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Analysis of 49 autosomal SNPs in an Iraqi population

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Abstract

Forty-nine of the 52 autosomal single nucleotide polymorphisms (SNPs) in the SNPforID 52plex were typed in 101 unrelated Iraqis living in Denmark. No significant deviation from HWE was found in all but one of the 49 SNP systems and no significant pairwise linkage disequilibrium was observed for any SNP pair. When 18 worldwide populations were compared (including populations in Iraq, Turkey, Israel, Pakistan, India, China, Taiwan, Japan, Siberia, Algeria, Somalia, Uganda, Mozambique, Angola, Nigeria, Denmark, Portugal, Spain), a significant global FST value was obtained. All but six FST values were statistically significant when pairwise comparisons were performed between the 18 populations. The Iraqi population did not show significant difference from the population in Turkey and it grouped together with other Middle-Eastern populations when a multidimensional scaling plot was drawn based on the pairwise FST values. The combined mean match probability and the typical paternity index for trios were 8.3 × 10−20 and 259,000, respectively, for the 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)

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