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The MinION system (Oxford Nanopore Technologies, United Kingdom) was used to directly sequence genomic DNAs of two recombinant Escherichia coli strains. One strain carried a plasmid with the gene for M.HpaII DNA methyltransferase, which methylates the second cytosine in a CCGG site. The other strain contained M.HspAI DNA methyltransferase, which modifies the central cytosine in a GCGC sequence. Either enzyme methylates cytosine to produce 5-methylcytosine. The presence of 5-methylcytosine was found to be detectable with high accuracy when DNA is sequenced at high coverage. In particular, 98.9% of the GCGC sites were identified as methylated at the first cytosine when DNA from the strain carrying the cloned M.HspAI gene was sequenced at 1300× coverage. Only 0.09% of the remaining tetranucleotides with a central CpG dinucleotide were false positives and were identified as methylated at the central cytosine. For the strain with M.HpaII, 91.3% of all CCGG sites were identified as methylated in a set of positions covered by more than 700 reads and only 0.13% of the other tetranucleotides with a central CpG dinucleotide were identified as sites with 5-methylcytosine in the second position. Thus, coverage of at least 700–1000× is necessary for accurately measuring 5-methylcytosine and eliminating false-positive results when using the method.

Cultured hydrocarbon-oxidizing bacteria have been isolated for the first time from bacterioplankton in urban Lake Beloye (Moscow). The taxonomic positions of two bacterial strains (2012B and 2012C) isolated from this lake have been determined. Lipids of the strain 2012B comprise C14:0–C19:0 fatty acids, the most abundant of them being C15:0 (54%), C16:0 (17%), C17:0 (10%), and 10-methyl С18:0 (3.5%). Lipids of the strain 2012C comprise C14:0–C19:0 fatty acids, the most abundant of them being C15:0 (45%), C16:0 (32%), and C17:0 (9%). A phylogenetic analysis of strain 2012B is performed using the nucleotide sequences of the 16S rRNA (KP779654.1) and alkB (KR422620.1) genes and the strain is identified as a typical member of the genus Rhodococcus spp. (Actinobacteria, Nocardiaceae). The combination of molecular identification and analysis of biochemical and physiological properties makes it possible to identify strain 2012B as Rhodococcusqingshengii 2012B. A phylogenetic analysis of strain 2012C is performed using the nucleotide sequences of 16S rRNA (MG966152) and shows the highest identity (99.57%) of strain 2012С with Pseudomonas psychrotolerans and Pseudomonas oryzihabitans

Congenital core myopathies are a clinically and genetically heterogenous group of congenital myopathies that share a specific histopathological feature: areas of reduced oxidative activity in muscle fibers. The relationship between clinical, genetic and morphological characteristics of this group of disorders remains understudied. The aim of this work was to compare clinical presentations and morphological phenotypes of patients with congenital myopathies/myodystrophy to the data yielded by massively parallel exome sequencing. Eight children were included in the study: 2 boys and 6 girls aged 3 to 14 years. Their biopsy material was analyzed by light and electron microscopy. Sequencing was performed on HiSeq2500. Mutations were detected in 7 (87.5%) of 8 participants. Six children had 8 mutations in the genes associated with congenital core myopathies; one patient had 2 mutations in the LAMA2 gene implicated in merosin-deficient muscular dystrophy. The proportions of patients with mutations in RYR1 and SEPN1 were equal (42.86%). Of 10 detected mutations, 3 had not been previously described, including c.7561G>A in RYR1, c.485C>A in SEPN1 and p.Cys1136Arg in LAMA2. The clinical and morphological features of core myopathies suggest that genetic causes of this group of disorders should not be limited to RYR1 and SEPN1 genes only. This necessitates the search for and the study of other genes implicated in congenital myopathies or myodystrophy using state-of-the-art molecular genetic tools.

Body mass index (BMI) is a highly heritable polygenic trait. It is also affected by various environmental and behavioral risk factors. We used a BMI polygenic risk score (PRS) to study the interplay between the genetic and environmental factors defining BMI. First, we generated a BMI PRS that explained more variance than a BMI genetic risk score (GRS), which was using only genome-wide significant BMI-associated variants (R2= 13.1% compared to 6.1%). Second, we analyzed interactions between BMI PRS and seven environmental factors. We found a significant interaction between physical activity and BMI PRS, even when the well-known effect of theFTOregion was excluded from the PRS, using a small dataset of 6,179 samples. Third, we stratified the study population into two risk groups using BMI PRS. The top 22% of the studied populations were included in a high PRS risk group. Engagement in self-reported physical activity was associated with a 1.66 kg/m2decrease in BMI in this group, compared to a 0.84 kg/m2decrease in BMI in the rest of the population. Our results (i) confirm that genetic background strongly affects adult BMI in the general population, (ii) show a non-linear interaction between BMI genetics and physical activity, and (iii) provide a standardized framework for future gene-environment interaction analyses.

Copy-number variants (CNVs) are an important part of human genetic variation. They can be benign or can play a role in human disease by creating dosage imbalances and disrupting genes and regulatory elements. Accurate identification and clinical annotation of CNVs is essential, however, manual evaluation of individual CNVs by clinicians is challenging on a large scale. Here, we present ClassifyCNV, an easy-to-use tool that implements the 2019 ACMG classification guidelines to assess CNV pathogenicity. ClassifyCNV uses genomic coordinates and CNV type as input and reports a clinical classification for each variant, a classification score breakdown, and a list of genes of potential importance for variant interpretation. We validate ClassifyCNV’s performance using a set of known clinical CNVs and a set of manually evaluated variants. ClassifyCNV matches the pathogenicity category for 81% of manually evaluated variants with the significance of the remaining pathogenic and benign variants automatically determined as uncertain, requiring a further evaluation by a clinician. ClassifyCNV facilitates the implementation of the latest ACMG guidelines in high-throughput CNV analysis, is suitable for integration into NGS analysis pipelines, and can decrease time to diagnosis. The tool is available at https://github.com/Genotek/ClassifyCNV.

Background Epilepsy with intellectual disability limited to females (Epileptic encephalopathy, early infantile, 9; EIEE9) is a rare early infantile epileptic encephalopathy characterized by an unusual X-linked inheritance: females with heterozygous mutations are affected, while hemizygous males are not. Case presentation We describe the clinical and molecular characteristics of 2 Russian patients with EIEE9 (females, ages 3 years and 7 years). In these patients seizures developed at the age of 3 years. Additionally, for our patients and for cases described in the literature we searched for a possible relationship between the type and localization of the mutation and the EIEE9 clinical phenotype. Conclusions We identified two novel PCDH19 mutations in EIEE9 patients: a missense mutation in exon 1 (c.1236C > A, p.Asp412Glu) and a frameshift in exon 3 (c.2386_2387insGTCT, p.Thr796fs). We conclude that the age of seizure onset and the presence of intellectual disability may depend not on the type and localization of PCDH19 mutations, but on the X-inactivation status. The study also highlights the need to screen for EIEE9 among young female epilepsy patients.

One of the most promising areas of research into the biological underpinnings of depression is genetic studies. However, the absence of generally accepted phenotyping methods leads to the difficulties in generalizing their results due to the heterogeneity of the samples. Thus, the development of a reliable and convenient phenotyping method that allows large sample sizes to be included in studies remains a top priority for the further development of genetic studies of depression.The aim of this study was to evaluate the applicability of the online version of the depression subscale of Hospital Anxiety and Depression Scale (HADS-D) for depression phenotype screening in the general population. Using online HADS-D we performed screening of depressive symptoms and compared results with known population patterns of depression.We conducted an online survey of 2610 Russian-speaking respondents over the age of 18. The overall HADS-D score was higher in women (p=0.003), in individuals under 30 y.o compared to participants over 42 y.o. (p=0.004) and in individuals reporting cardiovascular diseases (CVD) symptoms (pLinear regression showed that the presence of CVD leads to higher HADS-D scores (pThese results are consistent with the known data on the association of sex, age, and the presence of CVD with the prevalence of depression. The online version of HADS-D, given the ease of its usage, can be regarded as an effective tool for phenotyping depression in the general population.

Non-invasive prenatal testing (NIPT) for aneuploidy on Chromosomes 21 (T21), 18 (T18) and 13 (T13) is actively used in clinical practice around the world. One of the limitations of the wider implementation of this test is the high cost of the analysis itself, as high-throughput sequencing is still relatively expensive. At the same time, there is an increasing trend in the length of reads yielded by sequencers. Since extracellular DNA is short, in the order of 140&ndash, 160 bp, it is not possible to effectively use long reads. The authors used high-performance sequencing of cell-free DNA (cfDNA) libraries that went through additional stages of enzymatic fragmentation and random ligation of the resulting products to create long chimeric reads. The authors used a controlled set of samples to analyze a set of cfDNA samples from pregnant women with a high risk of fetus aneuploidy according to the results of the first trimester screening and confirmed by invasive karyotyping of the fetus using laboratory and analytical approaches developed by the authors. They evaluated the sensitivity, specificity, PPV (positive predictive value), and NPV (negative predictive value) of the results. The authors developed a technique for constructing long chimeric reads from short cfDNA fragments and validated the test using a control set of extracellular DNA samples obtained from pregnant women. The obtained sensitivity and specificity parameters of the NIPT developed by the authors corresponded to the approaches proposed earlier (99.93% and 99.14% for T21, 100% and 98.34% for T18, 100% and 99.17% for T13, respectively).

Background Neuronal ceroid lipofuscinoses (NCLs) are a group of neurodegenerative disorders characterized by an accumulation of lipofuscin in the body's tissues. NCLs are associated with variable age of onset and progressive symptoms including seizures, psychomotor decline, and loss of vision. Methods We describe the clinical and molecular characteristics of four Russian patients with NCL (one female and three males, with ages ranging from 4 to 5 years). The clinical features of these patients include cognitive and motor deterioration, seizures, stereotypies, and magnetic resonance imaging signs of brain atrophy. Exome sequencing was performed to identify the genetic variants of patients with NCL. Additionally, we tested 6,396 healthy Russians for NCL alleles. Results We identified five distinct mutations in four NCL‐associated genes of which two mutations are novel. These include a novel homozygous frameshift mutation in the CLN6 gene, a compound heterozygous missense mutation in the KCTD7 gene, and previously known mutations in KCTD7, TPP1, and MFSD8 genes. Furthermore, we estimated the Russian population carrier frequency of pathogenic and likely pathogenic variants in 13 genes associated with different types of NCL. Conclusion Our study expands the spectrum of mutations in lipofuscinosis. This is the first study to describe the molecular basis of NCLs in Russia and has profound and numerous clinical implications for diagnosis, genetic counseling, genotype–phenotype correlations, and prognosis., 5 distinct mutations were identified in 4 NCL‐caused genes, of which two mutations are novel. Also carrier frequency of pathogenic and likely pathogenic variants in 13 genes associated with different types of NCL were estimated in Russian population.

Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly, which is used for the analysis of genomic rearrangements, chromosome phasing, and reconstructing genomes without a reference, require solving tasks of high computational complexity. Here we demonstrate a method for solving genome assembly tasks with the use of quantum and quantum-inspired optimization techniques. Within this method, we present experimental results on genome assembly using quantum annealers both for simulated data and the $\phi$X 174 bacteriophage. Our results pave a way for an increase in the efficiency of solving bioinformatics problems with the use of quantum computing and, in particular, quantum annealing. We expect that the new generation of quantum annealing devices would outperform existing techniques for {\it de novo} genome assembly. To the best of our knowledge, this is the first experimental study of de novo genome assembly problems both for real and synthetic data on quantum annealing devices and quantum-inspired techniques., Comment: 9 pages, 4 figures

The rapid expansion of diagnostic technologies in general and of the genome-wide association studies method in particular brings us closer to the understanding of the etiopathogenetic fundamentals of endogenous mental disorders. The amount of accumulated experience in genome-wide association studies allows one to assess the importance of specific genetic markers in the development of the diseases of interest. The introduction of screening systems and the assessment of disease prognosis is yet to be implemented, due to conceptual and methodological contradictions. The present review aims at analyzing the current progress in the field of genetic studies of schizophrenia spectrum disorders. The prospects and limitations of existing methods and the obstacles to the efficient translational application of the achievements of GWAS and candidate gene studies are discussed. Along with the still poor understanding of the etiology and pathogenesis of schizophrenia spectrum disorders, such issues as the ongoing debate regarding the correct classification, as well as the large degree of symptom heterogeneity within this group of conditions, remain a cornerstone in biologicalresearch. A more accurate approach to phenotyping, including the application of deep phenotyping techniques, is required to form more homogenous samples for future genome-wide association and candidate gene studies of schizophrenia spectrum disorders.

The review is devoted to the analysis of the current state of pharmacogenetic research and their use in psychiatric practice. The main genes responsible for the pharmacodynamics and pharmacokinetics of drugs used in psychiatry are listed. Foreign pharmacogenetic clinical recommendations and progress on their implementation in medical practice in various countries of Europe and the USA are analyzed. The need to create Russian clinical guidelines on pharmacogenomics to improve the effectiveness of patient care and to implement a personalized approach to therapy is discussed.Статья представляет собой обзор, посвященый современному состоянию фармакогенетических исследований и возможностям их применения в области психиатрии. Перечислены основные гены, ответственные за фармакодинамику и фармакокинетику лекарственных средств, применяемых в клинической психиатрии. Представлен анализ соответствующих зарубежных фармакогенетических клинических рекомендаций и результатов их внедрению в медицинскую практику в различных странах Европы и США. Поставлен вопрос о необходимости создания российских клинических рекомендаций по фармакогеномике для повышения эффективности лечения пациентов и осуществления персонифицированного подхода к терапии.

Background Liddle syndrome is a monogenic disease with autosomal dominant inheritance. Basic characteristics of this disease are hypertension, reduced concentration of aldosterone and renin activity, as well as increased excretion of potassium leading to low level of potassium in serum and metabolic alkalosis. The cause of Liddle syndrome is missense or frameshift mutations in SCNN1A, SCNN1B, or SCNN1G genes that encode epithelial sodium channel subunits. Case presentation We describe a family with Liddle syndrome from Russia. 15-year-old proband has arterial hypertension, hypokalemia, hyporeninemia, metabolic alkalosis, but aldosterone level is within the normal range. At 12 years of age, arterial hypertension was noticed for the first time. We identified novel frameshift mutation c.1769delG (p.Gly590Alafs) in SCNN1G, which encodes the γ subunit of ENaC in vertebrates. The father and younger sister also harbor this heterozygous deletion. Treatment with amiloride of proband and his sister did not normalize the blood pressure, but normalized level of plasma renin activity. Conclusions Our results expand the mutational spectrum of Liddle syndrome and provide further proof that the conserved PY motif is crucial to control of ENaC activity. Genetic analysis has implications for the management of hypertension, specific treatment with amiloride and counselling in families with Liddle syndrome.

Background Cutis laxa (CL) is a rare connective tissue disorder characterized by loose, redundant, inelastic and wrinkled skin. Patients develop a prematurely aged appearance. Inheritance can be autosomal dominant or autosomal recessive. The X-linked form is now classified in the group of copper transport diseases. Autosomal dominant CL is characterized by wrinkled, redundant and sagging, inelastic skin and in some cases is associated with internal organ involvement. Case presentation We report a familial case of autosomal dominant CL, which includes a 33-year-old woman and her 11-year-old son with dry, thin and wrinkled skin that appeared prematurely aged. No serious involvement of internal organs was found. In both patients, we identified novel heterozygous mutation c.2323delG (p.Ala775fs) in exon 34 of elastin transcript NM_001278939.1. Similar frameshift mutations in the last exons of elastin gene were previously reported in patients with autosomal dominant CL. Conclusions Our results show a novel frameshift mutation that was found in patients with cutis laxa. Exome sequencing is effective and useful technology for properly diagnosis of diseases with similar phenotype to ensure proper treatment is provided.

Liability to alcohol dependence is heritable, but little is known about its complex polygenic architecture. We performed a genome-wide association study (GWAS) of self-reported alcohol consumption in 1798 of Russian individuals. No SNP reached genome-wide significance for any alcohol drinking patterns: never drinking, everyday drinking, once per week drinking and once per month drinking. Polymorphisms in previously reported genes of KLB and AUTS2 were significant associated with everyday drinking and once per week drinking patterns, respectively. We also found associations of genes involved in nervous system function and mental disorders with some alcohol drinking patterns. This study identifies novel gene associations that should be the focus of future studies investigating the neurobiology of alcohol consumption.

Background Neuronal ceroid lipofuscinoses (NCLs) are the most common autosomal recessive neurodegenerative disorders in children. Clinical manifestations include progressive cognitive decline, motor impairment, ataxia, visual loss, seizures and early death. To date more than 440 NCL-causing mutations in 13 genes are known. Case presentation We report clinical and genetic characteristics of a 5-year-old girl affected by ceroid lipofuscinosis type 7 (NCL7). She had progressive motor and mental deterioration since the age of 2,5 years. Later she developed progressive vision loss, stereotypies, action myoclonus and epilepsy. By the age of 5 years she stopped walking. Based on symptoms, diagnosis of Rett syndrome was suggested, but no abnormalities were detected in MeCP2. We identified a novel homozygous mutation in MFSD8 gene (c.525 T > A, p.Cys175Ter). To our knowledge, this is the first report of MFSD8 gene mutation in a Russian patient with variant late-infantile NCL. Conclusions Our results enlarge mutational spectrum of ceroid lipofuscinosis type 7 and demonstrate tremendous diagnosis value of exome sequencing for pediatric NCLs. Also we confirmed that NCL should be suspected in patients with Rett-like phenotype at onset and negative MECP2 mutation.

Polymorphisms in ACTN3 and ACE genes were previously reported to be associated with power and endurance performance. We estimated the relationship between their population frequencies in several countries and FIFA World averaged rating (FWAR). The entropy was used as the measure of uncertainty. The FWAR distribution entropy (in nats) was 1.38. The FWAR conditional distribution entropy given ACTN3 RR and ACE II frequencies was 1.27 and 1.24, respectively. Almost same FWAR conditional entropy (1.25) was after adjustment on GDP. Population frequencies of polymorphisms in power and endurance performance genes might be a cause of high or low FWAR (low frequency -- less football players) or an effect of ethnic origin and geographical location of countries, related to GDP.

We aimed to develop a pipeline for the bioinformatic analysis and interpretation of NGS data and detection of a wide range of single-nucleotide somatic mutations within tumor DNA. Initially, the NGS reads were submitted to a quality control check by the Cutadapt program. Low-quality 3¢-nucleotides were removed. After that the reads were mapped to the reference genome hg19 (GRCh37.p13) by BWA. The SAMtools program was used for exclusion of duplicates. MuTect was used for SNV calling. The functional effect of SNVs was evaluated using the algorithm, including annotation and evaluation of SNV pathogenicity by SnpEff and analysis of such databases as COSMIC, dbNSFP, Clinvar, and OMIM. The effect of SNV on the protein function was estimated by SIFT and PolyPhen2. Mutation frequencies were obtained from 1000 Genomes and ExAC projects, as well as from our own databases with frequency data. In order to evaluate the pipeline we used 18 breast cancer tumor biopsies. The MYbaits Onconome KL v1.5 Panel ("MYcroarray") was used for targeted enrichment. NGS was performed on the Illumina HiSeq 2500 platform. As a result, we identified alterations in BRCA1, BRCA2, ATM, CDH1, CHEK2, TP53 genes that affected the sequence of encoded proteins. Our pipeline can be used for effective search and annotation of tumor SNVs. In this study, for the first time, we have tested this pipeline for NGS data analysis of samples from patients of the Russian population. However, further confirmation of efficiency and accuracy of the pipeline is required on NGS data from larger datasets as well as data from several types of solid tumors.Tsel'iu issledovaniia byla razrabotka i testirovanie protokola dlia bioinformaticheskoĭ obrabotki NGS-dannykh dlia éffektivnogo poiska mutatsiĭ v genome solidnykh opukholeĭ. Soglasno razrabotannomu protokolu na nachal'nom étape provodili otsenku kachestva prochteniĭ nukleotidov. Nukleotidy s kachestvom prochteniia nizhe 10 udaliali s 3¢-kontsa s pomoshch'iu programmy Cutadapt. Dalee prochteniia kartirovali na referensnyĭ genom hg19 (GRCh37.p13) s pomoshch'iu programmy BWA. Deduplikatsiiu ridov vypolniali spetsializirovannoĭ programmoĭ SAMtools. Dlia raspoznavaniia odnonukleotidnykh variantov primeniali MuTect. Kompleksno otsenivali funktsional'nyĭ éffekt mutatsiĭ na osnove algoritma, vkliuchaiushchego annotirovanie i otsenku patogennosti s pomoshch'iu programmnogo resheniia SnpEff, a takzhe analiza takikh baz dannykh, kak COSMIC, dbNSFP, Clinvar, OMIM. Dopolnitel'no dlia otsenki éffekta na funktsiiu kodiruemogo belka primeniali utility SIFT i Poly-Phen2. Informatsiiu o chastote mutatsiĭ poluchali na osnove dannykh proektov 1000 Genomes i ExAC, a takzhe sobstvennoĭ bazy dannykh chastot. Dlia provedeniia testirovaniia protokola byl proveden analiz 18 obraztsov biopsii opukholeĭ molochnoĭ zhelezy. Sekvenirovanie obraztsov provodili na platforme Illumina. Dlia targetnogo obogashcheniia kodiruiushchikh regionov genoma ispol'zovali nabor reagentov MYbaits Onconome KL v1.5 Panel (“MYcroarray,” SShA). Po rezul'tatam bioinformaticheskoĭ obrabotki dannykh sekvenirovaniia obnaruzheno mnozhestvo mutatsiĭ v genakh BRCA1, BRCA2, ATM, CDH1, CHEK2, TP53, v tom chisle mutatsii-draĭvery, okazyvaiushchie vliianie na aminokislotnuiu posledovatel'nost' kodiruemogo belka. Takim obrazom, predlagaemyĭ nami bioinformaticheskiĭ protokol pozvoliaet éffektivno vypolniat' avtomaticheskuiu obrabotku NGS-dannykh obraztsov opukholeĭ i obnaruzhivat' mutatsii. Dannyĭ protokol dlia bioinformaticheskoĭ obrabotki dannykh vpervye aprobirovan na vyborke obraztsov opukholeĭ iz rossiĭskoĭ populiatsii. Dlia podtverzhdeniia éffektivnosti i tochnosti predlagaemogo protokola v dal'neĭshem neobkhodimo testirovanie algoritma na dannykh sekvenirovaniia razlichnykh form opukholeĭ.

Depression is one of the leading causes of decreased quality of life and social functioning of patients. In the context of preventive medicine, the prevention of depression becomes a priority. To achieve the goals of prevention, it is necessary to identify specific population risk groups - individuals with a high genetic risk of depression. The paper describes the project aimed at developing a genetic test system based on polygenic risk scores (PRS) for depression, considering the multi-ethnicity and multicultural diversity of the Russian population. As a result of the study, data on the genetic architecture of depression (GWAS) and PRS for depression will be obtained for the first time. The emergence of a genetic test system developed in the study of the Russian population and in the conditions of a constant decrease in the cost of genetic research will allow an effective transition to preventive medicine in the area of mental health.Депрессия является одной из ведущих причин снижения качества жизни и социального функционирования пациентов. В рамках превентивной медицины профилактика депрессии становится приоритетным направлением. Для достижения задач профилактики необходимы возможности выявления в популяции групп риска — индивидуумов с высоким уровнем генетического риска развития депрессии. В статье описываются методология и дизайн проекта, направленного на разработку генетической тест-системы на основе полигенных шкал риска (PRS) развития депрессии с учетом полиэтничности и мультикультурального характера российской популяции. В результате выполнения исследования должны быть впервые получены данные о генетической архитектуре депрессии (методом GWAS) и выявлены полигенные шкалы риска (PRS) развития депрессии. Появление генетической тест-системы, разработанной при изучении российской популяции и в условиях постоянного снижения стоимости генетических исследований, позволит осуществить эффективный переход к развитию превентивной медицины в области психического здоровья.

Prediction of mutation pathogenicity and its effect on the phenotype is an important task of modern bioinformatics. This task is particularly difficult in regard to single nucleotide polymorphisms, as their effect is very hard to predict. Information on pathogenic mutations is provided by curated databases such as Online Mendelian Inheritance in Man (OMIM) and The Human Gene Mutation Database (HGMD) which include data from experimental works. However, as different authors interpret the term “mutation pathogenicity” differently, it is necessary to double-check data before using them. We have assessed HGMD database quality using the most common bioinformatic tools, namely, snpEff, polyphen2 and SIFT. Our study relied on the characteristics specific for harmless mutations: high frequency in a population, weak effect on amino acid sequence of a protein, low pathogenicity as computed by the utilities used in the study. As a result, we have identified clearly harmless variants among those in the mutation database, as well as ambiguous ones in which a mutation type depends on characteristics and tools used for the analysis.

Whole Exome Sequencing (WES) is a promising method in human genetics. Because the majority of pathogenic mutations that lead to the development of diseases are localized in exons and splice sites, WES could become a major tool for the diagnosis of diseases with a complex hereditary nature. This tool appears to be particularly useful for hereditary neurological diseases, such as autism spectrum disorders, Charcot-Marie-Tooth disease and others. In our review, we discuss the clinical application of WES, with special emphasis on the diagnosis of hereditary neurological diseases.В статье обзорного характера представлено развитие методов современной молекулярной генетики, которые могут быть применены в клинической практике. Это показано на примере полноэкзомного секвенирования - WES (Whole Exome Sequencing), которое представлено в следующих разделах: особенности метода полноэкзомного секвенирования, захвата экзома, применение в клинической практике, стратегия выявления патогенной мутации, диагностика психических расстройств аутистического спектра, диагностика болезни Шарко-Мари-Тута, применение в клинико-диагностических лабораториях.

Background: Rheumatoid arthritis (RA) is a multi-factor disease with a key role of genetic component in its genesis. Development of osteoporosis and articular destruction is attributed with overexpression of pro-infl ammatory cytokines and reduced production of anti-infl ammatory ones. In this work probable associations of IFN-γ, IL-1α, IL-1β, IL-4, IL-6, IL-10, IL-18 and TNFα alleles with rheumatoid arthritis were studied among Russian ethnic group. Methods: A total of 69 Russian ethnical group patients with RA (cases) and 133 healthy control individuals (controls) were genotyped for variants in 8 cytokines genes (IFN-γ, IL-1α, IL-1β, IL-4,IL-6, IL-10, IL-18 and TNFα). Individual genotype and haplotype frequencies were compared between cases and controls. Odd ratios were calculated with asymptotic 95% confi dence intervals and P values less than 0.05 were considered statistically signifi cant. Results: The distribution of studied alleles of cytokine genes in Russian population is similar to other European populations. Genotype, allele and haplotype frequencies were equally distributed between RA cases and controls for IFN-γ (rs2430561), IL-1α (rs1800587), (rs17561), IL-1β (rs1143627), (rs16944), (rs1143634), IL-10 (rs1800871), IL- 18 (rs1946518) and TNFα (rs361525). Meanwhile, signifi cant associations (р

Background Torque teno virus (TTV) is a circular, single-stranded DNA virus that chronically infects healthy individuals of all ages worldwide. There is a lot of data on the prevalence and genetic heterogeneity of TTV in healthy populations and in patients with various diseases now available. However, little is known about TTV load among healthy human population. In this study we analyzed TTV load in the group of 512 Russian elite athletes, who are supposed to be, by some standards, the healthiest part of the human population. Results The prevalence rate of TTV among the Russian Olympic Reserve members was 94% (for test sensitivity about 1000 genome equivalents per 1 ml of blood). Quantities varied from 103 (which corresponded to detection limit) to 1010 copies per 1 ml of blood, with median at 2.7 × 106 copies. Conclusion About 94% of healthy individuals in Russian population have more than 1000 TTV genome copies per 1 ml of blood. This result exceeds the previously published data, and can be explained by either more sensitive PCR test system or by higher TTV distribution in Russian population or both. TTV viral load neither depends on gender, nor age.

Background: Tumor development in the human colon is commonly accompanied by epigenetic changes, such as DNA methylation and chromatin modifications. These alterations result in significant, inheritable changes in gene expression that contribute to the selection of tumor cells with enhanced survival potential. Results: A recent high-throughput gene expression analysis conducted by our group identified numerous genes whose transcription was markedly diminished in colorectal tumors. One of these, the protein-tyrosine phosphatase receptor type R (PTPRR) gene, was dramatically downregulated from the earliest stages of cellular transformation. Here, we show that levels of both major PTPRR transcript variants are markedly decreased (compared with normal mucosal levels) in precancerous and cancerous colorectal tumors, as well in colorectal cancer cell lines. The expression of the PTPRR-1 isoform was inactivated in colorectal cancer cells as a result of de novo CpG island methylation and enrichment of transcription-repressive histone-tail marks, mainly H3K27me3. De novo methylation of the PTPRR-1 transcription start site was demonstrated in 29/36 (80%) colorectal adenomas, 42/44 (95%) colorectal adenocarcinomas, and 8/8 (100%) liver metastases associated with the latter tumors. Conclusions: Epigenetic downregulation of PTPRR seems to be an early alteration in colorectal cell transformation, which is maintained during the clonal selection associated with tumor progression. It may represent a preliminary step in the constitutive activation of the RAS/RAF/ MAPK/ERK signalling, an effect that will later be consolidated by mutations in genes encoding key components of this pathway., Molecular cancer, 8, ISSN:1476-4598