Allele and haplotype frequencies of 12 X-STRs in Mexican population

Allele and haplotype frequencies of 12 X-STRs in Mexican population

Forensic Science International: Genetics 38 (2019) e11–e13 Contents lists available at ScienceDirect Forensic Science International: Genetics journa...

2MB Sizes 0 Downloads 33 Views

Forensic Science International: Genetics 38 (2019) e11–e13

Contents lists available at ScienceDirect

Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsigen

Correspondence Allele and haplotype frequencies of 12 X-STRs in Mexican population

T

ARTICLE INFO

ABSTRACT

Keywords: Argus X-12 X-STRs Human identification STRs Mexico FamLinkX

The use of X-chromosome short tandem repeats (X-STRs) to solve complex kinship cases has been facilitated by commercial human identification kits, such as the Argus X-12 kit (Qiagen), and the free-access software FamlinkX. For this purpose, allele and haplotype frequencies are required in the populations to be employed. Therefore, we obtained Argus X-12 haplotypes in 933 unrelated males from seven different geographic regions from Mexico. Forensic parameters for individual X-STRs and for three-loci linkage groups are reported. The observed homogeneity between the studied population samples support to use a global Mexican population database (Fst p-value > 0.05). In brief, forensic validation of the Argus X-12 kit was performed to facilitate incorporation of X-STRs in forensic casework in this country.

Dear editor, Mexico is one of the most populated countries in the world, occupying the 10th place with more than 120 million of inhabitants [1]. Most of the Mexican population (approximately 93%) is the result of around 500 years of admixture principally between Spaniards, Amerindians, and Africans in lesser extent. Admixed populations are commonly known as Mestizos; they speak Spanish and live in both urban and rural areas throughout the Mexican territory [2]. Forensic validation of different commercial Human Identification (HID) kits has been carried out in Mexican populations, including autosomal [2,3] and Ychromosome short tandem repeats (Y-STRs) [4]. However, X-chromosome STR (X-STR) loci have been scarcely studied in Mexico and, to our knowledge,only in female population samples [5,6]. X-STRs are important for resolution of complex kinship cases where at least one woman is involved; therefore, during the last decade, different X-STR systems have been included to the battery of markers available in forensic labs [7–9]. For instance, the Investigator® Argus X-12 kit (Qiagen, Germany) that allows obtaining three-loci X-STR haplotypes producing four linkage groups. In addition, the FamlinkX software has encouraged the incorporation of X-STR genetic systems making easier the statistical interpretation of haplotype data in forensic casework [10,11]. However, FamLinkX requires allele and haplotype frequencies directly obtained from male population samples [12,13], which are not available from any Mexican population. Consequently, the aim of this study is to create a Mexican population database with the Argus X-12 kit, and to report the required forensic parameters for HID purposes. We analyzed genomic DNA from 933 unrelated males from different geographic regions of Mexico: Northwest (n = 66), Northcenter (n = 342), Northeast (n = 103), West (n = 111), Center (n = 116), South (n = 94), and Southeast (n = 101) (Fig. 1). All volunteers signed an informed consent letter according to the Helsinki Declaration Ethical Guidelines. This project was approved by the Ethical Research Committee at the CUCiénega of the University of Guadalajara (UdeG) (N° 2911/05). DNA amplification with the Investigator® Argus X-12 kit (Qiagen, Germany) was carried out according to the manufacturer instructions.PCR products were analyzed by capillary electrophoresis https://doi.org/10.1016/j.fsigen.2018.10.012 Received 17 May 2018 Available online 23 October 2018 1872-4973/ © 2018 Elsevier B.V. All rights reserved.

using POP-7 polymer on ABI Prism™ 3130 Genetic Analyzer (Applied Biosystems, CA, USA)following the supplier recommendations. Genotyping process was helped by the allelic ladder incorporated within the Argus X-12 kit, and the software Genemapper version 3.2 (Applied Biosystems, CA, USA). Positive and negative controls were used as reference of suitable amplification.Our laboratory participates in the annual quality control exercise organized by the Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (https://ghep-isfg.org/), where the Investigator® Argus X-12 kit was included. The complete X-STR haplotype database, and the estimated allele frequencies in the total Mexican population sample are provided as Electronic Supplementary Material (ESM1 and 2, respectively). Similarly, haplotype frequencies calculatedby direct counting for each linkage group are supplied in this letter (ESM 3). A summary of this haplotype information is described in Table 1. The total population sample included 933 unrelated Mexican males, with 395, 299, 245, and 326 different haplotypes for the linkage groups I, II, III, and IV, respectively. The linkage group I was the most informative in MexicanMestizos, as previously described in German population [12]. The four linkage groups showed an elevated haplotype diversity (h≥98.35%). The percentage of unique haplotypes ranged between 44.4 and 57.3%, each with a frequency of 0.1%. Conversely, the haplotype 16-13-32 of the linkage group III was the most common with 56 observations(p = 0.06). As could be expected, pairwise LD tests between X-STRs of the Argus X-12 kit showed association between most of the loci from the same linkage group (ESM 4). Conversely, pairwise loci from different linkage groups were in equilibrium linkage (p > 0.01). The population relationships were evaluated by Fst distances and Fst p-values (ESM 5a) based upon haplotype frequencies ofthe seven Mexican population samples with the Arlequin 3.0 software [14].Because genetic homogeneity was demonstrated between the sampled geographic regions (pairwise Fst p-values > 0.99), a global Mexican population database compatible with the FamLinkX software was created (ESM 6: available upon request). However, due to the high haplotype diversity based on all 12 X-STRs, the sample sizes are too low for detecting significant differences, if they exist. In fact, when pairwise

Forensic Science International: Genetics 38 (2019) e11–e13

Correspondence

Fig. 1. Geographic location and sample size of the studied geographic regions in Mexican populations. Table 1 Summary of haplotype data of four linkage group included in the Investigator Argus X-12 Kit. Linkage group (n = 933)

Haplotype Diversity

Possible Haplotypes

Observed Haplotypes

Unique Haplotypes

Most common haplotype

Frequency of the most Frequent haplotype

I II III III

0.99428 0.99314 0.98355 0.99173

6296 3696 1575 8613

395 299 245 326

225 133 116 187

18-20-10 14-20-15 16-13-32 29-37-15

0.01929 0.01929 0.06002 0.03000

comparisons were done individually for each linkage group (ESM 5bc), some differences were the noticed, but principally implying the Northcenter region for the linkage group III, and -in lesser extent- IV, respectively. Therefore, the conclusion of genetic homogeneity between Mexican subpopulations should be considered as a preliminary finding to be confirmed with a larger population sample size. Given the lack FamLinkX-compatible databases from Latin-American populations, the attached file also could be useful for interpretation of complex kinship interpretation in different countries. In brief, we carried out the forensic validation of the Argus X-12 kit in Mexican population to facilitate its incorporation in forensic casework.

Appendix A. Supplementary data Supplementary material related to this article can be found, in the online version, at doi:https://doi.org/10.1016/j.fsigen.2018.10.012. References [1] United Nations, World Population Prospects: The 2015 Revision, Key Findings and Advance Tables, WorkingPaper No. ESA/P/WP.241 Department of Economic and Social Affairs, PopulationDivision, 2015. [2] R. Rubi-Castellanos, G. Martínez-Cortés, J.F. Muñoz-Valle, A. González-Martín, R.M. Cerda-Flores, M. Anaya-Palafox, H. Rangel-Villalobos, Pre-Hispanic Mesoamerican demography approximates the present-day ancestry of Mestizos throughout the territory of Mexico, Am. J. Phys. Anthropol. 139 (2009) 284–294. [3] J. Salazar-Flores, F. Zuñiga-Chiquette, R. Rubi-Castellanos, J.L. Álvarez-Miranda, A. Zetina-Hérnandez, V.M. Martínez-Sevilla, et al., Admixture and genetic relationships of Mexican Mestizos regarding Latin American and Caribbean populations based on 13 CODIS-STRs, Homo 68 (6) (2017) 44–59. [4] B. Ramos-González, J.A. Aguilar-Velázquez, M.L. Chávez-Briones, M.R. EscareñoHernández, E. Alfaro-Lopez, H. Rangel-Villalobos, Genetic population data of three Y-STR genetic systems in Mexican-Mestizos from Monterrey, Nuevo León (northeast, Mexico), Forensic Sci. Int. Genet. 29 (2017) e21–e22, https://doi.org/10. 1016/j.fsigen.2017.04.016. [5] I. Cortés-Trujillo, B. Ramos-González, O. Salas-Salas, F. Zuñiga-Chiquette, J.L. Álvarez-Miranda, G. Martínez-Cortés, M. Ruiz-Hernández, A. González-Martín, H. Rangel-Villalobos, Forensic efficiency parameters of the kit Investigator Argus X12 in two Mestizo and seven Amerindian populations from Mexico, Leg. Med. (Tokyo) 26 (2017) 62–64, https://doi.org/10.1016/j.legalmed.2017.03.006. [6] C. Mariscal Ramos, G. Martínez-Cortes, B. Ramos-González, H. Rangel-Villalobos, Forensic parameters of the X-STR Decaplex system in Mexican populations, Leg.

Conflict of interest Authors declare no conflicts of interest. Acknowledgments We are grateful with all the volunteers for generously collaborating in this study. We thank the technical support of A. Luna-Vázquez, G. Vilchis-Dorantes, A.P. Solis-Rivera, E. Arteaga-Jimenez, E. CastañonTorres, C.D. Muñoz-Rivas and L.G. Madrid-Pérez. We thank to CONACyT (grant N°129693) and to QIAGEN-México for the partial support to this project, and for the doctoral fellowship to I-CT. e12

Forensic Science International: Genetics 38 (2019) e11–e13

Correspondence

Benito Ramos-González Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León, Monterrey, Nuevo León, Mexico

Med. (Tokyo) 31 (2017) 38–41, https://doi.org/10.1016/j.legalmed.2017.12.013. [7] R. Szibor, M. Krawzack, S. Hering, J. Edelmann, E. Kuhlisch, D. Krause, Use of Xlinked markers for forensic purposes, Int. J. Leg. Med. 117 (2003) 67–74. [8] A. Barbaro, P. Comarci, A. Barbaro, X-STRs typing for an identification casework, Int. Congr. Ser. 1288 (2006) 513–515. [9] T.M. Diegoli, Forensic typing of short tandem repeat markers on the X and Y chromosomes, Forensic Sci. Int. Genet. 18 (2015) 140–151. [10] D. Kling, A. Tillmar, T. Egeland, P. Mostad, A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations, Int. J. Leg. Med. 129 (2014) 943–954, https://doi.org/10.1007/ s00414-014-1117-7. [11] D. Kling, B. Dell’ Amico, A. Tillmar, FamLinkX–implementation of a general model for likelihood computations for X-chromosomal marker data, Forensic Sci. Int. Genet. 17 (2015) 1–7, https://doi.org/10.1016/j.fsigen.2015.02.007. [12] J. Edelmann, S. Lutz-Bonengel, J. Naue, S. Hering, X-chromosomal haplotype frequencies of four linkage groupsusing the Investigator Argus X-12 kit, Forensic Sci. Int. Genet. 6 (2012) 24–34. [13] D. Kling, Curiosities of X chromosomal markers and haplotypes, Int. J. Leg. Med. 132 (2017) 361–371. [14] L. Excoffier, G. Laval, S. Schneider, Arlequin ver. 3.0: an integrated software package for population genetics data analysis, Evol. Bioinform. Online 1 (2005) 47–50.

Maria de Loures Chávez-Brionesa,b Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León, Monterrey, Nuevo León, Mexico b Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico a

Karely Liliana Islas-González, David Adrián Betancourt-Guerra Laboratorio de Genética Forense, Dirección de Servicios Periciales de la Fiscalía del Estado de Chihuahua, Ciudad Juárez, Chihuahua, Mexico Rocío Peralta-Coria Laboratorio de Genética Forense, Dirección de Servicios Periciales de la Procuraduría General de la República (PGR), Ciudad de México, Mexico Gabriela Martínez-Cortés, Héctor Rangel-Villalobos Instituto de Investigación en Genética Molecular, Universidad de Guadalajara (CUCI-UdeG), Ocotlán, Jalisco, Mexico E-mail addresses: [email protected], [email protected] (H. Rangel-Villalobos) ⁎

Irán Cortés-Trujillo Instituto de Investigación en Genética Molecular, Universidad de Guadalajara (CUCI-UdeG), Ocotlán, Jalisco, Mexico Fernando Zuñiga-Chiquette Laboratorio de Genética Forense, Servicios Periciales de la Procuraduría General de Justicia del Estado de Baja California, Tijuana, Baja California, Mexico

⁎ Corresponding author at: Instituto de Investigación en Genética Molecular, Universidad de Guadalajara, Av. Universidad #1115, CP 47810, Ocotlán, Jalisco, Mexico.

e13