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Short Tandem Repeat
(STR) Data for the AmpFlSTRâ
Profiler Loci of Samples from the Malay Population in Malaysia
Lim Kong
Boon
Primulapathi Jaya
Mohd Izuan Othman
Scientific Officers
N. Hithaya Jeevan
Head of Serology/DNA Section
Kee Sue Sing
Director of the Forensic Division
Lee Yoon Hin
Assistant Scientific Officer
Department of Chemistry
Ministry of Science, Technology, and the Environment
Malaysia
Abstract.......Introduction.......Materials
and Methods.......Statistical
Evaluation
Results and Discussion.......References
Abstract
The collection
and analysis of DNA from an ethnic population can be useful for
forensic evaluation. In this study, allele frequencies were generated
for the nine short tandem repeat (STR) genetic loci included in
the AmpFlSTRâ Profilerä Amplification Kit (PE Applied Biosystems, Foster
City, California). These frequencies were compared between two groups
of blood samples from unrelated individuals of the Malaysian Malay
population. The first group of blood samples was acquired from blood
banks of various hospitals, whereas the second group was acquired
from blood samples submitted for casework analysis. The combined
power of discrimination and mean paternity exclusion probability
of the nineplex was greater than 99.99999996 percent and 99.93 percent,
respectively for the two different groups. Only one of the nine
loci, CSF1PO of the blood bank samples (p=0.0087), deviated from
Hardy-Weinberg Equilibrium expectations using the exact test. Upon
comparison of the two blood sample groups, there were no significant
differences among their statistical estimates, and the scatter plot
demonstrated the similarity between the groups. This survey increased
the database's STR data for the AmpFlSTRâ
Profiler loci of samples from the Malay population in Malaysia.
Introduction
The collection
and analysis of DNA from an ethnic population can be useful for
forensic evaluation. Malaysia is a multiracial country comprised
mainly of three population-ethnic groups -- Malay, Chinese, and
Indian. The Malays comprise about 60 percent of the population.
STR allele frequencies for the AmpFlSTRâ
Profiler loci from these three ethnic population groups were compiled
using samples of blood from Malaysians who were donors to blood
banks of various hospitals for the statistical evaluation of forensic
DNA evidence (National Research Council 1996; Technical Working
Groups on DNA Analysis Methods 1995). Also DNA profiles of Malaysians
whose blood samples were submitted for casework during 1998-2000
were compiled. The data from both groups were pooled in the database,
increasing the size of the database for comparison and evaluation.
Materials
and Methods
Samples of blood
from Malay donors were acquired from the blood blanks of various
hospitals for forensic DNA evaluation. A total of 139 to156 samples
of this group were used. Samples were also used from 217 to 220
Malays whose blood samples were submitted for casework during 1998-2000.
DNA was extracted from whole blood from the blood bank samples with
phenol/chloroform/isoamyl alcohol after proteinase K digestion (PE
Applied Biosystems 1995, 1996A, 1996B, 1997). Quantifying was done
using agarose minigel electrophoresis with lambda DNA as the standard.
DNA was also
extracted from the casework whole blood samples using the chelex
extraction protocol (PE Applied Biosystems 1995, 1996A, 1996B, 1997)
and quantified using the Quanti-Blot technique. About 1-2 ng of
DNA were used for each amplification, which was done in a thin-walled
0.2 ml PCR reaction tube in a GeneAmpâ PCR
System (PE Applied Biosystems, Foster City, California). The thermal
cycling parameters were as follows: hold at 95oC
for 11 minutes, followed by 28 cycles of 94oC for 1 minute, 59oC
for 1 minute, 72oC for 1 minute, then hold at 60oC for 45 minutes.
Polyacrylamide gel electrophoresis and detection of alleles were
performed using the 377 DNA Sequencer with the GeneScanâ Analysis and GenoTyperâ software (PE Applied
Biosystems, Foster City, California) (Anderson et al. 1996; Schumm
et al. 1998).
Statistical
Evaluation
Allele frequencies
were calculated for each STR locus, and the number of heterozygotes,
both observed and expected (Hobs. and Hexp.), was determined (Chakraborty
et al. 1993). The Hardy-Weinberg Equilibrium was verified using
the exact test (P) (Brenner 2000). Only one of the nine loci, CSF1PO
of the blood bank samples (p=0.0087), deviated from Hardy-Weinberg
Equilibrium expectations. Power of discrimination (PD) and mean
paternity exclusion probability (MEP) were calculated for each locus
and for the combined nine STR loci (Brenner and Morris 1989; Morgan
and Cox 1995). The combined power of discrimination and mean paternity
exclusion probability of the nineplex was greater than 99.99999996
percent and 99.93 percent, respectively for the two different groups.
Ratios of the maximum-to-minimum frequency estimates and the scatter-plot
approach were evaluated using 145 different DNA profiles obtained
from crime samples (Budowle et al. 1994A; Budowle et al. 1994B).
Upon comparison of the two blood sample groups, there were no significant
differences among their statistical estimates, and the scatter plot
demonstrated the similarity between the groups.
Results
and Discussion
Examining the
results of the various statistical parameters evaluated between
the two different blood sample groups in Table
1, Table 2, and Table
3, the differences are as follows:
- Differences
in relative allele frequency vary from less than 0.0100 (for 49
of the total 84 alleles detected) to a high of 0.0846 (vWA-allele
14). A summary of the differences is shown in Table
4.
- Observed
and expected heterozygosity vary from 0.0040 (CSF1PO) to 0.0784
(THO1) and from 0.0004 (TPOX) to 0.0287 (FGA), respectively.
- Power of
discrimination and mean paternity exclusion probability vary from
0.0005 (FGA) to 0.0146 (THO1) and from 0.0026 (D13S317) to 0.0327
(THO1), respectively.
For the nine
genetic loci analyzed, there were only four alleles out of the total
of 84 alleles detected showing differences in relative allelic frequencies
greater than 0.05. They were FGA-allele 23 (0.0517), THO1-allele
7 (0.0534), D5S818-allele 10 (0.0737), and vWA-allele 14 (0.0846).
Ratios in Table
5 were determined by dividing the largest frequency by the smallest
frequency for each of the 145 crime DNA profile samples.
Most of the
145 DNA profiles used consisted of 9 genetic loci, whereas there
were 6 eight-loci profiles, 5 seven-loci profiles, and 2 six-loci
profiles.
More than 84
percent of the frequency estimates between the databases of the
blood bank and casework samples had differences of less than 3 fold
and less than 3 percent more than 5 fold (maximum difference of
about 6.3 fold). Therefore, there were no significant differences
among their statistical estimates using the databases from the two
different groups.
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Figure
1
Scatter Plot Comparison of the Frequency Estimates of 145 Crime
DNA Profile Samples Between the Databases of the Blood Bank
and Casework Samples. Click to enlarge
image. |
The
breadth of the scatter plot (Figure 1) is narrow, demonstrating
the similarity of the databases from the two different blood sample
groups. Data from both groups were combined to constitute the Malaysian
Malay population database for the statistical evaluation of DNA
evidence.
References
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F., Greenhalgh, M. J., Butler, H. R., Kilpatrick, S. R., Piercy,
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Parkin, B. H. Further validation of a multiplex STR system for use
in routine forensic identity testing, Forensic Science International
(1996) 78:47-64.
Brenner, C.
and Morris, J. Paternity index calculation in single locus hypervariable
DNA probes: Validation and other studies. In: Proceedings of
the International Symposium on Human Identification, Memorial
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DNA Forensic Analysis Programs, User’s Manual.
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Budowle, B.,
Monson, K. L., Giusti, A. M., and Brown, B. Evaluation of Hinf I-generated
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R., Srinivasan, M., and Daiger, S. P. Evaluation of standard error
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and Cox, K. J. Allele and Genotype Analysis: Statistical Package
(Version 2.23) Geoffrey Morgan, Queensland, Australia, 1995.
National Research
Council. The Evaluation of Forensic DNA Evidence, National
Academy Press, Washington, DC, 1996.
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AmpF/STRâ
Profiler PCR Amplification Kit. User's Manual. PE Applied
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Sprecher, C. J., Lins, A. M., Micka, K. A., Rabbach, D. R., Taylor,
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