623. [DOI: 10.1089/vim.2018.0028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Yerly Magnolia Useche
- Laboratorio de Genética Molecular, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Marcelo Ribeiro-Alves
- Laboratório de Pesquisa Clínica em DST-AIDS, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil
| | - Berta-Nelly Restrepo
- Instituto Colombiano de Medicina Tropical ICMT, Universidad CES, Sabaneta, Colombia
| | - Doris Martha Salgado
- Unidad de Infectología Pediátrica, Hospital Universitario de Neiva, Neiva, Colombia
- Programa de Medicina, Facultad de Salud, Universidad Surcolombiana, Neiva, Colombia
| | | | - Omer Campo
- Laboratorio de Genética Molecular, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Efrén Avendaño
- Grupo de Ciencias Básicas Aplicadas del Tecnológico de Antioquia, Tecnológico de Antioquia—Institución Universitaria, Medellín, Colombia
| | - Catalina Martínez
- Laboratorio de Genética Molecular, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan Camilo Chacon-Duque
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Gabriel Bedoya
- Laboratorio de Genética Molecular, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
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50
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Londoño J, Peláez Ballestas I, Cuervo F, Angarita I, Giraldo R, Rueda JC, Ballesteros JG, Baquero R, Forero E, Cardiel M, Saldarriaga E, Vásquez A, Arias S, Valero L, González C, Ramírez J, Toro C, Santos AM. Prevalence of rheumatic disease in Colombia according to the Colombian Rheumatology Association (COPCORD) strategy. Prevalence study of rheumatic disease in Colombian population older than 18 years. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.rcreue.2018.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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