Forensic Science International: Genetics 10 (2014) e4–e6

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Forensic Population Genetics – Letter to the Editor Genetic variation of 24 STR loci in a Mexican Mestizo population from Mexico D.F Dear Editor, In the present communication, twenty-four short tandem repeat (STR) loci (D3S1358, D1S1656, D2S441, D10S1248, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, DYS391, D8S1179, D12S391, D19S433, FGA, D22S1045 and D6S1043) were analyzed using the commercially available Powerplex1 Fusion System and Powerplex1 21 System (Promega, Madison, WI, USA) from a population sample of unrelated healthy Mexican mestizo individuals living in Mexico D.F. Further studies have characterized the Mestizo population from Mexico D.F. [1,2], but new highly polymorphism sites as D1S1656 [3] or D12S391 [4] have not been previously reported in this population. A total of 205 DNA samples were obtained through informed consent from unrelated donors from the Mexican population of Mexico D.F. specifically from paternity cases from the Centro de Estudios e Investigaciones ANIGEN and from anonymous donors from the faculty of Superior Studies Zaragoza (UNAM). About 25 ml of blood were spotted on FTA1 Whatman paper (Whatman, Clifton, NJ, USA). A 1.2 mm punch of FTA cards was used in each amplification without any preprocessing. Samples were amplified using Powerplex1 Fusion kit and Powerplex1 21 System (Promega) which contains 24 and 21 STRs as described by the manufacturer. The amplification was performed in a GeneAmp 9700 thermal cycler (Life Technologies, Carlsbad, CA, USA) with the following conditions: denaturation at 96 8C for 4 min followed by 27 cycles of 94 8C for 10 s, 59 8C for 60 s and 72 8C for 30 s, followed by 20 min at 60 8C. For amplification of the samples, the number of PCR cycles was reduced from 27 to 25 in order to decrease the amount of pull-up. The decrease in the number of PCR cycles from 27 to 25 made the analysis of samples without prior quantification possible. Amplification products were separated by electrophoresis in an Applied Biosystems ABI 3100 AVANT Genetic Analyzer (Life Technologies) and allele calls were determined automatically using GeneMapper v3.2 software (Life Technologies). Typing quality and allele designation were verified by simultaneous electrophoretic analysis of a control sample of known size. The alleles were named according to the number of repeated units, based on the sequenced allelic ladder according to the recommendations of the DNA commission of the ISFG (International Society of Forensic Genetics) [5,6]. ANIGEN Center of Studies and Investigations (Mexico D.F., Mexico) participate in the proficiency test of the DNA Analysis Latin American Working Group (GITAD) of the Latin American Academy of Forensic Sciences and Criminology (AICEF). Allelic frequencies, observed heterozygosity (Ho), expected heterozygosity (He) and deviation probability from the Hardy– Weinberg equilibrium (p) were calculated using the Arlequin 1872-4973/$ – see front matter ß 2014 Elsevier Ireland Ltd. All rights reserved. http://dx.doi.org/10.1016/j.fsigen.2014.02.001

v3.5.1.2 software [7]. Matching probability (MP), polymorphism information content (PIC), power of discrimination (PD), power of exclusion (PE) and typical paternity index (TPI) were calculated for each locus using the PowerStats v12 software [8]. Allele frequencies, PD, MP, were calculated for loci DYS391 using the PowerStats v12 software [8]. Gene diversity (GD) for loci DYS391 was calculated with the Arlequin v3.5.1.2 software [7] on a locus-bylocus basis. The Fst distances among Mexico D.F. population and other published population data (Metztitlan [9]; Yucatan [10]; Chihuahua [11]; Jalisco [10]; Nayarit [12]; Otomi from Sierra Madre (OtomiSM), Otomi from Ixmiquilpan (OtomiIS) and Huastecos [13]; USA Hispanos (HisUSA) [14]; and Spain (SpainEU), MartinezGonzalez et al. unpublished results) were calculated with Gendist from the package Phylip v3.69 [15]. To represent the distances in a more appropriate way, genetic distances (Reynolds, Nei and Cavalli-Sforza´s genetic-distance matrices) between the populations were graphically summarized by Euclidean representation, using the software SSPS v.20. Allele frequencies and statistic parameters for the 24 aSTR loci of the Mexican population are shown in Supplementary Table 1 and Supplementary Table 2 respectively. All loci analyzed but TH01 and D12S391 were in Hardy– Weinberg (HWE) equilibrium in the studied population (p > 0.05). However, after Bonferroni correction with 24 comparisons (p > 0.0021), the significant deviations from HWE were lost. The forensic parameter averages calculated for the aSTRs were: polymorphism information content (PIC) 74.65%; power of discrimination (PD) 90.96%; power of exclusion (PE) 57.51%; observed heterozygosity (Ho) 77.99%. Penta E showed the highest level of Ho (0.9317), PD (0.9818) and PIC (0.9079). D22S1045 had the lowest Ho (0.5659), PD (0.7831) and PIC (0.5298). The combined power of discrimination and the power of exclusion for the 23 aSTRs studied were 1–7.57287  10 27 and 99.999999% respectively. Gene diversity for DYS391 was 0.4953, PD was 50.92% and MP was 49.02%. Euclidean distance model of a multidimensional scale (MDS) and a representation plot is shown in Fig. 1. Mexican population can be divided into native (left part of the image) and Mestizos (right part). Admixture effects can be seen in Mestizos populations, where Mexico D.F. population can be found; closely located to Spanish and Hispanic American populations. These results are expected considering historical, geographic, linguistic and cultural factors. Genetic distances are summarized in Supplementary Table 3. According to these statistical parameters, the obtained data might be useful for population genetics research and for individual identification and paternity testing in forensic science. The use of standardized STR markers [16,17] to characterize populations as far as the determination of a very high number of markers will enable and facilitate the collaboration between forensic and population genetics laboratories. This paper follows

Forensic Population Genetics – Letter to the Editor / Forensic Science International: Genetics 10 (2014) e4–e6

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Fig. 1. Euclidean representation of Reynold’s genetic distances; stress value 0.05472.

the publication guidelines of population data requested by the journal [18]. Acknowledgments The authors wish to thank the DNA and blood donors, and everyone who assisted in the blood collection. The authors also wish to thank Dr. Jorge Antonio Zogbi Vela´zquez for his assistance, provision of the PCR kits and support. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.fsigen.2014.02.001. References [1] A. Luna-Vazquez, G. Vilchis-Dorantes, L.A. Paez-Riberos, F. Mun˜oz-Valle, A. Gonza´lez-Martin, H. Rangel-Villalobos, Population data of nine STRs of MexicanMestizos from Mexico City, Forensic Sci. Int. 136 (2003) 96–98. [2] T. Jua´rez-Cedillo, J. Zun˜iga, V. Acun˜a-Alonzo, N. Pe´rez-Herna´ndez, J.M. Rodrı´guezPe´rez, R. Barquera, et al., Genetic admixture and diversity estimations in the Mexican Mestizo population from Mexico City using 15 STR polymorphic markers, Forensic Sci. Int.: Genet. 2 (2008) e37–e39. [3] M.V. Lareu, S. Barrai, A. Salas, C. Pestoni, A. Carracedo, Sequence variation of a hypervariable short tandem repeat at the D1S1656 locus, Int. J. Legal Med. 111 (1998) 244–247. [4] M.V. Lareu, C. Pestoni, M. Schu¨renkamp, S. Rand, B. Brinkmann, A. Carracedo, A highly variable STR at the D12S391 locus, Int. J. Legal Med. 109 (1996) 134–138. [5] W. Ba¨r, B. Brinkmann, B. Budowle, A. Carracedo, P. Gill, P. Lincoln, et al., DNA recommendations. Further report of the DNA commission of the ISFG regarding the use of short tandem repeat systems, Forensic Sci. Int. 87 (1997) 179–184. [6] B. Olaisen, W. Ba¨r, B. Brinkmann, B. Budowle, A. Carracedo, P. Gill, et al., DNA recommendations 1997 of the international society for forensic genetics, Vox Sang. 74 (1998) 61–63. [7] L. Excoffier, H. Lischer, Arlequin suite ver3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resources 10 (2010) 564–567.

[8] A. Tereba, Tools for analysis of population statistics, Profiles in DNA 3 (1999) 14– 16. [9] A. Gorostiza, A. Gonza´lez-Martı´n, C.L. Ramı´rez, C. Sa´nchez, C. Barrot, M. Ortega, et al., Allele frequencies of the 15 AmpF/Str identifiler loci in the population of Metztitla´n (Estado de Hidalgo), Mexico, Forensic Sci. Int. 166 (2007) 230– 232. [10] R. Rubi-Castellanos, M. Anaya-Palafox, E. Mena-Rojas, D. Bautista-Espan˜a, J.F. Mun˜oz-Valle, H. Rangel-Villalobos, Genetic data of 15 autosomal STRs (identifiler kit) of three Mexican Mestizo population samples from the states of Jalisco (west), Puebla (center), and Yucatan (southeast), Forensic Sci. Int.: Genet. 3 (2009) e71– e76. [11] L.J. Martinez-Gonzalez, J.A. Lorente, E. Martinez-Espin, J. Carlos Alvarez, M. Lorente, E. Villanueva, et al., Intentional mixed buccal cell reference sample in a paternity case, J. Forensic Sci. 52 (2007) 397–399. [12] M.J. Alvarez-Cubero, L.J. Martinez-Gonzalez, D. Virgen-Ponce, E.A. Delgado-Najar, G.H. Moscoso-Caloca, J.C. Alvarez, et al., Genetic variation of 15 autosomal microsatellite loci in a Nayarit population (Mexico), Legal Med. 13 (2011) 323–327. [13] C. Barrot, C. Sa´nchez, M. Ortega, A. Gonza´lez-Martı´n, C. Brand-Casadevall, A. Gorostiza, et al., Characterisation of three Amerindian populations from Hidalgo State (Mexico) by 15 STR-PCR polymorphisms, Int. J. Legal Med. 119 (2005) 111– 115. [14] B. Budowle, B. Shea, S. Niezgoda, R. Chakraborty, CODIS STR loci data from 41 sample populations, J. Forensic Sci. 46 (2001) 453–489. [15] J. Felsenstein, PHYLIP (Phylogeny Inference Package) Documentation Files, Version 3.62c [computer program], Department of Genetics University of Washington, Seattle, WA, USA (2004). [16] Working Group ENFSI DNA, DNA-Database Management Review and 2012 http://www.enfsi.eu/sites/default/files/documents/ Recommendations, enfsi_document_on_dna-database_management_2012_0.pdf; 1–82. [17] P. Gill, L. Fereday, N. Morling, P.M. Schneider, The evolution of DNA databases— recommendations for new European STR loci, Forensic Sci. Int. 156 (2006) 242– 244. [18] A. Carracedo, J.M. Butler, L. Gusma˜o, W. Parson, L. Roewer, P.M. Schneider, Publication of population data for forensic purposes, Forensic Sci. Int.: Genet. 4 (2010) 145–147.

Erika Ramı´rez-Floresa,1 Marı´a Saizb,1,* Dora Villegas-Carmonaa Maria Jesus Alvarez-Cuberoc

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Forensic Population Genetics – Letter to the Editor / Forensic Science International: Genetics 10 (2014) e4–e6

Juan Carlos A´lvarezb Lourdes Vega-Navarretea a Anigen Center of Studies and Investigations, Municipio Libre 366, Col. Sta. Cruz Atoyac, Del. Benito Jua´rez C.P. 03310, Mexico b Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Universidad de Granada, Avda. de Madrid 11, 18071 Granada, Spain c Centre of Molecular Antropology for Ancient DNA Studies, Dipartimento di Biologia, Universita` di Roma ‘‘Tor Vergata," Rome, Italy

*Corresponding author at: Laboratory of Genetic Identification, Dept. Legal Medicine, Universidad de Granada, Granada, Spain. Tel.: +34 958249950; fax: +34 958246107 E-mail address: [email protected] (M. Saiz). 1

These authors contributed equally to this work. 12 September 2013 31 January 2014 1 February 2014

Genetic variation of 24 STR loci in a Mexican Mestizo population from Mexico D.F.

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