www.elsevier.com/locate/forsciint
Forensic Science International 167 (2007) 87–92
Announcement of Population Data
Allele frequencies of 15 autosomal STR loci in the Iraq population with
comparisons to other populations from the middle-eastern region
Filippo Barni a,*, Andrea Berti a, Antonio Pianese a, Antonio Boccellino a,Mark P. Miller b, Aldo Caperna c, Giampietro Lago a
a Carabinieri Scientific Investigation Department of Rome-Molecular Biology and Genetics Unit, Viale di Tor di Quinto 151, 00191 Rome, Italyb Department of Biology, 5305 Old Main Hill, Utah State University, Logan, Utah 84322-5305, USA
c Carabinieri Headquarter, Health Department, Viale Romania 45, 00197 Rome, Italy
Received 30 December 2005; received in revised form 27 January 2006; accepted 4 March 2006
Available online 17 April 2006
Abstract
Allele frequencies for the 15 autosomal STR loci included in the AmpFlSTR1 IdentifilerTM PCR Amplification Kit panel from Applied
Biosystems (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, TH01, TPOX, CSF1PO, D19S433, D2S1338,
D16S539) and several statistical parameters were estimated from a sample of 103 unrelated individuals, mostly Shia and Sunni Arabs, living in
most of central and southern Iraq provinces. We compared the allele frequency spectrum detected in the Iraqi population to allele frequencies from
11 other data sets from published studies of individuals from Turkey, Iraqi-Kurdistan, Saudi Arabia, Arab Emarates, Oman, Iran, Syria, and Jordan.
Significant global differences in allele frequencies were detected in 9 of the 11 comparisons following sequential Bonferroni corrections.
Comparisons with the two independent panels from Saudi Arabia were not significant after applying Bonferroni corrections, however, low P-values
(P < 0.05) associated with these two contrasts nonetheless suggested that at least slight genetic differences between populations may exist.
# 2006 Elsevier Ireland Ltd. All rights reserved.
Keywords: Iraq population; Shia and Sunni Arabs; STR DNA typing; Population data; Allele frequencies
Population: Buccal cells were collected by oral brushes
(Sterile Omni Swab or Sterile Foam Tipped Swabs, Whatman
International Ltd., Maidstone, UK) from 103 healthy, randomly
chosen individuals deriving from most of Iraq central and
southern provinces (Fig. 1). The number and ethnicity of
individuals were chosen in order to obtain a population sample
resembling the Iraq population structure and to achieve the
highest possible representation of the major ethno-religious and
tribal groups of the Country living in these central and southern
areas. Our sample was mainly constituted by Shia Arabs and,
secondly, by Sunni Arabs. Shia Arabs comprise about 65–70%
of the entire Iraq population while Sunni Arabs represent about
25% of Iraq population (Fig. 2).
DNA extraction: DNA from these samples was extracted
using QIAmp1 DNA Mini Kit (QIAGEN, Hagen, Germany)
according to manufacturer’s instructions.
* Corresponding author. Tel.: +39 347 1849158; fax: +39 02 700412617.
E-mail address: [email protected] (F. Barni).
0379-0738/$ – see front matter # 2006 Elsevier Ireland Ltd. All rights reserved.
doi:10.1016/j.forsciint.2006.03.005
DNA quantification: The total amount of human genomic
extracted DNA was determined by using QuantifilerTM Human
DNA Quantification Kit (Applied Biosystems, Foster City, CA,
USA) [1], which employs a TaqMan1 MGB Probe-based
technology (Applied Biosystems, Foster City, CA, USA) on
ABI Prism1 7000 Sequence Detection System (Applied
Biosystems, Foster City, CA, USA).
PCR: Simultaneous amplifications of 16 STR loci (multi-
plexed PCR) were performed by using the AmpFlSTR1
IdentifilerTM PCR Amplification Kit according to the user’s
manual recommendations [2]. The 16 loci amplified in this
study are D3S1358, vWA, FGA, D8S1179, D21S11, D18S51,
D5S818, D13S317, D7S820, TH01, TPOX, CSF1PO,
D19S433, D2S1338, D16S539 and the gender determination
marker, Amelogenin.
Typing: The separation and detection of amplified products
were conducted with the ABI Prism1 3100 Genetic Analyzer
16-capillary array system (Applied Biosystems, Foster City,
CA, USA) following manufacturer’s protocols. Data collection
was performed with Data Collection v. 2.0 software (Applied
Biosystems, Foster City, CA, USA) and samples were analyzed
F. Barni et al. / Forensic Science International 167 (2007) 87–9288
Fig. 1. Iraq administrative map showing the population density and the central and southern governorates where our samples came from (areas included in the black
circle) (Source: UNOSAT, www.unosat.org, United Nations).
by GeneMapper1 v. 3.2 software (Applied Biosystems, Foster
City, CA, USA).
Quality control: Experimental procedures were performed
according to the guidelines of the external blind proficiency test
of the GEDNAP (http://www.gednap.org) [3,4].
Statistical analyses: Several forensic and population
parameters such as the power of discrimination (PD), the a
priori chance of exclusion (CE), the polymorphism information
content (PIC), the paternity index (PI), the random match
probability (RMP) and marker’s observed and expected
heterozygosity (Ho and He, respectively) of the 15 loci were
estimated by using the statistical Microsoft WindowsTM-based
software Popgene v. 1.31 [5] and Cervus v. 2.0 [6,7] while
Hardy-Weinberg equilibrium analysis was performed for each
locus by the Chi-square test (x2).
Fig. 2. Iraq ethno-religious map showing the ethnic and religious population compos
and, secondly, by Sunni Arabs, where our samples came from (areas included in t
A set of interpopulation comparisons of allele frequencies
from this study and 11 additional published population data sets
were performed. Our analyses compared the Iraqi data to data
from Turkey [8,9], Iraqi-Kurdistan (northern Iraq) [10], Saudi
Arabia [11,12], Arabs Emirates [12], Oman [12], Iran [12,13],
Syria [14], and Jordan [15] whenever the same loci studied were
shared. In these cases, allele frequency data reported in these
studies were converted to counts by multiplying allele
frequencies from these publications by reported diploid (2N)
sample sizes. Tests for homogeneity of allele frequencies
between locus-specific data sets were performed using the
computer program R � C (M.P. Miller, available at http://
www.marksgeneticsoftware.net), which implements a Markov
Chain Monte Carlo variation of Fisher’s Exact test [16]. A global
P-value over shared loci from comparisons with each panel was
ition and the central and southern governorates, mostly constituted by Shia Arabs
he black circle) (Source: UNOSAT, www.unosat.org, United Nations).
F. Barni et al. / Forensic Science International 167 (2007) 87–92 89
obtained using Fisher’s Combined Probability Test [17]. Results
of global analyses were interpreted following application of
sequential Bonferroni tests for multiple comparisons [17].
Results and discussion: Allele frequencies and statistical
evaluations of the 15 autosomal STR loci analyzed from the
Iraqi population are reported in Table 1. No deviation of
observed genotype frequencies from those expected according
Table 1
Allele frequencies and statistical parameters of AmpFlSTR1 IdentifilerTM PCR A
Allele D8S1179 D21S11 D7S820 CSF1PO
6 – – – –
7 – – 0.0248 –
8 0.0146 – 0.1881 0.0147
9 0.0049 – 0.0990 0.0343
9.3 – – – –
10 0.0777 – 0.3317 0.2647
11 0.1165 – 0.2079 0.2843
12 0.1359 – 0.1139 0.3284
12.2 – – – –
13 0.2136 – 0.0347 0.0637
13.2 – – – –
14 0.1408 – – 0.0098
14.2 – – – –
15 0.2184 – – –
15.2 – – – –
16 0.0583 – – –
16.2 – – – –
17 0.0194 – – –
18 – – – –
19 – – – –
20 – – – –
20.2 – – – –
21 – – – –
21.2 – – – –
22 – – – –
22.2 – – – –
23 – – – –
23.2 – – – –
24 – – – –
24.2 – – – –
25 – – – –
26 – – – –
27 – 0.0248 – –
28 – 0.1139 – –
28.2 – – – –
29 – 0.2228 – –
29.2 – – – –
30 – 0.2426 – –
30.2 – 0.0149 – –
31 – 0.0396 – –
31.2 – 0.1040 – –
32 – – – –
32.2 – 0.1485 – –
33 – – – –
33.2 – 0.0693 – –
34 – 0.0050 – –
34.2 0.0099 – –
35 0.0050 – –
N 206 206 206 206
Ho 0.777 0.881 0.861 0.755
He 0.849 0.843 0.791 0.739
PI 2.242 4.202 3.597 2.041
RMP 0.056 0.053 0.092 0.129
PD 0.944 0.947 0.908 0.871
to Hardy-Weinberg equilibrium was detected at any of the 15
STR loci (Table 1). All loci showed a high degree of genetic
polymorphism, with observed heterozygosity (Ho) values
ranging from 0.621 (TPOX) to 0.881 (D21S11). The
polymorphism information content (PIC) values ranged from
0.568 for D18S51 to 0.852 for D2S1338, indicating good
informativeness of all STR markers. Overall, these parameters
mplification Kit loci in Iraq population
D3S1358 TH01 D13S317 D16S539
– 0.3058 – –
– 0.1699 – –
– 0.1311 0.2330 0.0340
– 0.2379 0.0388 0.1359
– 0.1359 – –
– 0.0194 0.0534 0.0874
– – 0.2233 0.3544
– – 0.3447 0.2913
– – – –
0.0049 – 0.0534 0.0874
– – – –
0.0388 – 0.0534 0.0097
– – – –
0.2282 – – –
– – – –
0.2379 – – –
– – – –
0.3641 – – –
0.1214 – – –
0.0049 – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
– – – –
206 206 206 206
0.806 0.825 0.767 0.806
0.746 0.789 0.771 0.758
2.577 2.857 2.146 2.577
0.120 0.085 0.089 0.097
0.880 0.915 0.911 0.903
F. Barni et al. / Forensic Science International 167 (2007) 87–9290
Table 1 (Continued )
Allele D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539
CE 0.522 0.512 0.410 0.322 0.333 0.399 0.379 0.361
PIC 0.826 0.819 0.757 0.689 0.700 0.752 0.732 0.718
P-value 0.060 0.135 0.393 0.533 0.824 0.936 0.660 0.250
Allele D2S1338 D19S433 vWA TPOX D18S51 D5S818 FGA
6 – – – 0.0049 – – –
7 – – – – – – –
8 – – – 0.5437 – 0.0049 –
9 – – – 0.0825 – 0.0485 –
9.3 – – – – – – –
10 – – – 0.1068 0.0098 0.0631 –
11 – 0.0049 – 0.2427 0.0196 0.3204 –
12 – 0.0922 – 0.0194 0.1471 0.3495 –
12.2 – 0.0097 – – – – –
13 – 0.1845 – – 0.1765 0.2039 –
13.2 – 0.0534 – – – – –
14 – 0.2282 0.0437 – 0.2010 0.0097 –
14.2 – 0.0243 – – – – –
15 0.0243 0.2184 0.0971 – 0.1225 – –
15.2 – 0.0728 – – – – –
16 0.0437 0.0583 0.3204 – 0.1029 – –
16.2 – 0.0437 – – – – –
17 0.2233 0.0097 0.2184 – 0.1029 – –
18 0.1165 – 0.2282 – 0.0588 – 0.0049
19 0.1019 – 0.0680 – 0.0490 – 0.0777
20 0.1796 – 0.0243 – 0.0049 – 0.0631
20.2 – – – – – – –
21 0.0340 – – – 0.0049 – 0.1650
21.2 – – – – – – –
22 0.0388 – – – – – 0.1602
22.2 – – – – – – –
23 0.1311 – – – – – 0.1990
23.2 – – – – – – –
24 0.0583 – – – – – 0.2087
24.2 – – – – – – 0.0049
25 0.0437 – – – – – 0.0728
26 0.0049 – – – – – 0.0340
27 – – – – – – 0.0097
28 – – – – – – –
28.2 – – – – – – –
29 – – – – – – –
29.2 – – – – – – –
30 – – – – – – –
30.2 – – – – – – –
31 – – – – – – –
31.2 – – – – – – –
32 – – – – – – –
32.2 – – – – – – –
33 – – – – – – –
33.2 – – – – – – –
34 – – – – – – –
34.2 – – – – – – –
35 – – – – – – –
N 206 206 206 206 206 206 206
Ho 0.825 0.796 0.748 0.621 0.824 0.728 0.816
He 0.870 0.848 0.785 0.630 0.868 0.731 0.851
PI 2.857 2.451 1.984 1.319 2.841 1.838 2.717
RMP 0.038 0.048 0.093 0.189 0.037 0.125 0.044
PD 0.962 0.952 0.907 0.811 0.963 0.875 0.956
CE 0.578 0.525 0.399 0.579 0.7812 0.314 0.528
PIC 0.852 0.825 0.749 0.579 0.568 0.680 0.829
P-value 0.473 0.344 0.058 0.377 0.399 0.450 0.710
N: number of alleles; Ho: observed heterozigosity; He: expected heterozigosity; PI: paternity index; RMP: random match probability; PD: power of discrimination;
CE: chance of exclusion; PIC: polymorphic information content; P-value: probability value of Chi-square test for Hardy-Weinberg equilibrium.
F. Barni et al. / Forensic Science International 167 (2007) 87–92 91
Table 2
Results of locus-specific and global tests over loci for genetic differentiation between the Iraqi population examined and other middle-eastern populations
Locus P-values from locus-specific contingency table analyses for each comparison
Eastern Anatolia,
Turkeya
Turkeyb Iraqi-
Kurdistanc
Saudi
Arabiad
Saudi
Arabiae
Arabs
Emiratesf
Omang Iranh Irani Syriaj Jordank
D8S1179 0.2790 0.0006 – – 0.3620 0.2138 0.2362 0.1314 0.0612 0.0958 –
D21S11 0.0558 0.2705 0.6063 – 0.9092 0.0215 0.0730 0.5622 0.4264 0.2456 –
D7S820 0.1872 0.1452 0.0773 – 0.2588 0.7204 0.5006 0.0280 0.1049 0.4228 –
CSF1PO 0.4050 0.3428 0.0595 0.1224 0.5310 0.7335 0.3152 0.3412 0.7682 0.1914 0.2576
D3S1358 – 0.0087 0.0996 – 0.7102 0.0970 0.0217 0.0411 0.1723 0.0396 –
TH01 0.3500 0.7788 0.9193 0.9315 0.0531 0.0550 0.0261 0.6529 0.7947 0.6890 –
D13S317 0.0001 0.0002 0.0057 – 0.0420 0.0077 0.0002 0.0010 0.0004 0.0142 –
D16S539 0.0026 0.1446 – – 0.4446 0.8835 0.3881 0.0852 0.6450 0.0344 0.9172
D2S1338 – 0.0344 – – 0.0182 0.0030 0.2033 0.0325 0.0215 – –
D19S433 – 0.0001 – – 0.1094 0.0052 0.0403 0.0256 0.0889 – –
vWA 0.2650 0.0001 0.0135 0.0806 0.8505 0.2186 0.4879 0.0063 0.0403 0.0384 –
TPOX 0.5810 0.1332 0.4341 0.0140 0.1195 0.2361 0.0067 0.6015 0.2716 0.0020 0.0001
D18S51 0.2747 0.5097 – – 0.1278 0.8735 0.7595 0.0972 0.8705 0.9302 –
D5S818 0.9943 0.7158 0.9032 – 0.7014 0.3803 0.0988 0.4181 0.5954 0.9677 –
FGA 0.0823 0.2694 0.5922 – 0.3000 0.3374 0.4425 0.5334 0.7792 0.4214 –
x2 57.27 105.9767 38.39 17.92 44.95 64.95 73.14 73.44 56.22 55.91 21.3065
d.f. 24 30 20 8 30 30 30 30 30 26 6
P-value 0.0002 <0.0001 0.0079 0.0219* 0.0390* <0.0001 <0.0001 <0.0001 0.0026 0.0006 0.0016
P-values indicate the significance of a test for allele frequency homogeneity between the Iraqi population examined and the populations listed at the top of the table. x2
indicates the test statistic derived from use of Fisher’s Combined Probability Test over loci and d.f. indicates degrees of freedom associated with the test. P-values
from the global test over loci are reported on the bottom row of the table.a Reference: [8].b Reference: [9].c Reference: [10].d Reference: [11].e Reference: [12].f Reference: [12].g Reference: [12].h Reference: [12].i Reference: [13].j Reference: [14].k Reference: [15].* Not significant following sequential Bonferroni corrections.
indicated the general utility of this STR loci panel for forensic
personal identification and paternity testing in the Iraq
population, thereby further confirming its efficacy for forensic
practice also in new populations.
Interpopulation comparisons were also performed by using
contingency table analyses and Fisher’s Combined Probability
Test. This investigation permitted us to assess the degree with
which Iraqi individuals are genetically differentiated from
other human populations in the middle-eastern region sur-
rounding or, at least, nearby central and southern Iraq [8–15].
Results of these analyses revealed multiple single loci with
significant allele frequency differences among populations
(Table 2). Furthermore, global analyses performed over loci
indicated that there were significant overall allele frequency
differences between the Iraqi population and 9 of the 11 other
populations used for comparison following use of sequential
Bonferroni corrections (Table 2). The exceptions to this pattern
were the allele frequency spectra detected in two independent
panels of individuals from Saudi Arabia [11,12], where
P-values nonetheless suggested approximately significant
levels of differentiation (P = 0.022 and 0.039 for [11] and
[12], respectively; Table 2).
Collectively, our data indicate that standardized multilocus
STR panels may be an useful forensic tool which can be applied
for identification purposes also in the Iraq population, but the
comparison among this population and other population from
the middle-eastern region demonstrated a remarkable and
statistically significant genetic differentiation across this area.
Hence, our results further suggest that proper DNA databases
should be generated and employed for forensic genetics
calculations, especially in populations where interpopulation
genetic exchange is extremely reduced both due to ethno-
religious and geographical reasons.
Access to the data: The complete data are available to any
interested researcher upon request to [email protected].
Other remarks: This paper follows the guidelines for
population data requested by the journal [18].
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