Allele Frequencies of 10 Autosomal STR Loci from Chakma and Tripura Tribal Populations in Bangladesh

Allele frequencies of ten autosomal STR loci, D3S1358, vWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01, and FGA were investigated in Chakma and Tripura tribal populations of Bangladesh. In both the populations, all loci were in Hardy-Weinberg equilibrium except for FGA locus in Chakma and D21S11 in Tripura. All the loci were highly polymorphic in Chakma population with an observed heterozygosity (Ho) of >0.7 and moderately polymorphic in Tripura population (Ho > 0.6). However, both the population showed least polymorphism at TH01 locus (Ho < 0.6). A comparison between Chakma and Tripura population data revealed statistically significant differences in allele frequency distribution for most of the loci. A similar comparison with the mainstream Bengali population using previously published data from this lab also showed significant difference in allele frequency with these two tribal populations.


Introduction
Short tandem repeats (STRs) are highly polymorphic sequences of nucleotides, which are abundant in eukaryotic genome. They form approximately 3% of the total human genome and occur on average in every 10 000 nucleotides [1]. Due to their small dimension, low mutation, and high level of polymorphism, these markers are intensely used as important genetic markers for mapping studies, disease diagnosis, and human identity testing [2]. STRs remained the mainstays in most of the forensic laboratories in the world for the last two decades, as these markers provide high statistical capability of discrimination and individualization [3]. With the growing number of laboratories which use STR markers, more and more population data are reported from all over the world.

Materials and Methods
Molecular Biology International

STR Typing.
PCR-amplified fragments were separated and analyzed on ABI Prism 3100-avant Genetic Analyzer (Applied Biosystems) using POP-4 polymer and data collection software ver. 1.1. Data were sized using GeneScan Software version 3.7 and internal GeneScan-500 ROX size standard. Genotype of each locus was determined after comparison with allelic ladder using Genotyper software version 3.7 NT.

Analysis of Data.
Allele frequencies at each locus and statistical parameters of forensic efficiency were calculated by using PowerStat Microsoft Excel Workbook template [5]. Possible divergence from Hardy-Weinberg equilibrium was evaluated by Fisher's exact test [6]. Population differentiation test using exact test was carried out using Arlequine 2.0 software [7].

Quality Control.
Positive control DNA and allelic ladder provided in AmpFlSTR SGM Plus PCR amplification kit (Applied Biosystems). Approximately 10% of samples from both the populations were regenotypes to ensure reproducibility and accuracy. All genotype results were in full concordance.

Results and Discussion
Allele frequencies of Chakma and Tripura tribal groups are shown in Tables 1 and 2, respectively. Forensic efficiency parameters for both the populations are summarized in Table 3. Population differentiation test per locus is summarized in Table 4. The combined probability of match (PM) for the 10 STR loci are 3.49 × 10 −12 (1 in 2.86 × 10 11 ) and Molecular Biology International 5 1.03 × 10 −11 (1 in 9.65 × 10 10 ), respectively, for Chakma and Tripura populations. The combined power of exclusion of paternity (PE) for the Chakma and Tripura were calculated to be 0.99997 and 0.9998, respectively. Significant deviation from Hardy-Weinberg equilibrium was observed for FGA locus in Chakma and D21S11 in Tripura population. Both the populations showed least polymorphism at TH01 locus (PIC < 0.6). This may be due to inbreeding and lack of admixture, which is a characteristic feature of these populations. Although both the populations achieved combined probability of match (PM) in the order of 10 10 to 10 11 , it would be reasonable to implement a "θ correction" while using this data in forensic casework, as recommended by the National Research Council (1996) [8] and by Foreman and Lambert [9]. Population differentiation test for each population pair per locus revealed significant difference in the allele frequency distribution for most of the loci (Table 4) between Chakma and Tripura populations. Both Chakma and Tripura populations also showed significant difference in the allele frequency distribution with the mainstream Bengali population when compared with previously published data from this lab [10]. Among the populations THO1 locus showed least differentiation whereas, highest differentiation was observed in D18S51 locus which was followed by D2S1338 locus (Table 4). The present study was undertaken from the standpoint of compiling own-population genetic database, owing to the fact that population and subpopulation differences at STR loci of forensic interest are growing up. In this context, we embarked on compiling the allele frequency database of two ethnolinguistic populations of Bangladesh. The obtained high combined PM and PE values demonstrated that STR loci employed in SGM Plus PCR amplification kit would be highly efficient for personal identification and paternity cases in spite of some population substructuring. Besides forensic benefits, we find this study very useful for regional and worldwide human population meta-analysis.