Sharif Akhteruzzaman

Haplotype diversity of 17 Y-chromosomal STR loci in the Bangladeshi population

Haplotype and allele frequencies of 17 Y-chromosomal STR loci were determined in 216 unrelated Bangladeshi males. AmpFlSTR Y-filer PCR Amplification kit (Applied Biosystems) was used to type the following Y-STR markers: DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS438, DYS439, DYS437, DYS448, DYS458, DYS456, DYS635, and Y-GATA-H4. A total of 211 haplotypes for the 17 Y-STR markers were detected and, of these, 206 haplotypes were unique. The haplotype diversity was 0.9998, indicating a high potential for differentiating between male individuals in this population. Comparison analysis via Analysis of Molecular Variance (AMOVA) and construction of Neighbor Joining Tree revealed a close association of Bangladeshi population with Indian Gaddi and Southern Indian populations.

Application of a subtractive genomics approach for in silico identification and characterization of novel drug targets in Mycobacterium tuberculosis F11

Extensive dead ends or host toxicity of the conventional approaches of drug development can be avoided by applying the in silico subtractive genomics approach in the designing of potential drug target against bacterial diseases. This study utilizes the advanced in silico genome subtraction methodology to design potential and pathogen specific drug targets against Mycobacterium tuberculosis, causal agent of deadly tuberculosis. The whole proteome of Mycobacterium tuberculosis F11 containing 3941 proteins have been analyzed through a series of subtraction methodologies to remove paralogous proteins and proteins that show extensive homology with human. The subsequent exclusion of these proteins ensured the absence of host cytotoxicity and cross reaction in the identified drug targets. The high stringency (expectation value 10−100) analysis of the remaining 2935 proteins against database of essential genes resulted in 274 proteins to be essential for Mycobacterium tuberculosis F11. Comparative analysis of the metabolic pathways of human and Mycobacterium tuberculosis F11 by KAAS at the KEGG server sorted out 20 unique metabolic pathways in Mycobacterium tuberculosis F11 that involve the participation of 30 essential proteins. Subcellular localization analysis of these 30 essential proteins revealed 7 proteins with outer membrane potentialities. All these proteins can be used as a potential therapeutic target against Mycobacterium tuberculosis F11 infection. 66 of the 274 essential proteins were uncharacterized (described as hypothetical) and functional classification of these proteins showed that they belonged to a wide variety of protein classes including zinc binding proteins, transferases, transmembrane proteins, other metal ion binding proteins, oxidoreductase, and primary active transporters etc. 2D and 3D structures of these 15 membrane associated proteins were predicted using PRED-TMBB and homology modeling by Swiss model workspace respectively. The identified drug targets are expected to be of great potential for designing novel anti-tuberculosis drugs and further screening of the compounds against these newly targets may result in discovery of novel therapeutic compounds that can be effective against Mycobacterium tuberculosis.

Forensic evaluation of STR data for the PowerPlex™ 16 System loci in a Bangladeshi population

Allele frequencies of 15 autosomal STR loci included in PowerPlex 16 System were determined from a sample of 148 unrelated Bangladeshi individuals. Forensic efficiency parameters such as, the power of discrimination (PD), observed and expected heterozygosity (H), polymorphism information content (PIC), probability of match (PM), power of exclusion (PE), and typical paternity index were calculated for the loci. These parameters indicated the usefulness of the loci in paternity testing and personal identification in the Bangladeshi population.

Phylogenetic and forensic studies of the Bangladeshi population using next-generation PowerPlex® Y23 STR marker system

Haplotype diversity and allele frequencies of 23 Y chromosomal short tandem repeat (STR) loci included in the next-generation PowerPlex® Y23 System were studied in 137 Bangladeshi Bengali males. A total of 134 different haplotypes were observed with a discrimination capacity (DC) of 0.978, indicating a high potential for differentiating between male individuals in this population. The highest allele frequency (0.818) was observed in locus DYS391. Locus DYS385a/b showed the highest gene diversity (0.945) while locus DYS391 showed the lowest gene diversity (0.302). Double alleles were detected in three loci. On the other hand, four null alleles were detected in a single haplotype at DYS448, DYS549, DYS392, and DYS385a/b locus, respectively. The haplotype data is available in the Y chromosome haplotype reference database under accession number YA003445. To understand the genetic diversity of Bangladeshi Bengali population, a pairwise genetic distances (Rst) was calculated by comparing with 23 population studies consisting 4249 haplotypes. The analysis placed the Bangladeshi population along with Indian Tamil and Indo-Pakistani population in a clade separated from the rest.

Population genetics of 17 Y-chromosomal STRs loci in Garo and Santal tribal populations in Bangladesh

Allele frequencies and haplotype diversity of 17 Y-chromosomal short tandem repeat (STR) loci included in Y-filer™ PCR amplification kit were studied in 120 Garo and 139 Santal male individuals residing in two distinct regions of Bangladesh. A total of 99 different haplotypes from Garo and 129 different haplotypes from Santal individuals were observed with a corresponding discrimination capacity (DC) of 0.825 and 0.928, respectively. A comparison of the studied data with the published data from Y-STR haplotype reference database (YHRD) based on AMOVA revealed that the Garo population is closely related to Tripuri population from Tripura, India and Santal population moderately close to Munda population from Jharkhand, India. The mainstream Bengali population resides at a significant genetic distance from these two studied populations.

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.

High resolution melting curve analysis targeting the HBB gene mutational hot-spot offers a reliable screening approach for all common as well as most of the rare beta-globin gene mutations in Bangladesh

BackgroundBangladesh lies in the global thalassemia belt, which has a defined mutational hot-spot in the beta-globin gene. The high carrier frequencies of beta-thalassemia trait and hemoglobin E-trait in Bangladesh necessitate a reliable DNA-based carrier screening approach that could supplement the use of hematological and electrophoretic indices to overcome the barriers of carrier screening. With this view in mind, the study aimed to establish a high resolution melting (HRM) curve-based rapid and reliable mutation screening method targeting the mutational hot-spot of South Asian and Southeast Asian countries that encompasses exon-1 (c.1 - c.92), intron-1 (c.92 + 1 - c.92 + 130) and a portion of exon-2 (c.93 - c.217) of the HBB gene which harbors more than 95% of mutant alleles responsible for beta-thalassemia in Bangladesh.ResultsOur HRM approach could successfully differentiate ten beta-globin gene mutations, namely c.79G > A, c.92 + 5G > C, c.126_129delCTTT, c.27_28insG, c.46delT, c.47G > A, c.92G > C, c.92 + 130G > C, c.126delC and c.135delC in heterozygous states from the wild type alleles, implying the significance of the approach for carrier screening as the first three of these mutations account for ~85% of total mutant alleles in Bangladesh. Moreover, different combinations of compound heterozygous mutations were found to generate melt curves that were distinct from the wild type alleles and from one another. Based on the findings, sixteen reference samples were run in parallel to 41 unknown specimens to perform direct genotyping of the beta-thalassemia specimens using HRM. The HRM-based genotyping of the unknown specimens showed 100% consistency with the sequencing result.ConclusionsTargeting the mutational hot-spot, the HRM approach could be successfully applied for screening of beta-thalassemia carriers in Bangladesh as well as in other countries of South Asia and Southeast Asia. The approach could be a useful supplement of hematological and electrophortic indices in order to avoid false positive and false negative results.

Forensic evaluation of 11 non-standard STR loci in Bangladeshi population.

Allele frequencies and forensic efficiency parameters of 11 non-standard autosomal STR loci, D21S1437, D22S683, D8S1110, D10S2325, D12S1090, D17S1294, D3S1744, D14S608, D20S470, D18S536 and D13S765 were evaluated in a sample of 102 unrelated Bangladeshi individuals. No significant deviation from Hardy-Weinberg equilibrium was observed in any of the loci studied. Statistical parameters of forensic importance, the power of discrimination (PD), observed and expected heterozygosity (H), polymorphism information content (PIC), matching probability (MP), power of exclusion (PE) and typical paternity index (TPI) were calculated for the loci. The most informative locus among the 11 STR loci was D10S2325 (PD=0.958), while the least informative was D17S129 (PD=0.876). The combined PD (1-PM) and MP was calculated to be 0.9999999999997 and 2.23×10(-23), respectively. These parameters indicated the usefulness of the loci in forensic personal identification and parentage testing among Bangladeshi population.

Allele-Specific Detection of SLC22A2 rs316019 Variants Associated with Metformin Disposition through the Kidney

Background: Metformin is prescribed as a first-line drug to treat type 2 diabetes. It is excreted directly and primarily through the SLC22A2 gene-encoded OCT2 transporter in the kidney. rs316019 (c.808G>T, p.270A>S) is the most common variant of SLC22A2, which affects its capacity to clear metformin from the body. Metformin increases the plasma lactate level in a concentration-dependent manner by inhibiting mitochondrial respiration and may lead to a condition known as metformin-associated lactic acidosis (MALA). MALA is a potentially life-threatening complication that can occur within the clinical doses of metformin. Therefore, dose adjustments based on the SLC22A2 rs316019 variants may be beneficial to maximize the efficacy and minimize the toxicity of metformin. Objective: This study was carried out to develop a simple and fast method to define genotype at the rs316019 locus. This method was applied to estimate the rs316019 allele frequencies in the Bangladeshi population. Methods: We designed allele-specific primers to determine genotype at the rs316019 locus using allele-specific polymerase chain reaction (AS-PCR). AS-PCR data were confirmed by targeted sequencing of randomly selected samples. Results: The DNA sequence chromatograms showed the exact genotypes predicted through the AS-PCR method. A proportion of 79.62, 18.01, and 2.37% of Bangladeshi individuals have GG, GT, and TT genotypes, respectively. Conclusion: We report here a simple and fast method to define genotypes at the rs316019 locus in diabetic patients who are under metformin regimen. Allele frequencies at the rs316019 locus in the Bangladeshi population are close to those reported in other populations.

Impaired acylcarnitine profile in transfusion-dependent beta-thalassemia major patients in Bangladesh

Graphical abstract