Research Article
Allele Frequency of Three Autosomal STR Loci D16S539, D7S820 and D13S317 in a Bangladeshi Population Sample
University of Dhaka, Bangladesh
Sharif Akhteruzzaman
University of Dhaka, Bangladesh
Microsatellites or Short Tandem Repeats (STRs) are loci with alleles composed of tandemly repeated short DNA sequences of 2-7 base pair in length (Weber and May, 1989). These sequences are widespread throughout the human genome and show sufficient variability among individuals of a population. Autosomal STRs now have become an indispensable tools for personal identification and paternity testing in forensics and criminal investigation (Edwards et al., 1992; Hammond et al., 1994; Santos et al., 1996; Sparkes et al., 1996). The use of polymerase chain reaction (PCR) for amplifying polymorphic DNA helps determining phenotypes of STR loci series in vary small and old biological evidences (Schumm, 1996). Their importance rises from the fact that they are the most informative genetic markers providing high statistical capability of discrimination and individualization (Edwards et al., 1991; Hochmeister et al., 1995; Linn et al., 1998).
Prior to the introduction of a new DNA profiling method a study of the allele frequencies and genotype distribution of any population needs to be undertaken. In this study, we present the allele distribution and forensic efficiency at three tetranucleotide STR loci, D16S539, D7S820 and D13S317 in a population sample of Bangladesh.
Whole blood obtained by venipuncture from 52 healthy unrelated individuals residing in Dhaka city, was collected in EDTA vacutainer tubes. Genomic DNA was extracted from the whole blood using standard published protocol (Gustincich et al., 1991). The quantity of recovered DNA was determined using the QuantiBlot® Human DNA Quantification Kit (Applied Biosystems, Foster City, USA). Amplification by polymerase chain reaction (PCR) was performed using GenePrint® SilverSTR III System (Promega Corporation, Madison, WI, USA) using 2.0-5.0 ng of template DNA in 9600 thermal cycler (Applied Biosystems) according to the manufacturers recommendations. PCR products were separated by electrophoresis on a 6% denaturing polyacrylamide gel. The bands were visualized by silver staining. STR alleles at each locus was determined after comparing the band with appropriate allelic ladder provided with the kit. The study was conducted in the Department of Biochemistry and Molecular Biology, University of Dhaka. Written informed consent was obtained from the study participants and local ethical review committee approved the design of the study.
STATISTICAL ANALYSIS
Allele frequencies and forensic efficiency parameters such as Heterozygosity (H), Polymorphism Information Content (PIC), Power of Discrimination (PD), Probability of Match (PM), Power of Exclusion (PE) and typical Paternity Index (PI) were calculated using the PowerStats Microsoft Excel workbook template provided by Promega Corporation (http://www.promega.com/geneticidtools/). Possible departures from hardy-Weinberg expectations at each locus was evaluated by Fishers exact test (Guo and Thompson, 1992).
The main biological characteristics of three STR loci are reported in Table 1. The overall distribution of the allele frequencies for each system was found to be in fair accordance with Hardy-Weinberg rule by compliance with the exact test (Gou and Thompson, 1992). The allele at all the three loci varied from 7 to 14, falling within the range observed for other local and world population. The most common allele at D16539 locus was 11, on the other hand at D7820 and D13S317 locus the most common alleles were 8, 10 and 8, 12, respectively. This data partly support an earlier study (Dobasi et al., 2005) where they found allele 11 as most common for all the three loci (Table 2).
Forensic efficiency parameters such as, the Power of Discrimination (PD), observed and expected Heterozygosity values (H), Polymorphism Information Content (PIC), Probability of Match (PM), Power of Exclusion (PE) and typical Paternity Index (PIt) are shown in Table 3. The observed heterozygosity was highest in D16S539 (0.846). The PIC values for all STR loci were highly informative (PIC≥0.7). The probability that two randomly chosen person have the same unspecified genotype at a locus is the sum squares of the frequencies of all genotypes at that locus (NRC, 1996).
Table 1: | Characteristics of three STR loci used in this study |
Table 2: | Observed allele frequency of three STR loci in Bangladeshi population |
Table 3: | Forensic efficiency parameters for the three STR loci |
Hobs: Observed heterozygosity; Hexp: Expected heterozygosity; PIC: Polymorphism Information Content; PD: Power of Discrimination; PM: Probability of Match; PE: Power of exclusion; PIt: Typical paternity index; P (Hardy-Weinberg equilibrium, exact test based on Monte Carlo Simulation) | |
This probability is designated as PM or individualization potential of a locus (Hammond et al., 1994) and is used to calculate the power of discrimination of a locus, 1-PM. The higher the discrimination power of a locus, the more efficient it is in discriminating between members of the population. The combined PM using these three loci was calculated to be 3.88x10-4 and therefore, the combined power of discrimination was 0.99961. This means when used together these loci can distinguish samples from different individuals with a probability of 99.96%.
Another parameters used to evaluate the strength of a locus to exclude falsely accused individuals is the power of exclusion or PE. It represents the percentage of individuals in the relevant population who would not share the same DNA profile presented in a paternity case (Brenner and Morris, 1990). The higher the PE value, the more non-fathers are excluded. Single locus PE values range from 0.543 to 0.687 (Table 3), which indicate low degree of exclusionary power of the loci when used individually. However, combined value using the three loci has increased the forensic utility to 0.9396. In conclusion, analysis of three STR loci by present multiplex PCR method was shown to be highly discriminating and suggesting it would be very useful in forensic practice.