Valery Ilinsky's research while affiliated with Genotek and other places
What is this page?
This page lists the scientific contributions of an author, who either does not have a ResearchGate profile, or has not yet added these contributions to their profile.
It was automatically created by ResearchGate to create a record of this author's body of work. We create such pages to advance our goal of creating and maintaining the most comprehensive scientific repository possible. In doing so, we process publicly available (personal) data relating to the author as a member of the scientific community.
If you're a ResearchGate member, you can follow this page to keep up with this author's work.
If you are this author, and you don't want us to display this page anymore, please let us know.
It was automatically created by ResearchGate to create a record of this author's body of work. We create such pages to advance our goal of creating and maintaining the most comprehensive scientific repository possible. In doing so, we process publicly available (personal) data relating to the author as a member of the scientific community.
If you're a ResearchGate member, you can follow this page to keep up with this author's work.
If you are this author, and you don't want us to display this page anymore, please let us know.
Publications (38)
Background
Overweight is the scourge of modern society and a major risk factor for many diseases. For this reason, understanding the genetic component predisposing to high body mass index (BMI) seems to be an important task along with preventive measures aimed at improving eating behavior and increasing physical activity.
Methods
We analyzed genet...
We present the results of the depression Genome-wide association studies study performed on a cohort of Russian-descent individuals, which identified a novel association at chromosome 7q21 locus. Gene prioritization analysis based on already known depression risk genes indicated MAGI2 (S-SCAM) as the most probable gene from the locus and potential...
Introduction
Because of different phenotypic approaches, data on depression prevalence is variable and controversial.
Objectives
The aim was to evaluate the prevalence of different depressive phenotypes in the Russian population (DSM criteria based self-report vs HADS questionnaire).
Methods
The data was from the on-line survey of 5116 clients of...
Introduction
Depression is a chronic, recurrent mental disorder with a moderate level of genetic impact. Modern GWAS of depression require extra-large sample sizes and new effective, clinically sensitive, objective and simple to fill online phenotyping tools for population studies are necessary today.
Objectives
Aim: to test online phenotyping too...
The Minusinsk Basin in Southern Siberia had unique conditions for the development of ancient societies, thanks to its geographical location, favorable climatic conditions, and relative isolation. Located at the northern periphery of the eastern Eurasian steppe, surrounded by the Altai-Sayan Mountains this area witnessed numerous ancient human migra...
Background
Lactase persistence — the ability to digest lactose through adulthood — is closely related to evolutionary adaptations and has affected many populations since the beginning of cattle breeding. Nevertheless, the contrast initial phenotype, lactase non-persistence or adult lactase deficiency, is still affecting large numbers of people worl...
Depression is one of the leading causes of reduced quality of life and social functioning in patients. The prophylaxis of depression is a priority in preventive medicine. Achievement of prophylaxis requires the opportunity to detect the risk group within the population. i.e., individuals at high genetic risk of developing depression. This review de...
Body mass index (BMI) is a highly heritable polygenic trait. It is also affected by various environmental and behavioral risk factors. We used a BMI polygenic risk score (PRS) to study the interplay between the genetic and environmental factors defining BMI. First, we generated a BMI PRS that explained more variance than a BMI genetic risk score (G...
Background
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there has been increasing urgency to identify pathophysiological characteristics leading to severe clinical course in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Human leukocyte antigen alleles (HLA) have been suggested as po...
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for de novo genome assembly, which is used for the analysis of genomic rearrangements, chromosome phasing, and reconstructing genomes without a r...
Introduction
To reduce the heterogeneity of depressive GWAS samples it seems relevant to evaluate and compare current instruments for depression phenotyping.
Objectives
The aim is to evaluate the agreement of DSM criteria and HADS scores in depression phenotyping for population studies.
Methods
The self-report data was obtained from 5116 clients...
One of the most promising areas of research into the biological underpinnings of depression is genetic studies. However, the absence of generally accepted phenotyping methods leads to the difficulties in generalizing their results due to the heterogeneity of the samples. Thus, the development of a reliable and convenient phenotyping method that all...
Non-invasive prenatal testing (NIPT) for aneuploidy on Chromosomes 21 (T21), 18 (T18) and 13 (T13) is actively used in clinical practice around the world. One of the limitations of the wider implementation of this test is the high cost of the analysis itself, as high-throughput sequencing is still relatively expensive. At the same time, there is an...
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for de novo genome assembly, which is used for the analysis of genomic rearrangements, chromosome phasing, and reconstructing genomes without a r...
Background: Non-invasive prenatal testing for aneuploidy on chromosomes 21, 18 and 13 is actively used in clinical practice around the world. One of the limitations of the wider implementation of this test is the high cost of the analysis itself, as the high throughput sequencing is still relatively expensive. At the same time, there is a trend of...
Depression is one of the leading causes of decreased quality of life and social functioning of patients. In the context of preventive medicine, the prevention of depression becomes a priority. To achieve the goals of prevention, it is necessary to identify specific population risk groups - individuals with a high genetic risk of depression. The pap...
Atypical hemolytic uremic syndrome (aHUS) is an orphan disease, associated with uncontrolled activation of the alternative complement pathway in 60-70% of cases, leading to complementmediated thrombotic microangiopathy (TMA). An unfavorable prognosis of overall and renal survival in the natural course of aHUS is obvious. The article presents a clin...
Congenital core myopathies are a clinically and genetically heterogenous group of congenital myopathies that share a specific histopathological feature: areas of reduced oxidative activity in muscle fibers. The relationship between clinical, genetic and morphological characteristics of this group of disorders remains understudied. The aim of this w...
Haplotypes defined by rs7041/rs4588 in GC gene modulate 25-hydroxyvitamin D (25(OH)D) and vitamin D-binding protein (DBP) levels. To investigate the distributions of GC polymorphisms, the rs7041 and rs4588 allele and haplotypes frequencies were analyzed in samples from different Eurasian regions. The GC1S haplotype associated with high level of ser...
Background
Cutis laxa (CL) is a rare connective tissue disorder characterized by loose, redundant, inelastic and wrinkled skin. Patients develop a prematurely aged appearance. Inheritance can be autosomal dominant or autosomal recessive. The X-linked form is now classified in the group of copper transport diseases. Autosomal dominant CL is characte...
The review is devoted to the analysis of the current state of pharmacogenetic research and their use in psychiatric practice. The main genes responsible for the pharmacodynamics and pharmacokinetics of drugs used in psychiatry are listed. Foreign pharmacogenetic clinical recommendations and progress on their implementation in medical practice in va...
Liability to alcohol dependence is heritable, but little is known about its complex polygenic architecture. We performed a genome-wide association study (GWAS) of self-reported alcohol consumption in 1798 of Russian individuals. No SNP reached genome-wide significance for any alcohol drinking patterns: never drinking, everyday drinking, once per we...
We describe COITR (https://github.com/Genotek/COITR) — Calculator Of Infant's TRaits — a novel algorithm for predicting phenotypic features of a child from genetic data of parents. We used data from open sources and a Bayesian approach for the prediction of externally visible traits. Based on genetic data of parents the developed algorithm can dete...
Polymorphisms in ACTN3 and ACE genes were previously reported to be associated with power and endurance performance. We estimated the relationship between their population frequencies in several countries and FIFA World averaged rating (FWAR). The entropy was used as the measure of uncertainty. The FWAR distribution entropy (in nats) was 1.38. The...
We aimed to develop a pipeline for the bioinformatic analysis and interpretation of NGS data and detection of a wide range of single-nucleotide somatic mutations within tumor DNA. Initially, the NGS reads were submitted to a quality control check by the Cutadapt program. Low-quality 3-nucleotides were removed. After that the reads were mapped to th...
Today, next generation sequencing (NGS) is extensively used in the research setting. However, high costs of NGS testing still prevent its routine use in clinical practice. One of the factors affecting the cost of sequencing is the number of reads per site, i.e. the number of times each nucleotide gets sequenced. On the one hand, lower coverage make...
Metagenomic sequencing is widely used in both scientific research and clinical practice for characterization of taxonomic profiles including estimation of relative abundance of prokaryotes in microbial communities in various media. Metagenomic sequencing of single marker genes is an excellent tool for studying the human microbiome. Unlike whole-gen...
Whole Exome Sequencing (WES) is a promising method in human genetics. Because the majority of pathogenic mutations that lead to the development of diseases are localized in exons and splice sites, WES could become a major tool for the diagnosis of diseases with a complex hereditary nature. This tool appears to be particularly useful for hereditary...
Supplementary Table 1. Expression of PTPRR transcript variants 1 and 2 in colorectal tumors and colorectal cancer cell lines as measured with real time quantitative RT-PCR. The expression of both isoforms in 9 polypoid adenomas, 11 colorectal cancers, and 16 colon cancer cell lines is shown.
Supplementary Table 2. Primer sequences and PCR conditions used in this study. All primer sequences and PCR conditions used for quantitative RT-PCR, methylation analysis, and ChIP are reported.
Supplementary Figure 1. Expression of the two PTPRR transcript variants in a series of normal human tissues. The expression of the two PTPRR isoforms in different normal human tissues as measured with real time quantitative RT-PCR is shown.
Tumor development in the human colon is commonly accompanied by epigenetic changes, such as DNA methylation and chromatin modifications. These alterations result in significant, inheritable changes in gene expression that contribute to the selection of tumor cells with enhanced survival potential.
A recent high-throughput gene expression analysis c...
Torque teno virus (TTV) is a circular, single-stranded DNA virus that chronically infects healthy individuals of all ages worldwide. There is a lot of data on the prevalence and genetic heterogeneity of TTV in healthy populations and in patients with various diseases now available. However, little is known about TTV load among healthy human populat...
Citations
... To address and possibly solve the enigma, the COVID-19 Host Genetic Initiative recently performed an enormously large study to identify genetic variants that account for the variability in individuals' susceptibility to SARS-CoV-2 and in the severity of COVID-19 [90,91]. In this comprehensive analysis, the genomes of more than 49,500 individuals with COVID-19 (including approximately 6200 critically ill patients) were compared with the genomes of around 2 million control individuals without known infection. ...
Reference: Post-COVID Syndrome in Adults—An Overview
... As would be expected, SARS-CoV-2 infection upregulated mediators of viral antigen presentation including HLA haplotypes HLA-B, HLA-I, and HLA-DRB. This observation is important as HLA-B and HLA-DRB have both been reported to influence COVID-19 disease severity (20,21) in association with preexisting medical comorbidities such as cardiovascular disease (22). B2M, a component of MHC class 1 molecules, was also upregulated in infected cells and has been implicated as a risk marker for coronary heart disease and stroke (23). ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/272568254988291-1441996744163_Q64/January-Weiner.jpg)
![[object Object]](https://i1.rgstatic.net/ii/profile.image/1004326914908160-1616461604562_Q64/Phillip-Suwalski.jpg)
![[object Object]](https://i1.rgstatic.net/ii/profile.image/986136348483585-1612124635966_Q64/Alexander-Rakitko.jpg)
![[object Object]](https://i1.rgstatic.net/ii/profile.image/278979522121734-1443525309509_Q64/Bettina-Heidecker-2.jpg)
... We aim to investigate the opportunities for systems biology approaches using this paradigm. While quantum computing has already found applications in other areas of biology, [23][24][25][26][27] we aim to evaluate the possibilities for using quantum computing for BNs as dynamic models of biological systems. Recent work by Qi et al. has demonstrated how Boolean time series can be generated by periodic quantum measurements resulting from a continuous Lindblad master equation based on an interaction graph. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/1000129175748609-1615460785676_Q64/A-Fedorov-12.jpg)
... The variability in drug response with respect to dosing efficacy and planning, as well as potentially controversial drug reactions, have long been considered as limiting factors to the overall improvement of patients' well-being in many medical domains including psychiatry and neurology [1][2][3][4][5][6]. It has been long known that the response and efficacy of a drug can be influenced by genes and genetic polymorphisms involved in signaling mechanisms linked to the metabolization of the drug [7][8][9], and by specific DNA variations, which may impact the activity of encoded proteins and the mechanisms of action of a drug. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/999735775223808-1615366991004_Q64/Gp-Kostyuk.jpg)
![[object Object]](https://i1.rgstatic.net/ii/profile.image/1151981464879138-1651665192638_Q64/Natala-Zaharova.jpg)
... It is known that there are significant ethnic differences in the genes encoding vitamin D-binding protein (DBP). Blacks are more likely to have variants of this gene, leading to low DBP levels and impaired vitamin D synthesis and metabolism (Nizamutdinov et al., 2019). In addition, the increase in melanin in black skin reduces the absorption of sunlight required to produce vitamin D (Nair and Maseeh, 2012;Cashman et al., 2016). ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/272188905357314-1441906300127_Q64/Igor-Nizamutdinov.jpg)
... For target enrichment, we used SureSelect XT2 (Agilent Technologies, Santa Clara, CA, USA). Enriched samples were sequenced using an Illumina HiSeq 2500 system (Illumina, San Diego, CA, USA) in paired-end mode (100 bp reads) and analyzed as described exactly in [32]. ...
... Optimization of library insert sizes has previously been discussed as a factor in genome assembly [24], or for exome-sequencing applications [25,26]. Here, we have observed the effect of insert size applied to resequencing of the human genome, but we expect the conclusions to be more widely applicable also to other genomes. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/629906102837248-1527192726369_Q64/Ivan-Stetsenko.jpg)
... The quality of generated reads was assessed using FastQC by studying theirs per base sequence quality plot, adapter content plot and per sequence quality score plots. Then, adapter trimming was done using Cutadapt [17]. We have provided a workf low adopted for the small RNA sequencing of miRNAs in Figure 1. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/1009618725646336-1617723270098_Q64/Daria-Plakhina.jpg)
![[object Object]](https://i1.rgstatic.net/ii/profile.image/308016530821126-1450448271260_Q64/Dmitriy-Korostin.jpg)
... Sequencing of individuals can identify millions of SNPs that differ between any two individual genomes (Bischoff et al., 2008), while good coverage ensures better identification of sequencing errors, increasing sequencing accuracy (Borisevich et al., 2017). Pools of DNA were sequenced for Afrikaner, Drakensberger and Nguni to discover new SNPs. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/530863756066817-1503579190280_Q64/Dmitrii-Borisevich.jpg)
... The final extension was conducted at 72°C for 10 min and the samples were held at 4°C. The second round of amplification added Illumina Dual Nextera XT indexes and sequencing adaptors [36]. Each library was quantified with a Qubit broad range dsDNA assay and equimolar amounts of each library were pooled. ...
