Transferability of the PRS estimates for height and BMI obtained from the European ethnic groups to the Western Russian populations

Genetic data plays an increasingly important role in modern medicine. Decrease in the cost of sequencing with subsequent increase in imputation accuracy, and the accumulation of large amounts of high-quality genetic data enable the creation of polygenic risk scores (PRSs) to perform genotype–phenotype associations. The accuracy of phenotype prediction primarily depends on the overall trait heritability, Genome-wide association studies cohort size, and the similarity of genetic background between the base and the target cohort. Here we utilized 8,664 high coverage genomic samples collected across Russia by “Evogen”, a Russian biomedical company, to evaluate the predictive power of PRSs based on summary statistics established on cohorts of European ancestry for basic phenotypic traits, namely height and BMI. We have demonstrated that the PRSs calculated for selected traits in three distinct Russian populations, recapitulate the predictive power from the original studies. This is evidence that GWAS summary statistics calculated on cohorts of European ancestry are transferable onto at least some ethnic groups in Russia

Особенности диагностики наследственных опухолевых синдромов с нетипичным проявлением: клинические случаи

Background: Germinal pathogenic variants are the cause of the development of hereditary cancer syndromes (HCS). Various genetic tests are used for HCS detect, from the «frequent» mutations of one or several genes analysis to the full-length gene sequence, next-generation sequencing (NGS) based panel, whole exome (WES) or whole genome sequencing (WGS).There are some HCS cases with atypical clinical manifestations and the family history does not allow one to suspect a specific HCS and limit oneself to the study of only one or a few genes. Conducting research using NGS to assess the selected sample of cancer patient’s genetic characteristics has revealed atypical HCS cases.Aim: To present the WGS diagnosis results for two atypical hereditary tumor syndromes cases.Materials and methods: DNA isolation was performed using Qiagen DNA Isolation kit.WGS for all samples was performed at DNBSEQ-T7 (MGI) and DNBSEQ-G400 (MGI) sequencing platforms using PCR-free protocol with average sample coverage 30x. A standard bioinformatics analysis pipeline was implemented for all the samples data processing.Potential clinically relevant variants were validated using Sanger sequencing. For all patients was received signed a written consent.Results: In the first case report, a pathogenic variant in the TP53 gene was identified: c. 637C > T, p. Arg213Ter, rs397516436, and Li – Fraumeni syndrome was confirmed. In the second case, we detected two pathogenic variants carrier — BRCA2: c. 6644_6647del, p. Tyr2215SerfsTer13, rs80359616 and MSH2: c. 1906G > C, p. Ala636Pro, rs63750875 associated with hereditary breast and ovarian cancer and hereditary colorectal cancer (Lynch syndrome).Conclusion: NGS, including WGS makes it easier to identify all clinically significant germline variants associated with hereditary cancer syndromes in cancer patients, as well as to trace their segregation in relatives.Актуальность: Герминальные патогенные варианты являются причиной развития наследственных опухолевых синдромов (НОС). Для выявления НОС применяются различные подходы, от анализа «частых» мутаций одного или нескольких генов до полного секвенирования кандидатного гена, мультигенной панели, полноэкзомного или полногеномного секвенирования. Иногда встречаются случаи с нетипичным клиническим проявлением, а семейный анамнез не позволяет своевременно заподозрить конкретный НОС у пациента и ограничиться исследованием одного или нескольких генов. Научные проекты с применением высокопроизводительного секвенирования для оценки генетических особенностей определенной выборки онкологических пациентов позволили выявить нетипичные случаи НОС.Цель исследования: Представить клиническое описание и результаты молекулярно-генетической диагностики двух нетипичных клинических случаев НОС.Материалы и методы: Представлены результаты молекулярной диагностики генетических причин, приводящих к развитию НОС, на примере двух клинических случаев. Полногеномное секвенирование проведено с использованием реагентов и оборудования производства MGI (Китай). Валидация клинически значимых вариантов, полученных по результатам полногеномного секвенирования, проведена секвенированием по Сэнгеру.Результаты: В первом клиническом случае выявлен патогенный вариант в гене TP53: c. 637C > T, p. Arg213Ter, rs397516436, и подтвержден синдром Ли – Фраумени. Во втором случае у пациента выявлено носительство двух патогенных вариантов — BRCA2: c. 6644_6647del, p. Tyr2215SerfsTer13, rs80359616 и MSH2: c. 1906G > C, p. Ala636Pro, rs63750875, ассоциированных с развитием наследственного рака молочной железы и яичника и наследственного колоректального рака (синдром Линча).Заключение: Использование расширенных методов генетического тестирования, в том числе полногеномного секвенирования позволяет выявить все клинически значимые герминальные варианты, ассоциированные с НОС, у онкологических пациентов, а также проследить их сегрегацию у родственников

Human gut microbiota community structures in urban and rural populations in Russia

The microbial community of the human gut has a crucial role in sustaining host homeostasis. High-throughput DNA sequencing has delineated the structural and functional configurations of gut metagenomes in world populations. The microbiota of the Russian population is of particular interest to researchers, because Russia encompasses a uniquely wide range of environmental conditions and ethnogeographical cohorts. Here we conduct a shotgun metagenomic analysis of gut microbiota samples from 96 healthy Russian adult subjects, which reveals novel microbial community structures. The communities from several rural regions display similarities within each region and are dominated by the bacterial taxa associated with the healthy gut. Functional analysis shows that the metabolic pathways exhibiting differential abundance in the novel types are primarily associated with the trade-off between the Bacteroidetes and Firmicutes phyla. The specific signatures of the Russian gut microbiota are likely linked to the host diet, cultural habits and socioeconomic status. © 2013 Macmillan Publishers Limited. All rights reserved

Злокачественное новообразование молочной железы в составе синдрома Коудена

Cowden syndrome is a rare disease characterized by multiple hamartomas and increased breast, thyroid, kidney and uterine neoplasm risk. The lifetime breast cancer risk for patients with Cowden syndrome is 85 %, with an average age of diagnosis between 38 and 46 years. The diagnostic criteria for Cowden syndrome have been established by the International Cowden Consortium (ICC) and the National Comprehensive Cancer Network (NCCN), and are regularly revised, but the diagnosis of Cowden syndrome remains difficult due to the variety of phenotypic and clinical features of the disease. At the same time, the genetic variants associated with Cowden syndrome analysis is not a standard for patients with breast cancer.Objective: To demonstrate the non‑BRCA hereditary breast cancer detection using whole genome sequencing on the Cowden syndrome clinical case example.Materials and methods: The article describes a clinical case of a 37‑year‑old female patient with breast cancer, normal intelligence and phenotype, structural abnormalities of the thyroid gland (multinodular goiter). Whole genome sequencing was used to identify clinically significant genetic variants associated with hereditary tumor syndromes.Clinical case: The article presents a brief literature review on the clinical presentation of Cowden syndrome and indications for its molecular diagnosis. Also, the presented clinical case describes patient R., 37 years old female with breast cancer, who underwent treatment in the City Clinical Oncological Hospital № 1 of the Moscow City Health Department in 2021. The patient was fully examined and enrolled in the whole genome sequencing project under the Order № 69 of Moscow Healthcare Department dated February 1, 2021 «Oncogenetic research organization in Moscow». The results revealed a pathogenic variant in the PTEN gene, previously associated with Cowden syndrome.Conclusion: The use of whole genome sequencing allows to identify hereditary tumor syndromes, the clinical manifestation of which may be breast cancer.Синдром Коудена характеризуется наличием множественных гамартом с высоким риском развития доброкачественных и злокачественных опухолей щитовидной железы, молочной железы, почек и эндометрия. Риск развития рака молочной железы у пациентов с синдромом Коудена в течение жизни составляет 85 %, при этом средний возраст постановки диагноза составляет от 38 до 46 лет. Диагностические критерии синдрома Коудена установлены Международным консорциумом по синдрому Коудена (ICC) и Американской ассоциацией онкологов (NCCN) и подвергаются регулярному пересмотру, однако диагностика синдрома Коудена по‑прежнему затруднена ввиду разнообразия фенотипических особенностей и клинических признаков заболеваний. В то же время, анализ генетических вариантов, ассоциированных с синдромом Коудена, не является стандартом обследования при диагностике рака молочной железы.Цель: продемонстрировать выявление методом полногеномного секвенирования наследственных опухолевых синдромов, клиническим проявлением которых могут быть злокачественные новообразования молочной железы, на примере синдрома Коудена.Материалы и методы: в статье описан клинический случай пациентки 37 лет с нормальным интеллектом и фенотипом, структурными поражениями щитовидной железы (многоузловой зоб), обратившейся по поводу рака молочной железы. В рамках научного исследования с целью выявления клинически значимых генетических вариантов, ассоциированных с наследственными опухолевыми синдромами, применен метод полногеномного секвенирования.Клинический случай: в статье представлен краткий обзор литературы, посвященный клинической характеристике синдрома Коудена, и показаний для молекулярной диагностики. Описан клинический случай пациентки Р., 37 лет, которая проходила лечение в ГБУЗ «Городская клиническая онкологическая больница № 1 ДЗМ» в 2021 г. по поводу рака молочной железы. С учетом диагностированного в возрасте до 50 лет злокачественного новообразования молочной железы пациентка включена в научный проект по проведению полногеномных исследований в рамках приказа Департамента Здравоохранения г. Москвы № 69 от 01.02.2021 «Об организации проведения онкогенетических исследований в городе Москве», по результатам генетического исследования выявлен патогенный вариант гена PTEN, ассоциированный с синдромом Коудена.Вывод: Применение полногеномного секвенирования позволяет выявлять наследственные опухолевые синдромы, клиническим проявлением которых могут быть злокачественные новообразования молочной железы

Genomic and phenotypic analysis of siderophore-producing Rhodococcus qingshengii strain S10 isolated from an arid weathered serpentine rock environment

© 2020, Springer-Verlag GmbH Germany, part of Springer Nature. The success of members of the genus Rhodococcus in colonizing arid rocky environments is owed in part to desiccation tolerance and an ability to extract iron through the secretion and uptake of siderophores. Here, we report a comprehensive genomic and taxonomic analysis of Rhodococcus qingshengii strain S10 isolated from eathered serpentine rock at the arid Khalilovsky massif, Russia. Sequence comparisons of whole genomes and of selected marker genes clearly showed strain S10 to belong to the R. qingshengii species. Four prophage sequences within the R. qingshengii S10 genome were identified, one of which encodes for a putative siderophore-interacting protein. Among the ten non-ribosomal peptides synthase (NRPS) clusters identified in the strain S10 genome, two show high homology to those responsible for siderophore synthesis. Phenotypic analyses demonstrated that R. qingshengii S10 secretes siderophores and possesses adaptive features (tolerance of up to 8% NaCl and pH 9) that should enable survival in its native habitat within dry serpentine rock

An allelic variant of congenital Salih myopathy

The paper describes the steps and problems of diagnosing congenital myopathy with early respiratory disorders. While differentially diagnosing, the authors consider congenital myopathies, in which early cardiac involvement is encountered. Since the course of the disease in an observed female patient differed from that of such nosological entities and appeared as not only muscle weakness, but also as early respiratory disorders, we could not identify what nosological entity the disease belonged to in view of its clinical presentation and the results of muscle histological examination and we decided to perform exome sequencing. Molecular genetic testing could find heterozygous mutations in the titin (TTN) gene. The findings are suggestive of congenital proximal myopathy with early respiratory failure, which is an allelic variant of Salih myopathy. This case is the first and so far only description of this disease in Russia

Aicardi–Goutieres syndrome in children with idiopathic epilepsy

This article describes 9 clinical cases of Aicardi–Goutières syndrome (AGS) in children admitted to the hospital of the Scientific and Practical Center of Medical Care for Children with Resistant Multifocal Epilepsy. Epilepsy, psychomotor retardation, and a loss of previously acquired skills were diagnosed during the investigation. Targeted exome sequencing in one child revealed a mutation in the RNASEH2B gene responsible for the development of this disease. AGS is an early-onset progressive encephalopathy with basal ganglia calcification, leukodystrophy, lymphocytosis, elevated interferon-alfa levels in the cerebrospinal fluid, and no evidence of viral infection. Noninfectious leukoencephalopathy concurrent with multifocal epilepsy in early childhood suggest that the syndrome is an inherited disease

Identification, Expression Analysis, and Target Prediction of Flax Genotroph MicroRNAs Under Normal and Nutrient Stress Conditions

Cultivated flax (Linum usitatissimum L.) is an important plant valuable for industry. Some flax lines can undergo heritable phenotypic and genotypic changes (LIS-1 insertion being the most common) in response to nutrient stress and are called plastic lines. Offspring of plastic lines, which stably inherit the changes, are called genotrophs. MicroRNAs (miRNAs) are involved in a crucial regulatory mechanism of gene expression. They have previously been assumed to take part in nutrient stress response and can, therefore, participate in genotroph formation. In the present study, we performed high-throughput sequencing of small RNAs extracted from flax plants grown under normal, phosphate deficient and nutrient excess conditions to identify miRNAs and evaluate their expression. Our analysis revealed expression of 96 conserved miRNAs from 21 families in flax. Moreover, 475 novel potential miRNAs were identified for the first time, and their targets were predicted. However, none of the identified miRNAs were transcribed from LIS-1. Expression of 7 miRNAs (miR168, miR169, miR395, miR398, miR399, miR408, and lus-miR-N1) with up- or down-regulation under nutrient stress (on the basis of high-throughput sequencing data) was evaluated on extended sampling using qPCR. Reference gene search identified ETIF3H and ETIF3E genes as most suitable for this purpose. Down-regulation of novel potential lus-miR-N1 and up-regulation of conserved miR399 were revealed under the phosphate deficient conditions. In addition, the negative correlation of expression of lus-miR-N1 and its predicted target, ubiquitin-activating enzyme E1 gene, as well as, miR399 and its predicted target, ubiquitin-conjugating enzyme E2 gene, was observed. Thus, in our study, miRNAs expressed in flax plastic lines and genotrophs were identified and their expression and expression of their targets was evaluated using high-throughput sequencing and qPCR for the first time. These data provide new insights into nutrient stress response regulation in plastic flax cultivars

Human gut microbiota community structures in urban and rural populations in Russia

The microbial community of the human gut has a crucial role in sustaining host homeostasis. High-throughput DNA sequencing has delineated the structural and functional configurations of gut metagenomes in world populations. The microbiota of the Russian population is of particular interest to researchers, because Russia encompasses a uniquely wide range of environmental conditions and ethnogeographical cohorts. Here we conduct a shotgun metagenomic analysis of gut microbiota samples from 96 healthy Russian adult subjects, which reveals novel microbial community structures. The communities from several rural regions display similarities within each region and are dominated by the bacterial taxa associated with the healthy gut. Functional analysis shows that the metabolic pathways exhibiting differential abundance in the novel types are primarily associated with the trade-off between the Bacteroidetes and Firmicutes phyla. The specific signatures of the Russian gut microbiota are likely linked to the host diet, cultural habits and socioeconomic status. © 2013 Macmillan Publishers Limited. All rights reserved