ABSTRACTBackgroundChromosome 3q29 duplication syndrome is a rare chromosomal disorder with a frequency of 1:5000 in patients with a neurodevelopmental phenotype. The syndrome is characterized by phenotypic polymorphism and reduced penetrance.MethodsPatients were investigated by performing a cytogenetic analysis of GTG‐banded metaphases, aCGH with the SurePrint G3 Human CGH Microarray 8×60K, qPCR, FISH, and WES.ResultsHere, we report five new patients with atypical duplications overlapping with the 3q29 duplication syndrome region and no other genetic findings. In two patients, duplications were found in the single BDH1 gene, a candidate gene for the 3q29 duplication phenotype. For the first time, we delineated and described the smallest minimal critical region, including the single BDH1 gene; in our patients, this region was associated with ASD, heart defects, biliary tract dysfunction, and obesity. The frequencies of the pathological phenotypes in duplication carriers reported in the literature were calculated and compared with those in patients with 3q29 deletions. Most of the phenotypes were observed in both groups but were significantly less common among individuals with 3q29 duplications. Mirrored phenotypes in patients with duplications and deletions included overweight and weight deficit. Schizophrenia, generalized anxiety disorder, and recurrent ear infections were unique phenotypes of patients carrying deletions.ConclusionChromosome 3q29 duplication syndrome is characterized by a complex genetic architecture and clinical polymorphism.

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).

The process of tuning of the piezoelectric filter consists in lowering the frequencies of the resonators as a result of removing the electrode layer by means of ion-beam etching (IBE) in an inert gas atmosphere. It is necessary to control frequencies of the first and second resonators, as well as the frequency spacing (distance between frequencies of the upper and lower resonances of the piezo system), dynamic impedance of partial resonators and insertion attenuation. We present the results of using ion-beam etching in tuning monolithic piezoelectric filters on volumetric acoustic waves. It is shown that tuning should be performed using frequencies of the upper and lower resonances of the piezo system under control of the insertion attenuation. It is also necessary to exclude the control operations for the frequencies of the first and second resonators. The optimum parameters of ion-beam etching electrodes of the resonators are determined: working pressure — 1.33 × 10 – 5 Pa, working gas flow — 1.75 m 3 · Pa/sec, ion beam energy — 1 keV, ion current density — 6 mA/cm 2 . Moreover, the dependence of the insertion damping and dynamic resistance on the frequency of the resonator was revealed. Characteristics of the obtained monolithic quartz filter are presented: nominal frequency — 21400.681 MHz, bandwidth by –3 dB — 32.66 kHz, insertion loss 0.5 dB. The obtained results can be used when tuning sections with smaller electrodes for filters at higher frequencies.

Interpreting the clinical significance of small supernumerary marker chromosomes (sSMCs) in prenatal diagnosis is still an urgent problem in genetic counselling regarding the fate of a pregnancy. We present a case of prenatal diagnosis of mosaic sSMC(10) in a foetus with a normal phenotype. Comprehensive cytogenomic analyses by array-based comparative genomic hybridization (aCGH), sSMC microdissection with next-generation sequencing (NGS) of microdissected library, fluorescence in situ hybridization (FISH) with locus-specific and telomere-specific DNA probes and quantitative real-time PCR revealed that sSMC(10) had a ring structure and was derived from the pericentromeric region of chromosome 10 with involvement of the 10p11.21-p11.1 and 10q11.21-q11.23 at 1.243 Mb and 7.173 Mb in size, respectively. We observed a difference in the length of sSMC(10) between NGS data of the DNA library derived from a single copy of sSMC(10), and aCGH results that may indicate instability and structural mosaicism for ring chromosomes in foetal cells. The presence of a 9 Mb euchromatin region in the analysed sSMC(10) did not lead to clinical manifestations, and a healthy girl was born at term. We suggest that the ring structure of sSMCs could influence sSMC manifestations and should be taken into account in genetic counselling during prenatal diagnosis.

Пренатальная диагностика хромосомных болезней в Томске и Томской области является неотъемлемой частью оказания медико-генетической помощи населению. В НИИ медицинской генетики внедрены эффективные методы хромосомного анализа практически на любом сроке беременности. За последние пять лет в клинико-диагностической лаборатории проведено 3503 пренатальных цитогенетических исследования, хромосомная патология выявлена в 300 случаях (8,5%). Наибольший процент хромосомной патологии отмечен в группе беременных после прохождения биохимического скрининга 1 триместра - 11,5%. При стандартном цитогенетическом исследовании исключается носительство анеуплоидий и полиплоидий, аномалий структуры хромосом, однако микроструктурные перестройки хромосом часто остаются не выявленными. Только применение комплексного молекулярно-цитогенетического обследования позволяет исключить хромосомную патологию с максимальной вероятностью. Prenatal diagnosis of chromosomal diseases in Tomsk and the Tomsk region is an integral part of the medical care. In the Research Institute of Medical Genetics of Tomsk National Research Medical Center effective methods for chromosomal analysis at almost any gestational age are widely used. In the past five years, 3503 prenatal cytogenetic studies have been carried out and 300 cases (8,5%) of chromosomal abnormalities were detected. The highest percentage of chromosomal pathology (11,5%) was found in pregnant women within first trimester biochemical screening. A standard cytogenetic studying allows eliminates aneuploidy and polyploidy, structural anomalies, especially if they disrupt the morphology of chromosomes, but submicroscopic chromosomal abnormalities often remains not identified. Using of complex molecular cytogenetic technologies allows to exclude chromosomal pathology with the maximum probability.

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.

To carry out the cytogenetic study of chromosome aberrations in epithelial tissue of the stomach, the patients were divided into 2 groups. Group I comprised 24 patients with chronic gastritis (12 patients with metaplasia and dysplasia and 12 patients without morphological changes in the epithelium). Group II consisted of 10 patients with histologically verified intestinal-type gastric cancer. Chromosome aberrations were detected in 9 of the 12 patients (75 %) having no morphological changes in the epithelium (15q11.2-q26 deletion was found in 66 %). In patients with epithelial dysplasia, amplification of the chromosomal region 3р12-р23 was most frequently found (55,5 %). The cytogenetic analysis showed the evidence of chromosome aberrations in all studied epithelial samples, while in cells of chronic inflammation focus, aberrations were detected in 70 % of patients. Deletions in chromosomal regions 19p13.2, 19q13.1-q13 and 18q12-q21 were frequently observed in tumor-adjacent epithelial tissue (30 %), while in tumor cells, the frequent chromosomal aberrations were deletions in chromosomal regions 5q12-q23 (30 %) and 18q11.2-q21(30 %) as well as amplifications 20p11.2-p13 (20 %).

Molecular-cytogenetic characteristics of gastric tissues were studied in 10 patients with chronic erosive gastritis. Chromosomal abnormalities were detected in 8 patients. Amplifications at 3p12-23 (37,5 %) with minimal overlapping regions 3p14 and 3p22 as well as 3q13.1-27 (37,5 %) with common regions 3q25-26.2 and 3q26.1 were the most common abnormalities followed by amplifications at 2p12-23 (25 %) with minimal regions 2p16; 2q14.1-32 (25 %) with minimal common region 2q31; 4q24-25 (25 %) with minimal overlapping region 4q25 as well as amplifications at 6q21 (25 %) and 6q22-24 (25 %). Furthermore, in one of the cases (№ 7), a trisomy of chromosome 19 was detected. The fact of the presence of high level of unbalanced chromosomal aberrations deserves great attention as a factor associated with development of dysplastic changes.

Chromosomal abnormalities are typical for almost all tumors, including breast cancer. The spectrum and frequency of chromosomal aberrations in breast aissues with benign (n=4) and malignant neoplasms (n=23) were investigated in 23 women using high-resolution comparative genomic hybridization. Multiple chromosomal abnormalities, including those specific to the breast cancer, were revealed in both groups. The presence of common chromosomal aberrations was found in tissues of patients with benign and malignant tumors providing evidence for a new cytogenetic marker of malignancy risk estimation. Our results indicate the possibility of application of the molecular-cytogenetic analysis in the diagnosing of chromosomal aberrations in benign tumors to predict the risk of the breast cancer.

Comparative Genomic Hybridization (CGH) is a molecular cytogenetic method for detecting chromosomal imbalances by comparing the copy number of DNA sequences in cells of tested tissue and the reference specimen. CGH is based on two-color fluorescence suppressive in situ hybridization of genomic test and reference DNAs, each labeled with a different fluorochrome, to metaphase chromosomes of a healthy individual. First described by Kallioniemi et al. in 1992, the CGH assay has been widely used for identification and characterization of both numerical and unbalanced structural chromosome abnormalities in cells of different tissues at various pathological conditions in humans, especially in tumor diseases. We discuss the specific features and quality control of comparative genomic hybridization, its advantages and limitations in detection of genomic imbalance and the prospects for development of this technology.

Comparative genomic hybridization (CGH) technique was used to examine a set of ten spontaneous abortions whose cell cultures were characterized by the lack of proliferation in vitro, and thereby, were not available for the analysis by means of routine cytogenetic methods. Five abortions (50%) had aneuploidy of autosomes, including trisomy 10, 14, 18, and 21, and monosomy 22. The latter variant of unbalanced chromosomal abnormalities is rarely detected in spontaneous abortions by use of conventional cytogenetic methods. The results were validated by using fluorescent in situ hybridization (FISH) analysis with centromere-specific DNA probes. Embryos with trisomy 10 and monosomy 22 displayed mosaicism with the frequencies of abnormal cell clones constituting 68 and 33% respectively. The advantages and limitations of the applying of CGH technique for detection of genomic abnormalities in both nonmosaic and mosaic forms are discussed.