We report a case of familial small supernumerary marker chromosome 15 in a phenotypically normal female with 4 recurrent spontaneous abortions and a healthy child. The initial karyotype showed a small, bisatellited, apparently metacentric marker chromosome, 47,XX,+idic(15)(q11.1), maternally inherited. The proband's mother was mosaic for the idic(15)(q11.1) without pregnancy loss. Reexamination of the proband's karyotype revealed cryptic mosaicism for 1 ring and 1 minute chromosome derived de novo from chromosome 9 in 2% of the metaphases. In FISH analysis, the patient's karyotype was mos 47,XX,+idic(15)(q11.1)mat[100]/49,XX,+idic(15)(q11.1)mat,+r(9;9;9;9),+der(9)dn[2]. The second spontaneous abortion had trisomy 9 (47,XX,+9); the third had mosaic trisomy 9 in 21% of the nuclei and isodicentric chromosome 15 in 36% of the nuclei (mos 48,XN,+9,+idic(15)(q11.1)/47,XN,+9/47,XN,+idic(15)(q11.1)/46,XN). The first and fourth abortions were not cytogenetically studied. The cause of the spontaneous abortions in this patient is likely the cryptic mosaicism for ring and minute chromosomes 9, and gonadal mosaicism is most probable, due to the 2 abortions.

As interest in genetic resequencing increases, so does the need for effective mathematical, computational, and statistical approaches. One of the difficult problems in genome annotation is determination of precise positions of transcription start sites. In this paper we present TransPrise-an efficient deep learning tool for prediction of positions of eukaryotic transcription start sites. Our pipeline consists of two parts: the binary classifier operates the first, and if a sequence is classified as TSS-containing the regression step follows, where the precise location of TSS is being identified. TransPrise offers significant improvement over existing promoter-prediction methods. To illustrate this, we compared predictions of TransPrise classification and regression models with the TSSPlant approach for the well annotated genome of Oryza sativa. Using a computer equipped with a graphics processing unit, the run time of TransPrise is 250 minutes on a genome of 374 Mb long. The Matthews correlation coefficient value for TransPrise is 0.79, more than two times larger than the 0.31 for TSSPlant classification models. This represents a high level of prediction accuracy. Additionally, the mean absolute error for the regression model is 29.19 nt, allowing for accurate prediction of TSS location. TransPrise was also tested in Homo sapiens, where mean absolute error of the regression model was 47.986 nt. We provide the full basis for the comparison and encourage users to freely access a set of our computational tools to facilitate and streamline their own analyses. The ready-to-use Docker image with all necessary packages, models, code as well as the source code of the TransPrise algorithm are available at (http://compubioverne.group/). The source code is ready to use and customizable to predict TSS in any eukaryotic organism.

The role of genetic polymorphisms in the pathogenesis of recurrent pregnancy loss (RPL) has been studied intensively. Complex diseases, including miscarriage, are believed to have a polygenic basis, and gene-gene interactions can play a significant role in the etiology of the disease. This study was conducted to investigate the association of gene-gene interactions with angiogenesis, endothelial dysfunction-related gene polymorphisms, and RPL.

This study investigated whether common polymorphisms of cytochrome P450 2J2 (CYP2J2), a major enzyme that controls the biosynthesis of vasoactive epoxyeicosatrienoic acids, are collectively involved in the molecular basis of essential hypertension (EH). A total of 2314 unrelated Russian subjects from the Kursk (discovery sample: 913 EH patients and 645 controls) and Belgorod (replication sample: 345 EH patients and 411 controls) regions were recruited for this study. Eight single nucleotide polymorphisms (SNPs), including rs890293, rs11572182, rs10493270, rs1155002, rs2280275, rs7515289, rs11572325, and rs10889162, of CYP2J2 were genotyped using the MassARRAY 4 system and TaqMan-based assays. Significant associations were identified among the SNPs rs890293 (OR = 2.17, 95%CI 1.30-3.65), rs2280275 (OR = 1.59, 95%CI 1.10-2.37) and rs11572325 (OR = 1.89, 95%CI 1.22-2.95) and the risk of EH in females from the Kursk population. Sixteen CYP2J2 genotype combinations only showed significant associations with EH risk only in females. A common haplotype, T-T-G-C-C-C-T-A, increased the risk of EH in females. The bioinformatic analysis enabled identification of the SNPs that possess regulatory potential and/or are located within the binding sites for multiple transcription factors that play roles in the pathways involved in hypertension pathogenesis. Moreover, the polymorphisms rs890293, rs2280275, and rs11572325 were found to be significantly associated with hypertension risk in the Belgorod population. In conclusion, the rs2280275 and rs11572325 SNPs of CYP2J2 may be considered novel genetic markers of hypertension, at least in Russian women. However, sex-specific associations between CYP2J2 gene polymorphisms and hypertension require further investigation to clarify the specific genetic and/or environmental factors that are responsible for the increased disease susceptibility of women compared to that of men.

Skin fibroblasts from a patient with developmental delay and chromosome 2p25.3 deletion syndrome were reprogrammed into induced pluripotent stem cells (iPSCs) and the clonal stem cell line ICAGi001-A (iTAF9-11) was established. ICAGi001-A pluripotency was demonstrated in vitro by three germ layer differentiation capacity. This line is a good model for studying of the developmental delay and brain disorder.

The human induced pluripotent stem cell (iPSC) lines, ICGi009-A, ICGi009-B, ICGi013-A and ICGi013-B, were generated from skin fibroblasts of two siblings with intellectual disability. Both patients were carriers of CNTN6 gene microdeletion (Kashevarova et al., 2014). iPSC lines have normal karyotype, express pluripotency markers, are able to differentiate in vitro into derivatives of all three germ layers and represent a unique tool to study neurodevelopmental disorders.

The 3p26.3 microduplication involving the CNTN6 gene cause developmental delay and the intellectual disability. However, the incomplete penetrance is described for this copy number variation (CNV). Here we describe ICAGi002-A line, which is supposed to use as a model for studying of the penetrance of the CNV in 3p26.3. The ICAGi002-A iPSCs line was obtained by the reprogramming of the skin fibroblasts from a healthy donor with 3p26.3 microduplication involving the CNTN6 gene. The ICAGi002-A cells was pluripotent as it was shown by the expression of the pluripotency-associated markers and in vitro differentiation into the cells of three germ layers.

Asthma and hypertension are complex diseases coinciding more frequently than expected by chance. Unraveling the mechanisms of comorbidity of asthma and hypertension is necessary for choosing the most appropriate treatment plan for patients with this comorbidity. Since both diseases have a strong genetic component in this article we aimed to find and study genes simultaneously associated with asthma and hypertension. We identified 330 shared genes and found that they form six modules on the interaction network. A strong overlap between genes associated with asthma and hypertension was found on the level of eQTL regulated genes and between targets of drugs relevant for asthma and hypertension. This suggests that the phenomenon of comorbidity of asthma and hypertension may be explained by altered genetic regulation or result from drug side effects. In this work we also demonstrate that not only drug indications but also contraindications provide an important source of molecular evidence helpful to uncover disease mechanisms. These findings give a clue to the possible mechanisms of comorbidity and highlight the direction for future research.

In a previous study using one-step CRISPR/Cas9 genome editing in mouse zygotes, we created five founders carrying a 1,137 kb deletion and two founders carrying the same deletion, plus a 2,274 kb duplication involving the Cntn6 gene (encoding contactin-6). Using these mice, the present study had the following aims: (i) to establish stage of origin of these rearrangements; (ii) to determine the fate of the deleted DNA fragments; and (iii) to estimate the scale of unpredicted DNA changes accompanying the rearrangements. The present study demonstrated that all targeted deletions and duplications occurred at the one-cell stage and more often in one pronucleus only. FISH analysis revealed that there were no traces of the deleted DNA fragments either within chromosome 6 or on other chromosomes. These data were consistent with the Southern blot analysis showing that chromosomes with deletion often had close to expected sizes of removed DNA fragments. High-throughput DNA sequencing of two homozygotes for duplication demonstrated that there were no unexpected significant or scale DNA changes either at the gRNA and joint sites or other genome sites. Thus, our data suggested that CRISPR/Cas9 technology could generate megabase-sized deletions and duplications in mouse gametes at a reasonably specific level.

Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require the presence of an archaic human reference genome. We find no evidence for archaic admixture in the Andaman Islands, as previously claimed, or on the island of Flores, where Homo floresiensis fossils have been found. However, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the strongest signal in Khoesan and Pygmy individuals from Southern and Central Africa. The locations of these putative archaic admixture tracts are weighted against functional regions of the genome, consistent with the long-term effects of purifying selection against introgressed genetic material.

The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world’s population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia. We catalogue genetic variation, population structure, disease associations and founder effects. We also explore the use of this dataset in imputation, to facilitate genetic studies in populations across Asia and worldwide.

Известно, что в течение жизни у людей происходит укорочение длины теломерных участков хромосом, ограничивающих количество делений клеток, которые имеют свой предел (предел Хейфлика). Считается, что эволюционно этот феномен является компромиссом для предотвращения риска развития рака. В то же время в современном обществе, в котором продолжительность жизни значительно возросла, укорочение теломерных участков хромосом может играть важную роль в развитии заболеваний связанных со старением, и в первую очередь с такой группой патологий, как сердечно-сосудистые заболевания, являющие в 35% случаев причиной смерти в пожилом возрасте. В обзоре представлена информация, посвященная исследованиям, направленным на определение роли длины теломер в риске развития сердечно-сосудистых заболеваний и описании факторов, оказывающих влияние на изменение длины теломерных участков хромосом, а также возможных причин формирования геномной нестабильности вследствие повреждения теломерных участков хромосом.

В статье обсуждаются ключевые вопросы о связи качественных и количественных характеристик мтДНК и риска развития атеросклероза и инфаркта миокарда. Проанализированы российские и зарубежные научные публикации, посвященные точковым и делеционным мутациям мтДНК и гетероплазмии в связи с рисками развития сердечно-сосудистых заболеваний и острых сердечно-сосудистых катастроф. Также обсуждается взаимосвязь между кардиоваскулярными событиями и выраженностью оксидативного стресса, количеством копий мтДНК как в клетках, так и плазме крови.

Актуальность: Преэклампсия (ПЭ) признана одним из наиболее тяжелых осложнений беременности и является ведущей причиной материнской и перинатальной заболеваемости и смертности, поскольку в настоящее время отсутствуют прогностические биомаркеры и эффективная фармакологическая терапия ПЭ, а ее этиопатогенез остается плохо изученным. В связи с этим, изучение генетической компоненты ПЭ представляется актуальным. Цель исследования: Изучение генетической компоненты ПЭ по системе регуляторных полиморфных вариантов (rSNP) нового гена-кандидата CORO2A и выявление роли естественного отбора в ее формировании. Материалы и методы: Проанализировано 925 образцов ДНК женщин из этнических выборок русских и якутов (группа больных ПЭ, N=412 чел.; контрольная группа, N=513 чел.). Поиск rSNP проводили с помощью ресурса «RegulomeDB». Генотипирование осуществляли методом MALDI-TOF масс-спектрометрии. Для сравнения частот аллелей и генотипов между анализируемыми группами использовали критерий X2 Пирсона или двусторонний точный тест Фишера. Для поиска сигналов естественного отбора в эволюционной линии парвотряда Catarrhini использовали метод INSIGHT. Результаты: В этнической выборке русских для аллеля C регуляторного полиморфного варианта rs10985257 показана ассоциация с развитием ПЭ (p=0.005, OR=2.33, CI:1.32-4.11), тогда как аллель A (p=0.005, OR=0.43, CI:0.24-0.76) и генотип AA (p=0.02, OR=0.45, CI:0.24-0.85) обладают протективными свойствами. В эволюционной линии парвотряда Catarrhini выявлено действие слабого очищающего отбора для rs10985257, rs2231656 и rs78486797. Заключение: Продемонстрирована значимая роль rs10985257 и его адаптивных изменений на макроэволюционном уровне в формировании наследственной предрасположенности к ПЭ.

Изучение причин и процессов, приводящих к внезапной смерти, - одна из важнейших задач кардиологии. Данные многочисленных исследований указывают на то, что значительную роль в патогенезе внезапной смерти играет дисфункция митохондрий. Недостаток АТФ, избыток активных форм кислорода и нарушение ионного баланса в митохондриях могут вызывать развитие жизнеугрожающей аритмии. Митохондриальная ДНК, кодирующая некоторые субъединицы дыхательной цепи митохондрий, характеризуется значительным полиморфизмом в популяциях человека. Показано, что распространенные в популяции варианты мтДНК могут влиять на интенсивность клеточного дыхания. Кроме того, получены данные об ассоциации полиморфизма мтДНК с предрасположенностью к различным заболеваниям сердечно-сосудистой системы, в том числе к состояниям, связанным с высоким риском внезапной смерти. Эти особенности энергетического метаболизма, характеризующие различные генотипы мтДНК, не оказывают существенного влияния на функцию миокарда в норме, но могут оказаться критически важными в условиях острой ишемии. Таким образом, митохондриальный геном можно рассматривать как одну из важных составляющих в патогенетике внезапной сердечной смерти.