Genetic polymorphisms of twelve X-STRs of the investigator Argus X-12 kit and additional six X-STR centromere region loci in an Egyptian population sample

https://doi.org/10.1016/j.fsigen.2014.02.007Get rights and content

Abstract

Recently, many researchers have focused on analysis of different X-chromosomal STRs as they bear the potential to efficiently complement the analysis of autosomal and Y-chromosomal STRs in solving special complex kinship deficiency cases. In the current study we examined a sample of 250 unrelated Egyptian males with the Investigator Argus X-12 kit (Qiagen GmbH, Hilden, Germany) which detects 12 X-STR markers distributed over the entire X-chromosome as four closely linked clusters. Microvariant off ladder alleles as well as null alleles have been detected in some loci. Furthermore, discordant results were observed between the Investigator Argus X-12 and the Mentype® Argus X-8 kits (Biotype AG, Dresden, Germany). New primers were designed for loci DXS10101, DXS10146 and DXS10148 to correct the allele drop outs observed in these loci with the Investigator Argus X-12 kit. Additionally, DNA sequence analysis revealed the polymorphisms responsible for the allele drop outs. Furthermore, six additional X-STRs (DXS10161, DXS10159, DXS10162, DXS10163, DXS10164 and DXS10165) located in the centromere region at Xp11.21–Xq11.1 were examined in a single multiplex reaction. Allele and haplotype frequencies as well as different forensic statistical parameters of the 18 X-STR loci tested indicated that they are highly informative in different forensic applications in the Egyptian population. However, some modifications still need to be performed on the Investigator Argus X-12 kit before its use in forensic casework is validated.

Introduction

X-chromosomal short tandem repeat markers (X-STRs) have special characteristics that make them particularly useful in certain forensic casework. The fact that males are hemizygous for their X-chromosome and a father passes his X-chromosome completely to his daughters made X-STR markers good candidates for efficiently complementing autosomal and Y-chromosomal short tandem repeat markers (Y-STRs) in solving kinship deficiency cases [1], [2], [3]. Furthermore, certain X-STR loci express strong linkage disequilibrium (LD) and segregate together as haplotypes [4], [5], [6], [7], [8], [9], [10], [11].

A great number of X-STR multiplex assays have been described in the literature, but only one commercial kit is currently available. That is the Investigator Argus X-12 kit (Qiagen GmbH, Hilden, Germany) which simultaneously detects 12 X-STR markers plus Amelogenin. Before the potential of this kit for use in a forensic setting can be fully estimated, it is crucial to thoroughly examine it with different populations.

Therefore we examined anonymized samples of unrelated Egyptian males with the commercially available Investigator Argus X-12 kit as well as with an ‘in-house’ prepared multiplex system described by Edelmann et al. [12]. The ‘in-house’ prepared multiplex detects 6 X-STRs, namely DXS10159, DXS10161, DXS10162, DXS10163, DXS1064 and DXS1065 which are located in the region between 56 and 64 Mb distanced from the Xp telomere at Xp11.1–Xq11.1.

The aim of the current study is to report population specific data of the 18 X-STRs tested in the samples of 250 males from Alexandria/Egypt.

Egypt is located on the Mediterranean Sea in Northeast Africa and acts as a crossroad between three continents: Africa, Asia, and Europe. Alexandria is Egypt's second largest city, located in Northern Egypt bordering the Mediterranean Sea and is considered as Egypt's major seaport. During its history, Egypt has been ruled by several occupying forces of different ethnicities. Moreover, over the years different migration waves took place between Egypt and the neighboring countries. This has consequently affected the Egyptian population structure. Several studies that have been conducted on polymorphisms of the Y-chromosome [13], [14] and of the mitochondrial DNA [15], [16], [17] of Egyptian population samples, concluded that the current Egyptian population represents a mixture of multiple ethnic origins, namely European, Middle Eastern and African. Additionally, Saunier et al. [17] observed that the haplotype breakdown of an Egyptian population sample from Alexandria, that they studied, consisted predominantly of European (67.5%), followed by African (20.6%) and then Asian (11.9%) mitochondrial DNA.

Section snippets

Samples and DNA extraction

After informed consent, DNA samples were collected from 250 healthy unrelated Egyptian male volunteers living in Alexandria. The samples were collected as buccal swabs and were anonymized before being processed. DNA extraction was carried out using the QIAamp® DNA Mini Kit (Qiagen GmbH, Hilden, Germany).

PCR amplification

All the 250 Egyptian male samples collected were amplified with the Investigator Argus X-12 kit. PCR amplification and capillary electrophoresis were performed according to the manufacturer's

Results and discussion

Among the 250 samples examined, allele drop outs as well as off ladder alleles were observed. Human reference genome and known genetic variations were inspected.

Conclusion and recommendations

In this study discordance has been observed between the Investigator Argus X-12 kit and the earlier generation Mentype Argus X-8 kit. This discordance is probably a result of using different primers with different primer binding sites.

Furthermore, null alleles have been observed with Argus X-12 in loci DXS10101, DXS10146 and DXS10148 in the Egyptian samples tested here. In loci DXS10101 and DXS10148 SNPs were detected in the sequenced samples, while in locus DXS10146 an insertion/deletion

Role of funding

No external funding was received to conduct this study.

Conflict of interest

None declared.

Acknowledgements

The authors would like to thank Ahmad Ashour and Mahmoud Ahmed for their enormous help in the sample collection.

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