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Legal Medicine 10 (2008) 153–156

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Announcement of Population Data

Allele frequencies of 14 STR loci in the population of Malta

M. Cassar a, C. Farrugia a, C. Vidal a,b,*

a
MLS BioDNA Ltd., KBIC Rooms 2150–2160, Industrial Estate, Kordin, Malta
b
Department of Physiology and Biochemistry, University of Malta, Malta

Received 7 August 2007; accepted 28 September 2007

Available online 26 November 2007

Abstract

Allele frequencies of 14 STR loci (D13S317, D16S539, D2S1338, vWA, TPOX, D18S51, D5S818, FGA, D8S1179, D21S11, D7S820,
CSF1PO, TH01 and D3S1358) observed in the population of Malta are being reported. Polymerase chain reaction (PCR) amplification
using the AmpFl STRÒ Identifiler kit was performed in a random sample of 157 subjects (314 chromosomes). Markers D2S1338, D18S51
and FGA had the highest power of discrimination (PD) values while TPOX was the least informative marker. Allele frequencies observed
in the Maltese population were also compared with those of other populations from the Mediterranean region, Europe and Africa.
Our data is useful for anthropological and other comparative studies of populations and is powerful for forensic and paternity testing
in the Maltese islands.
Ó 2007 Elsevier Ireland Ltd. All rights reserved.

Keywords: Maltese; STRs; Allele frequencies; Population data; AmpFl STRÒ Identifiler

Population: One hundred and fifty-seven unrelated indi-
viduals living in the island of Malta were randomly selected
from paternity cases submitted to our facility. An informed
consent was completed by each individual. Individuals that
were not of a Maltese origin were excluded from the anal-
ysis. Buccal swabs or peripheral blood in EDTA containers
were collected for DNA analysis.
DNA extraction: Genomic DNA was extracted from
peripheral blood leucocytes by a modified salting out tech-
nique [1]. DNA extraction from buccal swabs was per-
formed by using AccuPrepä Genomic DNA extraction
kit (Bioneer Corporation, Daejeon, Korea).
PCR: Amplification of 14 STRs and Amelogenin was
performed according to manufacturer’s instructions using
the AmpFl STRÒ Identifiler kit (Applied Biosystems, Fos-
ter City, CA) in a 12.5 ll total reaction volume.
Typing: Amplified products were analyzed with refer-
ence ladder using an ABI 3130 genetic analyzer (Applied
Biosystems, Foster City, CA). Analysis of data obtained
*
Corresponding author. Tel.: +356 23980148; fax: +356 23980161.
E-mail address: chrisv@mlsbiodna.com (C. Vidal).
from genetic analyzer was performed using GeneMapperÒ
software v3.5.
Results: Refer to Table 1.
Quality control: Participation in proficiency testing by
the College of American Pathologists (CAP) (http://
www.cap.org) and forensic inter-laboratory testing organ-
ised by Collaborative Testing Services Inc. (http://
www.collaborativetesting.com/).
Analysis of data: Forensic and paternity statistics includ-
ing power of discrimination (PD) and power of exclusion
(PE) were calculated with PowerStats v2.1 (Promega, Mad-
ison, WI, USA) [2]. Hardy–Weinberg equilibrium and het-
erozygosity were calculated for all loci using Linkage
Utility Programs by J. Ott [3] (http://linkage.rockefel-
ler.edu/). Deviation from Hardy–Weinberg equilibrium
was also analysed using FSTAT (http://www2.unil.ch/pop-
gen/softwares/fstat.htm) for those loci that deviated from
Hardy–Weinberg.
Genetic relationships between populations coming from
the Mediterranean region Europe and Africa were analysed
using previously published STR data. Populations used
were Sicilians [4], Italians [5], Greek [6], Spanish [7], Tuni-
sian [8], Turkish [9], German [10], Slovenian [11] and Afri-

1344-6223/$ - see front matter Ó 2007 Elsevier Ireland Ltd. All rights reserved.
doi:10.1016/j.legalmed.2007.09.004
 Author's personal copy

154 M. Cassar et al. / Legal Medicine 10 (2008) 153–156

Table 1
Allele frequencies of 14 STRs in the population of Malta (n = 157)
Allele D13S317 D16S539 D2S1338 vWA TPOX D18S51 D5S818 FGA D8S1179 D21S11 D7S820 CSF1PO TH01 D3S1358
6 0.006 0.162
7 0.003 0.016 0.003 0.162
8 0.118 0.006 0.500 0.020 0.041 0.134 0.022 0.086
9 0.105 0.121 0.103 0.046 0.010 0.080 0.061 0.242
9.3 0.338
10 0.070 0.035 0.110 0.013 0.030 0.054 0.271 0.274 0.010
11 0.252 0.341 0.248 0.016 0.336 0.080 0.287 0.315
12 0.318 0.341 0.032 0.178 0.352 0.115 0.169 0.252
12.2 0.003
13 0.096 0.115 0.151 0.197 0.347 0.035 0.045 0.003
14 0.038 0.038 0.109 0.171 0.010 0.175 0.010 0.029 0.054
15 0.003 0.141 0.125 0.118 0.269
16 0.038 0.215 0.086 0.003 0.054 0.199
17 0.218 0.282 0.115 0.295
18 0.128 0.186 0.076 0.010 0.003 0.170
19 0.099 0.048 0.030 0.076 0.003
19.2 0.003
20 0.163 0.019 0.020 0.089 0.006
21 0.058 0.007 0.146
22 0.058 0.010 0.219
22.2 0.007
23 0.135 0.003 0.203
23.2 0.003
24 0.067 0.106 0.003
24.2 0.016
25 0.035 0.099
26 0.036
27 0.042
28 0.123
29 0.252
29.2 0.003
30 0.248
30.2 0.003 0.045
31 0.071
31.2 0.065
32 0.016
32.2 0.071
33.2 0.045
35 0.003
Ho 0.797 0.740 0.870 0.808 0.667 0.875 0.723 0.855 0.810 0.842 0.793 0.758 0.770 0.771
HWp 0.547 0.188 0.585 0.436 0.367 0.538 0.999 0.387 0.980 <0.0001 0.503 0.664 0.599 0.767
MP 0.072 0.119 0.035 0.066 0.162 0.036 0.123 0.044 0.064 0.049 0.073 0.101 0.093 0.102
PD 0.928 0.881 0.965 0.934 0.838 0.964 0.877 0.956 0.936 0.951 0.927 0.899 0.907 0.898
PIC 0.77 0.70 0.85 0.78 0.62 0.86 0.67 0.84 0.79 0.82 0.76 0.71 0.73 0.73
PE 0.569 0.410 0.675 0.477 0.464 0.745 0.455 0.677 0.740 0.698 0.546 0.512 0.604 0.566
TPI 2.31 1.60 3.12 1.86 1.80 4.00 1.77 3.15 3.93 3.37 2.18 2.01 2.53 2.29
Ho, observed heterozygosity; HWp, Hardy–Weinberg equilibrium p-value; MP, matching probability; PD, power of discrimination; PIC, polymorphism
information content; PE, power of exclusion; TPI, typical paternity index.

can (Equatorial Guinea) [12]. Genetic divergence was based
on allele frequencies of five STRs (vWA, D18S51,
D8S1179, D21S11, D3S1358) commonly tested in all pop-
ulations. DA genetic distance was calculated as described
by Nei and colleagues [13], which is a more reliable esti-
mate of evolutionary relationships between closely related
populations than standard genetic distance (DS) [14]. DS
and DA were both used to construct phylogenetic trees by
neighbour-joining (NJ) clustering [15]. Bootstrap re-sam-
pling of 1000 replicates was performed to obtain the most
reliable dendrograms. These analyses were performed using
the software DISPAN [16].
Access to data: Complete data can be acquired upon
request to chrisv@mlsbiodna.com and from website
http://www.mlsbiodna.com/downloads.htm.
Other remarks: As shown in Table 1, all markers
showed high PD values (>0.800) the highest being that
observed for D2S1338 and lowest for TPOX. Marker
D18S51 was the most powerful marker used for pater-
nity testing with the highest PE and TPI. Deviation
from Hardy–Weinberg equilibrium was observed for
D21S11, however this deviation was not observed after
correction using FSTAT (p = 0.667; 2000
randomisations).
 Author's personal copy
M. Cassar et al. / Legal Medicine 10 (2008) 153–156
When compared to other populations from Europe,
Africa and the Mediterranean region, the Maltese popula-
tion was observed to be closely related to the Sicilian pop-
ulation and was genetically distant from the two African
populations. Figs. 1 and 2 show NJ-trees constructed
according to DA and DS genetic distances, respectively.
Consistent results between the Maltese and Sicilian popula-
tions were observed in both instances. A bootstrap value of
75%, supports clustering together of the two populations
for the DA statistic, that is superior to establish genetic
relationships than DS. These results must be interpreted
with caution due to the low number of loci compared
between populations.
Malta is a small island located just 90 km South of
Sicily. The first inhabitants of the Maltese islands were
thought to have come from Southern Italy approximately
7000 years ago. From that time, the inhabitants of the
islands mixed with a series of occupants and traders
including the Phoenicians, Romans and Arabs. Haplo-
type frequencies of the Y chromosome were different in
Greeks and Italians when compared to Asians and Slavs,
suggesting a possible common origin from sea-faring
people such as the Phoenicians rather than from Neo-
lithic European farmers [17]. On the other hand, recent
analysis of the Y-chromosome STRs in several popula-
tions from the Mediterranean basin revealed that Malta
forms part of the Central-East Mediterranean cluster
being closest to north western Sicilians, with southern
Fig. 1. NJ-Phylogenetic tree of five STRs commonly used between populations, using DA distances. The numbers of each branch is the bootstrap value
obtained for 1000 replicates.
Fig. 2. Phylogenetic tree of five STRs commonly used between populations, using Ds distances. The numbers of each branch is the bootstrap value.
155
Italy, Cyprus and Turkey also in the same group [18].
The authors reported that these results could show the
correctness when saying that near eastern populations
are evidence of the Neolithic expansion from the Middle
East towards Europe. Analysis of autosomal STR in our
study showed that the Italian population has a stronger
genetic relationship with the Greeks rather than with
Sicilian and Maltese populations. The Sicilian population
is known to be genetically heterogeneous with the wes-
tern settlement being more of a Phoenician/Arab and
Norman origin than the eastern part (Siculo/Greek).
The present Maltese population, although geographi-
cally isolated, is a genetically heterogeneous population
thought to have expanded exponentially from a much
smaller population during the last four hundred years with
a number of founder effects [19] introduced due to admix-
ture with other populations coming from Sicily, Mediterra-
nean and northern Africa [20]. During the time of the
Knights of St. John there was a constant contact between
Maltese people and Sicilians that were mainly mariners
and traders especially in harbour areas. Sicilian and Italian
influence on the Maltese population is supported by the
number of surnames of Sicilian and Italian origin and also
from linguistics where there was a larger Siculo-Italian
influence in port areas than in the internal rural villages.
Allele frequencies presented in this article are powerful
and useful for forensic and paternity testing in Malta and
genealogical studies.
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156 M. Cassar et al. / Legal Medicine 10 (2008) 153–156
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