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Hermansyah D, Firsty NN, Siagian RHN, Dwinda NN. Intercontinental Comparison of Immunohistochemical Subtypes Among Individuals With Breast Cancer in South-East Asia and South America: A Scoping Systematic Review and Meta-Analysis of Observational Studies. World J Oncol 2024; 15:355-371. [PMID: 38751698 PMCID: PMC11092420 DOI: 10.14740/wjon1788] [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: 01/29/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
Background Breast cancer (BC) remains a significant global concern, particularly among developing countries in South-East Asia (SEA) and South America (SA). The socioeconomic burdens of oncologic care in those countries were often originated from limited accessibility on attainable therapeutic options and reliability on identifying essential information of cancer cells, i.e., immunohistochemical (IHC) subtyping to determine suitable approaches. The triple-negative breast cancer (TNBC) is among the most aggressive category in breast malignancy, therefore, requiring more specific molecular pathway blocking to exhaust the cells. However, large-scale epidemiological investigation on its rate among BC remains unavailable to date. This study aimed to describe the prevalence of TNBC in the SEA and SA continents since it may guide the future direction of oncologic research and trials. Methods This review focuses on observational studies from the SEA and SA continents from the last decade. Each study represents its country or cities, period of observation, population size, and the TNBC-BC rate as the main outcomes. Therefore, we may also limit the reporting bias originated from same-patient data on the specific occasions. The analysis will be derived to SEA-SA comparison, plus SEA/SA-specific session as processed in Comprehensive Meta-Analysis (CMA) version 3.0. The statistical analysis will be performed in random effects model (REM) within 95% confidence interval (CI). Results From 46 studies included in the final analysis with a total enlisted population of 34,346 unique individuals with BC, the TNBC rate was higher in the SEA compared to the SA region (19.3% vs. 15.7%; P < 0.05 in 95% CI), with the highest prevalence observed in Vietnam (22.4%) and Peru (17.8%), if it was restricted on countries with two or more studies. Interestingly, both Laos and Argentina possessed significant differences compared to other countries within their respective continents, with the highest and lowest TNBC rates (P < 0.05). Conclusions The IHC characteristics in SEA differ from those in the SA continent as mainly represented by TNBC prevalence, possibly shaping the course of future trials in the respective region based on IHC expressivity status.
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Affiliation(s)
- Dedy Hermansyah
- Division of Surgical Oncology, Department of Surgery, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Naufal Nandita Firsty
- Graduate Program in Medicine, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
- Putri Hijau Level II Military Hospital, Medan, Indonesia
| | - Ruth Hasian Nami Siagian
- Graduate Program in Medicine, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
- Datu Sanggul Rantau Public Hospital, Tapin, Indonesia
| | - Najwa Nandita Dwinda
- Undergraduate Program in Public Health, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
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Vallejo-Azar MN, Arenaza B, Elizalde Acevedo B, Alba-Ferrara L, Samengo I, Bendersky M, Gonzalez PN. Hemispheric asymmetries in cortical grey matter of gyri and sulci in modern human populations from South America. J Anat 2024; 244:815-830. [PMID: 38183319 PMCID: PMC11021627 DOI: 10.1111/joa.14001] [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: 09/16/2021] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024] Open
Abstract
Structural asymmetries of brain regions associated with lateralised functions have been extensively studied. However, there are fewer morphometric analyses of asymmetries of the gyri and sulci of the entire cortex. The current study assessed cortical asymmetries in a sample of healthy adults (N = 175) from an admixed population from South America. Grey matter volume and surface area of 66 gyri and sulci were quantified on T1 magnetic resonance images. The departure from zero of the differences between left and right hemispheres (L-R), a measure of directional asymmetry (DA), the variance of L-R, and an index of fluctuating asymmetry (FA) were evaluated for each region. Significant departures from perfect symmetry were found for most cortical gyri and sulci. Regions showed leftward asymmetry at the population level in the frontal lobe and superior lateral parts of the parietal lobe. Rightward asymmetry was found in the inferior parietal, occipital, frontopolar, and orbital regions, and the cingulate (anterior, middle, and posterior-ventral). Despite this general pattern, several sulci showed the opposite DA compared to the neighbouring gyri, which remarks the need to consider the neurobiological differences in gyral and sulcal development in the study of structural asymmetries. The results also confirm the absence of DA in most parts of the inferior frontal gyrus and the precentral region. This study contributes with data on populations underrepresented in the databases used in neurosciences. Among its findings, there is agreement with previous results obtained in populations of different ancestry and some discrepancies in the middle frontal and medial parietal regions. A significant DA not reported previously was found for the volume of long and short insular gyri and the central sulcus of the insula, frontomarginal, transverse frontopolar, paracentral, and middle and posterior parts of the cingulate gyrus and sulcus, gyrus rectus, occipital pole, and olfactory sulcus, as well as for the volume and area of the transverse collateral sulcus and suborbital sulcus. Also, several parcels displayed significant variability in the left-right differences, which can be partially attributable to developmental instability, a source of FA. Moreover, a few gyri and sulci displayed ideal FA with non-significant departures from perfect symmetry, such as subcentral and posterior cingulate gyri and sulci, inferior frontal and fusiform gyri, and the calcarine, transverse collateral, precentral, and orbital sulci. Overall, these results show that asymmetries are ubiquitous in the cerebral cortex.
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Affiliation(s)
- Mariana N Vallejo-Azar
- Estudios en Neurociencias y Sistemas Complejos, ENyS (CONICET, Universidad Nacional Arturo Jauretche, Hospital El Cruce), Florencio Varela, Argentina
| | - Bautista Arenaza
- Department of Medical Physics and Instituto Balseiro, Centro Atómico Bariloche, CONICET, Bariloche, Argentina
| | - Bautista Elizalde Acevedo
- Estudios en Neurociencias y Sistemas Complejos, ENyS (CONICET, Universidad Nacional Arturo Jauretche, Hospital El Cruce), Florencio Varela, Argentina
- Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET-Universidad Austral, Bariloche, Argentina
| | - Lucía Alba-Ferrara
- Estudios en Neurociencias y Sistemas Complejos, ENyS (CONICET, Universidad Nacional Arturo Jauretche, Hospital El Cruce), Florencio Varela, Argentina
| | - Inés Samengo
- Department of Medical Physics and Instituto Balseiro, Centro Atómico Bariloche, CONICET, Bariloche, Argentina
| | - Mariana Bendersky
- Estudios en Neurociencias y Sistemas Complejos, ENyS (CONICET, Universidad Nacional Arturo Jauretche, Hospital El Cruce), Florencio Varela, Argentina
- Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula N Gonzalez
- Estudios en Neurociencias y Sistemas Complejos, ENyS (CONICET, Universidad Nacional Arturo Jauretche, Hospital El Cruce), Florencio Varela, Argentina
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Solloch UV, Giani AS, Pattillo Garnham MI, Sauter J, Bernas SN, Lange V, Barriga F, Fernández-Viña MA, Schmidt AH. HLA allele and haplotype frequencies of registered stem cell donors in Chile. Front Immunol 2023; 14:1175135. [PMID: 37313414 PMCID: PMC10258311 DOI: 10.3389/fimmu.2023.1175135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/15/2023] [Indexed: 06/15/2023] Open
Abstract
Patients in need of hematopoietic stem cell transplantation often rely on unrelated stem cell donors matched in certain human leukocyte antigen (HLA) genes. Donor search is complicated by the extensive allelic variability of the HLA system. Therefore, large registries of potential donors are maintained in many countries worldwide. Population-specific HLA characteristics determine the registry benefits for patients and also the need for further regional donor recruitment. In this work, we analyzed HLA allele and haplotype frequencies of donors of DKMS Chile, the first Chilean donor registry, with self-assessed "non-Indigenous" (n=92,788) and "Mapuche" (n=1,993) ancestry. We identified HLA alleles that were distinctly more abundant in the Chilean subpopulations than in worldwide reference populations, four of them particularly characteristic for the Mapuche subpopulation, namely B*39:09g, B*35:09, DRB1*04:07g, and DRB1*16:02g. Both population subsamples carried haplotypes of both Native American and European origin at high frequencies, reflecting Chile's complex history of admixture and immigration. Matching probability analysis revealed limited benefits for Chilean patients (both non-Indigenous and Mapuche) from donor registries of non-Chilean donors, thus indicating a need for ongoing significant donor recruitment efforts in Chile.
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Marrodan M, Piedrabuena MA, Gaitan MI, Fiol MP, Ysrraelit MC, Carnero Conttenti E, Lopez PA, Peuchot V, Correale J. Performance of McDonald 2017 multiple sclerosis diagnostic criteria and evaluation of genetic ancestry in patients with a first demyelinating event in Argentina. Mult Scler 2023; 29:559-567. [PMID: 36942953 DOI: 10.1177/13524585231157276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
BACKGROUND Information on performance of multiple sclerosis (MS) diagnostic criteria is scarce for populations from Latin America, Asia, or the Caribbean. OBJECTIVE To assess performance of revised 2017 McDonald criteria as well as evaluate genetic ancestry in a group of MS patients from Argentina experiencing a debut demyelinating event. METHODS Demographic and clinical characteristics, cerebrospinal fluid (CSF), and magnetic resonance imaging (MRI) findings and new T2 lesions were recorded at baseline and during relapses. Diagnostic accuracy in predicting conversion to clinically defined MS (CDMS) based on initial imaging applying revised 2017 criteria was evaluated and genetic ancestry-informative markers analyzed. RESULTS Of 201 patients experiencing their first demyelinating event (median follow-up 60 months), CDMS was confirmed in 67. We found 2017 diagnostic criteria were more sensitive (84% vs 67%) and less specific (14% vs 33%) than 2010 criteria, especially in a group of patients revised separately, presenting positive oligoclonal bands (88% vs 8%). Genetic testing performed in 128 cases showed 72% of patients were of European ancestry and 27% presented genetic admixture. CONCLUSION 2017 McDonald criteria showed higher sensitivity and lower specificity compared with 2010 criteria, shortening both time-to-diagnosis and time-to-treatment implementation.
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Affiliation(s)
| | | | | | - Marcela P Fiol
- Departamento de Neurología, Fleni, Buenos Aires, Argentina
| | | | - Edgar Carnero Conttenti
- Unidad de Neuroinmunología, Departamento de Neurociencias, Hospital Alemán, Buenos Aires, Argentina
| | - Pablo Adrian Lopez
- Unidad de Neuroinmunología, Departamento de Neurociencias, Hospital Alemán, Buenos Aires, Argentina
| | | | - Jorge Correale
- Departamento de Neurología, Fleni, Buenos Aires, Argentina/Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), CONICET/Universidad de Buenos Aires, Buenos Aires, Argentina
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Nguidi M, Flores R, Ribeiro J, Garzón A, Calvopiña M, Zapata S, Cabrera A, Yepez I, Gomes V, Gusmão L, Burgos G. The paternal heritage of self-declared Ecuadorian indigenous people. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Simão F, Ribeiro J, Vullo C, Catelli L, Gomes V, Xavier C, Huber G, Bodner M, Quiroz A, Ferreira AP, Carvalho EF, Parson W, Gusmão L. The Ancestry of Eastern Paraguay: A Typical South American Profile with a Unique Pattern of Admixture. Genes (Basel) 2021; 12:1788. [PMID: 34828394 PMCID: PMC8625094 DOI: 10.3390/genes12111788] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/25/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022] Open
Abstract
Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay.
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Affiliation(s)
- Filipa Simão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Julyana Ribeiro
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Carlos Vullo
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team, Córdoba 14001, Argentina; (C.V.); (L.C.)
| | - Laura Catelli
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team, Córdoba 14001, Argentina; (C.V.); (L.C.)
| | - Verónica Gomes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4099-002 Porto, Portugal;
- Institute of Pathology and Molecular Immunology, University of Porto (IPATIMUP), 4099-002 Porto, Portugal
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Alfredo Quiroz
- Instituto de Previsión Social, Asunción 100153, Paraguay;
| | - Ana Paula Ferreira
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Elizeu F. Carvalho
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
- Forensic Science Program, The Pennsylvania State University, State College, PA 16801, USA
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
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Tamburrini C, de Saint Pierre M, Bravi CM, Bailliet G, Jurado Medina L, Velázquez IF, Real LE, Holley A, Tedeschi CM, Basso NG, Parolin ML. Uniparental origins of the admixed Argentine Patagonia. Am J Hum Biol 2021; 34:e23682. [PMID: 34533260 DOI: 10.1002/ajhb.23682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 09/01/2021] [Accepted: 09/06/2021] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES We aimed to contribute to the understanding of the ancient geographic origins of the uniparentally inherited markers in modern admixed Argentinian populations from central Patagonia with new information provided for the city of Trelew. We attempted to highlight the importance of combining different genetic markers when studying population history. METHODS The mtDNA control region sequence was typified in 89 individuals and 12 Y-STR and 15 Y-SNP loci were analyzed in 66 males. With these data, analysis of molecular variance and Network analyses were carried out. We exhaustively compared the modern data with ancient mtDNA information. Finally, we tested the differences in continental origins estimated by uniparental and previously published biparental markers. RESULTS Native American mtDNAs (53.9%) increased when maternal ancestors were born in the northern (81.8%) and southern (58.5%) regions of Argentina or in Chile (77.8%). Population substructure was only observed for Y-chromosome haplotypes. Some mtDNA haplogroups have been present in the area for at least ca. 2762-2430 and ca. 500 (D1g and D1g4 haplogroups) and ca. 6736 and ca. 6620 (C1b and C1c haplogroups) years, respectively. In contrast, haplogroups B2i2 and C1b13, frequent in modern Patagonia populations, had not been found in previous ancient DNA studies of the region. CONCLUSIONS The results suggest that Native American ancestry is well preserved in the region. Trelew samples had characteristic native mtDNA haplogroups previously described in Chilean and Argentine Patagonian populations, but not observed in ancient samples until now. These findings support the idea that these lineages have a recent regional origin. Finally, the estimated proportions of continental ancestry depend on the genetic marker analyzed.
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Affiliation(s)
- Camila Tamburrini
- Instituto de Diversidad y Evolución Austral, (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina
| | - Michelle de Saint Pierre
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago de Chile, Chile
| | - Claudio Marcelo Bravi
- Laboratorio de Genética Molecular Poblacional, IMBICE (CCT-CONICET, CIC-PBA), Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Graciela Bailliet
- Laboratorio de Genética Molecular Poblacional, IMBICE (CCT-CONICET, CIC-PBA), Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Laura Jurado Medina
- Laboratorio de Genética Molecular Poblacional, IMBICE (CCT-CONICET, CIC-PBA), Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | | | - Luciano Esteban Real
- Instituto de Diversidad y Evolución Austral, (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina
| | - Alfredo Holley
- Instituto de Diversidad y Evolución Austral, (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina
| | | | - Néstor Guillermo Basso
- Instituto de Diversidad y Evolución Austral, (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina
| | - María Laura Parolin
- Instituto de Diversidad y Evolución Austral, (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina
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Patterns of genetic diversity in Colombia for 38 indels used in human identification. Forensic Sci Int Genet 2021; 53:102495. [PMID: 33743518 DOI: 10.1016/j.fsigen.2021.102495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/06/2021] [Indexed: 01/15/2023]
Abstract
The current population of Colombia has a genetic heterogeneity resulting from different migrations from other continents and within the country. In addition, there are small groups in their territory that have remained isolated and therefore have a different genetic pool in relation to that of the neighbouring urban populations. This population stratification must be considered in forensic analysis, being more complex for markers with marked intercontinental differentiation. In this study, population differentiation in Colombian admixed, native, and Afro-descendant populations was evaluated for a group of 38 indels described for forensic use. Allelic frequencies and parameters of forensic relevance were determined in each of the groups defined based on population differentiation analyses. In addition to the differences found between population groups, the results show that the set of 38 indels analysed could be useful in studies of individual identification in Colombia. The exclusion power presented by this set of markers suggests the need for joint use with other markers, being able to complement the STRs in paternity cases. High levels of both power of discrimination and exclusion were found when complementing the 38 HID-indels with a second multiplex, for a total of 83 indels.
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Fernández Souto D, Rosello J, Lazo L, Veloso F, Gamba C, Kuperman S, Roca V. HLA diversity in the Argentinian Umbilical Cord Blood Bank: frequencies according to donor's reported ancestry and geographical distribution. Sci Rep 2021; 11:4140. [PMID: 33602993 PMCID: PMC7892815 DOI: 10.1038/s41598-021-83282-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/01/2021] [Indexed: 11/09/2022] Open
Abstract
Umbilical cord blood (UCB) is a suitable source for hematopoietic stem cell transplantation. The study of HLA genes by next generation sequencing is commonly used in transplants. Donor/patient HLA matching is often higher within groups of common ancestry, however "Hispanic" is a broad category that fails to represent Argentina's complex genetic admixture. Our aim is to describe HLA diversity of banked UCB units collected across the country taking into consideration donor's reported ancestral origins as well as geographic distribution. Our results showed an evenly distribution of units mainly for 2 groups: of European and of Native American descent, each associated to a defined geographic location pattern (Central vs. North regions). We observed differences in allele frequency distributions for some alleles previously described in Amerindian populations: for Class I (A*68:17, A*02:11:01G, A*02:22:01G, B*39:05:01, B*35:21, B*40:04, B*15:04:01G, B*35:04:01, B*51:13:01) and Class II (DRB1*04:11:01, DRB1*04:07:01G/03, DRB1*08:02:01, DRB1*08:07, DRB1*09:01:02G, DRB1*14:02:01, DRB1*16:02:01G). Our database expands the current knowledge of HLA diversity in Argentinian population. Although further studies are necessary to fully comprehend HLA heterogeneity, this report should prove useful to increase the possibility of finding compatible donors for successful allogeneic transplant and to improve recruitment strategies for UCB donors across the country.
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Affiliation(s)
- Daniela Fernández Souto
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina
| | - Julieta Rosello
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina
| | - Laura Lazo
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina
| | - Florencia Veloso
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina
| | - Cecilia Gamba
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina
| | - Silvina Kuperman
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina
| | - Valeria Roca
- Cord Blood Bank, Hemotherapy Regional Center, Hospital de Pediatría Dr.Juan P. Garrahan, Combate de los Pozos 1881, (1245), Buenos Aires, Argentina.
- National Research Council, Buenos Aires, Argentina.
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Caputo M, Amador MA, Sala A, Riveiro Dos Santos A, Santos S, Corach D. Ancestral genetic legacy of the extant population of Argentina as predicted by autosomal and X-chromosomal DIPs. Mol Genet Genomics 2021; 296:581-590. [PMID: 33580820 DOI: 10.1007/s00438-020-01755-w] [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: 08/07/2020] [Accepted: 12/14/2020] [Indexed: 12/01/2022]
Abstract
Aiming to determine their ancestry diagnostic potential, we selected two sets of nuclear deletion/insertion polymorphisms (DIPs), including 30 located on autosomal chromosomes and 33 on the X chromosome. We analysed over 200 unrelated Argentinean individuals living in urban areas of Argentina. As in most American countries, the extant Argentinean population is the result of tricontinental genetic admixture. The peopling process within the continent was characterised by mating bias involving Native American and enslaved African females and European males. Differential results were detected between autosomal DIPs and X-DIPs. The former showed that the European component was the largest (77.8%), followed by the Native American (17.9%) and African (4.2%) components, in good agreement with the previously published results. In contrast, X-DIPs showed that the European genetic contribution was also predominant but much smaller (52.9%) and considerably larger Native American and African contributions (39.6% and 7.5%, respectively). Genetic analysis revealed continental genetic contributions whose associated phenotypic traits have been mostly lost. The observed differences between the estimated continental genetic contribution proportions based on autosomal DIPs and X-DIPs reflect the effects of autosome and X-chromosome transmission behaviour and their different recombination patterns. This work shows the ability of the tested DIP panels to infer ancestry and confirm mating bias. To the best of our knowledge, this is the first study focusing on ancestry-informative autosomal DIP and X-DIP comparisons performed in a sample representing the entire Argentinean population.
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Affiliation(s)
- M Caputo
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense Y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina. .,CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina. .,Department of Forensic Genetics and DNA Fingerprinting Service, School of Pharmacy and Biochemistry, Junin 956, 7th floor, C1113AAD, CABA, Argentina.
| | - M A Amador
- Laboratorio de Genética Humana E Médica, Departamento de Patologia, Universidade Federal Do Pará, Belém, Pará, Brazil
| | - A Sala
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense Y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina.,CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina
| | - A Riveiro Dos Santos
- Laboratorio de Genética Humana E Médica, Departamento de Patologia, Universidade Federal Do Pará, Belém, Pará, Brazil
| | - S Santos
- Laboratorio de Genética Humana E Médica, Departamento de Patologia, Universidade Federal Do Pará, Belém, Pará, Brazil
| | - D Corach
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense Y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina.,CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina
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Pujol F, Jaspe RC, Loureiro CL, Chemin I. Hepatitis B virus American genotypes: Pathogenic variants ? Clin Res Hepatol Gastroenterol 2020; 44:825-835. [PMID: 32553521 DOI: 10.1016/j.clinre.2020.04.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/19/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023]
Abstract
Hepatitis B virus (HBV) chronic infection is responsible for almost 900.000 deaths each year, due to cirrhosis or hepatocellular carcinoma (HCC). Ten HBV genotypes have been described (A-J). HBV genotype F and H circulate in America. HBV genotypes have been further classified in subgenotypes. There is a strong correlation between the genetic admixture of the American continent and the frequency of genotypes F or H: a high frequency of these genotypes is found in countries with a population with a higher ratio of Amerindian to African genetic admixture. The frequency of occult HBV infection in Amerindian communities from Latin America seems to be higher than the one found in other HBV-infected groups, but its association with American genotypes is unknown. There is growing evidence that some genotypes might be associated with a faster evolution to HCC. In particular, HBV genotype F has been implicated in a frequent and rapid progression to HCC. However, HBV genotype H has been associated to a less severe progression of disease. This study reviews the diversity and frequency of autochthonous HBV variants in the Americas and evaluates their association to severe progression of disease. Although no significant differences were found in the methylation pattern between different genotypes and subgenotypes of the American types, basal core promoter mutations might be more frequent in some subgenotypes, such as F1b and F2, than in other American subgenotypes or genotype H. F1b and probably F2 may be associated with a severe presentation of liver disease as opposed to a more benign course for subgenotype F4 and genotype H. Thus, preliminary evidence suggests that not all of the American variants are associated with a rapid progression to HCC.
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Affiliation(s)
- Flor Pujol
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, Caracas 1020A, Venezuela.
| | - Rossana C Jaspe
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, Caracas 1020A, Venezuela
| | - Carmen L Loureiro
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, Caracas 1020A, Venezuela
| | - Isabelle Chemin
- INSERM U1052, CNRS 5286, Université de Lyon, Université Claude Bernard Lyon 1, centre Léon Bérard, centre de recherche en cancérologie de Lyon, 69000, Lyon, France
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12
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Luisi P, García A, Berros JM, Motti JMB, Demarchi DA, Alfaro E, Aquilano E, Argüelles C, Avena S, Bailliet G, Beltramo J, Bravi CM, Cuello M, Dejean C, Dipierri JE, Jurado Medina LS, Lanata JL, Muzzio M, Parolin ML, Pauro M, Paz Sepúlveda PB, Rodríguez Golpe D, Santos MR, Schwab M, Silvero N, Zubrzycki J, Ramallo V, Dopazo H. Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina. PLoS One 2020; 15:e0233808. [PMID: 32673320 PMCID: PMC7365470 DOI: 10.1371/journal.pone.0233808] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/12/2020] [Indexed: 12/24/2022] Open
Abstract
Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previously published data for admixed individuals in the region and then compared to different reference panels specifically built to perform population structure analyses at a sub-continental level. Concerning the Native American ancestry, we could identify four Native American components segregating in modern Argentinean populations. Three of them are also found in modern South American populations and are specifically represented in Central Andes, Central Chile/Patagonia, and Subtropical and Tropical Forests geographic areas. The fourth component might be specific to the Central Western region of Argentina, and it is not well represented in any genomic data from the literature. As for the European and African ancestries, we confirmed previous results about origins from Southern Europe, Western and Central Western Africa, and we provide evidences for the presence of Northern European and Eastern African ancestries.
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Affiliation(s)
- Pierre Luisi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Angelina García
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Museo de Antropología, Córdoba, Argentina
| | - Juan Manuel Berros
- Consejo Nacional de Investigaciones Científicas y Técnicas - Laboratorio de Análisis de Datos, Biocódices S.A., Buenos Aires, Argentina
| | - Josefina M B Motti
- Núcleo de Estudios Interdisciplinarios de Poblaciones Humanas de Patagonia Austral (NEIPHA), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional del Centro de la Provincia de Buenos Aires, Quequén, Argentina
| | - Darío A Demarchi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Museo de Antropología, Córdoba, Argentina
| | - Emma Alfaro
- Instituto de Ecorregiones Andinas (INECOA), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Jujuy, Jujuy, Argentina.,Instituto de Biología de la Altura, Universidad Nacional de Jujuy, Jujuy, Argentina
| | - Eliana Aquilano
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Carina Argüelles
- Departamento de Genética, Grupo de Investigación en Genética Aplicada (GIGA), Facultad de Ciencias Exactas, Químicas y Naturales, Instituto de Biología Subtropical (IBS)-Nodo Posadas, Universidad Nacional de Misiones (UNaM)-Consejo Nacional de Investigaciones Científicas y Técnicas, Posadas, Argentina.,Cátedra de Biología Molecular, Carrera de Medicina, Facultad de Ciencias de la Salud, Universidad Católica de las Misiones (UCAMI), Posadas, Argentina
| | - Sergio Avena
- Instituto de Ciencias Antropológicas (ICA), Facultad de Filosofía y Letras, Universidad de Buenos Aires, Buenos Aires, Argentina.,Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina
| | - Graciela Bailliet
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Julieta Beltramo
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina.,Laboratorio de Análisis Comparativo de ADN, Corte Suprema de Justicia de la Provincia de Buenos Aires, La Plata, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Mariela Cuello
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Cristina Dejean
- Instituto de Ciencias Antropológicas (ICA), Facultad de Filosofía y Letras, Universidad de Buenos Aires, Buenos Aires, Argentina.,Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina
| | | | - Laura S Jurado Medina
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - José Luis Lanata
- Instituto de Investigaciones en Diversidad Cultural y Procesos de Cambio (IIDyPCa), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Río Negro, San Carlos de Bariloche, Argentina
| | - Marina Muzzio
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - María Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Consejo Nacional de Investigaciones Científicas y Técnicas - Centro Nacional Patagónico, Puerto Madryn, Argentina
| | - Maia Pauro
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Museo de Antropología, Córdoba, Argentina
| | - Paula B Paz Sepúlveda
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Daniela Rodríguez Golpe
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - María Rita Santos
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Marisol Schwab
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Natalia Silvero
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Virginia Ramallo
- Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH) - Consejo Nacional de Investigaciones Científicas y Técnicas-Centro Nacional Patagónico, Puerto Madryn, Argentina
| | - Hernán Dopazo
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas - Biocodices S.A., Buenos Aires, Argentina
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13
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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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Strauss M, Acosta-Herrera M, Alcaraz A, Casares-Marfil D, Bosch-Nicolau P, Lo Presti MS, Molina I, González CI, Martín J. Association of IL18 genetic polymorphisms with Chagas disease in Latin American populations. PLoS Negl Trop Dis 2019; 13:e0007859. [PMID: 31751351 PMCID: PMC6894881 DOI: 10.1371/journal.pntd.0007859] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 12/05/2019] [Accepted: 10/21/2019] [Indexed: 12/14/2022] Open
Abstract
Host genetic factors have been suggested to play an important role in the susceptibility to Chagas disease. Given the influence of interleukin 18 (IL-18) in the development of the disease, in the present study, we analyzed three IL18 genetic variants (rs2043055, rs1946518, rs360719) regarding the predisposition to Trypanosoma cruzi infection and the development of chronic Chagas cardiomyopathy (CCC), in different Latin America populations. Genetic data of 3,608 patients from Colombia, Bolivia, Argentina, and Brazil were meta-analyzed to validate previous findings with increased statistical power. Seropositive and seronegative individuals were compared for T. cruzi infection susceptibility. In the Colombian cohort, the allelic frequencies of the three variants showed a significant association, with adjustment for sex and age, and also after applying multiple testing adjustments. Among the Colombian and Argentinean cohorts, rs360719 showed a significant genetic effect in a fixed-effects meta-analysis after a Bonferroni correction (OR: 0.76, CI: 0.66-0.89, P = 0.001). For CCC, the rs2043055 showed an association with protection from cardiomyopathy in the Colombian cohort (OR: 0.79, CI: 0.64-0.99, P = 0.037), with adjustment for sex and age, and after applying multiple testing adjustments. The meta-analysis of the CCC vs. asymptomatic patients from the four cohorts showed no evidence of association. In conclusion, our results validated the association found previously in the Colombian cohort suggesting that IL18 rs360719 plays an important role in the susceptibility to T. cruzi infection and no evidence of association was found between the IL18 genetic variants and CCC in the Latin American population studied.
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Affiliation(s)
- Mariana Strauss
- Centro de Estudios e Investigación de la Enfermedad de Chagas y Leishmaniasis, FCM, INICSA-CONICET-UNC, Córdoba, Argentina
| | | | - Alexia Alcaraz
- Instituto de Parasitología y Biomedicina López-Neyra, IPBLN-CSIC, PTS Granada, Granada, España
| | - Desiré Casares-Marfil
- Instituto de Parasitología y Biomedicina López-Neyra, IPBLN-CSIC, PTS Granada, Granada, España
| | - Pau Bosch-Nicolau
- Unidad de Medicina Tropical y Salud Internacional Hospital Universitari Vall d'Hebron, PROSICS, Barcelona, España
| | - María Silvina Lo Presti
- Centro de Estudios e Investigación de la Enfermedad de Chagas y Leishmaniasis, FCM, INICSA-CONICET-UNC, Córdoba, Argentina
| | - Israel Molina
- Unidad de Medicina Tropical y Salud Internacional Hospital Universitari Vall d'Hebron, PROSICS, Barcelona, España
| | | | - Javier Martín
- Instituto de Parasitología y Biomedicina López-Neyra, IPBLN-CSIC, PTS Granada, Granada, España
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15
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Differential admixture, human leukocyte antigen diversity, and hematopoietic cell transplantation in Latin America: challenges and opportunities. Bone Marrow Transplant 2019; 55:496-504. [DOI: 10.1038/s41409-019-0737-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022]
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16
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Navarro P, Ramallo V, Cintas C, Ruderman A, de Azevedo S, Paschetta C, Pérez O, Pazos B, Delrieux C, González-José R. Body shape: Implications in the study of obesity and related traits. Am J Hum Biol 2019; 32:e23323. [PMID: 31506993 DOI: 10.1002/ajhb.23323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 08/06/2019] [Accepted: 08/25/2019] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES The diagnosis and treatment of obesity are usually based on traditional anthropometric variables including weight, height, and several body perimeters. Here we present a three-dimensional (3D) image-based computational approach aimed to capture the distribution of abdominal adipose tissue as an aspect of shape rather than a relationship among classical anthropometric measures. METHODS A morphometric approach based on landmarks and semilandmarks placed upon the 3D torso surface was performed in order to quantify abdominal adiposity shape variation and its relation to classical indices. Specifically, we analyzed sets of body cross-sectional circumferences, collectively defining each, along with anthropometric data taken on 112 volunteers. Principal Component Analysis (PCA) was performed on 250 circumferences located along the abdominal region of each volunteer. An analysis of covariance model was used to compare shape variables (PCs) against anthropometric data (weight, height, and waist and hip circumferences). RESULTS The observed shape patterns were mainly related to nutritional status, followed by sexual dimorphism. PC1 (12.5%) and PC2 (7.5%) represented 20% of the total variation. In PCAs calculated independently by sex, linear regression analyses provide statistically significant associations between PC1 and the three classical indexes: body mass index, waist-to-height ratio, and waist-hip ratio. CONCLUSION Shape indicators predict well the behavior of classical markers, but also evaluate 3D and geometric features with more accuracy as related to the body shape under study. This approach also facilitates diagnosis and follow-up of therapies by using accessible 3D technology.
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Affiliation(s)
- Pablo Navarro
- Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH), Centro Nacional Patagónico (CENPAT - CONICET), Puerto Madryn, Argentina.,Departamento de Informática (DIT), Facultad de Ingeniería, Universidad Nacional de la Patagonia San Juan Bosco, Trelew, Chubut, Argentina.,Laboratorio de Ciencias de las Imágenes, Departamento de Ingeniería Eléctrica y Computadoras, Universidad Nacional del Sur, Bahia Blanca, Argentina
| | - Virginia Ramallo
- Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH), Centro Nacional Patagónico (CENPAT - CONICET), Puerto Madryn, Argentina
| | | | - Anahí Ruderman
- Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH), Centro Nacional Patagónico (CENPAT - CONICET), Puerto Madryn, Argentina
| | - Soledad de Azevedo
- Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH), Centro Nacional Patagónico (CENPAT - CONICET), Puerto Madryn, Argentina
| | - Carolina Paschetta
- Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH), Centro Nacional Patagónico (CENPAT - CONICET), Puerto Madryn, Argentina
| | - Orlando Pérez
- Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH), Centro Nacional Patagónico (CENPAT - CONICET), Puerto Madryn, Argentina
| | - Bruno Pazos
- Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH), Centro Nacional Patagónico (CENPAT - CONICET), Puerto Madryn, Argentina.,Departamento de Informática (DIT), Facultad de Ingeniería, Universidad Nacional de la Patagonia San Juan Bosco, Trelew, Chubut, Argentina.,Laboratorio de Ciencias de las Imágenes, Departamento de Ingeniería Eléctrica y Computadoras, Universidad Nacional del Sur, Bahia Blanca, Argentina
| | - Claudio Delrieux
- Laboratorio de Ciencias de las Imágenes, Departamento de Ingeniería Eléctrica y Computadoras, Universidad Nacional del Sur, Bahia Blanca, Argentina
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH), Centro Nacional Patagónico (CENPAT - CONICET), Puerto Madryn, Argentina
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