AIM Due to increasing use of mitochondrial DNA (mtDNA) sequencing in both forensic practice and clinical disease research, this study explores the optimization of the next-generation sequencing (NGS) method for whole mitochondrial genome analysis on the Illumina MiSeq platform. METHODS Initial attempts using pre-made commercial primers were unsuccessful, leading to the design of novel custom-designed primers in our laboratory and optimization of sequencing chemistry and protocols. A comprehensive protocol was developed, involving long-range amplification, enzymatic fragmentation, and the use of IDT® for Illumina DNA/RNA UD Indexes and MiSeq Reagent Nano Kit v2 (300 cycles), whereby DNA extraction, quantification, and library preparation were all performed according to optimized protocols. RESULTS Successful amplification was confirmed using gel electrophoresis and Agilent Bioanalyzer, with optimized conditions yielding clear, specific amplicons 9.8 and 8.5 kb in length. Sequencing results demonstrated high-quality reads with an average coverage depth of 742x and a GC content of 43-45%. The study highlights the efficiency of custom primers and individual library normalization for reliable mtDNA sequencing. CONCLUSION These findings advance the application of NGS in forensic and clinical settings by enhancing the detection of rare mutations and mitochondrial heteroplasmy, paving the way for routine mtDNA analysis using NGS technology.

AimCOVID-19 pandemic, caused by SARS-CoV-2, has had a profound impact on global health, including in Bosnia and Herzegovina, which faced unique challenges due to limited testing and high mortality rates. This analysis aimed to identify mutations and detect different SARS-CoV-2 lineages across four pandemic waves.MethodologyA total of 127 SARS-CoV-2 samples were collected and sequenced from patients from the Federation of Bosnia and Herzegovina, providing a comprehensive overview of the viral genetic diversity in this region. Two sequencing platforms, Ion Torrent and Illumina, were used, whereby 37 samples were sequenced on the Ion Torrent platform, while others were sequenced on the Illumina platform.ResultsThis study presents a genomic analysis of SARS-CoV-2 variants circulating in the Federation of Bosnia and Herzegovina over four distinct pandemic waves, spanning from March 2020 to April 2023. Examination of genomic variations across these waves revealed key mutations associated with transmission and potential virulence.ConclusionThese genomic insights into SARS-CoV-2 evolution in Federation of Bosnia and Herzegovina emphasizes the importance of continuous surveillance to understand viral evolution and strengthen public health responses to future pandemics.

Objective: This comprehensive research aimed to thoroughly examine the effectiveness of a diode laser (445 nm) in combination with non-surgical treatment in patients with chronic periodontitis (CP) by evaluating a wide range of clinical and microbiological parameters. Materials and methods: Thirty-one subjects diagnosed with CP were included in this study. The total number of treated periodontal pockets was 862. The subjects were randomly assigned to group 1, which underwent scaling and root planing and laser therapy (SRP+L), and group 2, which underwent scaling and root planing (SRP) only. All respondents underwent a periodontal diagnostic protocol. The parameters plaque index (PI), gingival index (GI), bleeding on probing index (BOP), probing depth (PD), clinical attachment level (CAL), and tooth mobility (TM) were registered. Clinical periodontal measurements were performed at baseline and one and three months after therapy. Microbiological analysis was conducted on Aggregatibacter actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), and Tannerella forsythia (Tf) using real-time polymerase chain reaction (PCR). For microbiological analysis, samples were taken at baseline, immediately after therapy, and after three months. Laser irradiation was performed immediately after SRP. Results: All clinical parameters improved statistically from baseline to three months after therapy. For all examined clinical parameters, better results were achieved in group 1 than in group 2. This study showed a more significant reduction in Pg and Tf from baseline to three months in group 1 compared to group 2. Conclusion: These results showed that the diode laser wavelength 445 nm was also usable in treating periodontal diseases as an additional method to SRP.

Human mitochondrial genes MT-ATP6 and MT-ATP8 encode the subunits 6 and 8, respectively, of ATP synthase, a vital protein Complex V intricately involved in oxidative phosphorylation and ATP metabolism. This enzyme produces ATP from ADP in the mitochondrial matrix utilizing energy provided by the proton electrochemical gradient. Pathogenic mutations within these genes have been linked to various syndromes such as NARP syndrome, Leigh syndrome, mitochondrial myopathy with reversible cytochrome C oxidase deficiency, and progressive spastic paraparesis, among others. In our investigation, we sequenced 24 complete human mitochondrial genomes of healthy adult individuals from Bosnia and Herzegovina, each representing unique maternal lineage. Employing the Illumina MiSeq NGS platform and the Nextera XT DNA library preparation protocol, we obtained raw NGS reads. Subsequent analysis utilizing SAMtools enabled the identification of genetic variants within the MT-ATP6 and MT-ATP8 genes. We identified a total of 11 SNPs, including three in MT-ATP8 and eight in MT-ATP6, with none of them being associated with any mitochondrial diseases or conditions. Our results align well with previously reported genome variation data for European populations and set the groundwork for future mtDNA analysis for clinical purposes in Bosnia and Herzegovina.

Background: Tuberous Sclerosis Complex (TSC) is an autosomal dominant genetic disorder and involves multiple organs, intellectual disability and epilepsy. Mutations in TSC1 and TSC2 genes are responsible for the molecular disease mechanism. Objective: The aim is to determine molecular background of a patient with a suspicion of TSC. Case presentation: In this case report, we describe a seven year old patient with the clinical manifestation of TSC that includes supratentorial changes, subependymal hamartomas and angifibromas in the facial area. Besides the brain and skin changes, no other TSC characteristics were observed. The patient was referred to molecular genetic testing using Next Generation Sequencing (NGS). Results: Clinical exome sequencing revealed intronic TSC2 c.4849+2T>G variant. The variant was confirmed using Sanger sequencing on the subject. However, the variant was not detected in the parents, which indicated that it arose de-novo. The RegSNP-intron, Mutation Taster and Human Splicing Finder were used as a bioinformatic tools to predict the possible effect on protein. Using bioinformatic tools, it was determined that the variant is possibly damaging to protein. Conclusion: This data suggest that observed splicing intronic variant could be the cause of TSC in this pediatric patient.

Background: MitoWizz is an advanced bioinformatics tool designed for the analysis of the human mitochondrial genome, offering precise and efficient data interpretation. It enables comparisons of sequencing results obtained from various instrumental methods with the reference Andersen genome (rCRS), aiding in the identification of alterations. This capability is particularly valuable in forensic and clinical mitochondrial DNA analysis. Objective: The primary goal of developing MitoWizz is to automate and streamline mitochondrial DNA analysis, providing researchers and forensic experts with a fast, reliable, and comprehensive tool for sequence comparison, variation detection, and data validation. Methods: MitoWizz compares query sequences in opposed to the reference genome and allows direct comparison of two sequences to identify genetic variations. To ensure accuracy, the results are validated through the Clustal Omega W by aligning sequences with the human mitochondrial DNA reference from GenBank (NC_012920.1). Results: The software detected genetic variations and generated a visual report, as demonstrated in an analysis where 11 mutations were identified in various genes, with an 88% sequence identity to the reference genome. The accuracy of the detected alterations was further validated using the Omega Clustal W program. Conslusion: MitoWizz significantly reduces analysis time and enhances result reliability by integrating multiple analytical steps into a single platform. By automating mtDNA comparisons and validation, it provides forensic and research laboratories with a high-throughput, efficient solution for precise mitochondrial genome analysis.

Introduction: COVID-19 has been a major focus of scientific research since early 2020. Due to its societal, economic, and clinical impact worldwide, research efforts aimed, among other questions, to address the effect of host genetics in susceptibility and severity of COVID-19. Methods: We, therefore, performed next-generation sequencing of coding and regulatory regions of 16 human genes, involved in maintenance of the immune system or encoding receptors for viral entry into the host cells, in a subset of 60 COVID-19 patients from the General Hospital Tešanj, Bosnia and Herzegovina, classified into three groups of clinical conditions of different severity (“mild,” “moderate,” and “severe”). Results: We confirmed that the male sex and older age are risk factors for severe clinical picture and identified 13 variants on seven genes (CD55, IL1B, IL4, IRF7, DDX58, TMPRSS2, and ACE2) with potential functional significance, either as genetic markers of modulated susceptibility to SARS-CoV-2 infection or modifiers of the infection severity. Our results include variants reported for the first time as potentially associated with COVID-19, but further research and larger patient cohorts are required to confirm their effect. Discussion: Such studies, focused on candidate genes and/or variants, have a potential to answer the questions regarding the effect of human genetic makeup on the expected infection outcome. In addition, loci we identified here were previously reported to have clinical significance in other diseases and viral infections, thus confirming a general, broader significance of COVID-19-related research results following the end of the pandemic period.

Background: All viral genomes, including the SARS-CoV-2 virus, mutate over time, and some of these mutations can affect the characteristics of the virus, such as the ease of spread, the severity of the patient’s clinical picture, or the effect of vaccines, therapeutic drugs, diagnostic tools or other measures of public health and social protection. Because of all the above, it is imperative to carry out continuous sequencing of this pathogen. Objective: The main goal of this research was to obtain the highest quality genomic sequences of the SARS-CoV-2 virus, to compare the obtained sequences with the reference Wuhan-Hu-1 sequence and to obtain a high-quality genomic alignment in order to reconstruct the appropriate phylogenetic tree. Methods: For the purposes of this research, a next-generation semiconductor sequencing method was chosen. In this research, a total of 47 samples of nasopharyngeal and oropharyngeal swabs from patients from the human population of Bosnia and Herzegovina with a clinical diagnosis of COVID-19 were collected. Results: In the processed 47 samples, there are several monophyletic groups on the constructed phylogenetic tree, of which one sample belongs to the same monophyletic group as the Wuhan-Hu-1 reference sequence. Conclusion: The greater number of samples is needed for a more comprehensive approach. Therefore, the results of this research can act as a guideline for the design of effective measures and strategies in order to solve problems regarding future pandemics as efficiently as possible.

Aim To analyze an additional set of Y-chromosome genetic markers to acquire a more detailed insight into the diversity of the Croatian population. Methods A total of 518 Yfiler Plus profiles were genotyped. Allele frequencies, haplotype frequencies, and haplotype diversity were calculated by using the STRAF software v. 2.0.4. Genetic distances were quantified by Rst with AMOVA online tool from the YHRD. The evolutionary history was inferred with the neighbor-joining method of phylogenetic tree construction in the MEGAX software. Whit Athey's Haplogroup Predictor v. 5 was used for additional comparison with regional and other European populations. Results A total of 507 haplotypes were used for genetic STR analysis. An interpopulation study on 17 Y-STR markers showed the lowest genetic diversity between the Croatian and Bosnian-Herzegovinian populations and the highest between the Croatian and Irish populations. Additional interpopulation comparison with the original 27 Y-STR markers (for the population with available data) was also performed. A total of 518 haplotypes were used in the determination of haplogroup diversity. Haplogroup I with its sublineage I2a expressed the highest prevalence. The second most prevalent haplogroup was R, with its major sublineage R1a, except for the subpopulation of Hvar, where E1b1b was the second most prevalent haplogroup. Rare haplogroups also confirmed in this study were L, T, and Q. G1 was detected for the first time in the Croatian population. Conclusion We obtained a new insight into the differences between examined subpopulations of Croatia and their possible (dis)similarities with neighboring and distant populations.