Cystic fibrosis (CF) is a hereditary disease that leads to impaired functioning of chloride channels in cells, and, as a result, to a decrease in the viscoelastic properties of the secretion of all exocrine glands. Cystic fibrosis is the result of mutations in the cystic fibrosis transmembrane conductance regulator ( CFTR ) gene, which encodes the CFTR protein. In this study, induced pluripotent stem cells (iPSCs) were obtained from the skin fibroblasts of a patient with a homozygous mutation F508del CFTR (NM_000492.3(CFTR):c.1521_1523del). This deletion is the most common for cystic fibrosis. The resulting iPSC line had a normal karyotype, retained the original genotype, and also demonstrated the presence of pluripotency markers (OCT4, SOX2, NANOG, SSEA4, TRA-1-60) and the ability to differentiate into derivatives of three germ layers.

Long QT syndrome is a rare ion channel cardiac disorder, the main manifestations of which are prolongation of the QT interval on the ECG and ventricular arrhythmias, which can cause sudden cardiac death at a young age. Diagnosis and treatment of this syndrome is an urgent problem, since the disease is heterogeneous and effective therapy requires molecular genetic diagnosis to accurately determine the type of this pathology. This review discusses clinical and genetic characteristics of different types of congenital long QT syndrome.

Background. Approximately 5–10 % of cases of Parkinson’s disease (PD) are monogenic, in other cases the pathology has a multifactorial etiology. One of recognized pathogenetic pathways of PD is mitochondrial dysfunction, in particular the accumulation of damage in mitochondrial DNA. Hence, the genes of DNA repair proteins are promising candidate genes for multifactorial forms of PD.The aim. To study the involvement of genes of DNA repair proteins in the development of Parkinson’s disease.Materials and methods. The associative analysis was carried out while comparing a group of patients with PD (n = 133) with a Tomsk population sample (n = 344). SNaPshot analysis was used to study 8 SNPs in genes of DNA repair proteins (rs560191 (TP53BP1); rs1805800 and rs709816 (NBN); rs473297 (MRE11A); rs1189037 and rs1801516 (ATM); rs1799977 (MLH1); rs1805321 (PMS2)).Results. Common alleles and homozygous rs1801516 genotypes in the ATM gene predispose the development of PD (odds ratio (OR) – 3.27 (p = 0.000004) and OR = 3.46 (p = 0.00008) for risk alleles and genotype respectively) and rs1799977 in the MLH1 gene (OR = 1.88 (p = 0.0004) and OR = 2.42 (p = 0.00007) respectively); heterozygotes have a protective effect (OR = 0.33 (p = 0.0007) and OR = 0.46 (p = 0.0007) for ATM and MLH1, respectively). The rare rs1805800 allele in the NBN gene (OR = 1.62 (p = 0.019)) and a homozygous genotype for it (OR = 2.28 (p = 0.016)) also predispose to PD. Associations with PD of the ATM, MLH1, NBN genes were revealed for the first time.Conclusion. Mitochondrial dysfunction is one of the key factors in the pathogenesis of PD, while at least two of the three protein products of associated genes are involved in the development of mitochondrial dysfunction. Accordingly, it can be assumed that associated genes are involved in the pathogenesis of PD precisely through mitochondrial dysfunction.

Xenobiotic metabolism system in the current populations is involved in the biotransformation of a wide range of endogenous substrates and various xenobiotics, which can contribute to developing the diseases of various organ systems, and, in some cases, comorbid conditions where increased biotransformation system activity is observed. In this regard, it is of great interest to study the involvement of polymorphism in xenobiotic metabolism genes in the development of both isolated pathology and various comorbid conditions. Aim . The goal of study was to investigate the involvement of rs4244285 in the CYP2C19 gene in the development of isolated pathology and comorbidities. Material and Methods. The frequencies of alleles and genotypes were studied in groups of patients with comorbid conditions including groups of coronary artery disease (CAD) with hypertension (HTN) (CAD_HTN, n = 133) and bronchial asthma (BA) with HTN (BA_HTN, n = 178), in group of isolated BA ( n = 135), and in the population sample of the city of Tomsk ( n = 377). Association analysis covered three initial groups of patients (CAD, BA, and BA_HTN) and subgroups assigned based on the presence of absence of HTN diagnosis taking into account comorbid conditions both in patient samples and in population control. Results and Discussion. The study demonstrated the predisposing eff ect of GA genotype on the development of comorbid BA and HTN (OR = 1.94, p = 0.038) and comorbid CAD and HTN (OR = 2.26, p = 0.009) compared to isolated BA. The AA genotype was observed 3.98 times less often in HTN patients than in normotensive individuals. However, the diff erences did not reach the level of statistical signifi cance due to the low occurrence of this genotype. Conclusion . The obtained results may be explained by the involvement of CYP2C19 -metabolites of arachidonic acid in the regulation of vascular tone, which requires further study.

The study aimed to search for mutations in the ATP7B gene using massively parallel sequencing in patients with Wilson disease in the Tomsk region. For 42 patients with suspected Wilson's disease (aged from 1 to 33 years) was performed molecular genetic analysis. Enrichment of the interest genome regions was carried out by the long-range PCR. DNA libraries with ligated adapters were constructed with Nextera DNA Flex (Illumina, USA) kit. Sequencing was performed on the Illumina MiSeq platform (Illumina, USA). As a result of this work, we identified 9 pathogenic genetic variants. All variants were previously described in the literature and were found in patients with Wilson's disease. Five missense mutations, one splice site mutation, and 3 frameshift mutations were identified. In patients with Wilson's disease in the Tomsk region, the most common variant was c.3207C>A, this variant is the most common both in the Russian Federation and in other European populations. Also, a pathogenic variant c.3036dupC was found, which is probably endemic to the Russian Federation.

Хронический вирусный гепатит С (ХВГС) является многофакторным заболеванием со сложной генетической компонентой. В настоящем исследовании была изучена вовлеченность гена PMS2 в развитие ХВГС и прогрессирование фиброза до цирроза печени. Проанализированы частоты аллелей и генотипов rs1805321 в гене PMS2 у пациентов с ХВГС (n=150) и популяционной выборке г. Томска (n=345). Установлена ассоциация изученного маркера с ХВГС: к развитию патологии предрасполагают аллель С (p=0,00005) и генотип СС (p=0,013), генотип TT является протективным (p=0,00002). Показано, что аллель С предрасполагает к развитию цирроза печени (p=0,038). Изученный полиморфный вариант может также влиять на темп прогрессирования фиброза печени при ХВГС. Chronic viral hepatitis C (HCVC) is a multifactorial disease with a complex genetic component. The present study examined the involvement of the PMS2 gene in the development of HCVC and the progression of fibrosis to cirrhosis. The frequencies of alleles and genotypes of rs1805321 in the PMS2 gene were analyzed in patients with chronic hepatitis C (n=150) and in a population samples from the Tomsk (n=345). The association of the studied marker with HCVC was established: the C allele (p=0.00005) and the CC genotype (p=0.013) predispose to the development of pathology, the TT genotype is protective (p=0.00002). Allele C has been shown to predispose to the development of liver cirrhosis (p = 0.038). The studied SNP may also affect the rate of progression of liver fibrosis in HCVC.

The "Mendelian code" hypothesis postulates a relationship between Mendelian (monogenic) and common pathologies. In this hypothesis, polymorphisms in the genes of Mendelian diseases may have a significant contribution to predisposition to common diseases in which the same biochemical pathways may be involved. In this review a group of genes encoding various proteins participating in the DNA repair, with a particular focus on the BRCA1-associated genome surveillance complex (BASC), is presented through the prism of the "Mendelian code" hypothesis. Here we discuss (1) their main functions in the repair of DNA double-strand breaks (ATM, MRE11, NBN, RAD50, BRCA1, and BLM) and mismatch repair (MSH2, MSH6, MLH1, PMS2, RF-C, and PCNA); (2) the mitochondrial involvement of these proteins; (3) the involvement of BASC proteins in the development of an adaptive immune response. For 13 out of 16 BASC protein encoding genes, mutations leading to monogenic diseases have already been described; for 11, there are associations with common diseases or individual biological processes. Patients with mutations in the genes of the BASC complex and patients with severe combined immunodeficiency share similar symptoms. Polymorphisms within DNA repair genes may play a role in the development of common diseases through the involvement of the immune response. The pleiotropic effects of these genes suggest their participation in the development of various conditions, both in health and pathology.

Wilson's disease is a rare autosomal recessive disorder of copper metabolism. The copper accumulation in the viscera appears due to the functional impairment of copper-transporting ATPase, which is encoded by the ATP7B gene. In this study, PBMCs of a patient with two ATP7B mutations were reprogrammed. The first mutation is a missense mutation p.H1069Q, which is the most frequent mutation in the human population. At the same time, the second one is a frameshift mutation p.Lys1013fs. The generated iPSC line had a normal karyotype, maintained the original genotype, expressed pluripotency markers, and demonstrated the ability to differentiate into derivatives of the three germ layers.

Болезнь Вильсона-Коновалова - редкое аутосомно-рецессивное заболевание, которое характеризуется патологическим накоплением меди в печени, головном мозге и других тканях. Дифференциальная диагностика болезни Вильсона-Коновалова представляет собой сложную задачу вследствие выраженной гетерогенности клинических проявлений. Это подчеркивает важность разработки как новых методов диагностики, так и усовершенствования существующих. В рамках настоящего исследования было проведено сравнение клинической диагностики заболевания с результатами молекулярно-генетических исследований. Проанализировано 42 пациента с подозрением на болезнь Вильсона-Коновалова. Произведена оценка значения биохимических показателей метаболизма меди (концентрация церулоплазмина, щелочной фосфатазы, общего билирубина, АСТ, АЛТ сыворотки крови, содержание меди в печени, экскреция меди с мочой) согласно Лейпцигской количественной шкале. Для молекулярно-генетического анализа использовали геномную ДНК. Обогащение интересуемых регионов генома проводилось с помощью ПЦР длинных фрагментов. Для подготовки ДНК библиотек был использован набор Nextera DNA Flex (Illumina, США). Секвенирование проводилось на приборе Illumina MiSeq (Illumina, США). В результате исследования в 62,5% случаев у пациентов, направленных на подтверждение диагноза (по Лейпцигской количественной шкале), были найдены мутации в гене ATP7B, что подтверждает ценность комплексной диагностики по Лейпцигской количественной шкале с учетом клинической симптоматики и лабораторных показателей метаболизма меди. Wilson’s disease is a rare autosomal recessive disorder characterized by abnormal accumulation of copper in the liver, brain, and other tissues. Wilson’s disease differential diagnosis is a difficult task due to the pronounced clinical heterogeneity. This emphasizes the importance of developing both new diagnostic methods and improving existing ones. As part of this study, we compared clinical diagnostics with the results of molecular genetic studies. We analyzed 42 patients with suspected Wilson’s disease. The biochemical parameters copper metabolism values were assessed (serum ceruloplasmin concentration, liver copper content, urinary copper excretion, alkaline phosphatase, total bilirubin, AST, ALT) according to the Leipzig quantitative scale. We used genomic DNA for molecular genetic analysis. Regions of interest in the genome was enriched using long-range PCR. The Nextera DNA Flex kit (Illumina, USA) was used to prepare DNA libraries. Sequencing was performed on an Illumina MiSeq device (Illumina, USA). As a result of the study, in 62.5% of cases in patients aimed at confirming the diagnosis (according to the Leipzig quantitative scale), we found mutations in the ATP7B gene, which confirms the value of a comprehensive diagnosis according to the Leipzig quantitative scale, taking into account the clinical symptoms and copper metabolism laboratory parameters.

For more than 100 years of existence of Wilson–Konovalov disease as an independent nosological form, the etiology and pathogenesis of this disease have been studied from different points of view—both clinical and genetic. However, to this day, new information is emerging not only about mutations in the ATP7B gene itself but also about modifying factors affecting the clinical picture of the disease. From a genetic point of view, the influence of modifier genes is undeniable, because owing to their action (protective or compensatory), some forms of Wilson–Konovalov disease can be explained and it is possible to further use this knowledge in the framework of personalized patient treatment. In this review, the authors consider the influence of various modifiers (intra- and extra-gene) on the course and manifestation of the clinical forms of Wilson–Konovalov disease. The authors show the possible mechanisms for the occurrence of milder or more severe forms of Wilson–Konovalov disease with the participation of certain genes.

Using massively parallel sequencing, the COL1A1 and COL1A2 genes were analyzed in 16 patients from 10 families with osteogenesis imperfecta types I, III, and IV. To analyze the mutations in these genes, a panel of primers was developed for sequencing the complete gene sequence. As a result of the work, 10 mutations were revealed: six of them are in the COL1A1 gene, four mutations in the COL1A2 gene. All mutations, except one, were previously described in the literature and were found in patients with various types of osteogenesis imperfecta. Missense mutations were identified in five families, nonsense mutations in two families, splice site mutations in two cases, and a frameshift mutation in one patient. Unique mutations that were not repeated in unrelated patients were found in all families. The revealed high heterogeneity of the spectrum of mutations in the COL1A1 and COL1A2 genes in osteogenesis imperfecta indicates the effectiveness of using MPS-based methods for the diagnosis of this pathology.

Гены белков репарации ДНК интересны с точки зрения их роли в формировании многофакторных заболеваний. Нами изучена изменчивость 8 SNP в 6 генах белков репарации ДНК в разных возрастных когортах жителей г. Томска. Для rs473297 в гене MRE11 выявлены возраст-зависимые изменения частот аллелей и генотипов: для старшей возрастной когорты зарегистрированы различия по частотам аллелей и генотипов как с младшей когортой (p=0,04 и p=0,047 соответственно), так и с долгожителями (p=0,02 и p=0,047 соответственно). Аллель T rs473297 ассоциирован, с одной стороны, с долгожительством (p=0,02 за счет генотипов TT и GT), с другой - со смертностью от сердечно-сосудистых заболеваний в возрасте до 55 лет (только генотипы TT, p=0,03). То есть, rs473297 в гене MRE11 может быть вовлечен в определение продолжительности жизни через селективную выживаемость носителей разных генотипов, больных сложно-наследуемыми заболеваниями. Genes of DNA repair proteins are interesting from the point of view of involvement of formation of common diseases. We studied variability of 8 SNP in the six DNA repair proteins genes in different age cohorts of residents of Tomsk. For rs473297 (MRE11), age-dependent changes alleles and genotypes frequencies were identified: for the older age cohort of the population sample, differences in alleles and genotypes frequencies were recorded with both the younger cohort (p=0.04 and p=0.047, respectively) and long-livers (p=0.02 and p=0.047, respectively). Allele T rs473297 is associated, on the one hand - with longevity (p=0.02, due to genotypes TT and GT), on the other - with mortality from cardiac death under 55 years of age (only homozygotes TT, p=0.03). That is, rs473297 (MRE11) may be involved in determining lifetime through selective survival of carriers of different genotypes suffering from common diseases.

Проведен поиск мутаций в генах KCNQ1, KCNH2 и SCN5A методом массового параллельного секвенирования (МПС) у 10 пациентов из 8 семей с диагнозом «синдром удлиненного интервала QT» (СУИQT). Для пробоподготовки использована методика целевого обогащения участков ДНК, относящихся к исследуемым генам. В результате проведенной работы выявлено 8 мутаций: 5 из них расположены в гене KCNQ1, 2 мутации - в гене KCNH2, 1 мутация - в гене SCN5A. Во всех случаях были найдены уникальные мутации, не повторяющиеся у неродственных пациентов. Результаты проведенной работы указывают на эффективность использования таргетных панелей для поиска генетических аномалий при СУИQT. We searched for mutations in the KCNQ1, KCNH2 and SCN5A genes using mass parallel sequencing (MPS) in 10 patients from 8 families with a diagnosis of “long QT syndrome” (LQTS). For sample preparation, we used the targeted enrichment of DNA regions method related to the studied genes. As a result of the work, 8 mutations were revealed: 5 of them are located in the KCNQ1 gene, 2 mutations in the KCNH2 gene, 1 mutation in the SCN5A gene. In all cases, we found unique mutations that did not recur in unrelated patients. The results of this work indicate the effectiveness of using targeted panels to search for genetic abnormalities in LQTS.

Изучение генетических особенностей дистропных заболеваний (в том числе, астмы и туберкулеза), определяющих формирование взаимоисключающих фенотипов на клиническом уровне, важно для лучшего понимания их патогенеза. Цель настоящего исследования заключалась в оценке значимости генетического полиморфизма гена NBN в формировании предрасположенности к астме и туберкулезу. Изучена изменчивость rs1805800 и rs709816 гена NBN в выборках больных бронхиальной астмой (БА), туберкулезом (ТБ) и популяционной выборке г. Томска (ПВ), общая выборка составила 683 человека. Показано разнонаправленное изменение частот аллелей, генотипов, сочетаний генотипов по rs1805800 и rs709816 гена NBN между группами больных БА и ТБ по сравнению с популяционной выборкой. Для развития БА генотип CT rs1805800 обладает рисковым (OR=1,66, χ2=5,41, p=0,02); а генотипа СС - протективным (OR=0,57, χ2=5,57, p=0,018) эффектом. Статистически значимые различия между группами БА и ТБ выявлены также по частотам сочетаний генотипов rs1805800/rs709816 в гене NBN (χ2 = 12,88; p=0,045). The research of genetic features of dystropic diseases (including asthma and tuberculosis) that determine the formation of mutually exclusive phenotypes at the clinical level is important for a better understanding of their pathogenesis. The aim of this study was to assess the significance of the genetic polymorphism of the NBN gene in the formation of a predisposition to asthma and tuberculosis. The variability of rs1805800 and rs709816 of the NBN gene in the samples of patients with bronchial asthma (BA), tuberculosis (TB) and the population sample of Tomsk (PV) was studied, the total sample was 683 people. The different-directional change of frequencies of alleles, genotypes, combinations of genotypes by rs1805800 and rs709816 of the NBN gene between groups of patients with BA and TB compared to the population sample is shown. For the development of BA, the genotype CT rs1805800 is risky (OR=1.66, χ2=5.41, p=0.02); And the SS genotype is a protective (OR=0.57, χ2=5.57, p=0.018) effect. Statistically significant differences between BA and TB groups are also revealed by the frequencies of combinations of the genotypes rs1805800/rs709816 in the NBN gene (χ2=12.88; p=0,045).

Болезнь Вильсона-Коновалова (БВК) - аутосомно-рецессивное заболевание, развивающееся вследствие накопления меди в организме при повреждениях гена АТР7В. В настоящем исследовании проводился поиск мутаций в этом гене методом массового параллельного секвенирования у больных с БВК. Для целевого обогащения интересуемых регионов была разработана панель праймеров для ПЦР длинных фрагментов. У 6 пациентов из 12 проанализированных выявлены патогенные и вероятно патогенные варианты нуклеотидной последовательности гена АТР7В. Полученные результаты указывают на то, что разработанный метод таргетного массового параллельного секвенирования позволяет эффективно выявлять мутации в гене ATP7B. Wilson’s disease is an autosomal recessive disease that develops as a result of the accumulation of copper in the organism when the ATP7B gene is damaged. The present study searched for mutations in this gene using massively parallel sequencing in patients with Wilson’s disease. For targeted enrichment of the regions of interest, a primer panel for PCR of long fragments was developed. In 6 patients out of 12 analyzed, pathogenic and probably pathogenic variants of the nucleotide sequence of the ATP7B gene were identified. The obtained results indicate that the developed method of targeted massively parallel sequencing allows efficient detection of mutations in the ATP7B gene.