A case report of Pallister-Killian syndrome with an unusual mosaic supernumerary marker chromosome 12 with interstitial 12p13.1-p12.1 duplication.

Pallister-Killian syndrome (PKS) is a rare inherited disease with multiple congenital anomalies, profound intellectual disability, and the presence in the karyotype of sSMC - i(12)(p10). The frequency of PKS may be underestimated due to problems with cytogenetic diagnosis caused by tissue-specific mosaicism and usually a low percentage of peripheral blood cells containing sSMC. Such tissue-specific mosaicism also complicates a detailed analysis of the sSMC, which, along with the assessment of mosaicism in different tissues, is an important part of cytogenetic diagnosis in PKS. Unfortunately, a full-fledged diagnosis in PKS is either practically impossible or complicated. On the one hand, this is due to problems with the biopsy of various tissues (skin biopsy with fibroblast culture is most often used in practice); on the other - a low percentage of dividing peripheral blood cells containing sSMC, which often significantly complicates the analysis of its composition and organization. In the present study, a detailed analysis of sSMC was carried out in a patient with a characteristic clinical picture of PKS. A relatively high percentage of peripheral blood cells with sSMC (50%) made it possible to perform a detailed molecular cytogenetic analysis of de novo sSMC using chromosomal in situ suppression hybridization (CISS-hybridization), multicolor FISH (mFISH), multicolor chromosome banding (MCB), array CGH (aCGH), and quantitative real-time PCR (qPCR), and short tandem repeat (STR) - analysis. As a result, it was found that the sSMC is not a typical PKS derivative of chromosome 12. In contrast to the classical i(12)(p10) for PKS, the patient's cells contained an acrocentric chromosome consisting of 12p material. Clusters of telomeric repeats were found at the both ends of the sSMC. Furthemore, the results of aCGH and qPCR indicate the presence of interstitial 8.9 Mb duplication at 12p13.1-p12.1 within the sSMC, which leads to different representations of DNA from different segments of 12p within cells containing sSMC. The obtained data raise the question of the instability of the sSMC and, as a consequence, the possible presence of additional rearrangements, which, in traditional cytogenetic analysis of patients with PKS, are usually described as i(12)(p10).

Expression of the NUP153 and YWHAB genes from their canonical promoters and alternative promoters of the LINE-1 retrotransposon in the placenta of the first trimester of pregnancy.

The placenta has a unique hypomethylated genome. Due to this feature of the placenta, there is a potential possibility of using regulatory elements derived from retroviruses and retrotransposons, which are suppressed by DNA methylation in the adult body. In addition, there is an abnormal increase in the level of methylation of the LINE-1 retrotransposon in the chorionic trophoblast in spontaneous abortions with both normal karyotype and aneuploidy on different chromosomes, which may be associated with impaired gene transcription using LINE-1 regulatory elements. To date, 988 genes that can be expressed from alternative LINE-1 promoters have been identified. Using the STRING tool, genes (NUP153 and YWHAB) were selected, the products of which have significant functional relationships with proteins highly expressed in the placenta and involved in trophoblast differentiation. This study aimed to analyze the expression of the NUP153 and YWHAB genes, highly active in the placenta, from canonical and alternative LINE-1 promoters in the germinal part of the placenta of spontaneous and induced abortions. Gene expression analysis was performed using real-time PCR in chorionic villi and extraembryonic mesoderm of induced abortions (n = 10), adult lymphocytes (n = 10), spontaneous abortions with normal karyotype (n = 10), and with the most frequent aneuploidies in the first trimester of pregnancy (trisomy 16 (n = 8) and monosomy X (n = 6)). The LINE-1 methylation index was assessed in the chorionic villi of spontaneous abortions using targeted bisulfite massive parallel sequencing. The level of expression of both genes from canonical promoters was higher in blood lymphocytes than in placental tissues (p < 0.05). However, the expression level of the NUP153 gene from the alternative LINE-1 promoter was 17 times higher in chorionic villi and 23 times higher in extraembryonic mesoderm than in lymphocytes (p < 0.05). The expression level of NUP153 and YWHAB from canonical promoters was higher in the group of spontaneous abortions with monosomy X compared to all other groups (p <0.05). The LINE-1 methylation index negatively correlated with the level of gene expression from both canonical (NUP153 - R = -0.59, YWHAB - R = -0.52, p < 0.05) and alternative LINE-1 promoters (NUP153 - R = -0.46, YWHAB - R = -0.66, p < 0.05). Thus, the observed increase in the LINE-1 methylation index in the placenta of spontaneous abortions is associated with the level of expression of the NUP153 and YWHAB genes not only from alternative but also from canonical promoters, which can subsequently lead to negative consequences for normal embryogenesis.

Influence of human peripheral blood samples preprocessing on the quality of Hi-C libraries.

The genome-wide variant of the chromatin conformation capture technique (Hi-C) is a powerful tool for revealing patterns of genome spatial organization, as well as for understanding the effects of their disturbance on disease development. In addition, Hi-C can be used to detect chromosomal rearrangements, including balanced translocations and inversions. The use of the Hi-C method for the detection of chromosomal rearrangements is becoming more widespread. Modern high-throughput methods of genome analysis can effectively reveal point mutations and unbalanced chromosomal rearrangements. However, their sensitivity for determining translocations and inversions remains rather low. The storage of whole blood samples can affect the amount and integrity of genomic DNA, and it can distort the results of subsequent analyses if the storage was not under proper conditions. The Hi-C method is extremely demanding on the input material. The necessary condition for successfully applying Hi-C and obtaining high-quality data is the preservation of the spatial chromatin organization within the nucleus. The purpose of this study was to determine the optimal storage conditions of blood samples for subsequent Hi-C analysis. We selected 10 different conditions for blood storage and sample processing. For each condition, we prepared and sequenced Hi-C libraries. The quality of the obtained data was compared. As a result of the work, we formulated the requirements for the storage and processing of samples to obtain high-quality Hi-C data. We have established the minimum volume of blood sufficient for conducting Hi-C analysis. In addition, we have identified the most suitable methods for isolation of peripheral blood mononuclear cells and their long-term storage. The main requirement we have formulated is not to freeze whole blood.

Comparision of fluorimetric and mass spectrometric methods for Fabry disease newborn screening.

Fabry disease is an X-linked hereditary lysosomal storage disorder caused by mutations in the GLA gene. Neonatal screening for Fabry disease in males is feasible by measurement of α-galactosidase A activity in DBS using either the mass spectrometric or fluorigenic substrate. The aim of the study: to assess the possibility of introducing the compared methods into the practice of neonatal screening. In the both assays performed a statistically significant difference of the enzyme activity between affected individuals and controls is reported. The slight modification of the fluorimetric method by centrifugation of a 96-well microplate before measurement could improve signal to noise ratio.

Generation of iPSC line ICGi024-A from human skin fibroblasts of a patient with ring chromosome 18.

Ring chromosome 18 is a rare chromosomal disorders that usually originate de novo and correlate with clinical manifestation: developmental delay as well as microcephaly, brain and ocular malformations, hypotonia and skeletal abnormalities. We generate iPSC clonal cell line ICGi024-A with pluripotency properties which were demonstrated in vitro by three germ layer differentiation capacity. ICGi024-A can be used for disease modeling and fundamental investigation of ring chromosome instability.

Establishment of an induced pluripotent stem cell line (ICGi025-A) from fibroblasts of a patient with 46,XY,r(8)/45,XY,-8 mosaicism.

Ring chromosomes are structural aberrations commonly associated with disease phenotype. We consider necessary to create the iPSCs with a ring chromosome 8, which can be used for disease modeling and related research. The ICGi025-A iPSCs line was obtained by the reprogramming of the skin fibroblasts from a 1-year-old boy with 46,XY,r(8)/45,XY,-8 mosaicism, developmental delay, microcephaly, dysmorphic features, diffuse muscle hypotonia, moderate proximal muscle weakness, feeding problems, and motor alalia. The iPSCs had expression of the pluripotency-associated markers. In vitro differentiated cells expressed the markers of the cells of three germ layers. That data allowed us to conclude that ICGi025-A cells were pluripotent.

Generation of four iPSC lines from two siblings with a microdeletion at the CNTN6 gene and intellectual disability.

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.

Generation of the induced pluripotent stem cell line, ICAGi002-A, from unaffected carrier megabase scaled duplication involving the CNTN6 gene.

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.

Induced pluripotent stem cell line, ICAGi001-A, derived from human skin fibroblasts of a patient with 2p25.3 deletion and 2p25.3-p23.3 inverted duplication.

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.

[Open, non-comparative phase III clinical study to evaluate the efficacy and safety of sapropterin in patients with phenylketonuria and hyperphenylalaninemia].

BACKGROUND: Phenylketonuria (PKU) is an autosomal recessive inherited disease associated with impaired metabolism of the amino acids phenylalanine (Phe) and tyrosine. The main criterion for diagnosis of PKU is high blood Phe level determined during neonatal screening. In case where PKU patient is responsive to tetrahydrobiopterin treatment, sapropterin restores the impaired activity of the enzyme phenylalanine hydroxylase, resulting in the stimulation of normal Phe metabolism and thereby enhancing patient tolerance to natural products. AIM: The present open, non-comparative clinical study was initiated to assess the degree and frequency of response after 8-day sapropterin administration and assess the safety of 6-week sapropterin treatment in patients with PKU and hyperphenylalaninemia. PATIENTS AND METHODS: The study enrolled 90 patients with PKU. The criterion of response to 8-day sapropterin therapy was the reduction of Phe blood levels ≥ 30% compared with the baseline value. RESULTS: Positive response to treatment was observed in 30 (33.3%) patients (95% CI 23.7-44.1). The mean percentage change in Phe blood levels after the 8-day response test period compared to Phe levels prior to dosing was 14.1 ± 28.4% in the overall subject population (95% CI 8.2-20.1) and 44.3 ± 15.1% in the subpopulation of patients with a positive response (95% CI 38.6-49.9). During the study, adverse events were reported in 24 (26.7%) patients in the overall population in 16 (53.3%) patients in the subpopulation who had a response. CONCLUSION: The study results confirmed the efficacy and safety of sapropterin therapy in patients with PKU, which is consistent with international clinical trials data.

[Clinical and genetic analysis of idiopathic intellectual disability based on array comparative genomic hybridization].

In this study authors searched for chromosomal aberrations in 71 children with developmental delay or idiopathic mental retardation using Human Genome CGH Microarray Kits 4×44K and 8×60K (Agilent Technologies, USA). Microdeletions and microduplications, as well as CNV, which may be related to intellectual disability and associated with regions of known hereditary diseases or chromosomal syndromes were identified in 14 (20%) children (these patients are described in this article). During the analysis, candidate genes localized within the regions of aberrations and associated with development and functioning of nervous system were denoted.

[Prevalence of hereditary pathology in Altai Republic]. / Rasprostranennost' nasledsvennoi patologii u naseleniia respubliki Altai.

Medical genetic study of the population of Altai Republic (Russia) has been performed. The population sample comprises 203 148 subjects, including 59 196 Altaians, 134 972 Russians, and 8980 Kazakhs. For each nosological group, the loads of Mendelian pathology with different modes of inheritance and their prevalence rates in urban and rural populations have been determined. Thirty-six autosomal dominant (AD) diseases have been found in a total of 121 subjects, with hereditary syndromes being the most prevalent. Autosomal recessive (AR) pathology is represented by 24 diseases found in 158 subjects, with metabolic disorders being the most prevalent; and X-linked pathology, by four diseases in nine subjects. The prevalence rate has been calculated for each nosological form in the district where it has been found. The loads of AD, AR, and X-linked pathologies in the urban population were, respectively, 2.98 and 9.62 per 1000 people and 0.56 per 1000 men in Altaians; 0.86 and 0.94 per 1000 people and 0.23 per 1000 men in Russians; 0.34 and 1.16 per 1000 people in Kazakhs. In the rural population, the genetic load has been calculated for each district. The spectrum of hereditary pathology in the populations studied is described.

[Epidemiology of congenital malformations in Gorno-Altaisk, Altai Republic, Russia]. / Epidemiologii vrozhdennykh porokov razvitiia v g. Gorno-Altaisk (Respublica Altai).

A retrospective epidemiological study has been performed using the data from healthcare institutions of the city of Gorno-Altaisk, Altai Republic, Russia for the period from 1983 to 2001. Congenital malformations (CMFs) have been studied in newborns, infants that died at ages under one year, and fetuses after 22 weeks of gestation. The most frequent malformations are those of the musculoskeletal and cardiovascular systems and multiple malformations, which account for 37.68, 18.22, and 8.9% of all congenital malformations, respectively. Their frequencies are 7.38, 3.57, and 1.74 per thousand, respectively. The frequency of congenital malformations subject to registration by the national system of CMF monitoring of the Russian Federation (21 malformation forms) is 6.08 per 1000 births and varies from 8.59 to 21.24. The frequency of the Down syndrome is 0.93 per 1000 births; it did not vary significantly during the period studied. The frequency of limb reduction deformities in the urban population of Altai Republic (0.32 per 1000 births) is higher than in other Siberian regions, including the cities of Kyzyl (Tyva Republic) and Tomsk and the Nyurba and Ust-Aldan uluses of Sakha Republic (Yakutia).

[Multiaberrant cell formation caused by exposure to internal densely-ionizing irradiation]. / Mul'tiabberantnye kletki pri vnutrennem obluchenii istochnikami plotno-ionizuiushchego izlucheniia.

The origin of multiaberrant cells (MACs) was studied by comparing the structure and intensity of chromosome damage in peripheral blood lymphocytes of two groups of people: workers of Siberian Chemical Plant differing in the content of plutonium-239 in their bodies, and inhabitants of a non-polluted settlement (control group). Plutonium-239 is known to be a long-lived densely-ionizing source of alpha-radiation with high linear energy delivery; therefore, it has a stronger effect on cell hereditary structures than gamma-rays. In persons with the content of plutonium-239 higher than 13 nCu, the frequency of MAC was 0.105% which at least tenfold exceeds the spontaneous level. The chromosome-type aberrations that are usually induced by ionizing radiation predominated in MACs. Our results suggest that MAC formation may be caused by internal body irradiation with the incorporated sources of densely-ionizing radiation.

[A search for mutations in the DIA1 gene in case of hereditary methemoglobinemia type I in the iakut population]. / Poisk mutatsii v gene DIA1 pri nasledstvennoi metgemoglobinemii I tipa v iakutskoi populiatsii.

In the patients with enzymopenic hereditary methemoglobinemia type I, a disease widely distributed on the territory of Yakutia, a search for the mutations in exons 3 and 4 of the DIA1 gene encoding NADH-cytochrome b5 reductase was carried out. It was shown that Yakut patients have none of three missence mutations, Arg57Gln, Leu72Pro, and Val105Met, described in case of this disease in the neighboring populations, Chinese and Japanese, inhabiting the territories south of Yakutia.

Characterization of a small supernumerary ring marker derived from chromosome 2 by forward and reverse chromosome painting.

A small ring-shaped supernumerary marker chromosome (SMC) was detected in 50% of metaphase cells in an 18-month-old boy with mental retardation and multiple congenital anomalies. Conventional cytogenetic methods had failed to identify the origin of the marker. When the patient was age 11.5 years, we defined the origin of the SMC by fluorescence in situ hybridization using a battery of centromere-specific DNA probes. The marker was positive with the probe for locus D2Z. More detailed characterization was achieved by using chromosome 2 arm-specific and marker-specific DNA libraries, which were constructed by microdissection of the two arms chromosome 2 and SMC with subsequent amplification of the chromosomal material by a degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR). The marker was identified as r(2)(p11.2-->q14.1). The propositus had dolichocephaly, coarse hair, low-set ears, exophthalmos, epicanthal folds, strabismus, depressed nasal bridge, high-arched palate, excess of skin on the neck, tapered fingers with mild clinodactyly, talipes varus on the right, inguinal hernia, hypogenitalism, muscular hypotonia, and mental retardation. This is the first case of SMC derived from chromosome 2 that was characterized by forward and reverse chromosome painting.

Keratosis pilaris and ulerythema ophryogenes associated with an 18p deletion caused by a Y/18 translocation.

We present a patient with partial monosomy of the short arm of chromosome 18 caused by de novo translocation t(Y;18) and a generalized form of keratosis pilaris (keratosis pilaris affecting the skin follicles of the trunk, limbs and face-ulerythema ophryogenes). Two-color FISH with centromere-specific Y and 18 DNA probes identified the derivative chromosome 18 as a dicentric with breakpoints in p11.2 on both involved chromosomes. The patient had another normal Y chromosome. This is a third report the presence of a chromosome 18p deletion (and first case of a translocation involving 18p and a sex chromosome) with this genodermatosis. Our data suggest that the short arm of chromosome 18 is a candidate region for a gene causing keratosis pilaris. Unmasking of a recessive mutation at the disease locus by deletion of the wild type allele could be the cause of the recessive genodermatosis.

[Identification of marker chromosomes and translocations in man using a computerized diagnostic database and fluorescent in situ hybridization]. / Identifikatsiia markernykh khromosom i translokatsii cheloveka s pomoshch'iu komp'iuternoi diagnosticheskoi bazy dannykh i fliuorestsentnoi gibridizatsii in situ.

Cytogenetic analysis revealed five carriers of supernumerary marker chromosomes and two carriers of unbalanced chromosome translocations in patients of the medical genetic consultation clinic. A new method for exact identification of such chromosome rearrangements requiring additional molecular cytogenetic diagnosis was proposed. The method involves computer analysis of abnormal phenotypic traits with the use of diagnostic databases and fluorescent in situ hybridization (FISH) to DNA probes specific for the most probable computer-selected chromosome syndromes. On average, the method allowed the number of necessary DNA probes to be decreased four times. In the tested patients, supernumerary marker chromosomes were shown to be derived from chromosomes 2, 9, and 15, and translocations were identified as dic(Y;18) and ins(6;21). Limited possibilities of using the method when (1) a chromosome syndrome is not clearly defined in a diagnostic system or (2) phenotypic expression of a marker chromosome is not significant are discussed. Presumably, the method will allow a reliable estimation of the efficiency of various diagnostic systems.

[Dynamics of the marital structure with respect to the nationality and birthplace of spouses in a modern urbanized Siberian population (as exemplified by Tomsk)]. / Dinamika struktury brakov po natsional'nosti i mestam rozhdeniia suprugov v sovremennoi urbanizirovannoi sibirskoi populiatsii (na primere g. Tomska).

To analyze a population's marital structure with respect to the ethnicity and birthplace of the spouses and to estimate the indices of endogamy, migration, and marriage assortativeness, the records of marriages in Tomsk during two periods of time (1970-1972 and 1985-1990) were studied. The parameters of the population-genetic and demographic structure proved to change during the studied period: the endogamy index and the indices of marriage assortativeness increased, and the migration index decreased. These data suggest that the genetic structure of the Tomsk urbanized population stabilized with time and that the intrapopulation subdivision decreased (a tendency for panmixia).

[Genetic-demographic characteristics of farming regions and small cities of the Tomsk district]. / Genetiko-demograficheskaia kharakteristika sel'skikh raionov i malykh gorodov Tomskoi oblasti.

In nine of the sixteen rural regions and three small towns in Tomskaya oblast, marriage structure with regard to birth place and ethnicity of spouses was genetically and demographically studied by selectively analyzing marriage records from 1970-1985. Migration processes of high intensity were shown to be characteristic of rural and urban inhabitants of Tomskaya oblast. High values of the migration index (0.56 for rural regions and 0.75 for small towns) and low values of the local endogamy index (0.22 and 0.08 respectively) were obtained. Analysis of marriage assortativeness according to birth place and ethnicity of spouses demonstrated, in total, low but statistically significant estimates of marriage assortativeness. Subdivision of oblast populations was determined mainly by ethnicity.