Forensic Science International 313 (2020) 110348

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Forensic Science International

journal homepage: www.elsevier.com/locate/forsciint

Allele frequency comparative study between the two main Egyptian

ethnic groups
Tarek Tahaa , Sagy Elzalabanyb , Sahar Fawzic , Ahmed Hishamc , Khaled Amerb ,
Olfat Shakerd,*
a
Department of Immune Diseases, Egyptian Army Central Medical Laboratories, Cairo, Egypt
b
Egypt Center for Research and Regenerative Medicine, Cairo, Egypt
c
Department of Systems and Biomedical Engineering, Faculty of Engineering, CairoUniversity, Cairo 12613, Egypt
d
Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Cairo, Egypt

A R T I C L E I N F O A B S T R A C T

Article history: The study of genetic correlation between ethnic groups, constituting one nation, is an important issue.
Received 29 April 2020 This work aims to study the correlation between allele frequencies of nine Short Tandem Repeats (STRs)
Accepted 24 May 2020 autosomal loci (D3S1358, VWA, FGA, THO1, TPOX, CSF1PO, D5S818, D13S317, and D7S820) for the main
Available online 27 May 2020
two Egyptian ethnic groups, Muslims and Christians, in order to test the hypothesis of a common
ancestral for the whole Egyptian population. Each group is represented by a sample of 100 unrelated
Keywords:
healthy individuals. The genetic correlation of the two ethnic groups is investigated using alleles’
STRs
frequencies statistics, forensic efficiency parameters and populations’ homogeneity charts. Graphical
Population genetics
Allele frequency
methods were used to check the harmony between the two ethnic groups. The results support that
Egyptian Muslims and Egyptian Christians genetically originate from the same ancestors.
© 2020 Elsevier B.V. All rights reserved.

1. Introduction The aim of this study is to compare alleles’frequencies of nine

STR is a common and effective technique used for population
genetics characterization [1]. Studying the variation of autosomal
STRs loci has become possible due to the presence of highly
efficient DNA amplification systems, such as AmpFlSTR Profiler and
AmpFlSTR SGM Plus. Therefore, the detection of autosomal STRs isa
powerful tool for genetic variations study.
The obtained genetic datasets – from the DNA Sequencer –
could be on the form of either genotype or phenotype. Genotype is
the set of genes that a person has. It may refer to the entire genome
of a person or to the alleles carried at a particular locus. Phenotype
is the physical features of a person. It refers to any aspect of an
organism’s morphology, behavior, or physiology. A person’s
phenotype is affected by its genotype and by its environment [2].
Previous studies compared between the Egyptian Muslims and
Egyptian Christians. The first one [3] supported the homogeneity
hypothesis between the two ethnic groups. On the other hand, the
second [4] found that the two ethnic groups had significant
differences in six STRs loci.
* Corresponding author.
E-mail address: olfat.shaker@kasralainy.edu.eg (O. Shaker).
STRs autosomal loci for Egyptian Muslims and Egyptian Christians
usinga sample collected from all around Egypt. Moreover, it aims to
evaluate genetic correlation and convergence between both
groups statistically, graphically and by calculating their forensic
efficiency parameters [5–8].
2. Methods
2.1. Populations
A database was established based on 9 STRs loci (D3S1358,
VWA, FGA, THO1, TPOX, CSF1PO, D5S818, D13S317, and D7S820) of
100 blood samples for each of the two ethnic groups. These 200
unrelated healthy individuals originate from different geographi-
cal spots covering all over Egypt.
Random Subject Selection rules were applied to select subjects
to be included in the study.
Data fairness is warranted since every member is given equal
opportunity of being selected. The data sample used in this
research is guaranteed to be from an Egyptian person with
Egyptian parents and grandparents as they are following the
regulations of the Egyptian army.

http://dx.doi.org/10.1016/j.forsciint.2020.110348
0379-0738/© 2020 Elsevier B.V. All rights reserved.
2 T. Taha et al. / Forensic Science International 313 (2020) 110348

2.1.1. DNA extraction
DNA was isolated from whole EDTA blood using (QiA amp1
DNA blood by Qiagen-Gmph) [9].
2.1.1.1. PCR. Aliquots of 1.25 mL of the extract with DNA content of
approximately 2 ng/ul was amplified in biometra thermal cycler
(Applied Biosystems) by following the manufacturer’s instructions
for the AmpFlSTR Profiler PCR Amplification Kit. The samples were
amplified in single reactions for all 9 loci using fluorescently
labeled primers.
2.1.1.2. Typing. Separation was made by capillary electrophoresis
in an ABI 3130 Genetic Analyzer using the separation medium
Performance Optimized Polymer (POP) 7 and 36 cm capillaries
array (Applied Biosystems). The LIZ labeled ladder (Gene Scan 500
LIZ) was used for sizing the determinations of the amplified
fragments in combination with Gene Mapper ID v4 (Applied
Biosystems). Allelic calls and genotyping were carried out by
comparison to the reference allelic ladder included in the kit, using
Gene Mapper ID v4 (Applied Biosystems). The genotyped data
obtained from the Gene Mapper software was used to calculate the
rateof appearance for each allele in a population, which known as
allele frequency.
2.2. Statistics
A score value is assigned to each individual sample proportional
to its allelic contents. For each individual, the sample score is
calculated as the summation of the frequencies of its alleles
appeared in its blood sample. The mean sample score is the
summation of the phenotypic alleles' scores divided by the total
number of samples.
Mode is the sample score value that occurs most often and
median is the middle score value of the samples.
Skewness is the degree of distortion from the symmetrical bell
curve or normal distribution in a dataset [10]. The mean and
median of negatively skewed data will be less than the mode.
Kurtosis indicates how the tails of a distribution differ from the
normal distribution. Whereas skewness differentiates extreme
values in one versus the other tail, kurtosis measures extreme
values in either tail [11].
Zygosity (Ho, He), Combined Matching Probability (CMP),Power
of Discrimination (PD), Exclusion Probability (EP), Polymorphism
Information Content (PIC), and Typical Paternity Index (TPI) were
calculated using Promega, a Microsoft Excel-Power status program
statistical tool [12]. Moreover, statistical techniques,such as
correlation coefficient and p-value, were used for genetic
correlation assessments and hypothesis testing.
2.2.1. Zygosity
It is the degree of similarity of the alleles for a trait in an
organism. If both of the copies of the gene for a particular trait are
the same, then the individual is homozygous for that trait. On the
other hand, if an individual has two different alleles for a particular
trait, then they are heterozygous for that trait [13]. The frequency
of each allele for each locus and the observed heterozygosity (Ho)
were calculated from the number of observed genotypes in the
sample as shown in (1). In addition, expected heterozygosity (He)
was estimated as shown in (2):
X
k
Ho ¼ Pi 2 ð1Þ
i¼0
X
k

Standard Error (SE) measures the difference between the true He ¼ 1  Pi 2 ð2Þ
i¼0
population mean and the samples mean. It is used to validate the
accuracy of multiple samples by analyzing deviations within the Where P is the frequency of the ith allele and k is the total number
means. of alleles. Population with low heterozygosity are small, closed,

Table 1
The alleles frequencies of Egyptian Muslims and Egyptian Christians Ethnic groups.

D3S1358 vWA FGA THO1 TPOX CSF1PO D5S818 D13S317 D7S820

Mus. Ch. Mus. Ch. Mus. Ch. Mus. Ch. Mus. Ch. Mus. Ch. Mus. Ch. Mus. Ch. Mus. Ch.
5.3 0.010
6 0.200 0.195 0.015 0.005
7 0.215 0.230 0.010 0.015 0.015
8 0.150 0.100 0.475 0.540 0.005 0.015 0.035 0.040 0.115 0.155 0.180 0.160
8.3 0.005
9 0.360 0.370 0.200 0.140 0.020 0.020 0.075 0.075 0.110 0.080 0.105 0.135
9.3 0.065 0.070
10 0.010 0.020 0.055 0.085 0.300 0.265 0.105 0.160 0.060 0.030 0.330 0.300
11 0.245 0.205 0.290 0.365 0.255 0.225 0.210 0.280 0.220 0.255
12 0.005 0.010 0.015 0.330 0.250 0.365 0.350 0.420 0.280 0.115 0.130
13 0.015 0.005 0.005 0.040 0.085 0.155 0.140 0.070 0.145 0.035 0.005
14 0.040 0.055 0.065 0.055 0.015 0.010 0.010 0.015 0.030
15 0.365 0.285 0.110 0.105
16 0.205 0.290 0.285 0.230
17 0.230 0.220 0.255 0.340
18 0.140 0.140 0.190 0.180 0.015 0.005
19 0.005 0.010 0.075 0.075 0.050 0.060
20 0.010 0.005 0.080 0.120
21 0.005 0.005 0.125 0.165
22 0.210 0.165
23 0.145 0.135
23.2 0.160
24 0.105 0.140
25 0.075 0.135
26 0.005 0.030
27 0.015 0.030
28 0.010 0.010
29 0.005
 T. Taha et al. / Forensic Science International 313 (2020) 110348 3

and high consanguinity population. Egypt has an open population

with random matching, those nine loci are neutral, and they are not
affected by natural selection. Therefore, all alleles at each locus
have the same opportunity to be selected in to gametes. This means
that the probability of random sample matching is low.

2.2.2. Power of discrimination (PD)

In order to obtain PD, Combined Matching Probability (CMP)
should be calculated. CMP is the probability that two randomly
chosen persons would have identical match in DNA profiles. It is
the sum of the squares of the observed genotype frequencies in a
database as represented by equation (3). CMP should be less than 1
in a billion (1  109) for unrelated individuals
X 2
CMP ¼ P
i i
ð3Þ

Where Pi is the frequency of the genotype i at a given locus in the

population.Power of Discrimination is defined as the probability of
discrimination between two unrelated individuals. Thus, it is
correlated to CMP. For one locus, PD is calculated as in (4).
PD ¼ 1  CMP ð4Þ

Fig. 2. Egyptian Muslims samples histogram.

2.2.3. Exclusion probability (EP)
It is the probability that a random man could never be the
biological father of a child. The acceptable exclusion probability
value for all loci should be e more than 0.5, the higher the number
the more informative the locus is. PE is calculated as shown in
equation (5):
2 2
PE = h . (1  2.h.H )
Where h is the proportion of heterozygous individuals and H is the
proportion of homozygous individuals in the population sample.
2.2.4. Polymorphism information content (PIC)
PIC is the probability of the ability to deduce the allele
transmitted to the child by his parent. It is a measure of a marker's
usefulness for linkage analysis. In case the parentsare heterozy-
gous, their gametes will usually be informative. On the other hand,
In caseboth parents and child are heterozygous for the same
genotype, the origins of child’s alleles are ambiguous. Assume the
probability of occurrence of this situation is C, then:
PIC ¼ H  C ð6Þ
(5) Where H is the probability that an individual is heterozygous.The
idealPIC value equals to one, which means that the polymorphism
is informative in any random matching and the ideal heterozygos-
ity is 100%.
2.2.5. Typical Paternity Index (TPI)
It is generated for a single genetic locus as a meanof measuring
the strength of that locus in favor of or against parentage given the
phenotypes of the tested participants and the inheritance scenario.
The TPI is a likelihood ratio that is generated by comparing two
probabilities as shown in (7):
TPI = X / Y (7)
Where X is the probability that some event will occur given a
certain set of circumstances or conditions, Y is the probability that
some event will occur given a different set of circumstances or
conditions.

Fig. 1. Egyptian Christians samples histogram. Fig. 3. Egyptian Muslims and Christians homogeneity chart.
4 T. Taha et al. / Forensic Science International 313 (2020) 110348

Fig. 4. Egyptian Population, Egyptian Muslims An Egyptian Christians Allele Frequency Trajectories (AFTs) in 9 SRTs.

3. Results and discussion
3.1. Genotype allele
The allele frequency comparison between Egyptian Muslims
and Egyptian Christians groups results are shown in Table 1.
3.2. Graphical representation
Allele frequencies are obtained for all individuals comprising
ethnic group samples. The obtained data should undergo statistical
analysis to ensure their randomization and homogeneity. The
samples scores were used to represent each sample in statistical
analysis as each sample score is based on the allelic content of the
sample with respect to the population allele frequency.
Fig. 1 shows the histogram for the Egyptian Christians samples,
while Fig. 2 shows the histogram for the Egyptian Muslims
samples. The Gaussian distribution appeared on both histograms
indicates that the date is well randomly distributed.
Fig. 3 shows the homogeneity chart for the samples of the
Egyptian Muslims and Christians by plotting the obtained samples
scores for both ethnic groups versus samples serial numbers.
The chartvisually indicates great homogeneity between the two
ethnic groups with almost nooutliers.
 T. Taha et al. / Forensic Science International 313 (2020) 110348 5

Table 2

D7S820
Descriptive statistics for both Ethnic Groups.

0.563
0.750
0.250
0.090

0.719
0.917

2.170
Statistical Parameters Muslims Christians
Mean 34.290 29.370

D13S317
Standard Error 0.340 0.280

0.581
0.280

0.902
0.720

0.735
0.074

1.420
Median 34.360 29.520
Mode 34.360 30.550
Standard Deviation 3.380 2.780

D5S818
Sample Variance 11.390 7.720

2.000
0.563
0.780
0.220
0.089
0.920

0.770
Kurtosis 0.430 0.390
Skewness 0.260 0.330
Range 15.450 15.960

CSF1PO
Minimum Score 25.640 20.850

0.834
0.428
0.639
0.290

1.850
0.710
Maximum Score 41.080 36.810

0.14
Scores Sum 3429.380 2937.040
Samples Count 100.000 100.000

0.620
0.380

0.372

1.400
Confidence Level (95.0 %) 0.670 0.550

0.813
TPOX

0.619
0.143
THO1

2.400
0.730

0.091
0.901

0.733
0.270

0.473
The Allele Frequency Trajectories (AFTs) for Egyptian popula-
tion, Egyptian MuslimsandEgyptian Christians [14], was applied on

0.966

0.843
0.840

0.028

0.732

1.900
2.94  1010 (1 in 3.4  109)
0.160
versus the two ethnic groups. Fig. 4 demonstrates the strong

Egyptian Christians Group

FGA
relationship and the great matching between theEgyptian
population and the two groups.

0.590
0.078
0.730
0.270

1.700
0.742
0.911
VWA

0.999999999706
3.3. Population statistics

0.999872
D3S1358
A descriptive statistical comparison based on phenotypic

0.892
0.522
0.260
0.740

0.710
2.100
0.125
alleles' sample scores of both ethnic groups was performed as
shown in Table 2. D7S820

2.200
0.089
0.233

0.729
0.578
0.767

0.918
1) The mean of the Muslim group is (34.290), which is greater
than the mean of the Christian group (29.370). This indicates
that the phenotypic alleles' scores of Muslims are higher
D13S317

than those of the Christians, which means the allelic content

0.758

0.581
0.753
0.920
0.242
0.072

1.450
of the Muslim group tends to have higher frequencies alleles
(population common alleles) than the Christian group.
D5S818

2) Regarding the Standard Error, both groups have low SE

0.753

0.559
0.094

0.762
0.247

0.911

2.110

values, which indicates that both of them are well

representing the Egyptian population.
3) The skewness value for both groups is negative, which
CSF1PO

0.872
0.727
0.273

0.641
0.470

1.920

means that the tail of the left side of the distribution is longer
0.133

than the tail on the right side “left-skewed”.

4) The negative kurtosis value for both ethnic groups means
0.663

0.881

0.630
0.337

1.500
TPOX

0.410
0.140

thattheir distributionsare flatter than the normal distribu-

tion.Datasets with negative kurtosis values tend to have lack
Rensic Efficiency Parameters of Egyptian Muslim And Christian Groups.

of outliers.
THO1

2.400
0.328

0.889
0.462
0.094
0.672

0.721

Table 3 illustrate a comparison based on forensic efficiency

parameters of the nine STRs loci in 100 unrelated Egyptian
2.200
0.834

0.852
0.772
0.031
0.971

2.9  1010 (1 in 3.44  109)

0.166
FGA

Muslimsand Christians.
Egyptian Muslims Group

For the Muslims group, the matching probability (MP) ranged

from TPOX (0.140) to FGA (0.031), the power of discrimination (PD)
0.806

0.620
0.933
0.075

0.763
1.900
0.194
VWA

0.99999999971

from FGA (0.971) to CSF1PO (0.872), the power of exclusion (EP)

from FGA (0.772) to TPOX (0.410), the polymorphism content (PIC)
0.999932
D3S1358

from FGA (0.852) to TPOX (0.630), and the typical paternity index
2.200
0.225

0.550
0.775

0.740
0.912
0.120

(TPI) from THO1 (2.400) to D13S317 (1.450).

For the Christians group, the matching probability (MP) ranged
from TPOX (0.143) to FGA (0.028), the power of discrimination (PD)
Power of discrimination
Heterozygosity Content

Typical paternity index

from FGA (0.966) to CSF1PO (0.834), the power of exclusion (EP)

Polymorphism content
Homozygosity Content
Matching probability

from FGA (0.732) to TPOX (0.372), the polymorphism content (PIC)

Power of exclusion

from FGA (0.843) to TPOX (0.619), and the typical paternity index
(TPI) from THO1 (2.400) to D13S317 (1.400).
For both ethnic groups, the Combined Matching Probability
(CMP) for Muslims and Christians groups are (2.9  1010) and
Table 3

CMP

(2.94  1010) respectively, which is an ideal result of matching

CPD
CEP

probability for unrelated individuals. In addition, both groups have

6 T. Taha et al. / Forensic Science International 313 (2020) 110348
high Combined Powerof Discrimination (CPD) with
(0.99999999971) for the Muslims groupand (0.99999999706) for
the Christians group. Furthermore, the Combined Exclusion
Probability (CEP) for Muslims is (0.999932) and for Christians is
(0.999872), both values are accepted as they are greater than (0.5).
This comparison revealed, both ethnic groups – Muslims and
Christians – have the same discriminative loci for all the forensic
efficiency parameters.Moreover, these results prove that both
Egyptian ethnic groups mayhave descended from a common
ancestral population. Using STRs results, two previous studies
made a comparison between the Egyptian Muslims and Egyptian
Christians. The first study (Tahir et al., 2003) analyzed the results
obtained from a sample of volunteers consists of 148Egyptian
Muslims versus 28Egyptian Christians. This study supports the
homogeneity of the two ethnic groups. It is obvious that its results
must had been affected by the significant difference in sample size
between the two ethnic groups. In the contrast, the second study
(Coudray et al., 2007) found that Copts sub-population from Adima
village have significant difference from general Egyptian Muslims
population in loci D3S1358, D18S51, D13S317, D8S1179, FGA, and
THO1.
These differences may be due to the isolated locality that had
been selected in that study. In addition, the samples did not
represent the whole Egyptian population gene pool.However, the
results of our study agree with the first study, which noticed that
there is no difference between upper Egyptian population and
general Caucasian population from Cairo with the Egyptian
Christian population from Cairo.
4. Conclusion
In this paper, we aimed to, study the genetic correlation
between the two Egyptian ethnic groups Muslims and Christians,
based on the study of the allele frequencies of nine STRs autosomal
loci. Several statistical and visualization techniques were applied.
Both groups show small SE values, which indicate that both of
them represent the Egyptian population very well. Moreover, the
forensic efficiency parameters showed a great genetic homogenei-
ty and correlation between the two ethnic groups. CMP for
Muslims and Christians groups are (2.9  1010) and (2.94  1010)
respectively, which is an ideal result of matching probability for
unrelated individuals. The PD for Muslims group is
(0.99999999971) and for Christians group is (0.99999999706),
which is considered as a high probability of discrimination.
Moreover, PE values for Muslims and Christians are accepted,
(0.999932) and (0.999872) respectively, as they are greater than
(0.5). Also, both groups have the same discriminative loci for all the
forensic efficiency parameters such as FGA is the most discrimi-
nating locus for both ethnic groups. Furthermore, The AFTs of the
Egyptian population showed the great matching between the two
groups. Therefore, from these results we conclude that Egyptian
Muslims and Egyptian Christians genetically originate from the
same ancestors.
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