Background Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type—whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs). Methods We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy. Results Applied to 66 human samples Exo-C achieved 100% recall and 73% precision in detecting chromosomal translocations and SNVs. We further benchmarked its performance for inversions and CNVs and demonstrated its utility in detecting mosaic SVs and resolving diagnostically challenging cases.
Conclusions Through several case studies, we demonstrate how Exo-C’s multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders.

Background and objectives: In the post-genomic era, long non-coding RNAs (lncRNAs) have emerged as critical regulators in various cancers and hold potential as minimally invasive diagnostic biomarkers. This study aimed to perform microarray analysis of the peripheral blood mononuclear cell (PBMC) transcriptome to evaluate differential lncRNA expression in women with luminal A breast cancer. Methods: A one-color microarray analysis was conducted using SurePrint G3 Human Unrestricted 8×60K arrays and a SureScan Microarray Scanner (Agilent Technologies, USA). The study cohort comprised 16 participants: eight patients diagnosed with luminal A breast cancer and eight healthy controls. Bioinformatic analysis was performed using the “limma” and “tidyverse” packages in the R statistical environment. Functional enrichment analysis was conducted to identify significantly differentially expressed gene clusters. The false discovery rate-adjusted p-value (padj) was applied to ensure methodological rigor. Associations between lncRNAs and disease progression were explored using the LncRNADisease 2.0 database. Results: Differential expression was observed for long intergenic non-coding (LINC), LOC, and antisense RNA genes. Notably, LINC RNA 974 (LINC00974) exhibited significant differential expression (log fold change > |1.5|, padj < 0.05) after multiple comparison correction. Analysis using the LncRNADisease 2.0 database revealed associations between LINC and antisense RNAs and other oncological disorders. Conclusions: This study is the first to demonstrate differential lncRNA expression in PBMCs of patients with luminal A breast cancer. Despite the limited sample size, the study demonstrates statistically significant differences between groups, highlighting the potential of PBMC-derived lncRNAs as minimally invasive biomarkers. These findings enhance our understanding of the utility of PBMC-derived lncRNAs as biomarkers for breast cancer.

Background. Studies of comorbid (syntropic) and inversely comorbid (rarely occurring together, i.e., dystropic) diseases have focused on the search for molecular causes of this phenomenon. Materials. We investigated DNA methylation levels in regulatory regions of 23 apoptosis-associated genes as candidate loci associated with the “cancer–neurodegeneration” dystropy in patients with Huntington’s disease (HD) and patients with non–small cell lung cancer (LC). Results. Statistically significant differences in methylation levels between the HD and LC groups were found for 41 CpG sites in 16 genes. The
results show that five genes (SETDB1, TWIST1, HDAC1, SP1, and GRIA2) are probably involved in the phenomenon of inverse comorbidity of these diseases. For these genes, the methylation levels of the studied CpG sites were altered in opposite directions in the two groups of patients, compared to the control group. Conclusions. For the SP1 gene, the above hypothesis is supported by our analysis of open-access data on gene expression in patients with the aforementioned diagnoses and fits a probable mechanism of the “HD–LC” dystropy.

Since 2023, the Russian Federation (RF) has implemented an expanded newborn screening (NBS) program for 36 hereditary disorders, which now includes 5q spinal muscular atrophy (5q SMA). As a result of newborn screening for 5q SMA conducted in the RF during 2023–2024, 288 newborns with a homozygous deletion of exon 7 in the SMN1 gene were identified by molecular genetic methods. The overall observed incidence of 5q SMA was 1 in 8439 newborns, which does not significantly differ from the expected incidence of 1 in 7953 newborns, established by previous pilot screening projects (p > 0.05). A comparison
of the genotypes of patients identified through selective and newborn screening showed statistically significant differences in the proportions of patients carrying two, three, and four or more copies of the SMN2 gene. These findings demonstrate that the NBS program is effective in detecting both individuals with more severe phenotypes, as expected, and those with milder forms of the disease.

COVID-19 – тяжелая острая респираторная инфекция, вызванная вирусом SARS-CoV-2. Исследования в области генетики организма-хозяина способствуют открытию новых геномных маркеров прогрессирования коронавирусной инфекции. В представленной статье разработан метод мультиплексного генотипирования однонуклеотидных полиморфных вариантов генов, ассоциированных с тяжестью течения COVID-19, основанный на многолокусной ПЦР и MALDI-TOF-масс-спектрометрии молекул ДНК. Охарактеризованы частоты 45 однонуклеотидного полиморфизма генов кандидатов COVID-19 в популяционной выборке русских г. Томска. Полученные результаты сопоставлены с данными для мировых популяций из проекта “1000 геномов”.

Коронавирусная инфекция COVID-19 – быстро распространившееся по всему миру и переросшее в глобальную пандемию в 2020 г. инфекционное вирусное заболевание. Клинические проявления COVID-19 разнообразны и варьируют от полного отсутствия симптомов до развития дыхательной недостаточности и летального исхода. На сегодняшний день этиологические основы особенностей течения COVID-19 до конца не изучены, предполагается участие множества факторов, в том числе генетических. В настоящей работе проведен репликативный анализ ассоциации с тяжестью течения COVID-19 варианта последовательности rs73064425 гена LZTFL1, связанного по результатам GWAS с развитием тяжелой формы COVID-19. Полученные данные свидетельствуют о наличии ассоциации между однонуклеотидным изменением rs73064425 гена LZTFL1 и тяжелой формой COVID-19 в популяции русских г. Томска. Обсуждаются возможные механизмы вовлечения изученного SNV в патогенетику заболевания. Обнаружена вариабельность частот рискового аллеля Т rs73064425 в популяциях мира.

The Forest and Tundra Nenets in different areas of the Yamalo-Nenets Autonomous Okrug were studied using Y-chromosome markers. The results of analyzing the genetic structure of Nenets clans using 44 STR markers of the Y chromosome are presented, taking into account their presence in subethnoses (Tundra and Forest Nenets), as well as to the Kharyuchi (“true Nenets”) and Vanuito (“foreigners”) phratries. The number of the Nenets (N = 606) includes the Tundra (N = 536) and Forest (N = 70) Nenets. Sublineage N1a2b1b1a~-B170 is specific for the clans in the Kharyuchi phratry, and sublineage N1a2b1b1b-B172, for the clans in the Vanuito phratry. Most Forest Nenets clans have haplogroup N1a2b1-B478. All males of the Pyak clan, which is prevalent in the Forest Nenets, have a specific haplogroup, N1a1a1a1a2a1c1~. The results of the study suggest that the Nenets clan associations typically have a common ancestor in the male line and are characterized by a recent founder effect. Each Nenets clan has its own specific cluster of haplotypes, equidistant from each other. The structure of Y-chromosome haplotypes and haplogroups in the Nenets gene pool includes the Nenets heritage from the Khanty and Enets. Many samples from these sample sets were shown to have rare haplotypes that were absent from the baseline data and to differ significantly from the other haplotypes found in the populations. They belong to various rare branches of the Y-chromosome haplogroups found only in these sample sets. Some samples form haplotype variants that have not been described previously and allow us to characterize the phylogeny of these lineages in more detail. The Forest and Tundra Nenets differ greatly in the composition of haplogroups, which is fully consistent with ethnological and linguistic data on the origin of these populations. The predominant haplogroups are N1a1a1a1a2a1c1~-Y13850, Y13852, Y28540 CTS9108 (xY24219, Y24375) and N1a2b1-B478, Z35080, Z35081, Z35082, Z35083, Z35084 (xB169) in the Forest Nenets, and N1a2b1b1a~-B170 (xZ35104), N1a1a1a1a2a1c~-Y13850, Y13852, Y13138, PH3340 (xY24219, Y24365) and N1a2b1b1b-B172, Z35108 in the Tundra Nenets.

Genetic mechanisms regulating gene expression encompass complex processes such as transcription, translation, epigenetic modifications, and interactions of regulatory elements. These mechanisms play a crucial role in shaping phenotypic diversity in humans. High-throughput technologies, such as expression microarrays and next-generation sequencing (NGS), have enabled precise analysis of transcripts for thousands of genes genome-wide. These methods have enabled researchers to measure gene expression levels in various tissues and cells and to gain deeper insights into previously inaccessible biological processes. Numerous studies show that gene expression varies significantly among individuals. However, there are also notable differences between populations from different continental groups, driven by genetic, epigenetic, environmental factors, and natural selection. Furthermore, disease states represent an important factor influencing gene activity, as they can significantly alter the transcriptomic profiles of individual cells. In this context, comparative population genetic studies help uncover the molecular mechanisms underlying complex phenotypic traits and identify population-specific features of transcriptomic profiles in both health and disease. However, despite significant progress in this field, many aspects remain underexplored. Specifically, the distribution of gene expression variability among populations, the degree of research coverage for specific ethnic groups, the spectrum of biological materials used, and the contribution of population affiliation to observed differences in gene expression during pathological conditions require further investigation. This review presents an overview of contemporary research focused on analyzing variability in expression profiles across different human populations. It summarizes findings from individual studies, outlines the advantages and limitations of the methods employed, highlights key research directions in population transcriptomics, and discusses potential practical applications of the data obtained.

Crouzon syndrome, which is a hereditary craniosynostosis, can be the result of inheritance from either parent, as well as de novo mutations in the FGFR2 gene. With a confirmed molecular genetic diagnosis, preimplantation genetic testing for monogenic diseases (PGT-M) is available for high-risk families. However, there is currently little information in the literature about using this approach to prevent this condition. The aim of our study was to describe the clinical case of IVF/ICSI with PGT-M for Crouzon syndrome with a successful outcome and confirmatory diagnostics. PGT-M was planned and performed for a married couple (aged 24 and 25), in which the husband had Crouzon syndrome. The husband’s father had a milder form of Crouzon syndrome and the pathogenic variant of the FGFR2 gene was in a mosaic form. During preparation, a testing system was selected for the pathogenic variant NM_000141.5(FGFR2):c.1007A>G (p.Asp336Gly) of the FGFR2 gene, and gene-linked polymorphic microsatellite markers. The STR markers in the husband’s father excluded chimerism for the pathogenic variant and indicated mosaicism with the involvement of germ cells. Molecular genetic analysis was performed using а nested PCR, with detection by fragment analysis for STRs and restriction analysis of the pathogenic variant. During the IVF program, superovulation stimulation and embryological procedures were performed according to standard protocols. Fertilization was achieved using the ICSI method, and blastocyst biopsy was done on the sixth day of development. For PGT-M, a direct analysis of pathogenic variants and an indirect analysis of selected informative STRs were used. The thawed embryos were transferred based on the results of preimplantation testing. We selected twelve STRs flanking the FGFR2 gene, eight informative ones were used during PGT-M. In the IVF program, 15 mature oocytes were obtained, then four blastocysts were biopsied. One of the four embryos inherited a normal paternal chromosome, the other three had the pathogenic variant and the associated risk haplotype. A singleton pregnancy has occurred as a result of embryo transfer recommended after PGT-M. Following the child’s birth, molecular diagnostics were performed, confirming the PGT-M result. The presented clinical case provides an effective example of IVF with PGT-M to prevent the birth of affected children in families with hereditary craniosynostosis.

Human mitochondrial DNA (mtDNA) exhibits high population-level polymorphism. While certain pathogenic mtDNA variants are known to cause hereditary mitochondrial syndromes, often presenting with cardiac arrhythmias, life-threatening ventricular tachycardia (VT) itself is a major risk factor for sudden death in cardiovascular diseases. The aim of the work was to study rare (“private”) missense substitutions in the mtDNA of patients with documented episodes of ventricular tachycardia in comparison with patients with ischemic heart disease without life-threatening heart arrhythmias and individuals without clinical manifestations of cardiovascular diseases. The sequencing of mtDNA was performed using high-throughput sequencing methods. Specialized algorithms predicting the effect of gene variants were used to assess the effect of missense substitutions. Comparative analysis of the spectrum of the identified amino acid substitutions in the studied groups showed that about 40 % of the individuals in all three groups were carriers of “private” missense variants in mtDNA. However, among such substitutions, the variants classified by the APOGEE2 predictor as “variants of uncertain significance” (VUS) were more common in the group of patients with heart arrhythmias than in the control group, where “private” missense substitutions of the VUS category were not detected (p = 0.0063 for Fisher’s exact test). In addition, the groups differed in their phred-ranked Combined Annotation Dependent Depletion (CADD) scores, which were lower for individuals in the control group. The results indicate that rare mtDNA variants may contribute to predisposition to cardiovascular disease – in particular, to the risk of developing ventricular tachycardia by some patients.

Interstitial deletions of the short arm of chromosome 6 are even rarer than distal deletions of 6p24-pter, with an incidence rate of 1:1,000,000 (according to MalaCards, https://www.malacards.org/). These deletions are associated with developmental delays, autism spectrum disorders, congenital anomalies, and dysmorphic features. The objective of our study was to identify chromosomal abnormalities in twins from a Yakut family exhibiting severe psycho-speech developmental delays, intellectual disability combined with dysmorphisms, and congenital anomalies. In this paper, two new cases involving monozygotic twins from a Yakut family, who underwent array comparative genomic hybridization (aCGH), were reported. The diagnostic results revealed a rare interstitial deletion in the region 6p22.3-p24.3, measuring 7.5 Mb, which was subsequently confirmed using a conventional cytogenetics (GTG-banding) method. According to the cytogenetic analysis, the karyotypes of the parents were normal, indicating a de novo structural chromosomal rearrangement in the patients. Additionally, a comparative phenotypic analysis of these twins with each other and with other previously reported patients was performed; they were found to have overlapping deletions in the 6p22-p24 region. Furthermore, a literature review and an analysis of the gene content of the deleted region 6p22.3-p24.3 were conducted, and so was a discussion of the genotype-phenotype correlation. The results of the phenotypic analysis revealed both common and distinct dysmorphogenic features, including craniofacial dysmorphisms, deformities of the auricles, and abnormalities in the development of the upper and lower limbs, which are often mentioned in the literature. However, the analyzed data, both from the literature and our observations, showed that all patients lacked a common deleted region in the 6p22-p24 area, creating challenges in establishing an accurate diagnosis. The findings indicate the complexity of defining the minimally overlapping region responsible for the observed phenotypic and behavioral traits and highlight the importance of a systematic and multi-level approach to diagnosing severe psycho-speech developmental delays.

Transposable elements (TEs), comprising over one-third of the human genome, play a crucial role in its evolution, serving as a significant source of regulatory sequences. Under normal circumstances, their activity is tightly controlled by DNA methylation mechanisms; however, the effectiveness of this suppression varies substantially across tissues. The placenta, characterized by global hypomethylation, represents a unique environment where retroviruses and retrotransposons, typically silenced in somatic cells, gain the opportunity for activation. This distinct epigenetic landscape of the placenta allows transposons to participate in the regulation of genomic activity, influencing processes ranging from early embryogenesis to postnatal development. DNA hypomethylation in the placenta not only promotes TE mobilization, but also opens the possibility of using their components as independent genes and regulatory elements – promoters, enhancers, and other functional modules. These elements are involved in key aspects of placental development, including syncytiotrophoblast formation, extravillous trophoblast invasion, spiral artery remodeling, and endometrial decidualization. Importantly, TEs can serve as sources of alternative promoters for neighboring genes, and ancient mammalian transposons contain multiple transcription factor binding sites, enabling coordinated regulation of genes sharing a common function. Despite the growing interest in the role of transposable elements in placental development and function, many questions remain unanswered. In particular, the mechanisms of non-long terminal repeat (non-LTR) retrotransposon function during pregnancy remain poorly understood. A deep understanding of these processes is necessary to elucidate regulatory disorders in the placenta associated with major obstetric syndromes. This review examines the contribution of transposable elements to the functioning of the human genome, particularly their impact on gene expression, in the context of pregnancy and placental development.

Genetic factors contribute to the etiology of intellectual disability in 25–50 % of cases. Chromosomal abnormalities, such as microdeletions and microduplications, are the most significant genetic causes. We examined a family where two boys, aged 8 and 7, were diagnosed with mild intellectual disability. Using array-based comparative genomic hybridization, we detected a duplication of Xq28 in both brothers on the X chromosome inherited from a healthy mother with skewed (88 %) X-chromosome inactivation. The size of the rearrangement is 439.6 kilobases (kb). Eight genes are located in this region, including F8, MTCP1, BRCC3, VBP1, RAB39B, CLIC2, FUNDC2, and CMC4. This chromosomal region overlaps with the region of Xq28 duplication syndrome (OMIM 300815), characterized by intellectual disability, behavioral and psychiatric disorders, recurrent infections, atopic diseases, and specific facial features in affected male individuals. Whole-exome sequencing did not reveal pathogenic or likely pathogenic variants associated with neurodevelopmental disorders. These disorders have been previously linked to X-linked recessive single-nucleotide variants in RAB39B (OMIM 300271, 311510) and CLIC2 (OMIM 300886). An assessment of the clinical significance of the identified duplication, using the AutoCNV internet resource and original data, allowed us to classify this variant as pathogenic. This implies that the identified duplication may be the cause of intellectual disability in patients.

Администрация и коллектив Томского НИМЦ, Научно-исследовательского института медицинской генетики Томского НИМЦ, Российское общество медицинских генетиков, редакционная коллегия журнала «Медицинская генетика» сердечно поздравляют Вадима Анатольевича Степанова с юбилеем, желают здоровья, благополучия, верных единомышленников и учеников на творческом пути, неиссякаемой энергии и новых свершений на благо генетики человека и медицинской генетики.