Short communicationAnalysis of 49 autosomal SNPs in an Iraqi population
Section snippets
Population and samples
The Iraqi population is heterogeneous and includes a number of ethnic groups. Around 75–80% of the total Iraqi population are Arabs. Kurds represent 15–20% of the total population, while approximately 5% of the population is constituted by minority groups such as Turkomans, Yazidis, Assyrians and Armenians [1]. According to the Danish Statistic Bank (“Statistikbanken®” [2]), 29,859 individuals from Iraq were registered as residents in Denmark in July 2011. In order to establish a frequency
DNA extraction
DNA from approximately half the samples was extracted from 200 μL blood using the QIAamp DNA blood mini kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer's recommendations. DNA from the other half of the samples was extracted from 4 μL of blood using the DNA Investigator kit (Qiagen) and a BioRobot® EZ1 Workstation (Qiagen) according to the manufacturer's instructions.
SNP genotyping and quality control
Forty-nine of the 52 autosomal SNPforID SNPs [4] were analyzed using a single PCR and two single base extension (SBE) reactions as previously described [3]. The SBE products were run in an ABI3130xl Genetic Analyzer (AB) with 36 cm capillary arrays and POP-4™ polymer (AB). The GeneScan® 3.7 (AB) and Genotyper® 3.7 software (AB) were used to analyze the resulting electropherograms. Previously described criteria for homo- and heterozygote allele calling were used [4]. Each sample was run two
Data analyses
Population genetic analyses were performed using Arlequin 3.5.1.2 software [5]. Possible departures from Hardy–Weinberg equilibrium (HWE) were tested as described by Guo and Thompsom [6]. Linkage disequilibrium between pairs of loci was tested using an extension of the Fisher's exact test [7]. Data regarding the 49 autosomal SNPs analyzed in populations from Turkey, Israel, Pakistan, India, China, Taiwan, Japan, Siberia, Algeria, Somalia, Uganda, Mozambique, Angola, Nigeria, Denmark, Portugal
Results and discussion
Allele frequencies and observed and expected heterozygosities for the 49 SNPs studied in the Iraqi population are provided in Supplementary Table 1. The minimum allele frequency observed for the 49 autosomal SNPs analyzed in the Iraqi population varied from 0.178 (rs938283) to 0.500 (rs8037429). All but one SNP (rs2107612) showed the number of heterozygotes expected under HWE. The heterozygosity observed for the SNP system rs2107612 (0.287) was significantly lower (P < 0.05, after step-down
Acknowledgements
We thank Trine L. Hansen and Anja Jørgensen for technical assistance. IED and EM are recipients of an ERASMUS fellowship from Universitat de Barcelona and a MOBINT fellowship from AGAUR (Agència de Gestió d’Ajuts Universitaris i de Recerca, Generalitat de Catalunya). Authors agree and accept the guidelines for publication of population genetic data requested by the journal editorial [12].
References (12)
- et al.
Validation of a single nucleotide polymorphism (SNP) typing assay with 49 SNPs for forensic genetic testing in a laboratory accredited according to the ISO 17025 standard
Forensic Sci. Int. Genet.
(2009) - et al.
Allele frequencies of 15 autosomal STR loci in the Iraq population with comparisons to other populations from the middle-eastern region
Forensic Sci. Int.
(2007) - et al.
Publication of population data for forensic purposes
Forensic Sci. Int. Genet.
(2010) - et al.
A multiplex assay with 52 single nucleotide polymorphisms for human identification
Electrophoresis
(2006)
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