Reference population database for 24 STR loci of selected provinces of Argentina.

doi:10.21203/rs.3.rs-2617057/v1

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Reference population database for 24 STR loci of selected provinces of Argentina.

https://doi.org/10.21203/rs.3.rs-2617057/v1

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published 23 May, 2023

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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). 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. 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.

Autosomal STR

reference database

Argentina

Argentinean population is the result of 20 generations of admixture between South Amerindians, Europeans and to a lesser degree, Africans [1]. Since the advent of forensic molecular genetics, the construction of local reference databases (RDB) became mandatory [2]. Initially, our laboratory generated RDBs for metropolitan populations and Native American groups inhabiting Argentina [3–17]

In parallel, a considerable number of publications focusing on forensic-oriented STR RDBs were developed and published by other authors [18–30]. Nevertheless, there is only one dataset, at present, under the quality guidelines established by STRidER (STRs for identity ENFSI Reference database) [31] deposited and published by Bobillo in 2019 for the Argentinean province of La Pampa (STRidER reference STR000114) [32].

Aiming to further extend the RDB of Argentina and fine control its technical quality, under STRider requirements, we present herein the allele frequencies for 24 autosomal STRs, including D22S1045, and SE33 (not previously reported for Argentina in STRidER).

Genotypes of 6454 unrelated individuals (3761 males and 2694 females) from 13 out of 23 provinces were analysed. We analyzed urban populations including: Buenos Aires, n = 1996; Misiones, n = 454; La Pampa, n = 255; Formosa, n = 698; Rio Negro, n = 1444; Chubut, n = 335; Corrientes, n = 752; Chaco, n = 256; Salta, n = 91; Santa Cruz, n = 32; Santiago del Estero, n = 47; Santa Fe, n = 64 and Neuquén, n = 30). We used the following commercial kits: PowerPlex (PP)16, PP18, PP21, PPFusion (PPF), PPF6C (Promega Corp., Madison, USA), and AmpFLSTR Identifiler and VeriFiler Express (ThermoFisher Scientific, USA). Genotypes were obtained along a period of 10 years, hence not all the samples were typed with all the STRs, whose number increased from 15 (PP16) to 24 STRs (PPF6C). We obtained DNA from peripheral blood spotted onto Whatman 3MM paper (Millipore, USA) following the method described in of the manufacture of the semiautomated Maxwell 16 robot (Promega, Madison, USA) or manually as proposed by [33]. Unrelated participants of paternity tests were randomly selected. All participants read and signed a written consent statements, approved by the Ethical Committee of the School of Pharmacy and Biochemistry of Buenos Aires University. PCR amplification reactions were performed following the manufacturer’s instructions and amplicons were separated by electrophoresis in an ABI3500 Genetic Analyzer (Invitrogen, Palo Alto, USA). Data analysis was performed using Gene Mapper ID-X V.1.1 and V.1.4 softwares (Applied Biosystems, Invitrogen, USA). The exact test of Hardy-Weinberg equilibrium (HWE) for each locus was evaluated using Arlequin v.3.5.1 software [34]. The allele frequencies, forensic parameters: Polymorphic Information Content (PIC), Match Probability (MP), and paternity parameters including Power of Exclusion (PE), Power of Discrimination (PD), Observed Heterozigosity (Hobs), Typical Paternity Index (TPI), and Genetic Diversity (GD) were calculated using the online software STRAF (https://straf-p7bdrhm3xq-ew.a.run.app/) [35]. According to the revised guidelines for the publication of genetic population data, the results were submitted passing STRidER quality control standards (QC), receiving the reference number STR000327 v.2.

Allele frequencies and forensic/paternity parameters are shown in Table S1. No departures from HWE were observed after Bonferroni’s correction. The observed heterozygosity (H obs) ranged from 0.661 (TPOX) to 0.941 (SE33). Although the lowest number of chromosomes analyzed involved locus SE33 (n = 372), it was revealed to be the most informative marker, which presented the highest values for PIC (0.955), GD (0.952), TPI (8.455) and PE (0.879). This supports the importance of incorporating SE33 within the set of markers for individual identification, which has been widely shown to be the most polymorphic marker [36–37]. On the other hand, TPOX turned out to be the least informative marker: PIC (0.618), GD (0.669), and PE (0.371).

This study is the most extensive for Argentina and complements the already reported information concerning the autosomal STRs commonly used in forensic identification. In addition, it also includes new valuable data of forensic interest as those for D22S1045, described for the first time in Argentina. The possibility offered by the analysis of a high number of samples allowed detecting microvariants and new alleles all of them in heterozygous condition. Thus, alleles with low frequency were detected in loci: CSF1PO (allele 6, 1/6454 samples); D16S539 (allele 5, 1/6454), D21S11 (allele 36, 4/6454). We also detected microvariants in the following loci: D18S51 (allele 24.1, 1/6454 samples); PENTA D (3.2, 1/6253); PENTA E (10.4 and 15.3, 1/6253 each); and at locus D6S1043, (16.1, 1/1234; 19.3 and 23.3, 8/1234 each).

Our laboratory participates yearly in the Proficiency testing of the Spanish and Portuguese Speaking Working Group (GHEP) of the International Society for Forensic Genetics (ISFG) (http://www.gepisfg.org) and the proficiency test of the Argentine Society for Forensic Genetics (SAGF) (http://www.sagf.org.ar) carried out yearly.

Comparative Quality Controls results and certificates are available at http://www.ffyb.uba.ar/shdg/certificados-de-los-controles-de-calidad

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