Characteristics of Genomic Distribution of Runs of Homozygosity in the Indigenous Population of Northern Eurasia Abstract Populations of the indigenous ethnic groups of Northern Eurasia are of considerable interest for population genomics, both because they have been relatively poorly studied with the use of modern genomic technologies and owing to the specificity of their gene pools that developed in various genetic-demographic conditions. We used genotype data on 242 179 autosomal SNPs of 876 individuals to search for regions with runs of homozygosity of more than 1 Mb. For Siberian populations, the number of runs of homozygosity and their total length was higher than for other populations of Northern Eurasia.

Study of the Individual Radiosensitivity in Humans Based on the Assessment of the Frequency of Chromosome Aberrations and Micronuclei in Peripheral Blood T Lymphocytes Abstract The influence of low-dose ionizing radiation on a human being is increasing in the modern world (medical diagnostics etc.). The issue of the effect of low-doses on human health is topical and controversial. It is known that in the population up to 15% of people react to radiation exposure differently from what has been expected, which, according to the published data, happens owing to their genome peculiarities. The objective of the current study was to investigate the influence of chronic lowdose rate exposure (doses to red bone marrow varied within the range 3—4600 mGy) of the Techa River residents (South Urals) on the radiosensitivity of T cells in vivo and in vitro under additional gamma exposure of peripheral blood T lymphocytes (0.5, 1, and 2 Gy). Such cytogenetic parameters as frequency of unstable chromosome aberrations and micronuclei were used as irradiation markers. Persons were considered radiosensitive if the obtained values of the analyzed parameters for them exceeded the 90% percentile. On the basis of the findings of the performed study, the following conclusions were drawn: about 10% of donors demonstrated increased radiosensitivity; moreover, the effect did not depend on the dose of chronic exposure; no age dependence of radiosensitivity in the studied age range (49–89 years) of the donors was revealed. In most cases, we did not detect a reproducible radiosensitivity effect in the same donor under different irradiation regimes.

Epigenetic Mosaicism in Genomic Imprinting Disorders Abstract Differential gene expression during development is maintained by complex regulatory epigenetic mechanisms that provide the formation of different specialized cell types. Subsequently, a multicellular organism is a mosaic of cells with differing epigenetic characteristics. It seems likely that exceeding the limits of normal epigenetic variability may cause the occurrence of pathological mosaic states in which one part of the cell population has a normal epigenotype, while the other part carries modified epigenetic information. In this review, using the genomic imprinting as a classical epigenetic phenomenon, for the first time, the prevalence of epigenetic mosaicism and the mechanisms of its origin, as well as its role in the etiology of hereditary disorders, determined by the dysfunction of imprinted genomic loci are summarized.

Detection of Point Mutations and Chromosomal Translocations Based on Massive Parallel Sequencing of Enriched 3C Libraries Abstract The diagnosis and treatment of patients with hereditary diseases require the creation of efficient methods for the study of individual genomes. The existing approaches either are aimed at searching for a narrow set of genomic variants or are too expensive to use in routine practice. We studied the possibility of detection point mutations and interchromosomal translocations using sequencing of enriched 3C libraries. We demonstrated that enriched 3C libraries are more informative from the point of view of detecting the variants in exons than whole genome libraries, but are inferior to whole exome data. At the same time, translocations significantly change the profile of the chromatin spatial contacts, which makes it possible to detect efficiently such rearrangements when analyzing enriched 3C libraries.

The Baseline Level of Cytogenetic Damage in Lymphocytes and Buccal Epitheliocytes of Lung Cancer Patients Abstract The results of the study of chromosomal aberrations and micronuclei in blood lymphocytes, as well as micronuclei in buccal epithelium cells of 50 untreated men with lung cancer (LC) and 62 control donors, are presented. Using a variety of cytogenetic tests, a significant unidirectional increase in the base level of genetic instability in the cells of the patients was detected compared to the control. It was shown that, in LC patients, the elimination of damaged cells occurs predominantly by necrosis, whereas the frequencies of cells at the apoptosis stage do not differ in patients and control. The age of the patient, smoking status, type, and stage of LC do not have a significant impact on the performance of the baseline level of genetic damage. This fact suggests that the cytogenetic instability of the somatic cells of untreated LC patients is a constant sign that characterizes the genome response to the effect of the oxidative stress accompanying the neoplastic process.

Signals of Positive Selection in Human Populations of Siberia and European Russia Abstract Human adaptation to extreme climatic and geographic conditions mediated by natural selection may be one of the major factors for formation of genetic structure in North Eurasian populations. Using data on a genome-wide set of single nucleotide polymorphisms (SNPs), we searched for the signals of positive selection in five populations of Siberia and the Russian European North. From 113 to 185 genomic regions with extended homozygous haplotypes blocks containing altogether 771 genes were found in each of the populations. Cross-population search of the selection targets resulted in about 150 genomic regions, 57 of which overlap with the results of haplotype analysis in individual populations. Genomic loci with the most profound signals of positive selection in northern populations include regions of SLC30A9, CACNA1C, KCNQ5, ABCA1, ALDH1A2, CSMD1, RBFOX1, and WWOX, as well as some other genes. Bioinformatics analysis demonstrated that major biological processes where selection targets are implicated are those conferring the response to external stimuli, including proteins, nutrients, and glucose, and defense reactions, including inflammatory immune response. The network of protein-protein interactions of genes under positive selection forms distinct clusters related to a number of biological processes indicated above. Results of the study indicate that non-neutral microevolution mechanisms may play a substantial role in genetic structuring of the human populations during long-term adaptation to unfavorable environmental conditions.

Chromosomal Instability and Karyotype Correction in Human Induced Pluripotent Stem Cells Abstract Human induced pluripotent stem cells (iPSCs) are a promising source of cells for regenerative medicine, study of the pathogenesis of various diseases, screening of pharmacological drugs, and other clinical and basic research. However, the maintenance of the genetic stability of the cells during reprogramming, long-term culture, and directed differentiation is necessary for the use of iPSCs. Large chromosomal aberrations affect the quality of iPSCs most adversely, so the review focuses on the analysis of chromosomal abnormalities, including the recurrent aneuploidy; the sources of its origin, the effect of reprogramming, and long-term culture on the accumulation of chromosome aberrations are discussed. Cases of spontaneous correction of the iPSCs karyotype and the possibility of induced correction of the large chromosomal abnormalities by removing or silencing the extra homologue are considered.

Noninvasive Prenatal Testing Using Next Generation Sequencing: Pilot Experience of the D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology Abstract In recent years, noninvasive prenatal testing (NIPT) for fetal chromosomal abnormalities has come into wide use. NIPT allows detection of fetal chromosomal abnormalities without invasive sampling of fetal material: by analyzing cell-free fetal DNA in maternal blood. Here, we report on the pilot results of using NIPT at the D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology (St. Petersburg, Russia). The results obtained in 149 blood samples from pregnant women proved the clinical value of NIPT for detection of fetal trisomies 21, 18, and 13. Aneuploidy was detected in 20 out of 149 samples. Among these 20 aneuploid cases, trisomy 21 amounted to 60%, trisomy 18 – to 25%, and trisomy 13 to 5% of cases. In one sample, double aneuploidy involving chromosomes 13 and 21 was detected, and in one case, trisomy X was identified. In 100% of cases, aneuploidies were confirmed by prenatal karyotyping advocating for the absence of false positive NIPT results. The observed high specificity was consistent with the declared test specificity level of >99.9%. The sensitivity of the method was 100%. To summarize, NIPT is a new reliable technique that will probably soon replace the conventional first trimester combined screening. The only disadvantages of implementing NIPT in Russia are its relatively high cost and the lack of coverage by insurance companies. NGS-based NIPT is suitable for clinical practice and will be widely deployed due to a further cost decrease.

Clinical Utility of MLPA and QF-PCR Techniques in the Genetic Testing of Miscarriages Abstract Most common reasons for pregnancy loss are chromosomal anomalies of the fetus. They are found in as much as half of the miscarriages. The standard technique for assessment of chromosomal abnormalities in spontaneously aborted fetuses has been karyotyping, however, it needs cell culture which is the most vulnerable element of a diagnostic process. At present, there are a number of molecular methods, which skip the necessity of cell culture. In this study, we assess retrospectively the diagnostic yield of two commonly used molecular techniques (MLPA and QF-PCR) for aneuploidy detection in miscarriages. A total of 674 samples were analyzed. The QF-PCR assay for chromosomes 13, 15, 16, 18, 21, 22, X and Y was used. Two subtelomeric and subcentromeric probe kits covering all chromosomes were used in MLPA tests. In QF-PCR test, chromosomal abnormalities were found in 49.5% of cases. Trisomies constituted 25.7%, monosomies X— 12.9% and triploidies—10.9%. In the MLPA series, a total of 55.1% samples turned out to carry a chromosomal aberration. Trisomies were found in 43.2% of all good quality samples, chromosome X monosomies accounted for 13.4% of samples, and triploidies were detected in 11.3%. Both QF-PCR and MLPA methods may be successfully implemented as an alternative for standard karyotype in testing material from spontaneous abortion. QF-PCR has lower sensitivity comparing to MLPA in detecting aneuploidies, however, it is an effective tool for the detection of polyploidies. It should be noted, that using these techniques, the maternal cell contamination should be considered as an important issue.

Interpretation of FISH Results in the Case of Nonuniform Internal Radiation Exposure of Human Body with the Use of Model Approach Abstract The fluorescence in situ hybridization (FISH) technique allows for the estimation of the number of stable chromosomal aberrations (translocations) in human blood T-lymphocytes decades after radiation exposure. Therefore, it is used for retrospective assessment of irradiation doses received by red bone marrow (RBM). Cytogenetic analysis of individuals exposed on the Techa River in the 1950s to 89,90Sr, locally irradiating RBM, showed that dose assessment based on FISH data led to underestimation of the actual dose estimated from measurements of whole-body 90Sr content. The purpose of current study was to evaluate the dose–effect relationship and the frequency of translocations per 1 Gy of RBM irradiation dose and T-lymphocytes dose for donors living in Techa riverside villages (n = 178; translocation yield = 2389; number of genome equivalents GE = 96 446). Irradiation doses were estimated using the latest version of the Techa River dosimetry system and the T-cell irradiation model. Statistical analysis showed that the frequency of translocations per 1000 GE per 1 Gy of RBM dose was 8.0 ± 0.7; this value was statistically significantly lower than the value estimated for Sellafield radiation workers under external exposure (11.6 ± 1.6). At the same time, the use of T-cell and their progenitor doses led to re-evaluation (increase) in the slope of the dose–response curve to 11.8 ± 1.6 per 1 Gy per 1000 GE, which agreed well with the published data. The obtained estimates of the background frequencies of translocations also were close to the published values ​​for unexposed donors. These findings demonstrate the legitimacy of using a model approach for estimation of irradiation doses in T-lymphocytes and their progenitors and the need to take into account complex T-cell dynamics in interpretation of cytogenetic data for the purposes of biodosimetry.