Цель исследования − оценить частоту и структуру хромосомных аномалий при исследовании абортивного материала с помощью SNP - хромосомного микроматричного анализа (ХМА). 2109 образцов ДНК, выделенной из ворсин хориона и тканей плодов, предоставленных на анализ при потере беременности, исследовано методом SNP-ХМА с использованием SNPолигонуклеотидных микроматриц CytoScan Optima (ThermoFisher Scientific, США)

Технологии секвенирования нового поколения (NGS) имеют важное значение в диагностике заболеваний нервной системы. Преимуществом их использования является широкий охват исследуемых генов, что позволяет повысить выявляемость причин в такой клинически и генетически гетерогенной группе заболеваний. Цель настоящей работы - определить эффективность секвенирования генома для выявления генетических причин у пациентов с вероятно наследственными заболеваниями нервной системы. В нашем исследовании секвенирование генома позволило выявить причину заболевания у 28,6% таких пациентов. При отрицательном результате анализа панели генов секвенирование генома позволило выявить причину заболевания у 9% пациентов. NGS-based technologies play an important role in the diagnosis of diseases of the nervous system. The advantage of their using is the wide coverage of the analyzed genes, which allows to increase the detection of causes in such a clinically and genetically heterogeneous group of diseases. The purpose of this work is to determine the effectiveness of genome sequencing to identify genetic causes in patients with likely hereditary diseases of the nervous system. In our study, genome sequencing revealed the cause of the disease in 28.6%. In cases with a negative result from the analysis of the gene panel, genome sequencing revealed the cause of the disease in 9% of patients.

Цель исследования - оценить распространенность и типы хромосомных аномалий у пациентов с множественными врожденными пороками развития (МВПР), комплексами малых аномалий развития (МАР), задержкой развития, умственной отсталостью (ЗР/УО) и расстройствами аутистического спектра (РАС) за период с 2013 по 2019 гг. Методом хромосомного микроматричного анализа (ХМА) было обследовано 6516 пациентов с МВПР, ЗР/УО, РАС и МАР. В результате проведенного анализа причина заболевания была обнаружена у 1212 (18,6%) пациентов, у 4868 (74,7%) пациентов хромосомный дисбаласнс отсутствовал, а 436 (6,7%) пациентов имели варианты, возможно имеющие отношение к причине заболевания. Вывод: Полученные нами результаты указывают на необходимость использования ХМА в качестве теста первой линии, вместо стандартного кариотипирования, в постнатальной диагностике.

Микроделеционные и микродупликационные синдромы выявляются примерно у 8% плодов с врожденными пороками развития (ВПР), однако диагностика патогенных CNVs в пренатальном периоде в данный момент не регламентирована и зачастую основана на технических возможностях лаборатории. Представлены результаты исследования плодов, которые имели ВПР и/или маркеры хромосомной патологии, установленные по УЗИ, методом хромосомного микроматричного анализа (ХМА). В выборке (N=1048) у 10,3% плодов были обнаружены числовые аномалии хромосом и у 7,4% плодов были выявлены патогенные хромосомные аномалии, которые невозможно выявить при стандартном кариотипировани из-за их малого размера. Результаты нашего анализа согласуются с данными литературы, демонстрирующей большую эффективность SNP-микроматриц по сравнению с классическими цитогенетическими методами. Microdeletion and microduplication syndromes are detected in approximately 8% of fetuses with congenital malformations, however, the diagnosis of pathogenic CNVs in the prenatal period, at the moment, is unregulated and often based on the technical capabilities of the laboratory. The thesis presents the result of a study of fetuses that had congenital malformations and / or markers of chromosomal abnormalities, determined by ultrasound, by the method of chromosomal microarray analysis. Using chromosomal microarray analysis in our sample (N = 1048), numerical chromosome abnormalities were detected in 10.3% of the fetuses and pathogenic chromosome imbalance was revealed in 7.4% of the fetuses, which cannot be detected by standard karyotyping. The results of our analysis are consistent with the data of the scientific literature, which demonstrates the greater efficiency of using SNP microarrays in comparison with classical cytogenetic methods.

Детский церебральный паралич (ДЦП) - распространенная, клинически гетерогенная группа заболеваний, нарушающих двигательную функцию и поддержание позы. Предполагалось, что генетическую этиологию ДЦП имеют не более чем 2% пациентов. Целью данной работы является определение эффективности высокопроизводительного секвенирования для диагностики причин ДЦП. В нашем исследовании, генетическая этиология установлена у 31,8 % пациентов с ДЦП, возможная причина ДЦП выявлена у 17,5 % пациентов. Cerebral palsy (CP) is a common, clinically heterogeneous group of disorders affecting movement and posture. It was assumed that the genetic etiology of CP does not exceed 2%. The aim of this work is to determine the effectiveness of high-throughput sequencing for diagnosing the causes of CP. In our study, a genetic etiology was found in 31.8% of patients with CP, a possible cause was identified in 17.5% of patients with CP.

Study objective is to assess the prevalence of rare mutations in the EGFR, KRAS, NRAS, BRAF genes, as well as the proportion of the mutant allele frequency (AF) in the samples of patients with lung cancer and colorectal cancer. Materials and Methods: 199 samples of DNA isolated from paraffin blocks was studied using next generation sequencing. Study Results: rare mutations in colorectal cancer were detected in 12.8% of patients. 20% of the samples had AF <15%. Rare mutations in lung cancer were observed in 24.2%. 27% of the samples had AF <15%. Conclusion: Next Generation Sequencing (NGS) may be recommended as a routine method for detecting somatic mutations in a tumor. NGS has great diagnostic capabilities compared to PCR or Sanger sequencing.

Цель исследования - оценить распространенность и типы хромосомных аномалий (ХА) в абортивном материале за период с 2015 по 2019 гг. Методом хромосомного микроматричного анализа был исследован 2201 образец ДНК, выделенной из абортивного материала при неразвивающейся беременности. ХА были обнаружены в 49,57% случаев, из них анеуплоидии, в том числе нескольких хромосом и мозаичные формы, составляют 79,65%, триплоидия - 10,72%, другие ХА, возможно имеющие клиническое значение, - 8,62%, тетраплоидия - 1,01%. Таким образом, хромосомный микроматричный анализ может быть рекомендован как рутинный метод для поиска несбалансированных ХА в абортивном материале при невынашивании беременности. Study objective is to assess the prevalence and pattern of chromosomal abnormalities (CAs) in products of conception (POC) for the period from 2015 to 2019. Materials and Methods: 2201 samples of POC were studied by the chromosomal microarray analysis. Study Results: CAs were detected in 49.57% of cases, of which aneuploidy, including several chromosomal and mosaic forms, were detected in 79.65%, triploidy - 10.72%, other CAs with possible clinical significance - 8.62%, tetraploidy - 1.01%. Conclusion: chromosomal microarray analysis can be recommended as a routine method for searching of unbalanced CAs in POC.

Использование высокопроизводительного секвенирования в пренатальной диагностике позволило значительно увеличить выявляемость причин аномалий развития плода, определенных при УЗИ. Установление релевантного варианта является важным для постановки диагноза и оценки прогноза. Цель настоящей работы - определить распространенность и структуру моногенных заболеваний, являющихся причиной пороков развития плода при использовании секвенирования нового поколения (NGS). В нашем исследовании было проанализировано 60 образцов ДНК плодов, аномалии развития которых были выявлены при УЗИ во время беременности. Патогенные варианты, являющиеся причиной аномалий развития были найдены у 71% плодов. The use of high-throughput sequencing in prenatal diagnostics has significantly increased the detection of the causes of fetal abnormalities identified by ultrasound. Establishing a relevant option is important for making a diagnosis and evaluating the prognosis. The purpose of this work is to determine the prevalence and structure of monogenic diseases that cause fetal malformations using next generation sequencing (NGS). In our study, we analyzed 60 samples of fetal DNA whose abnormalities were detected by ultrasound during pregnancy. Pathogenic variants were found in 71% of fetuses.

Achromatopsia (ACHM) is a rare autosomal recessive disease. Its mutation spectrum is well described in other populations, but the data on ACHM prevalence and features in Russia are insufficient. Purpose . To describe clinically and genetically the Russian cohort of AHCM for the potential use of targeted treatment approaches, including gene therapy. Material and methods . Out of 18 patients with clinical manifestations of ACHM, 10 patients were chosen (6 with no kinship relatedness and 4 with kinship relatedness) aged 12.3 ± 5.8 years. These patients underwent standard ophthalmologic examination: visometry, perimetry, biomicroscopy, ophthalmoscopy, as well as optical coherence tomography, electroretinography, and color test on distinguishing color shades, in order to determine the clinical characteristics of ACHM. Molecular genetic confirmation of the clinical diagnosis was performed by high-performance parallel DNA sequencing. An in silico analysis of pathogenetic pathways of the clinical picture in 10 patients with confirmed ACHM was performed. Results . In the examined Russian patients, previously determined mutations in the CNGA3 and CNGB3 genes were confirmed. The most common mutation was a single nucleotide deletion with a reading frame shift in the 10th exon of the CNGB3 gene; a missense mutation in the 8th exon of the CNGA3 gene was second frequent. One patient had mutations in the CNGA3 and CNGB3 genes. Segregation analysis confirms the autosomal recessive nature of disease inheritance. Mutations in the CNGB3 gene have been observed to lead to more serious clinical manifestations than mutations in CNGA3. Conclusions . The analysis of the Russian ACHM cohort shows that mutations in the CNGA3 and CNGB3 genes are the main cause of the development of the disease. A complete molecular genetic confirmation of the clinical diagnosis has been obtained, which is necessary for prescribing targeted treatment to patients, including gene therapy.

Цель исследования - оценить распространённость редких мутаций в генах EGFR, KRAS, NRAS, BRAF, а также долю мутантного аллеля (AF) в образцах у пациентов с раком легкого и колоректальным раком. Методом секвенирования следующего поколения (NGS) (NGS) было исследовано 199 образцов ДНК, выделенной из парафиновых блоков, содержащих образцы опухоли. Редкие мутации при колоректальном раке выявлены у 12,8% пациентов; 20% образцов имели AF<15%. Редкие мутации при раке легкого найдены у 24,2% пациентов; 27% образцов имели AF<15%. NGS может быть рекомендовано как рутинный метод исследования соматических мутаций в опухоли. NGS обладает большими диагностическими возможностями в сравнении с ПЦР-тестами или секвенированием по Сэнгеру. Study objective is to assess the prevalence of rare mutations in the EGFR, KRAS, NRAS, BRAF genes, as well as the proportion of the mutant allele frequency (AF) in the samples of patients with lung cancer and colorectal cancer. Materials and Methods: 199 samples of DNA isolated from paraffin blocks was studied using next generation sequencing. Study Results: rare mutations in colorectal cancer were detected in 12.8% of patients. 20% of the samples had AF <15%. Rare mutations in lung cancer were observed in 24.2%. 27% of the samples had AF <15%. Conclusion: Next Generation Sequencing (NGS) may be recommended as a routine method for detecting somatic mutations in a tumor. NGS has great diagnostic capabilities compared to PCR or Sanger sequencing.

The article presents a comparative analysis of methods used for the diagnosis of genetic pathology in fetuses with malformations and / or developmental abnormalities. The standard cytogenetic analysis of the karyotype is most widely implemented and used, however, the low resolution of this method in 8Mb does not allow for the detection of microdeletions and microduplications, which in turn in 5-6% of cases are the causes of malformations and / or developmental abnormalities in the fetus. When using chromosomal microarray analysis (CMA) it increases the diagnostic efficacy of prenatal diagnosis, which allows making a diagnosis in a timely manner, determining the prognosis for the life of the child after birth. The choice of method for diagnosing genetic pathology in fetuses with congenital malformations and / or developmental abnormalities is currently not regulated and is often based on the technical capabilities of the laboratory. At the moment, a large amount of data has been accumulated confirming the effectiveness of the use of SNP microarrays compared to classical cytogenetic methods.

Sporadic angiomyolipoma of the kidney is the most common type of renal benign tumors with an estimated frequency of 1 case per 250 people. Despite the asymptomatic course, with the increase of the tumor size, the risk of rupture of micro- and macroaneurysms also increases, which threatens the patient’s life. The use of mTOR protein kinase inhibitors leads to tumor reduction. However, such drugs are prescribed only if the patient has a somatic or germline mutation in the TSC1 or TSC2 genes the products of which are endogenous mTOR inhibitors in the reaction cascade of the PI3K/Akt/mTOR pathway. According to the COSMIC database, driver mutations in the TSC1 and TSC2 genes were identified only in 57% of angiomyolipoma cases, whereas the causes of the remaining cases are still not clear. We have conducted a loss of heterozygosity (LOH) screening in 20 sporadic kidney AML samples by use of the NGS. In seven of the twenty samples, LOH was found in different chromosome regions. In five samples, LOH encompasses the 16p13.3 region, where the TSC2 gene is located. In two samples with the normal allelic state of the 16p13.3 region, we have detected alternative LOH events encompassing 15q14q15.1 in one case, and multiple chromosomal regions in another (high chromosomal instability).

There are various methods for the analysis of chromosomal rearrangements in embryos aborted in miscarriage. Chromosomal microarray analysis is one of the modern diagnostic methods. Studies to determine the diagnostic yield of CMA in comparison to standard karyotyping are of significant scientific and practical interest. Aim. The aim of the present study is to compare the results of CMA and karyotyping of products of conception from women with miscarriage. Materials and methods. A comparative analysis of the two diagnostic methods is based on the study of abortive material from 885 women. In 1st group, 632 women whose products of conception were analysed by CMA were included. The 2nd group comprised 253 women, whose material was directed to a cytogenetic study. Results and discussion. There were no significant differences between study groups in the proportions of samples with a normal and pathological chromosome set. However, the structure of chromosomal abnormalities spectrum in the study groups was different. In both groups, autosomal trisomies were found most frequently - 33.5% in the 1st group and 28.5% in the 2nd group among all the samples. Structural anomalies were significantly more frequent when using CMA - 4.4% of all effective studies in group 1, and only 0.8% (2 cases) in group 2. A higher frequency of polyploidy was revealed during cytogenetic examination. In the 1st group, triploidy was found in 35.8% cases, and tetraploidy in 0.5%. In the 2nd group, triploidy was detected in 10.0%, and tetraploidy - in 5.2% of cases. Conclusions. Traditional karyotyping and CMA have specific relative advantages and disadvantages. The number of chromosomal abnormalities detected using these methods is approximately the same, but the spectum of these anomalies is different. CMA reveals structural rearrangements more often, while karyotyping reveals more cases of multiple anomalies and polyploidy. Identification of structural anomalies has greater clinical significance since it may indicate an unbalanced translocation that is hereditary. The impossibility of detecting balanced translocations with CMA is a limitation of the method that is not as much clinically relevant since it is extremely rare in this type of material.