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Low vitamin D status is linked to disturbance in cognitive performance. This study explored possible ways how composition and functional capacity of the gut microbiome affects vitamin D metabolism, directing serum vitamin D (VitD) levels and memory impairmets. It was found that gut microbiome composition, characterized by an increase in the relative abundance of Enterococcus and correlated with vitamin D deficiency and, as consequence, with memory impairments. A key mechanism identified in the study was the differential utilization of short-chain fatty acids (SCFAs) produced by gut bacteria as substrates for synthesizing vitamin D3 precursor in the skin. This finding confirms a complex interplay between the gut microbiome, host metabolism, and cognitive health, highlighting the potential significance of targeting Enterococcus dysbiosis in future preventive and therapeutic strategies to address VitD deficiency-related memory impairments. These results underscore the importance of understanding and modulating gut microbiome composition to optimize VitD status and cognitive function., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2025 The Author(s).)

Epilepsy is one of the most common neurological disorders affecting approximately 50 million people worldwide. It impacts people of all genders and ages, but evidence suggests a higher incidence rate in children and the elderly. Given that childhood epilepsy has the risk of causing developmental epileptic encephalopathy, which is associated with intellectual, behavioral, and/or motor disabilities, proper assessment of children with new-onset epilepsy at an early stage is essential to prevent threats affecting neurodevelopmental processes. The aim of this study was to investigate whole genome sequencing data of children diagnosed with epilepsy. Our results revealed an identification of a novel mutation in a 2-year-old male patient who suffered from recurrent epileptic seizures of unknown etiology. The detected variant is heterozygous and located in gene CHRNA2 (chr8:27321348, NM_000742, c.612G > A, p.Trp204∗) in exon 6. The databases such as Varsome, GeneCards, and NCBI did not reveal any matches with previously identified variants, implying the novelty of the finding. Moreover, according to various prediction tools (MutationTaster, SIFT, CADD, FATHMM-MKL, LRT, DANN, Eigen, and BayesDel), the mutation is characterized as pathogenic, which corresponds to the American College of Medical Genetics and Genomics (ACMG) classification. According to the findings, mutation of the CHRNA2 gene is closely associated with two disorders known as autosomal dominant nocturnal frontal epilepsy (ADNFLE), and benign familial infantile epilepsy (BFIS). Comparison of proband's clinical manifestations showed that it is difficult to attribute precisely the patient's symptoms to either of the conditions, however the evidence suggests that the patient's symptoms are more consistent with those of ADNFLE. In this report, we expanded the spectrum of existing variations in the CHRNA2 gene contributing and associated with the development of epilepsy with the important and novel causative genetic variant., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Genomic repeats are functionally ubiquitous structural units found in all genomes. Studying these repeats of different origins is essential for understanding the evolution and adaptation of a given organism. These repeating patterns have manifold signatures and structures with varying degrees of homology, making their identification challenging. To address this challenge, we developed a new algorithm and software that can rapidly and accurately detect any repeated sequences de novo with varying degrees of homology in genomic sequences in interspersed or clustered repeats. Numerous forms of repeated sequences and complex patterns can be identified, even for complex sequence variants and implicit or mixed types of repeat blocks. Direct and inverted-repeat elements, perfect and imperfect microsatellite repeats, and any short or long tandem repeat belonging to a wide range of higher-order repeat structures of telomeres or large satellite sequences can be detected. By combining precision and versatility, our tool contributes significantly to elucidating the intricate landscape of genomic repeats., Competing Interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2024.)

Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

The success of DNA analytical methods, including long-read sequencing, depends on the availability of high-quality, purified DNA. Previously, we developed a method and device for isolating high-molecular-weight (HMW) DNA for long-read sequencing using a high-salt gel electroelution trap. Here, we present an improved version of this method for purifying nucleic acids with high yield and purity from even the most challenging biological samples. The proposed method is a significant improvement over the previously published procedure, offering a simple, fast, and efficient solution for isolating HMW DNA and smaller DNA and RNA molecules. The method utilizes vertical gel electrophoresis in two nested, partially overlapping electrophoretic columns. The upper, smaller-diameter column has a thin layer of agarose gel at the bottom, which separates nucleic acids from impurities, and an electrophoresis buffer on top. After the target nucleic acid has been gel-purified on the upper column, a larger-diameter column with a layer of high-salt gel overlaid with electrophoresis buffer is inserted from below. The purified nucleic acid is then electroeluted into the buffer-filled gap between the separating gel and the high-salt gel, where excess counterions from the high-salt gel slow its migration and cause it to accumulate. The proposed vertical purification system outperforms the previously described horizontal system in terms of ease of use, speed, scalability, and compatibility with high-throughput workflows. Furthermore, the vertical system allows for the sequential purification of several nucleic acid species from the same sample using interchangeable salt-gel columns.

Objective: Tuberculosis is a major health problem in many countries, including Kazakhstan. Host genetics can affect TB risk, and epidemiological and social factors may contribute to disease progression. Due to the high incidence of pulmonary tuberculosis in the country, our research aimed to study the epidemiological and genetic aspects of pulmonary tuberculosis in Kazakhstan., Material and Methods: 1026 participants of Central Asian origin were recruited in the study: 342 individuals diagnosed with active PTB, 342 household contacts, and 342 controls without a family history of TB. Genetic polymorphisms of selected genes were determined by real-time polymerase chain reaction. The association between the risk of pulmonary TB and polymorphisms was evaluated using logistic regression and assessed with the ORs and their corresponding 95 % CIs, and the significance level was determined as p < 0.05., Results: Epidemiological data revealed that underweight BMI (χ² = 89.97, p < 0.001), employment (χ² = 39.28, p < 0.001), and diabetes (χ² = 12.38, p < 0.001) showed a significant association with PTB. A/T polymorphism of the IFG gene showed a lower risk, and A/A polymorphism showed an increased risk of susceptibility to TB. A/A polymorphism of the IFG gene was associated with an almost 3-fold increased risk of PTB, and A/T polymorphism of the IFG gene was associated with a decreased risk of PTB (OR = 0.67, 95 % CI = 0.49-0.92, p = 0.01). The analysis revealed a decreased risk of PTB for A/A polymorphism of the VDR ApaI (OR = 0.67, 95 % CI = 0.46-0.97, p < 0.05). A/A polymorphism of the TLR8 gene was associated with a 1.5-fold increased risk of PTB (OR = 1.53, 95 % CI = 1.00-2.33, p < 0.05)., Conclusion: Results showed that gender, employment, underweight BMI and diabetes are associated with PTB incidence in our study cohort. The A/A genotype of the IFG (rs2430561) and an A/A genotype of the TLR8 (rs3764880) genes were associated with an increased risk of PTB. A/T polymorphism of the IFG (rs2430561) and A/A polymorphism of the VDR ApaI were associated with a decreased risk of PTB., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Background: Tuberculosis (TB) is a major public health emergency in many countries, including Kazakhstan. Despite the decline in the incidence rate and having one of the highest treatment effectiveness in the world, the incidence rate of TB remains high in Kazakhstan. Social and environmental factors along with host genetics contribute to pulmonary tuberculosis (PTB) incidence. Due to the high incidence rate of TB in Kazakhstan, our research aimed to study the epidemiology and genetics of PTB in Kazakhstan., Materials and Methods: 1,555 participants were recruited to the case-control study. The epidemiology data was taken during an interview. Polymorphisms of selected genes were determined by real-time PCR using pre-designed TaqMan probes., Results: Epidemiological risk factors like diabetes ( χ 2  = 57.71, p  < 0.001), unemployment (χ 2  = 81.1, p  < 0.001), and underweight-ranged BMI (<18.49, χ 2  = 206.39, p  < 0.001) were significantly associated with PTB. VDR FokI (rs2228570) and VDR BsmI (rs1544410) polymorphisms were associated with an increased risk of PTB. A/A genotype of the TLR8 gene (rs3764880) showed a significant association with an increased risk of PTB in Asians and Asian males. The G allele of the rs2278589 polymorphism of the MARCO gene increases PTB susceptibility in Asians and Asian females. VDR BsmI (rs1544410) polymorphism was significantly associated with PTB in Asian females. A significant association between VDR ApaI polymorphism and PTB susceptibility in the Caucasian population of Kazakhstan was found., Conclusion: This is the first study that evaluated the epidemiology and genetics of PTB in Kazakhstan on a relatively large cohort. Social and environmental risk factors play a crucial role in TB incidence in Kazakhstan. Underweight BMI (<18.49 kg/m2), diabetes, and unemployment showed a statistically significant association with PTB in our study group. FokI (rs2228570) and BsmI (rs1544410) polymorphisms of the VDR gene can be used as possible biomarkers of PTB in Asian males. rs2278589 polymorphism of the MARCO gene may act as a potential biomarker of PTB in Kazakhs. BsmI polymorphism of the VDR gene and rs2278589 polymorphism of the MARCO gene can be used as possible biomarkers of PTB risk in Asian females as well as VDR ApaI polymorphism in Caucasians., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Yerezhepov, Gabdulkayum, Akhmetova, Kozhamkulov, Rakhimova, Kairov, Zhunussova, Kalendar and Akilzhanova.)

Esophageal squamous cell carcinoma (ESCC) is the predominant subtype of esophageal cancer in Central Asia, often diagnosed at advanced stages. Understanding population-specific patterns of ESCC is crucial for tailored treatments. This study aimed to unravel ESCC's genetic basis in Kazakhstani patients and identify potential biomarkers for early diagnosis and targeted therapies. ESCC patients from Kazakhstan were studied. We analyzed histological subtypes and conducted in-depth transcriptome sequencing. Differential gene expression analysis was performed, and significantly dysregulated pathways were identified using KEGG pathway analysis ( p -value < 0.05). Protein-protein interaction networks were constructed to elucidate key modules and their functions. Among Kazakhstani patients, ESCC with moderate dysplasia was the most prevalent subtype. We identified 42 significantly upregulated and two significantly downregulated KEGG pathways, highlighting molecular mechanisms driving ESCC pathogenesis. Immune-related pathways, such as viral protein interaction with cytokines, rheumatoid arthritis, and oxidative phosphorylation, were elevated, suggesting immune system involvement. Conversely, downregulated pathways were associated with extracellular matrix degradation, crucial in cancer invasion and metastasis. Protein-protein interaction network analysis revealed four distinct modules with specific functions, implicating pathways in esophageal cancer development. High-throughput transcriptome sequencing elucidated critical molecular pathways underlying esophageal carcinogenesis in Kazakhstani patients. Insights into dysregulated pathways offer potential for early diagnosis and precision treatment strategies for ESCC. Understanding population-specific patterns is essential for personalized approaches to ESCC management., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Sharip, Rakhimova, Molkenov, Ashenova, Kozhamkulov, Akhmetollayev, Zinovyev, Zhukov, Omarov, Tuleutaev, Rakhmetova, Terwilliger, Lee, Zhumadilov, Akilzhanova and Kairov.)

Objectives: The data presented in this study were collected with the aim of obtaining the complete genomes of specific strains of Bacillus bacteria, namely, Bacillus licheniformis T5. This strain was chosen based on its enzymatic activities, particularly amylolytic activity. In this study, nanopore sequencing technology was employed to obtain the genome sequences of this strain. It is important to note that these data represent a focused objective within a larger research context, which involves exploring the biochemical features of promising Bacilli strains and investigating the relationship between enzymatic activity, phenotypic features, and the microorganism's genome., Data Description: In this study, the whole-genome sequence was obtained from one Bacillus strain, Bacillus licheniformis T5, isolated from soil samples in Kazakhstan. Sample preparation and genomic DNA library construction were performed according to the Ligation sequencing gDNA kit (SQK-LSK109) protocol and NEBNext module. The prepared library was sequenced on a MinION instrument (Oxford Nanopore Technologies nanopore sequencer with a maximum throughput of up to 30 billion nucleotides per run and no limit on read length), using a flow cell for nanopore sequencing FLO-MIN106D. The genome de novo assembly was performed using the long sequencing reads generated by MinION Oxford Nanopore platform. Finally, one circular contig was obtained harboring a length of 4,247,430 bp with 46.16% G + C content and the mean contig 428X coverage. B. licheniformis T5 genome assembly annotation revealed 5391 protein-coding sequences, 81 tRNAs, 51 repeat regions, 24 rRNAs, 3 virulence factors and 53 antibiotic resistance genes. This sequence encompasses the complete genetic information of the strain, including genes, regulatory elements, and noncoding regions. The data reveal important insights into the genetic characteristics, phenotypic traits, and enzymatic activity of this Bacillus strain. The findings of this study have particular value to researchers interested in microbial biology, biotechnology, and antimicrobial studies. The genomic sequence offers a foundation for understanding the genetic basis of traits such as endospore formation, alkaline tolerance, temperature range for growth, nutrient utilization, and enzymatic activities. These insights can contribute to the development of novel biotechnological applications, such as the production of enzymes for industrial purposes. Overall, this study provides valuable insights into the genetic characteristics, phenotypic traits, and enzymatic activities of the Bacillus licheniformis T5 strain. The acquired genomic sequences contribute to a better understanding of this strain and have implications for various research fields, such as microbiology, biotechnology, and antimicrobial studies., (© 2023. The Author(s).)

Long-read sequencing technologies require high-molecular-weight (HMW) DNA of sufficient purity and integrity, which can be difficult to obtain from complex biological samples. We propose a method for purifying HMW DNA that takes advantage of the fact that DNA's electrophoretic mobility decreases in a high-ionic-strength environment. The method begins with the separation of HMW DNA from various impurities by electrophoresis in an agarose gel-filled channel. After sufficient separation, a high-salt gel block is placed ahead of the DNA band of interest, leaving a gap between the separating gel and the high-salt gel that serves as a reservoir for sample collection. The DNA is then electroeluted from the separating gel into the reservoir, where its migration slows due to electrostatic shielding of the DNA's negative charge by excess counterions from the high-salt gel. As a result, the reservoir accumulates HMW DNA of high purity and integrity, which can be easily collected and used for long-read sequencing and other demanding applications without additional desalting. The method is simple and inexpensive, yields sequencing-grade HMW DNA even from difficult plant and soil samples, and has the potential for automation and scalability.

In Kazakhstan, there is insufficient data on genetic epilepsy, which has its own clinical and management implications. Thus, this study aimed to use whole genome sequencing to identify and evaluate genetic variants and genetic structure of early onset epilepsy in the Kazakhstani pediatric population. In this study, for the first time in Kazakhstan, whole genome sequencing was carried out among epilepsy diagnosed children. The study involved 20 pediatric patients with early onset epilepsy and no established cause of the disease during the July-December, 2021. The average age at enrolment was 34.5 months, with a mean age at seizure onset of 6 months. Six patients (30%) were male, and 7 were familial cases. We identified pathogenic and likely pathogenic variants in 14 (70%) cases, among them, 6 novel disease gene variants (KCNQ2, CASK, WWOX, MT-CO3, GRIN2D, and SLC12A5). Other genes associated with the disease were SCN1A (x2), SLC2A1, ARX, CACNA1B, PCDH19, KCNT1, and CHRNA2. Identification of the genetic causes in 70% of cases confirms the general structure of the etiology of early onset epilepsy and the necessity of using NGS in diagnostics. Moreover, the study describes new genotype-phenotypic correlations in genetic epilepsy. Despite certain limitations of the study, it can be concluded that the genetic etiology of pediatric epilepsy in Kazakhstan is very broad and requires further research., (© 2023. The Author(s).)

We developed a comprehensive multiplexed set of primers adapted for the Oxford Nanopore Rapid Barcoding library kit that allows universal SARS-CoV-2 genome sequencing. This primer set is designed to set up any variants of the primers pool for whole-genome sequencing of SARS-CoV-2 using single- or double-tiled amplicons from 1.2 to 4.8 kb with the Oxford Nanopore. This multiplexed set of primers is also applicable for tasks like targeted SARS-CoV-2 genome sequencing. We proposed here an optimized protocol to synthesize cDNA using Maxima H Minus Reverse Transcriptase with a set of SARS-CoV-2 specific primers, which has high yields of cDNA template for RNA and is capable of long-length cDNA synthesis from a wide range of RNA amounts and quality. The proposed protocol allows whole-genome sequencing of the SARS-CoV-2 virus with tiled amplicons up to 4.8 kb on low-titer virus samples and even where RNA degradation has occurred. This protocol reduces the time and cost from RNA to genome sequence compared to the Midnight multiplex PCR method for SARS-CoV-2 genome sequencing using the Oxford Nanopore., (© 2023. The Author(s).)

Background: Kazakhstan has a high burden of multidrug-resistant tuberculosis in the Central Asian region. This study aimed to perform genomic characterization of Mycobacterium tuberculosis strains obtained from Kazakhstani patients with pre-extensively drug-resistant tuberculosis diagnosed in Kazakhstan., Methods: Whole-genome sequencing was performed on 10 pre-extensively drug-resistant M. tuberculosis strains from different regions of Kazakhstan. All strains had high-confidence resistance mutations according to the resistance grading system previously established by the World Health Organization. The genome analysis was performed using TB-Profiler, Mykrobe, CASTB, and ResFinder., Results: Valuable information for understanding the genetic diversity of tuberculosis in Kazakhstan can also be obtained from whole-genome sequencing. The results from the Phenotypic Drug Susceptibility Testing (DST) of bacterial strains were found to be consistent with the drug resistance information obtained from genomic data that characterized all isolates as pre-XDR. This information can help in developing targeted prevention and control strategies based on the local epidemiology of tuberculosis. Furthermore, the data obtained from whole-genome sequencing can help in tracing the transmission pathways of tuberculosis and facilitating early detection of outbreaks., Conclusions: The results from whole-genome sequencing of tuberculosis clinical samples in Kazakhstan provide important insights into the drug resistance patterns and genetic diversity of tuberculosis in the country. These results can contribute to the improvement of tuberculosis control and management programs in Kazakhstan.

Arteriovenous malformations of the brain (bAVMs) are plexuses of pathological arteries and veins that lack a normal capillary system between them. Intracranial hemorrhage (hemorrhagic stroke) is the most frequent clinical manifestation of AVM, leading to lethal outcomes that are especially high among children and young people. Recently, high-throughput genome sequencing methods have made a notable contribution to the research progress in this subject. In particular, whole-exome sequencing (WES) methods allow the identification of novel mutations. However, the genetic mechanism causing AVM is still unclear. Therefore, the aim of this study was to investigate the potential genetic mechanism underlying AVM. We analyzed the WES data of blood and tissue samples of a 30-year-old Central Asian male diagnosed with AVM. We identified 54 polymorphisms in 43 genes. After in-silica overrepresentation enrichment analysis of the polymorphisms, the SIRT1 gene variant (g.67884831C>T) indicated a possible molecular mechanism of bAVM. Further studies are required to evaluate the functional impact of SIRT1 g.67884831C>T, which may warrant further replication and biological investigations related to sporadic bAVM.

Severe acute respiratory syndrome (SARS-CoV-2) is responsible for the worldwide pandemic, COVID-19. The original viral whole-genome was sequenced by a high-throughput sequencing approach from the samples obtained from Wuhan, China. Real-time gene sequencing is the main parameter to manage viral outbreaks because it expands our understanding of virus proliferation, spread, and evolution. Whole-genome sequencing is critical for SARS-CoV-2 variant surveillance, the development of new vaccines and boosters, and the representation of epidemiological situations in the country. A significant increase in the number of COVID-19 cases confirmed in August 2021 in Kazakhstan facilitated a need to establish an effective and proficient system for further study of SARS-CoV-2 genetic variants and the development of future Kazakhstan's genomic surveillance program. The SARS-CoV-2 whole-genome was sequenced according to SARS-CoV-2 ARTIC protocol (EXP-MRT001) by Oxford Nanopore Technologies at the National Laboratory Astana, Kazakhstan to track viral variants circulating in the country. The 500 samples kindly provided by the Republican Diagnostic Center (UMC-NU) and private laboratory KDL "Olymp" were collected from individuals in Nur-Sultan city diagnosed with COVID-19 from August 2021 to May 2022 using real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR). All samples had a cycle threshold (Ct) value below 20 with an average Ct value of 17.03. The overall average value of sequencing depth coverage for samples is 244X. 341 whole-genome sequences that passed quality control were deposited in the Global initiative on sharing all influenza data (GISAID). The BA.1.1 ( n = 189), BA.1 ( n = 15), BA.2 ( n = 3), BA.1.15 ( n = 1), BA.1.17.2 ( n = 1) omicron lineages, AY.122 ( n = 119), B.1.617.2 ( n = 8), AY.111 ( n = 2), AY.126 ( n = 1), AY.4 ( n = 1) delta lineages, one sample B.1.1.7 ( n = 1) belongs to alpha lineage, and one sample B.1.637 ( n = 1) belongs to small sublineage were detected in this study. This is the first study of SARS-CoV-2 whole-genome sequencing by the ONT approach in Kazakhstan, which can be expanded for the investigation of other emerging viral or bacterial infections on the country level., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Kairov, Amanzhanova, Karabayev, Rakhimova, Aitkulova, Samatkyzy, Kalendar, Kozhamkulov, Molkenov, Gabdulkayum, Sarbassov and Akilzhanova.)

Kazakhstan, the ninth-largest country in the world, is located along the Great Silk Road and connects Europe with Asia. Historically, its territory has been inhabited by nomadic tribes, and modern-day Kazakhstan is a multiethnic country with a dominant Kazakh population. We sequenced and analyzed the genomes of five ethnic Kazakhs at high coverage using the Illumina HiSeq2000 next-generation sequencing platform. The five Kazakhs yielded a total number of base pairs ranging from 87,308,581,400 to 107,526,741,301. On average, 99.06% were properly mapped. Based on the Het/Hom and Ti/Tv ratios, the quality of the genomic data ranged from 1.35 to 1.49 and from 2.07 to 2.08, respectively. Genetic variants were identified and annotated. Functional analysis of the genetic variants identified several variants that were associated with higher risks of metabolic and neurogenerative diseases. The present study showed high levels of genetic admixture of Kazakhs that were comparable to those of other Central Asians. These whole-genome sequence data of healthy Kazakhs could contribute significantly to biomedical studies of common diseases as their findings could allow better insight into the genotype-phenotype relations at the population level., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Kairov, Molkenov, Sharip, Rakhimova, Seidualy, Rhie, Kozhamkulov, Zhabagin, Kim, Lee, Terwilliger, Seo, Zhumadilov and Akilzhanova.)

Summary: We developed BIODICA, an integrated computational environment for application of independent component analysis (ICA) to bulk and single-cell molecular profiles, interpretation of the results in terms of biological functions and correlation with metadata. The computational core is the novel Python package stabilized-ica which provides interface to several ICA algorithms, a stabilization procedure, meta-analysis and component interpretation tools. BIODICA is equipped with a user-friendly graphical user interface, allowing non-experienced users to perform the ICA-based omics data analysis. The results are provided in interactive ways, thus facilitating communication with biology experts., Availability and Implementation: BIODICA is implemented in Java, Python and JavaScript. The source code is freely available on GitHub under the MIT and the GNU LGPL licenses. BIODICA is supported on all major operating systems. URL: https://sysbio-curie.github.io/biodica-environment/., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Polymerase chain reaction (PCR) is a simple and rapid method that can detect nucleotide polymorphisms and sequence variation in basic research applications, agriculture, and medicine. Variants of PCR, collectively known as allele-specific PCR (AS-PCR), use a competitive reaction in the presence of allele-specific primers to preferentially amplify only certain alleles. This method, originally named by its developers as Kompetitive Allele Specific PCR (KASP), is an AS-PCR variant adapted for fluorescence-based detection of amplification results. We developed a bioinformatic tool for designing probe sequences for PCR-based genotyping assays. Probe sequences are designed in both directions, and both single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) may be targeted. In addition, the tool allows discrimination of up to four-allelic variants at a single SNP site. To increase both the reaction specificity and the discriminative power of SNP genotyping, each allele-specific primer is designed such that the penultimate base before the primer's 3' end base is positioned at the SNP site. The tool allows design of custom FRET cassette reporter systems for fluorescence-based assays. FastPCR is a user-friendly and powerful Java-based software that is freely available (http://primerdigital.com/tools/). Using the FastPCR environment and the tool for designing AS-PCR provides unparalleled flexibility for developing genotyping assays and specific and sensitive diagnostic PCR-based tests, which translates into a greater likelihood of research success., Competing Interests: Author RK is the owner and director of PrimerDigital. Author RK is an employee of PrimerDigital. This affiliation does not alter our adherence to publication policies on sharing data and materials. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Kalendar, Shustov, Akhmetollayev and Kairov.)

Tuberculosis (TB) is an infectious disease that remains an essential public health problem in many countries. Despite decreasing numbers of new cases worldwide, the incidence of antibiotic-resistant forms (multidrug resistant and extensively drug-resistant) of TB is increasing. Next-generation sequencing technologies provide a high-throughput approach to identify known and novel potential genetic variants that are associated with drug resistance in Mycobacterium tuberculosis ( Mtb ). There are limited reports and data related to whole-genome characteristics of drug-resistant Mtb strains circulating in Kazakhstan. Here, we report whole-genome sequencing and analysis results of eight multidrug-resistant strains collected from TB patients in Kazakhstan. Genotyping and validation of all strains by MIRU-VNTR and spoligotyping methodologies revealed that these strains belong to the Beijing family. The spectrum of specific and potentially novel genomic variants (single-nucleotide polymorphisms, insertions, and deletions) related to drug resistance was identified and annotated. ResFinder, CARD, and CASTB antibiotic resistance databases were used for the characterization of genetic variants in genes associated with drug resistance. Our results provide reference data and genomic profiles of multidrug-resistant isolates for further comparative studies and investigations of genetic patterns in drug-resistant Mtb strains., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Daniyarov, Molkenov, Rakhimova, Akhmetova, Yerezhepov, Chingissova, Bismilda, Toksanbayeva, Rakisheva, Akilzhanova, Kozhamkulov and Kairov.)

Independent Component Analysis is a matrix factorization method for data dimension reduction. ICA has been widely applied for the analysis of transcriptomic data for blind separation of biological, environmental, and technical factors affecting gene expression. The study aimed to analyze the publicly available esophageal cancer data using the ICA for identification and comprehensive analysis of reproducible signaling pathways and molecular signatures involved in this cancer type. In this study, four independent esophageal cancer transcriptomic datasets from GEO databases were used. A bioinformatics tool « BiODICA-Independent Component Analysis of Big Omics Data» was applied to compute independent components (ICs). Gene Set Enrichment Analysis (GSEA) and ToppGene uncovered the most significantly enriched pathways. Construction and visualization of gene networks and graphs were performed using the Cytoscape, and HPRD database. The correlation graph between decompositions into 30 ICs was built with absolute correlation values exceeding 0.3. Clusters of components-pseudocliques were observed in the structure of the correlation graph. The top 1,000 most contributing genes of each ICs in the pseudocliques were mapped to the PPI network to construct associated signaling pathways. Some cliques were composed of densely interconnected nodes and included components common to most cancer types (such as cell cycle and extracellular matrix signals), while others were specific to EC. The results of this investigation may reveal potential biomarkers of esophageal carcinogenesis, functional subsystems dysregulated in the tumor cells, and be helpful in predicting the early development of a tumor., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Ashenova, Daniyarov, Molkenov, Sharip, Zinovyev and Kairov.)

Background: High-throughput sequencing platforms generate a massive amount of high-dimensional genomic datasets that are available for analysis. Modern and user-friendly bioinformatics tools for analysis and interpretation of genomics data becomes essential during the analysis of sequencing data. Different standard data types and file formats have been developed to store and analyze sequence and genomics data. Variant Call Format (VCF) is the most widespread genomics file type and standard format containing genomic information and variants of sequenced samples., Results: Existing tools for processing VCF files don't usually have an intuitive graphical interface, but instead have just a command-line interface that may be challenging to use for the broader biomedical community interested in genomics data analysis. re-Searcher solves this problem by pre-processing VCF files by chunks to not load RAM of computer. The tool can be used as standalone user-friendly multiplatform GUI application as well as web application (https://nla-lbsb.nu.edu.kz). The software including source code as well as tested VCF files and additional information are publicly available on the GitHub repository (https://github.com/LabBandSB/re-Searcher)., Competing Interests: The authors declare there are no competing interests., (©2021 Karabayev et al.)

Objectives: Kazakhstan is a Central Asian crossroad of European and Asian populations situated along the way of the Great Silk Way. The territory of Kazakhstan has historically been inhabited by nomadic tribes and today is the multi-ethnic country with the dominant Kazakh ethnic group. We sequenced and analyzed the whole-genomes of five ethnic healthy Kazakh individuals with high coverage using next-generation sequencing platform. This whole-genome sequence data of healthy Kazakh individuals can be a valuable reference for biomedical studies investigating disease associations and population-wide genomic studies of ethnically diverse Central Asian region., Data Description: Blood samples have been collected from five ethnic healthy Kazakh individuals living in Kazakhstan. The genomic DNA was extracted from blood and sequenced. Sequencing was performed on Illumina HiSeq2000 next-generation sequencing platform. We sequenced and analyzed the whole-genomes of ethnic Kazakh individuals with the coverage ranging from 26 to 32X. Ranging from 98.85 to 99.58% base pairs were totally mapped and aligned on the human reference genome GRCh37 hg19. Het/Hom and Ts/Tv ratios for each whole genome ranged from 1.35 to 1.49 and from 2.07 to 2.08, respectively. Sequencing data are available in the National Center for Biotechnology Information SRA database under the accession number PRJNA374772.

Background: Ventricular tachycardia (VT) is a major cause of sudden cardiac death (SCD). Clinical investigations can sometimes fail to identify the underlying cause of VT and the event is classified as idiopathic (iVT). VT contributes significantly to the morbidity and mortality in patients with coronary artery disease (CAD) and dilated cardiomyopathy (DCM). Since mutations in arrhythmia-associated genes frequently determine arrhythmia susceptibility screening for disease-predisposing variants could improve VT diagnostics and prevent SCD in patients., Methods: Ninety-two patients diagnosed with coronary heart disease (CHD), DCM, or iVT were included in our study. We evaluated genetic profiles and variants in known cardiac risk genes by targeted next generation sequencing (NGS) using a newly designed custom panel of 96 genes. We hypothesized that shared morphological and phenotypical features among these subgroups may have an overlapping molecular base. To our knowledge, this was the first study of the deep sequencing of 96 targeted cardiac genes in Kazakhstan. The clinical significance of the sequence variants was interpreted according to the guidelines developed by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) in 2015. The ClinVar and Varsome databases were used to determine the variant classifications., Results: Targeted sequencing and stepwise filtering of the annotated variants identified a total of 307 unique variants in 74 genes, totally 456 variants in the overall study group. We found 168 mutations listed in the Human Genome Mutation Database (HGMD) and another 256 rare/unique variants with elevated pathogenic potential. There was a predominance of high- to intermediate pathogenicity variants in LAMA2 , MYBPC3 , MYH6 , KCNQ1 , GAA, and DSG2 in CHD VT patients. Similar frequencies were observed in DCM VT, and iVT patients, pointing to a common molecular disease association. TTN, GAA, LAMA2, and MYBPC3 contained the most variants in the three subgroups which confirm the impact of these genes in the complex pathogenesis of cardiomyopathies and VT. The classification of 307 variants according to ACMG guidelines showed that nine (2.9%) variants could be classified as pathogenic, nine (2.9%) were likely pathogenic, 98 (31.9%) were of uncertain significance, 73 (23.8%) were likely benign, and 118 (38.4%) were benign. CHD VT patients carry rare genetic variants with increased pathogenic potential at a comparable frequency to DCM VT and iVT patients in genes related to sarcomere function, nuclear function, ion flux, and metabolism., Conclusions: In this study we showed that in patients with VT secondary to coronary artery disease, DCM, or idiopathic etiology multiple rare mutations and clinically significant sequence variants in classic cardiac risk genes associated with cardiac channelopathies and cardiomyopathies were found in a similar pattern and at a comparable frequency., Competing Interests: The authors declare there are no competing interests., (©2021 Guelly et al.)

Drug-resistant tuberculosis (TB) is a major public health problem. Clinical Mycobacterium tuberculosis (MTB) isolate with Extensively drug-resistant tuberculosis (MTB-XDR) profile was subjected to whole-genome sequencing using a next-generation sequencing platform (NGS) Roche 454 GS FLX+ followed by bioinformatics sequence analysis. Quality of read was checked by FastQC, paired-end reads were trimmed using Trimmomatic. De novo genome assembly was conducted using Velvet v.1.2.10. The assembled genome of XDR-TB-1599 strain was functionally annotated using the PATRIC platform. Analysis of de novo assembled genome was performed using ResFinder, CARD, CASTB and TB-Profiler tools. MIRU&#95;VNTR genotyping on 12 loci and spoligotyping have been performed for XDR-TB-1599 isolate. M. tuberculosis XDR-TB-1599 strain yielded an average read depth of 21-fold with overall 4 199 325 bp. The assembled genome contains 5528 protein-coding genes, including key drug resistance and virulence-associated genes and GC content of 65.4%. We identified that all proteins encoded by this strain contain conserved domains associated with the first-line anti-tuberculosis drugs such as rifampicin, isoniazid, streptomycin and ethionamide. TB-Profiler had higher average concordance results with phenotypic DST (drug susceptibility testing) in comparison with ResFinder, CARD, CASTB profiling to first-line (75% vs 50%) and second-line (25% vs 0%) of anti-TB drugs, correspondingly. To our knowledge, this is the first report of a highly annotated and characterized whole-genome sequence and de novo assembled XDR-TB M.tuberculosis strain isolated from a sputum of new TB case-patient from Kazakhstan performed on Roche 454 GS FLX+ platform. This report highlights an important role of whole-genome sequencing technology and analysis as an advanced approach for drug-resistance investigations of circulated TB isolates., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2020 The Author(s).)

EWSR1-FLI1, the chimeric oncogene specific for Ewing sarcoma (EwS), induces a cascade of signaling events leading to cell transformation. However, it remains elusive how genetically homogeneous EwS cells can drive the heterogeneity of transcriptional programs. Here, we combine independent component analysis of single-cell RNA sequencing data from diverse cell types and model systems with time-resolved mapping of EWSR1-FLI1 binding sites and of open chromatin regions to characterize dynamic cellular processes associated with EWSR1-FLI1 activity. We thus define an exquisitely specific and direct enhancer-driven EWSR1-FLI1 program. In EwS tumors, cell proliferation and strong oxidative phosphorylation metabolism are associated with a well-defined range of EWSR1-FLI1 activity. In contrast, a subpopulation of cells from below and above the intermediary EWSR1-FLI1 activity is characterized by increased hypoxia. Overall, our study reveals sources of intratumoral heterogeneity within EwS tumors., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Motivation: Matrix factorization (MF) methods are widely used in order to reduce dimensionality of transcriptomic datasets to the action of few hidden factors (metagenes). MF algorithms have never been compared based on the between-datasets reproducibility of their outputs in similar independent datasets. Lack of this knowledge might have a crucial impact when generalizing the predictions made in a study to others., Results: We systematically test widely used MF methods on several transcriptomic datasets collected from the same cancer type (14 colorectal, 8 breast and 4 ovarian cancer transcriptomic datasets). Inspired by concepts of evolutionary bioinformatics, we design a novel framework based on Reciprocally Best Hit (RBH) graphs in order to benchmark the MF methods for their ability to produce generalizable components. We show that a particular protocol of application of independent component analysis (ICA), accompanied by a stabilization procedure, leads to a significant increase in the between-datasets reproducibility. Moreover, we show that the signals detected through this method are systematically more interpretable than those of other standard methods. We developed a user-friendly tool for performing the Stabilized ICA-based RBH meta-analysis. We apply this methodology to the study of colorectal cancer (CRC) for which 14 independent transcriptomic datasets can be collected. The resulting RBH graph maps the landscape of interconnected factors associated to biological processes or to technological artifacts. These factors can be used as clinical biomarkers or robust and tumor-type specific transcriptomic signatures of tumoral cells or tumoral microenvironment. Their intensities in different samples shed light on the mechanistic basis of CRC molecular subtyping., Availability and Implementation: The RBH construction tool is available from http://goo.gl/DzpwYp., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2019. Published by Oxford University Press.)

Independent component analysis (ICA) is a matrix factorization approach where the signals captured by each individual matrix factors are optimized to become as mutually independent as possible. Initially suggested for solving source blind separation problems in various fields, ICA was shown to be successful in analyzing functional magnetic resonance imaging (fMRI) and other types of biomedical data. In the last twenty years, ICA became a part of the standard machine learning toolbox, together with other matrix factorization methods such as principal component analysis (PCA) and non-negative matrix factorization (NMF). Here, we review a number of recent works where ICA was shown to be a useful tool for unraveling the complexity of cancer biology from the analysis of different types of omics data, mainly collected for tumoral samples. Such works highlight the use of ICA in dimensionality reduction, deconvolution, data pre-processing, meta-analysis, and others applied to different data types (transcriptome, methylome, proteome, single-cell data). We particularly focus on the technical aspects of ICA application in omics studies such as using different protocols, determining the optimal number of components, assessing and improving reproducibility of the ICA results, and comparison with other popular matrix factorization techniques. We discuss the emerging ICA applications to the integrative analysis of multi-level omics datasets and introduce a conceptual view on ICA as a tool for defining functional subsystems of a complex biological system and their interactions under various conditions. Our review is accompanied by a Jupyter notebook which illustrates the discussed concepts and provides a practical tool for applying ICA to the analysis of cancer omics datasets.

Purpose: To scrutinize the apoptotic and genotoxic effects of low-intensity ultrasound and an ultrasound contrast agent (SonoVue; Bracco Diagnostics Inc., EU) on human peripheral mononuclear blood cells (PMBCs)., Methods: PMBCs were subjected to a low-intensity ultrasound field (1-MHz frequency; spatial peak temporal average intensity 0.18 W/cm2) followed by analysis for apoptosis and DNA damage (single-strand breaks + double-strand breaks). The comet assay was then repeated after 2 h to examine the ability of cells to repair DNA breaks., Results: The results demonstrated that low-intensity ultrasound was capable of selectively inducing apoptosis in leukemic PMBCs, but not in healthy cells. The introduction of ultrasound contrast agent SonoVue resulted in an increase in apoptosis in both groups. DNA analysis after ultrasound exposure indicated that ultrasound triggered DNA damage in leukemic PMBCs (66.05 ± 13.36%), while the damage was minimal (7.01 ± 0.89%) in control PMBCs. However, both cell lines demonstrated an ability to repair DNA single- and double-strand breaks 2 h after sonication., Conclusions: The study demonstrated that low-intensity ultrasound selectively induced apoptosis in cancer PMBCs. Ultrasound-induced DNA damage was observed primarily in leukemic PMBCs. Nevertheless, both cell lines were able to repair ultrasound-mediated DNA strand breaks.

Background: Independent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the number of components (factors) to compute. The optimal choice of this parameter, related to determining the effective data dimension, remains an open question in the application of blind source separation techniques to transcriptomic data., Results: Here we address the question of optimizing the number of statistically independent components in the analysis of transcriptomic data for reproducibility of the components in multiple runs of ICA (within the same or within varying effective dimensions) and in multiple independent datasets. To this end, we introduce ranking of independent components based on their stability in multiple ICA computation runs and define a distinguished number of components (Most Stable Transcriptome Dimension, MSTD) corresponding to the point of the qualitative change of the stability profile. Based on a large body of data, we demonstrate that a sufficient number of dimensions is required for biological interpretability of the ICA decomposition and that the most stable components with ranks below MSTD have more chances to be reproduced in independent studies compared to the less stable ones. At the same time, we show that a transcriptomics dataset can be reduced to a relatively high number of dimensions without losing the interpretability of ICA, even though higher dimensions give rise to components driven by small gene sets., Conclusions: We suggest a protocol of ICA application to transcriptomics data with a possibility of prioritizing components with respect to their reproducibility that strengthens the biological interpretation. Computing too few components (much less than MSTD) is not optimal for interpretability of the results. The components ranked within MSTD range have more chances to be reproduced in independent studies.

Here, we report the draft genome sequences of two clinical isolates of Mycobacterium tuberculosis (MTB-476 and MTB-489) isolated from sputum of Kazakh patients., (Copyright © 2015 Kairov et al.)

Introduction: The human genome sequence will underpin human biology and medicine in the next century, providing a single, essential reference to all genetic information. Extraordinary technological advances and decreases in the cost of DNA sequencing have made the possibility of whole genome sequencing (WGS) feasible as a highly accessible test for numerous indications. The international project "Genetic architecture of Kazakh population" is well underway to determine the complete DNA. Next generation sequencing is a powerful tool for genetic analysis, which will enable us to uncover the association of loci at specific sites in the genome associated with disease. The aim of this study was to introduce first data on WGS of 6 Kazakh individuals., Methods: This pilot study is among the first WGS performed on 6 healthy Kazakh individuals, using next generation sequencing platform HiSeq2000, Illumina by manufacturer's protocols. All generated *.bcl files were simultaneously converted and demultiplexed using bcl2fasta application. Alignment of sequence reads performed using bwa-mem against human b19 reference genome. Sorting, removing of intermediate files, *.bam files assembling, and marking duplicates were performed using PicardTools package. GATK haplotype caller tool was used for variant calling. ClinVar, SNPedia, and Cosmic databases were processed to identify clinical genomic variants in 6 Kazakh whole genomes. Java Runtime Environment and R. Bioconductor packages were installed to perform raw data processing and run program scripts., Results: The sequence alignment and mapping procedures on reference genome hg19 of each 6 healthy Kazakh individual were completed. Between 87,308,581,400 and 107,526,741,301 total base pairs were sequenced with average coverage x29.85. Between 98.85% and 99.58% base pairs were totally mapped and on average 96.07% were properly paired. Het/Hom and Ti/Tv ratios for each whole genome ranged from 1.35 to 1.52 and from 2.07 to 2.08, respectively. We compared and analyzed each genome with on existing clinical databases ClinVar, SNPedia, Cosmic and found from 20 to 25, from 269 to 288, from 7 to 12 SNP records, respectively. The availability of a reference Kazakh genome sequences provides the basis for studying the nature of sequence variation, particularly single nucleotide polymorphisms., Conclusion: The first whole genome sequencing of Kazakhs were performed. In this pilot study, we identified SNPs associated with different conditions. Further studies of WGS on Kazakh population are needed to identify possible unique genetic variants in Kazakhs.

Introduction: Tuberculosis (TB) is caused by bacterium Mycobacterium tuberculosis (MTB), and according to the WHO, up to 30% of world population is infected with latent TB. Pathogenesis of TB is multifactorial, and its development depends on environmental, social, microbial, and genetic factors of both the bacterium and the host. The number of TB cases in Kazakhstan has decreased in the past decade, but multidrug-resistant (MDR) TB cases are dramatically increasing. Polymorphisms in genes responsible for immune response have been associated with TB susceptibility. The objective of this study was to investigate the risk of developing pulmonary TB (PTB) associated with polymorphisms in several inflammatory pathway genes among Kazakhstani population., Methods: 703 participants from 3 regions of Kazakhstan were recruited for a case-control study. 251 participants had pulmonary TB (PTB), and 452 were healthy controls (HC). Males and females represented 42.39% and 57.61%, respectively. Of all participants, 67.4% were Kazakhs, 22.8% Russians, 3.4% Ukrainians, and 6.4% were of other origins. Clinical and epidemiological data were collected from medical records, interviews, and questionnaires. DNA samples were genotyped using TaqMan assay on 4 polymorphisms: IFNγ (rs2430561) and IL1β (rs16944), TLR2 (rs5743708) and TLR8 (rs3764880). Statistical data was analyzed using SPSS 19., Results: Genotyping by IFγ, IL1β, TLR2 showed no significant association with PTB susceptibility ( p > 0.05). TLR8 genotype A/G was significantly higher in females (F/M - 41.5%/1.3%) and G/G in males (M/F - 49%/20.7%) (χ2=161.43, p < 0.001). A significantly increased risk of PTB development was observed for TLR A/G with an adjusted OR of 1.48 (95%, CI: 0.96 - 2.28), and a protective feature was revealed for TLR8 G/G genotype (OR: 0.81, 95%, CI: 0.56 - 1.16, p = 0.024). Additional grouping by gender revealed that TLR8 G/G contributes as protective genotype (OR: 1.83, 95%, CI: 1.18 - 2.83, p = 0.036) in males of the control group., Conclusion: Results indicate that heterozygous genotype A/G of TLR8 increases the risk of PTB development, while G/G genotype may serve as protection mechanism. A/A genotype is strongly associated with susceptibility to PTB. To clarify the role of other polymorphisms in susceptibility to PTB in Kazakhstani population, further investigations are needed.

Background: Tuberculosis is a major public health problem which infects one third of the world's population, resulting in more than two million deaths every year. The emergence of whole genome sequencing (WGS) technologies as a primary research tool has allowed for the detection of genetic diversity in Mycobacterium tuberculosis (MTB) with unprecedented resolution. WGS has been used to address a broad range of topics, including the dynamics of evolution, transmission, and treatment. To our knowledge, studies involving WGS of Kazakhstani strains of M. tuberculosis have not yet been performed., Aim: To perform whole genome sequencing of M. tuberculosis strains isolated in Kazakhstan and analyze sequence data (first experience and preliminary data)., Results: In the present report, we announce the whole-genome sequences of the two clinical isolates of Mycobacterium tuberculosis, MTB-489 and MTB-476, isolated from the Almaty region. These strains were part of a repository that was created during our project "Creating prerequisites of personalized approach in the diagnosis and treatment of tuberculosis, based on whole genome-sequencing of M. tuberculosis". Two strains were isolated from sputum samples of patients P1 and P2. Phenotypically, two isolates were drug-susceptible M. tuberculosis. Sequence data was compared with the publicly available data on M. tuberculosis laboratory strain H37Rv and others. The sequencing of the strains was performed on a Roche 454 GS FLX+ next-generation sequencing platform using a standard protocol for a shotgun genome library. The whole genome sequencing was performed for two M.tuberculosis isolates MTB-476 and MTB-489. 96 M bp with an average read length of 520 bp, approximately 21.8X coverage and 104.2 M bp with an average read length of 589 bp and approximately 23.7X coverage were generated for the MTB-476 and MTB-489, respectively. The genome of MTB-476 consists of 257 contigs, 4204 CDS, 46 tRNAs and 3 rRNAs. MTB-489 has 187 contigs, 4183 CDS, 45 tRNAs and 3rRNAs., Conclusion: The results of genome assembling have been submitted into NCBI GenBank and are available for public access under the accession numbers AZBA00000000 and AZAZ00000000. These genome assemblies can be useful for comparative genome analysis and for identification of novel SNPs and gene variants in genomes of M.tuberculosis.

Muscular dystrophy is a condition potentially predisposing for cancer; however, currently, only Myotonic dystrophy patients are known to have a higher risk of cancer. Here, we have searched for a link between facioscapulohumeral dystrophy (FSHD) and cancer by comparing published transcriptome signatures of FSHD and various malignant tumours and have found a significant enrichment of cancer-related genes among the genes differentially expressed in FSHD. The analysis has shown that gene expression profiles of FSHD myoblasts and myotubes resemble that of Ewing's sarcoma more than that of other cancer types tested. This is the first study demonstrating a similarity between FSHD and cancer cell expression profiles, a finding that might indicate the existence of a common step in the pathogenesis of these two diseases., (© 2013 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.)

Introduction: Vitamin D receptor (VDR) plays an important role in activating the immune response against various infectious agents. It is known that the active metabolite of ligand receptor Vitamin D (1,25 - dihydroxyvitamin D) is encoded by VDR and helps mononuclear phagocytes to suppress the intracellular growth of M. tuberculosis . The VDR gene harbors approximately 200 polymorphisms, some of which are linked to differences in receptor Vitamin D uptake and therefore can be considered as candidate disease risk variants. The relation between VDR gene polymorphisms and susceptibility to TB has been studied in different populations. There is not a great deal of information regarding the association of these SNPs with TB risk in the Kazakh population. The four most commonly investigated VDR polymorphisms in association with different diseases, including susceptibility to tuberculosis, are located in exon 2 (rs2228570 or FokI), intron 8 (rs1544410 or BsmI and rs7975232 or ApaI), and exon 9 (rs731236 or TaqI). The aim of our study was to determine whether these four VDR gene single nucleotide polymorphisms were associated with TB and whether they were a risk for the development of TB in the Kazakh Population in Almaty city and Almaty area., Methods: This study was a hospital-based case-control analysis of 283 individuals (99 TB patients and 184 healthy controls). Genotyping was performed by Taqman SNP allelic discrimination using commercial TaqMan SNP Genotyping assays. Statistical analysis was conducted using SPSS Version 19.0 software., Results: Genotype frequencies for the Kazakh population are close to world (HapMap) data on Asian populations. FokI and ApaI polymorphisms genotypes tend to be associated with TB risk under the co-dominant model [OR=1.18; 95%CI: (0.68, 2.07), p=0.15] for FokI and [OR=1.33; 95%CI: (0.61, 2.91), p=0.6] for ApaI. No significant association between the disease and TaqI, BsmI genotypes was observed., Conclusions: In summary, we explored potential associations between SNPs in the VDR (FokI, ApaI) gene and susceptibility to tuberculosis in the Kazakh Population, which requires further detailed analysis with a larger sample size and greater geographic diversity including other regions of Kazakhstan.

Introduction: Lactobacilli are a bacteria commonly found in the gastrointestinal tract. Some species of this genus have probiotic properties. The most common of these is Lactobacillus rhamnosus , a microoganism, generally regarded as safe (GRAS). It is also a homofermentative L-(+)-lactic acid producer. The genus Lactobacillus is characterized by an extraordinary degree of the phenotypic and genotypic diversity. However, the studies of the genus were conducted mostly with the unequally distributed, non-random choice of species for sequencing; thus, there is only one representative genome from the Lactobacillus rhamnosus clade available to date. The aim of this study was to characterize the genome sequencing of selected strains of Lactobacilli ., Methods: 109 samples were isolated from national domestic dairy products in the laboratory of Center for life sciences. After screaning isolates for probiotic properties, a highly active Lactobacillus spp strain was chosen.Genomic DNA was extracted according to the manufacturing protocol (Wizard® Genomic DNA Purification Kit). The Lactobacillus rhamnosus strain was identified as the highly active Lactobacillus strain accoridng to its morphological, cultural, physiological, and biochemical properties, and a genotypic analysis., Results: The genome of Lactobacillus rhamnosus was sequenced using the Roche 454 GS FLX (454 GS FLX) platforms. The initial draft assembly was prepared from 14 large contigs (20 all contigs) by the Newbler gsAssembler 2.3 (454 Life Sciences, Branford, CT)., Conclusion: A full genome-sequencing of selected strains of lactic acid bacteria was made during the study.

Two blind source separation methods (Independent Component Analysis and Non-negative Matrix Factorization), developed initially for signal processing in engineering, found recently a number of applications in analysis of large-scale data in molecular biology. In this short review, we present the common idea behind these methods, describe ways of implementing and applying them and point out to the advantages compared to more traditional statistical approaches. We focus more specifically on the analysis of gene expression in cancer. The review is finalized by listing available software implementations for the methods described., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Many genome-scale studies in molecular biology deliver results in the form of a ranked list of gene names, accordingly to some scoring method. There is always the question how many top-ranked genes to consider for further analysis, for example, in order creating a diagnostic or predictive gene signature for a disease. This question is usually approached from a statistical point of view, without considering any biological properties of top-ranked genes or how they are related to each other functionally. Here we suggest a new method for selecting a number of genes in a ranked gene list such that this set forms the Optimally Functionally Enriched Network (OFTEN), formed by known physical interactions between genes or their products. The method allows associating a network with the gene list, providing easier interpretation of the results and classifying the genes or proteins accordingly to their position in the resulting network. We demonstrate the method on four breast cancer datasets and show that 1) the resulting gene signatures are more reproducible from one dataset to another compared to standard statistical procedures and 2) the overlap of these signatures has significant prognostic potential. The method is implemented in BiNoM Cytoscape plugin (http://binom.curie.fr).