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Caputo M, Sala A, Corach D. Reference population database for 24 STR loci of selected provinces of Argentina. Mol Biol Rep 2023:10.1007/s11033-023-08497-z. [PMID: 37219673 DOI: 10.1007/s11033-023-08497-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Argentinean population is the result of admixture between South Amerindians, Europeans and to a lesser degree, Africans. Since the advent of forensic molecular genetics, the construction of local reference databases became mandatory. Aiming to further extend the technical quality reference database of Argentina, we present herein the allele frequencies for 24 autosomal STRs, including D22S1045, and SE33 (not previously reported for Argentina in STRidER). CONCLUSIONS Genotypes of 6454 unrelated individuals (3761 males and 2694 females) from 13 out of 23 provinces were analysed. Forensic parameters were calculated for each marker. The observed heterozygosity ranged from 0.661 (TPOX) to 0.941 (SE33). The locus SE33 was revealed to be the most informative marker showing the highest values for PIC (0.955), GD (0.952), TPI (8.455) and PE (0.879). On the other hand, TPOX turned out to be the least informative marker: PIC (0.618), GD (0.669), and PE (0.371). The high number of analyzed individuals allowed detecting low frequency alleles and microvariants in CSF1PO; D16S539 and D21S11 D18S51; PENTA D; PENTA E and at locus D6S1043. METHODS AND RESULTS This study is the most extensive for Argentina and complements the already reported information concerning the autosomal STRs commonly used in forensic identification. The results were submitted passing STRidER quality control standards (QC), receiving the reference number STR000327 v.2.
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Affiliation(s)
- Mariela Caputo
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Biotecnología, Inmunología y Genética. Catedra de Genética Forense, Centro de Referencia en Identificación Humana y Servicio de Huellas Digitales Genéticas (SHDG), Universidad de Buenos Aires, CABA, Argentina.
- CONICET. Consejo Nacional de Investigaciones Científicas y Técnicas, CABA, Argentina.
| | - Andrea Sala
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Biotecnología, Inmunología y Genética. Catedra de Genética Forense, Centro de Referencia en Identificación Humana y Servicio de Huellas Digitales Genéticas (SHDG), Universidad de Buenos Aires, CABA, Argentina
- CONICET. Consejo Nacional de Investigaciones Científicas y Técnicas, CABA, Argentina
| | - Daniel Corach
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Biotecnología, Inmunología y Genética. Catedra de Genética Forense, Centro de Referencia en Identificación Humana y Servicio de Huellas Digitales Genéticas (SHDG), Universidad de Buenos Aires, CABA, Argentina
- CONICET. Consejo Nacional de Investigaciones Científicas y Técnicas, CABA, Argentina
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Russo MG, Mendisco F, Avena SA, Dejean CB, Seldes V. Pre-Hispanic Mortuary Practices in Quebrada de Humahuaca (North-Western Argentina): Genetic Relatedness among Individuals Buried in the Same Grave. Ann Hum Genet 2016; 80:210-20. [PMID: 27346733 DOI: 10.1111/ahg.12159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/25/2016] [Accepted: 05/12/2016] [Indexed: 12/01/2022]
Abstract
Almost all pre-Hispanic societies from Quebrada de Humahuaca (north-western Argentina) buried their defuncts in domestic areas, demonstrating the importance of death and its daily presence among the living. Presumably, the collective graves contained related individuals, a hypothesis that can be tested through the study of ancient DNA. This study analyzes autosomal and uniparental genetic markers in individuals from two archaeological sites in Quebrada de Humahuaca occupied during the Late Formative (1450-1050 BP) and Regional Developments I (1050-700 BP) periods. Mitochondrial and Y-chromosome haplotypes were compared in order to establish possible maternal and paternal relatedness. Genotypes for 15 autosomal STRs were used to calculate pairwise relatedness coefficients and pedigree probabilities. High kinship levels among individuals buried in the same graves were found in both sites. Although only two particular cases were analyzed, these results represent an important contribution to the study of mortuary practices in the region by means of ancient DNA.
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Affiliation(s)
- M Gabriela Russo
- Universidad Maimónides, CONICET, CEBBAD, Equipo de Antropología Biológica, Fundación Azara, Hidalgo 775, CP 1405, Ciudad Autónoma de, Buenos Aires, Argentina
| | - Fanny Mendisco
- University Paul Sabatier, AMIS, CNRS, UMR 5288, F-31073, Toulouse, France
| | - Sergio A Avena
- Universidad Maimónides, CONICET, CEBBAD, Equipo de Antropología Biológica, Fundación Azara, Hidalgo 775, CP 1405, Ciudad Autónoma de, Buenos Aires, Argentina.,Sección de Antropología Biológica, ICA, FFyL, UBA, Puán 480, CP 1405, Ciudad Autónoma de, Buenos Aires, Argentina
| | - Cristina B Dejean
- Sección de Antropología Biológica, ICA, FFyL, UBA, Puán 480, CP 1405, Ciudad Autónoma de, Buenos Aires, Argentina.,Universidad Maimónides, CEBBAD, Equipo de Antropología Biológica, Fundación Azara, Hidalgo 775, CP 1405, Ciudad Autónoma de, Buenos Aires, Argentina
| | - Verónica Seldes
- UBA, CONICET, Instituto Interdisciplinario Tilcara, FFyL, Belgrano 445, CP 4624, Tilcara, Jujuy, Argentina
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Analysis of 17 STR data on 5362 southern Portuguese individuals—an update on reference database. Forensic Sci Int Genet 2016; 21:e10-2. [DOI: 10.1016/j.fsigen.2015.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 10/20/2015] [Accepted: 11/18/2015] [Indexed: 11/18/2022]
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Mexican mestizo population sub-structure: effects on genetic and forensic statistical parameters. Mol Biol Rep 2012; 39:10139-56. [DOI: 10.1007/s11033-012-1888-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 08/22/2012] [Indexed: 10/27/2022]
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Baca M, Doan K, Sobczyk M, Stankovic A, Węgleński P. Ancient DNA reveals kinship burial patterns of a pre-Columbian Andean community. BMC Genet 2012; 13:30. [PMID: 22524324 PMCID: PMC3470988 DOI: 10.1186/1471-2156-13-30] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 03/27/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A detailed genetic study of the pre-Columbian population inhabiting the Tompullo 2 archaeological site (department Arequipa, Peru) was undertaken to resolve the kin relationships between individuals buried in six different chullpas. Kin relationships were an important factor shaping the social organization in the pre-Columbian Andean communities, centering on the ayllu, a group of relatives that shared a common land and responsibilities. The aim of this study was to evaluate whether this Andean model of a social organization had an influence on mortuary practices, in particular to determine whether chullpas served as family graves. RESULTS The remains of forty-one individuals were analyzed with both uniparental (mtDNA, Y-chromosome) and biparental (autosomal microsatellites) markers. Reproducible HVRI sequences, autosomal and Y chromosomal STR profiles were obtained for 24, 16 and 11 individuals, respectively. Mitochondrial DNA diversity was comparable to that of ancient and contemporary Andean populations. The Tompullo 2 population exhibited the closest relationship with the modern population from the same region. A kinship analysis revealed complex pattern of relations within and between the graves. However mean relatedness coefficients regarding the pairs of individuals buried in the same grave were significantly higher than those regarding pairs buried in different graves. The Y chromosome profiles of 11 males suggest that only members of one male line were buried in the same grave. CONCLUSIONS Genetic investigation of the population that inhabited Tompullo 2 site shows continuity between pre-Columbian and modern Native Amerindian populations inhabiting the Arequipa region. This suggests that no major demographic processes have influenced the mitochondrial DNA diversity of these populations during the past five hundred years. The kinship analysis involving uni- and biparental markers suggests that the community that inhabited the Tompullo 2 site was organized into extended family groups that were buried in different graves. This finding is in congruence with known models of social organization of Andean communities.
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Affiliation(s)
- Mateusz Baca
- Center for Precolumbian Studies, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927, Warsaw, Poland
| | - Karolina Doan
- Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Pawińskiego 5A, 02–106, Warsaw, Poland
| | - Maciej Sobczyk
- Center for Precolumbian Studies, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927, Warsaw, Poland
| | - Anna Stankovic
- Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Pawińskiego 5A, 02–106, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Piotr Węgleński
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawińskiego 5A, 02-106, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
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Typing of Amerindian Kichwas and Mestizos from Ecuador with the SNPforID multiplex. Forensic Sci Int Genet 2011; 5:e105-7. [DOI: 10.1016/j.fsigen.2011.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 03/05/2011] [Indexed: 11/18/2022]
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Carnese FR, Mendisco F, Keyser C, Dejean CB, Dugoujon JM, Bravi CM, Ludes B, Crubézy E. Paleogenetical study of pre-Columbian samples from Pampa Grande (Salta, Argentina). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 141:452-62. [DOI: 10.1002/ajpa.21165] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Correspondence analysis approach for finding allele associations in population genetic study. Comput Stat Data Anal 2007. [DOI: 10.1016/j.csda.2006.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Toscanini U, Gusmão L, Berardi G, Amorim A, Carracedo A, Salas A, Raimondi E. Testing for genetic structure in different urban Argentinian populations. Forensic Sci Int 2007; 165:35-40. [PMID: 16846710 DOI: 10.1016/j.forsciint.2006.02.042] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Revised: 02/14/2006] [Accepted: 02/14/2006] [Indexed: 11/19/2022]
Abstract
Fifteen autosomal short tandem repeat (STR) markers (D3S1358, HUMTH01, D21S11, D18S51, PENTA E, D5S818, D13S317, D7S820, D16S539, CSF1PO, PENTA D, HUMvWA, D8S1179, HUMTPOX, FGA) were analyzed in 1734 individuals living in urban areas of cities from six different Argentinian provinces (Buenos Aires, Neuquén, Tucumán, La Pampa, San Luis, Santa Cruz) in order to determine if a common urban database could be used in Argentina for forensic purposes. Frequencies estimates, Hardy-Weinberg equilibrium (HWE), and other parameters of forensic interest were computed. Comparisons between the six populations, and with published data from one Native American population from Argentina and other urban populations from Argentina and Europe were also performed. Our results reveal evidences for population structure, both when testing for genetic differentiation and when comparing frequencies distributions between different pairs of populations. Therefore, caution should be taken when using a common pooled database with general forensic purposes in Argentina.
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Affiliation(s)
- Ulises Toscanini
- PRICAI-Fundacion Favaloro, Av. Belgrano 1782, 1er Subsuelo, 1093 Capital Federal, Buenos Aires, Argentina
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Ricaut FX, Fedoseeva A, Keyser-Tracqui C, Crubézy E, Ludes B. Ancient DNA analysis of human neolithic remains found in northeastern Siberia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2005; 126:458-62. [PMID: 15756672 DOI: 10.1002/ajpa.20257] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We successfully extracted DNA from a bone sample of a Neolithic skeleton (dated 3,600 +/- 60 years BP) excavated in northeastern Yakutia (east Siberia). Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by sequencing of the hypervariable region I (HV1) of the mitochondrial DNA (mtDNA) control region. The STR profile, the mitochondrial haplotype, and the haplogroup determined were compared with those of modern Eurasian and Native American populations. The results showed the affinity of this ancient skeleton with both east Siberian/Asian and Native American populations.
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Affiliation(s)
- François-Xavier Ricaut
- Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, 67085 Strasbourg, France.
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Carpio Y, Sainz de la Peña MV, Santiesteban M, Amaro F, Ferreira R, Lleonart R. Genetic structure of a Cuban population based on nine short tandem repeat loci. Int J Legal Med 2005; 119:137-41. [PMID: 15711979 DOI: 10.1007/s00414-005-0522-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Accepted: 01/07/2005] [Indexed: 10/25/2022]
Abstract
Cuba is a multiethnic and multiracial society. Here we describe the genetic variation of a sample of the Cuban population, which include the three most common racial groups, Caucasians, Negroids and Mestizos, by means of a set of nine microsatellites (HUMTH01, HUMTPOX, HUMCFS1PO, HUMVWA, HUMFESFPS, HUMF13A, HUMF13B, HUMLPL and HUMHPRTB). The analysis presented here indicates that these STR loci are highly informative for forensic purposes. The genetic data on the major racial groups is in good agreement with current demographic tendencies and with historic events that took place during the formation of the Cuban population.
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Affiliation(s)
- Yamila Carpio
- Center for Genetic Engineering and Biotechnology, PO Box 6162, Havana 10600, Cuba
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