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95 Publications visible to you, out of a total of 95
The Topology of the Grapevine Genome – Admixture meets SOMmelier

Abstract (Expand)

Inferring the genetic structure of populations at the subpopulation level is crucial for understanding the evolutionary forces and demographic histories that shape genetic diversity. Among the most … widely used approaches in population genetics are methods based on admixture and structure modeling—named after the respective software tools—which have become standard due to their intuitive, interpretable outputs. In this study, we address a key methodological question: how does traditional admixture-based decomposition of genetic components in multilocus population data relate to clustering approaches that leverage machine learning, specifically Self-Organizing Maps (SOMs)? We implemented this approach through our custom SOM-based tool, SOMmelier, which enables the portrayal of genetic structure by identifying modules of co-mutated SNPs and arranging them in a topology-aware genetic landscape. In this context, topology-awareness refers to the organization of genetic modules in a two-dimensional map, where their spatial proximity reflects mutual similarity. As a case study, we applied SOMmelier to investigate the population genetics of European grapevine. Based on prior literature, we considered up to six genetic components, which formed a genetic landscape that closely mirrors the geographic expanse of the classical Mediterranean world—from Western Asia through the Caucasus to Western Europe. The resulting topology reflects the dynamic spatial and temporal nature of grapevine domestication and diffusion. SOMmelier thus represents a complementary and powerful framework for genetic data analysis. By integrating the topological structure of SNP co-variation, it offers new perspectives on population structure, evolutionary history, and trait associations in grapevine—and has broader applicability to other species and systems in population genetics.

Author: Anush Baloyan, Tomas Konecny, Emma Hovhannisyan, Nate Zadirako, Maria Nikoghosyan, Hans Binder

Date Published: No date defined

Publication Type: Unpublished

SARS-CoV-2 detection by extraction-free qRT-PCR for massive and rapid COVID-19 diagnosis during a pandemic in Armenia

Abstract (Expand)

COVID-19 pandemic severely impacted the healthcare and economy on a global scale. It is widely recognized that mass testing is an efficient way to contain the spread of SARS-CoV-2 infection as well as … aid in the development of informed policies for disease management. However, the current COVID-19 worldwide infection rates increased the demand for rapid and reliable screening of infection. We compared the performance of qRT-PCR in direct heat-inactivated (H), heat-inactivated and pelleted (HC) samples against RNA in a group of 74 subjects (44 positive and 30 negative). Then we compared the sensitivity of HC in a larger group of 196 COVID-19 positive samples. Our study suggests that HC samples show higher accuracy for SARS-CoV-2 detection PCR assay compared to direct H (89 % vs 83 % of the detection in RNA). The sensitivity of detection using direct samples varied depending on the sample transport and storage media as well as the viral loads (as measured by qRT-PCR Ct levels). Altogether, all the data suggest that purified RNA provides more accurate results, however, direct sample testing with qRT-PCR may help to significantly increase testing capacity. Switching to the direct sample testing is justified if the number of tests is doubled at least.

Authors: Diana Avetyan, Andranik Chavushyan, Hovsep Ghazaryan, Ani Melkonyan, Ani Stepanyan, Roksana Zakharyan, Varduhi Hayrapetyan, Sofi Atshemyan, Gisane Khachatryan, Tamara Sirunyan, Suren Davitavyan, Gevorg Martirosyan, Gayane Melik-Andreasyan, Shushan Sargsyan, Armine Ghazazyan, Naira Aleksanyan, Xiushan Yin, Arsen Arakelyan

Date Published: No date defined

Publication Type: Journal

Genetic Variations Associated with Brain Disorders: Focus on Synaptic Plasticity and Apoptosis Regulatory Genes in Schizophrenia, Posttraumatic Stress Disorder and Ischemic Stroke

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Epidemiologic, clinical and experimental data indicates that a majority of brain disorders including schizophrenia (SCZ), posttraumatic stress disorder (PTSD), and ischemic stroke (IS) are multifactorial … disorders with strong and complex genetic component. Identification of all genetic variations associated with these disorders may sufficiently contribute to understanding of their basic pathomechanisms and encourage development of new innovative approaches to their early diagnosis and treatment. The aim of this review article is to provide overview of our recent studies on evaluation of potential association of SCZ, PTSD and IS with functional single nucleotide polymorphisms (SNPs) of synaptic plasticity and apoptosis regulatory genes in Armenian population. Here, our attention was focused on genes encoding netrin G1 (NTNG1), brain-derived neurotrophic factor (BDNF), complexin-2 (CPLX2), nerve growth factor (NGF) and its receptor (NGFR), annexin family proteins - annexin A5 and annexin A11 (ANXAV, ANXA11), and B-cell lymphoma 2 (Bcl-2) family proteins - Bcl-2 proper and Bcl-2-associated X protein (BCL2, BAX). Genomic DNA samples of diseased and healthy individuals were genotyped for a number of SNPs of the mentioned genes using polymerase chain reaction with sequence-specific primers (PCR-SSP). The significance of differences in genotype and allele frequencies and minor allele carriage between patients and healthy control subjects was determined using Pearson’s Chi-square test. P-values less than 0.05 were considered statistically significant. Significant associations were found between: (1) SCZ and BDNF rs6265, CPLX2 rs1366116, rs3892909, NGF rs6330, rs4839435, NGFR rs734194, rs11466155, rs2072446, ANXAV rs11575945, BAX rs1057369 SNPs; (2) PTSD and CPLX2 rs1366116, BCL2 rs956572 SNPs; (3) IS and NTNG1 rs628117, CPLX2 rs1366116, ANXAV rs11575945 SNPs. The obtained results indicated the involvement of genetically determined alterations in synaptic plasticity and apoptosis in pathomechanisms of SCZ, PTSD and IS. The minor T allele of the CPLX2 gene rs1366116 polymorphism represents risk factor for all studied diseased conditions indicating important functional significance of this genetic variation in maintenance of synaptic plasticity. Another important conclusion of these studies is that minor alleles of some polymorphic variants of genes, encoding synaptic plasticity and apoptosis regulatory proteins, may play a protective role relative to SCZ decreasing the risk for development of this disorder. In summary, our studies emphasize the important contribution of changes in synaptic plasticity and apoptosis regulation to pathomechanisms of SCZ, PTSD, and IS as well as significant input of genetic factors to these changes.

Authors: Anna Boyajyan, Ani Stepanyan, Diana Avetyan, Hovsep Ghazaryan, Sofi Atshemyan, Roksana Zakharyan, Kristina Pirumyan, Gohar Tsakanova

Date Published: No date defined

Publication Type: Journal

Genetic polymorphisms of complement factor H in schizophrenia and ischemic stroke

Abstract (Expand)

Objectives: Alterations in the immune response are involved in pathogenesis of many neuropsychiatric disorders including schizophrenia and stroke. Our recent studies indicated alterations in the … complement system, including hyperactivation of the alternative complement pathway in patients with schizophrenia and ischemic stroke. In the present study we investigated functional single nucleotide polymorphisms (SNPs) of gene encoding factor H (CFH), a negative regulator of the alternative complement cascade, in patients with schizophrenia, ischemic stroke, and healthy controls. Methods: Genomic DNA samples of study subjects were genotyped using polymerase chain reaction with sequence specific primers. The distribution of genotypes for the selected SNP was checked for correspondence to the H–W equilibrium. In order to investigate potential association of the selected polymorphisms with schizophrenia and stroke, their allele and phenotype frequencies in patients and control subjects were compared using Pearson’s chi-squared test. Results: According to the results obtained, CFH rs424535 (2783- 526T >A) SNP was positively associated with schizophrenia, while have no association with stroke. On the contrary, CFH rs800292 (184G >A) SNP was positively associated with stroke and no association between this SNP and schizophrenia was found. Conclusions: In summary, we concluded that rs424535*A minor allele of the CFH gene may represent a risk factor for schizophrenia, and rs800912 minor allele of the CFH gene might be considered as a risk factor for ischemic stroke.

Authors: A. Boyajyan, H. Ghazaryan, A. Stepanyan, R. Zakharyan

Date Published: No date defined

Publication Type: Journal

Association of Genetic Variants of Dopamine and Serotonin In Schizophrenia

Abstract (Expand)

Background Several studies indicated that antipsychotic treatment response and side effect manifestation can be different due to inter-individual variability in genetic variations. Aim of the study … Here we perform a case-control study to explore a potential association between schizophrenia and variants within the antipsychotic drug molecular targets (DRD1, DRD2, DRD3, HTR2A, HTR6) and metabolizing enzymes (CYP2D6, COMT) genes in Armenian population including also analysis of their possible relationship with disease clinical symptoms. Methods A total of 18 SNPs was studied in patients with schizophrenia (n = 78) and healthy control subjects (n = 77) using MassARRAY genotyping. Results: We found that two studied genetic variants, namely DRD2 rs4436578*C and HTR2A rs6314*A are underrepresented in the group of patients compared to healthy subjects. After the correction for multiple testing, the rs4436578*C variant remained significant while the rs6314*A reported borderline significance. No significant differences in minor allele frequencies for other studied variants were identified. Also, a relationship between the genotypes and age of onset as well as disease duration has been detected. Conclusions The DRD2 rs4436578*C genetic variant might have protective role against schizophrenia, at least in Armenians.

Authors: Roksana Zakharyan, Hovsep Ghazaryan, Lenka Kocourkova, Andranik Chavushyan, Artur Mkrtchyan, Veronika Zizkova, Arsen Arakelyan, Martin Petrek

Date Published: No date defined

Publication Type: Journal

Telomere shortening in blood leukocytes of patients with posttraumatic stress disorder

Abstract (Expand)

Telomeres are protective fragments on chromosome ends involved in maintaining genome stability, preventing chromosomal fusions, regulation of cell division. It was shown that telomere attrition rate … is accelerated in age-related diseases, as well as in response to physiological and psychosocial stress. The aim of this study was to evaluate relative leukocyte telomere length (LTL) in patients with post traumatic stress disorder (PTSD), as well as to investigate association of functional SNPs of telomerase TERC and TERT genes with LTL and PTSD. The relative LTL was measured by multiplex quantitative PCR method; genotyping of TERC rs12696304, TERT rs7726159 and rs2736100 was performed by PCR with sequence specific primers. Comparison of LTL in diseased and healthy subjects showed that PTSD patients had shorter average LTL than controls. Also, the frequency and the carriage rate of the TERT rs2736100*T allele was higher in PTSD patients compared to controls. Overall our results are in line with previous research in different populations. Furthermore, we have demonstrated that rs2736100 of TERT gene was significantly associated with PTSD and the minor allele of this polymorphism may be considered as a risk factor for PTSD in the Armenian population.

Authors: Diana Avetyan, Roksana Zakharyan, Martin Petrek, Arsen Arakelyan

Date Published: No date defined

Publication Type: Journal

Brain-derived neurotrophic factor blood levels are decreased in schizophrenia patients and associate with rs6265 genotypes

Abstract (Expand)

Objectives: A growing number of studies implicate brain-derived neurotrophic factor (BDNF), an important promoter of synaptic transmission and neural plasticity, in the pathogenesis of schizophrenia. … However, the existing data are controversial, that may reflect population differences between studied groups. Design and methods: In the present study we performed a comparative analysis of BDNF plasma levels and its relation with rs6265 (G196A; Val66Met) polymorphism of BDNF gene (BDNF) in schizophrenia-affected and healthy subjects (controls) of the Armenian population. To check the influence of antipsychotics on BDNF plasma levels both medicated and non-medicated patients were involved in this study. Patients with paranoid form of schizophrenia chronically treated with typical antipsychotics (n=103), age- and sex-matched controls (n=105), and 25 antipsychotic-naive first-episode schizophrenia patients were involved. The levels of BDNF in the blood plasma were measured with a solid-phase enzyme-linked immunosorbent assay. Results: Decreased plasma levels of BDNF in both medicated and non-medicated schizophrenia patients compared to controls were observed. No significant difference in BDNF levels between medicated and non-medicated patients was detected. It was also detected that, compared to individuals homozygous for the standard allele (G/G) of rs6265, carriers of the rs6265 minor allele (A/G+A/A), which is significantly more frequent in schizophrenia patients than in controls, had decreased BDNF levels. Conclusions: The data obtained suggested that the pathogenesis of schizophrenia is characterized by genetically predetermined decreased blood levels of BDNF. These results indicated that genetically determined alterations of neuroimmune modulators may be among the risk factors of schizophrenia and contribute to disease-specific pathologic changes in functional activity of both the neuronal synaptic plasticity and the immune system. Keywords: Brain-derived neurotrophic factor; Plasma levels; Schizophrenia; rs6265 Polymorphism.

Authors: Roksana Zakharyan, Anna Boyajyan

Date Published: No date defined

Publication Type: Journal

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