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Gusmão L, Antão-Sousa S, Faustino M, Abovich MA, Aguirre D, Alghafri R, Alves C, Amorim A, Arévalo C, Baldassarri L, Barletta-Carrillo C, Berardi G, Bobillo C, Borjas L, Braganholi DF, Brehm A, Builes JJ, Cainé L, Carvalho EF, Carvalho M, Catelli L, Cicarelli RMB, Contreras A, Corach D, Di Marco FG, Diederiche MV, Domingues P, Espinoza M, Fernandéz JM, García MG, García O, Gaviria A, Gomes I, Grattapaglia D, Henao J, Hernandez A, Ibarra AA, Lima G, Manterola IM, Marrero C, Martins JA, Mendoza L, Mosquera A, Nascimento EC, Onofri V, Pancorbo MM, Pestano JJ, Plaza G, Porto MJ, Posada YC, Rebelo ML, Riego E, Rodenbusch R, Rodríguez A, Rodríguez A, Sanchez-Diz P, Santos S, Simão F, Siza Fuentes LM, Sumita D, Tomas C, Toscanini U, Trindade-Filho A, Turchi C, Vullo C, Yurrebaso I, Pereira V, Pinto N. X-chromosomal STRs: Metapopulations and mutation rates. Forensic Sci Int Genet 2025; 76:103232. [PMID: 39893847 DOI: 10.1016/j.fsigen.2025.103232] [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: 09/06/2024] [Revised: 01/15/2025] [Accepted: 01/26/2025] [Indexed: 02/04/2025]
Abstract
The analysis of STRs located on the X chromosome has been one of the strategies used to address complex kinship cases. Its usefulness is, however, limited by the low availability of population haplotype frequency data and lack of knowledge on the probability of mutations. Due to the large amount of data required to obtain reliable estimates, it is important to investigate the possibility of grouping data from populations with similar profiles when calculating these parameters. To better understand the partition of genetic diversity among human populations for the X-STRs most used in forensics, an analysis was carried out based on data available in the literature and new data (23,949 haplotypes in total; from these 10,445 new) obtained through collaborative exercises within the Spanish and Portuguese Working Group of the International Society for Forensic Genetics. Based on the available population data, a similarity in X-STR profiles was found in European populations, and in East Asian populations, except for some isolates. A greater complexity was found for African, South American, and South and Southeast Asian populations, preventing their grouping into large metapopulations. New segregation data on 2273 father/mother/daughter trios were also obtained, aiming for a more thorough analysis of X-STR mutation rates. After combining our data with published information on father/mother/daughter trios, no mutations were detected in 13 out of 37 loci analyzed. For the remaining loci, mutation rates varied between 2.68 × 10-4 (DXS7133) and 1.07x10-2 (DXS10135), being 5.2 times higher in the male (4.16 ×10-3) than in the female (8.01 ×10-4) germline.
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Affiliation(s)
- L Gusmão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - S Antão-Sousa
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Portugal; Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
| | - M Faustino
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
| | - M A Abovich
- Banco Nacional de Datos Genéticos, Buenos Aires, Argentina and Sección Histocompatibilidad, Unidad Inmunología e Histocompatibilidad, Hospital General de Agudos Dr. Carlos G. Durand, CABA, Buenos Aires, Argentina
| | - D Aguirre
- Laboratorio Genes SAS, Medellín, Colombia
| | - R Alghafri
- General Department of Forensic Sciences and Criminology, Dubai Police General Head Quarters, Dubai, United Arab Emirates
| | - C Alves
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Portugal
| | - A Amorim
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Portugal; Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
| | - C Arévalo
- Laboratorio Biología-ADN, Comisaría General de Policía Científica, Madrid, Spain and Instituto Universitario de Investigación en Ciencias Policiales (IUICP), Universidad de Alcalá de Henares, Madrid, Spain
| | - L Baldassarri
- Laboratorio di Genetica Forense de la Università Cattolica del Sacro Cuore di Roma, Rome, Italy
| | - C Barletta-Carrillo
- Laboratorio de Genética Humana, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - G Berardi
- PRICAI - Fundación Favaloro, Buenos Aires, Argentina
| | - C Bobillo
- Servicio de Huellas Digitales Genéticos (SHDG) and Cátedra de Genética y Bioquímica Molecular, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina
| | - L Borjas
- Laboratorio de Genética Molecular, Unidad de Genética Médica, Facultad de Medicina, Universidad del Zulia, Zulia, Venezuela
| | - D F Braganholi
- Laboratório de Investigação de Paternidade-NAC, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo, Brazil
| | - A Brehm
- Laboratório de Genética Humana, Universidade da Madeira, Campus da Penteada, Funchal, Portugal
| | - J J Builes
- Laboratorio Genes SAS, Medellín, Colombia
| | - L Cainé
- Serviço de Genética e Biologia Forenses, Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. - Delegação do Norte, Porto, Portugal; Faculdade de Medicina da Universidade do Porto, Portugal
| | - E F Carvalho
- DNA Diagnostic Laboratory, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - M Carvalho
- Serviço de Genética e Biologia Forenses, Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. - Delegação do Centro, Coimbra, Portugal
| | - L Catelli
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team (EAAF), Córdoba, Argentina
| | - R M B Cicarelli
- Laboratório de Investigação de Paternidade-NAC, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo, Brazil
| | - A Contreras
- Laboratorio Regional de Genética Forense - Poder Judicial de Rio Negro, Rio Negro, Argentina
| | - D Corach
- Servicio de Huellas Digitales Genéticos (SHDG) and Cátedra de Genética y Bioquímica Molecular, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina
| | - F G Di Marco
- Laboratorio ManLab, Area de Filiaciones, Buenos Aires, Argentina
| | - M V Diederiche
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz - UESC, Ilhéus, Bahia, Brazil
| | - P Domingues
- DNA Diagnostic Laboratory, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - M Espinoza
- Departamento de Ciencias Forenses, Sección de Bioquímica, Unidad de Genética Forense, Poder Judicial, San José, Costa Rica
| | - J M Fernandéz
- Departamento de Biología, Servicio de Criminalística, Dirección General de la Policía y la Guardia Civil, ámbito Guardia Civil, Spain
| | - M G García
- Laboratorio ManLab, Area de Filiaciones, Buenos Aires, Argentina
| | - O García
- Sección de Genética Forense, Area de Laboratorio Ertzaintza, Bizkaia, Spain
| | - A Gaviria
- Laboratorio de Genética Molecular and Hemocentro Nacional - Cruz Roja Ecuatoriana, Quito, Ecuador
| | - I Gomes
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Portugal; Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal
| | - D Grattapaglia
- Heréditas Tecnologia em Análise de DNA, Brasília, Brazil
| | - J Henao
- Laboratorio de Genética Médica, Universidad Tecnológica de Pereira, Facultad de Ciencias de la Salud, Pereira, Colombia
| | - A Hernandez
- Instituto Nacional de Toxicología y Ciencias Forenses, Delegación de Canarias, Santa Cruz de Tenerife, Spain
| | - A A Ibarra
- Laboratorio IdentiGEN - Universidad de Antioquia, Medellín, Colombia
| | - G Lima
- Serviço de Genética e Biologia Forenses, Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. - Delegação do Norte, Porto, Portugal
| | - I M Manterola
- Servicio Genómica - SGIker - Universidad del País Vasco (UPV-EHU), Bilbao, Spain
| | - C Marrero
- Laboratorio Genomik C.A., Valencia, Venezuela
| | - J A Martins
- Research Centre for Biochemistry and Molecular Biology at the Medical School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil
| | - L Mendoza
- Laboratorio Genes SAS, Medellín, Colombia
| | - A Mosquera
- Forensic Genetics Unit, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - E C Nascimento
- Coordenação de Genética Forense, Departamento de Polícia Técnica da Bahia, Salvador, Brazil
| | - V Onofri
- Legal Medicine Unit, Azienda Ospedaliero-Universitaria delle Marche, Ancona, Italy
| | - M M Pancorbo
- Banco de ADN, Universidad del País Vasco (UPV/EHU), Vitoria, Gasteiz, Spain
| | - J J Pestano
- Laboratorio de Genética Forense, Facultad de Medicina, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | - G Plaza
- NEODIAGNOSTICA, SL, Lleida, Spain
| | - M J Porto
- Serviço de Genética e Biologia Forenses, Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. - Delegação do Centro, Coimbra, Portugal
| | - Y C Posada
- Laboratorio IdentiGEN - Universidad de Antioquia, Medellín, Colombia
| | - M L Rebelo
- Serviço de Genética e Biologia Forenses, Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. - Delegação do Norte, Porto, Portugal
| | - E Riego
- Unidad de Parentesco e Identificación Humana por ADN, Referencia Laboratorio Clínico, Dominican Republic
| | - R Rodenbusch
- Laboratório PeritosLab Forense, Porto Alegre, Brazil
| | - A Rodríguez
- Departamento de Ciencias Forenses, Sección de Bioquímica, Unidad de Genética Forense, Poder Judicial, San José, Costa Rica
| | - A Rodríguez
- Forensic Genetics Unit, University of Santiago de Compostela, Santiago de Compostela, Spain
| | | | - S Santos
- Human and Medical Genetics Laboratory, Federal University of Pará, Belém, Brazil
| | - F Simão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | | | - D Sumita
- Genomic Engenharia Molecular Ltda., São Paulo, Brasil
| | - C Tomas
- Section of Forensic Genetics - Department of Forensic Medicine, Faculty of Health and Medical Sciences - University of Copenhagen, Copenhagen, Denmark
| | - U Toscanini
- PRICAI - Fundación Favaloro, Buenos Aires, Argentina
| | - A Trindade-Filho
- Instituto de Pesquisa de DNA Forense - Polícia Civil do Distrito Federal, Brasília, Brazil
| | - C Turchi
- Section of Legal Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - C Vullo
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team (EAAF), Córdoba, Argentina
| | - I Yurrebaso
- Sección de Genética Forense, Area de Laboratorio Ertzaintza, Bizkaia, Spain
| | - V Pereira
- Section of Forensic Genetics - Department of Forensic Medicine, Faculty of Health and Medical Sciences - University of Copenhagen, Copenhagen, Denmark
| | - N Pinto
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Portugal; Centro de Matemática da Universidade do Porto (CMUP), Porto, Portugal.
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Alwi AR, Mahat NA, Salleh FM, Ishar SM, Kamaluddin MR, Rashid MRA, Rahayu Karmilla Syed Hassan SN, Iyavoo S. Population data for 12 X-STRs loci in Malaysian Malay and Chinese populations. Heliyon 2024; 10:e38054. [PMID: 39391492 PMCID: PMC11466538 DOI: 10.1016/j.heliyon.2024.e38054] [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: 03/27/2024] [Revised: 08/21/2024] [Accepted: 09/17/2024] [Indexed: 10/12/2024] Open
Abstract
The utilization of X-chromosome short tandem repeats (X-STRs) for human identification particularly in resolving complex kinship cases has been advocated. Since, forensic statistical parameters vary among different populations, and because the X-STRs population data representing the diverse population of Peninsular Malaysia remain unavailable, the specific attempt reported here for the Malays (n = 224) and Chinese (n = 201) populations appears forensically relevant to support the evidential value of the 12 X-STRs markers for human identification in Malaysia. Results derived from the Qiagen Investigator® Argus X-12 kit revealed that DXS10135 as the most polymorphic locus with high genetic diversity, polymorphic information content, heterozygosity as well as power of exclusion. Based on allele frequencies, the combined power of discrimination as well as the mean exclusion chance (MECKrüger, MECKishida, MECDesmarais and MECDesmaraisDuo) values for the Malays and Chinese were individually ≥0.999995532964908. As for the combined power of discrimination as well as the mean exclusion chance (MECKrüger, MECKishida, MECDesmarais and MECDesmaraisDuo) calculated based on haplotype frequencies, the values were ≥0.9999986410567 for the Malays and Chinese populations. In addition, results from the genetic distance, neighbor-joining phylogenetic tree and principal component analysis revealed close biogeographical distributions of the studied populations with other South East Asian populations. Hence, the utilization of the X-STRs data for identifying individuals among the Malays and Chinese populations in Peninsular Malaysia for forensic application appears as highly supported.
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Affiliation(s)
- Aedrianee Reeza Alwi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia (UTM), 81310 Johor Bahru, Johor, Malaysia
- Department of Chemistry Malaysia Johor State, Jalan Abdul Samad, 80100 Johor Bahru, Johor, Malaysia
| | - Naji Arafat Mahat
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia (UTM), 81310 Johor Bahru, Johor, Malaysia
- Investigative and Forensic Sciences Research Group, Universiti Teknologi Malaysia (UTM), 81310 Johor Bahru, Johor, Malaysia
- Centre for Sustainable Nanomaterials, Ibnu Sina Institute for Scientific and Industrial Research, Universiti Teknologi Malaysia (UTM), 81310 Johor Bahru, Johor, Malaysia
- Centre of Research for Fiqh Forensics and Judiciary, Faculty of Syariah and Law, Universiti Sains Islam Malaysia (USIM), Bandar Baru Nilai, 71800, Nilai, Negeri Sembilan, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia (UTM), 81310 Johor Bahru, Johor, Malaysia
- Investigative and Forensic Sciences Research Group, Universiti Teknologi Malaysia (UTM), 81310 Johor Bahru, Johor, Malaysia
| | - Seri Mirianti Ishar
- Forensic Science Program, Faculty of Health Sciences, Universiti Kebangsaan Malaysia (UKM), 43600 Bangi, Selangor, Malaysia
| | - Mohammad Rahim Kamaluddin
- Centre for Research in Psychology and Human Well-Being, Faculty of Social Sciences and Humanities, Universiti Kebangsaan Malaysia (UKM), 43600 Bangi, Selangor, Malaysia
| | - Mohd Radzniwan A. Rashid
- Family Medicine Unit, Faculty of Medicine and Health Science, Universiti Sains Islam Malaysia (USIM), Bandar Baru Nilai, 71800, Nilai, Negeri Sembilan, Malaysia
| | | | - Sasitaran Iyavoo
- School of Natural Sciences, College of Health and Science, University of Lincoln, Lincoln, United Kingdom
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Aizpurua-Iraola J, Rasal R, Prieto L, Comas D, Bonet N, Casals F, Calafell F, Vásquez P. Population analysis of complete mitogenomes for 334 samples from El Salvador. Forensic Sci Int Genet 2023; 66:102906. [PMID: 37364481 DOI: 10.1016/j.fsigen.2023.102906] [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: 03/22/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023]
Abstract
The use of mitochondrial DNA (mtDNA) in the field of forensic genetics is widely spread mainly due to its advantages when identifying highly degraded samples. In this sense, massive parallel sequencing has made the analysis of the whole mitogenome more accessible, noticeably increasing the informativeness of mtDNA haplotypes. The civil war (1980-1992) in El Salvador caused many deaths and disappearances (including children) all across the country and the economic and social instability after the war forced many people to emigration. For this reason, different organizations have collected DNA samples from relatives with the aim of identifying missing people. Thus, we present a dataset containing 334 complete mitogenomes from the Salvadoran general population. To the best of our knowledge, this is the first publication of a nationwide forensic-quality complete mitogenome database of any Latin American country. We found 293 different haplotypes, with a random match probability of 0.0041 and 26.6 mean pairwise differences, which is similar to other Latin American populations, and which represent a marked improvement from the values obtained with just control region sequences. These haplotypes belong to 54 different haplogroups, being 91% of them of Native American origin. Over a third (35.9%) of the individuals carried at least a heteroplasmic site (excluding length heteroplasmies). Ultimately, the present database aims to represent mtDNA haplotype diversity in the general Salvadoran populations as a basis for the identification of people that disappeared during or after the civil war.
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Affiliation(s)
- Julen Aizpurua-Iraola
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Raquel Rasal
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Lourdes Prieto
- Instituto de Ciencias Forenses, Universidad de Santiago de Compostela, Santiago de Compostela, Spain; Comisaría General de Policía Científica. DNA Laboratory, Madrid, Spain
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Patricia Vásquez
- Asociación Pro-Búsqueda de Niñas y Niños Desaparecidos de El Salvador, San Salvador, El Salvador
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De Oliveira TC, Secolin R, Lopes-Cendes I. A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations. Front Genet 2023; 14:1091269. [PMID: 36741309 PMCID: PMC9893294 DOI: 10.3389/fgene.2023.1091269] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.
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Affiliation(s)
- Thais C. De Oliveira
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Rodrigo Secolin
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
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Casals F, Rasal R, Anglada R, Tormo M, Bonet N, Rivas N, Vásquez P, Calafell F. A forensic population database in El Salvador: 58 STRs and 94 SNPs. Forensic Sci Int Genet 2021; 57:102646. [PMID: 34875492 DOI: 10.1016/j.fsigen.2021.102646] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 12/31/2022]
Abstract
We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in a sample of 248 men and 143 women from El Salvador, Central America. Regional division (Centro, Oriente, Occidente) showed in almost all cases FST values not significantly different from 0, and further analyses were applied only to the undivided, country-wide population. The overall random match probability (RMP) decreased from 6.79 × 10-31 in length-based genotypes in the 27 autosomal STRs to 1.47 × 10-34 in repeat-sequence based genotypes. Combining the autosomal loci in this set, RMP reaches 2.97 × 10-70. In a population genetic analysis, El Salvador showed the lowest FST values with US Hispanics both for autosomal and X-STRs; however, it was much closer to Native Americans for the latter than for the former, in accordance with the well-known gender-biased admixture that created most Latin American populations.
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Affiliation(s)
- Ferran Casals
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadísitca, Universitat de Barcelona, Barcelona, Spain
| | - Raquel Rasal
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Roger Anglada
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Marc Tormo
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain; Scientific IT Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Nury Rivas
- Instituto de Medicina Legal Dr. Roberto Masferrer, San Salvador, El Salvador
| | - Patricia Vásquez
- Asociación Pro-Búsqueda de Niñas y Niños Desaparecidos de El Salvador, 27 calle Pnte. No.1329 Colonia Layco, San Salvador, El Salvador
| | - Francesc Calafell
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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