Single Nucleotide Polymorphism Variants Research Articles

Cross-phenotype association analysis of gastric cancer: in-silico functional annotation based on the disease-gene network.

A gene or variant has pleiotropic effects, and genetic variant identification across multiple phenotypes can provide a comprehensive understanding of biological pathways shared among different diseases or phenotypes. Discovery of genetic loci associated with multiple diseases can simultaneously support general interventions. Several meta-analyses have shown genetic associations with gastric cancer (GC); however, no study has identified associations with other phenotypes using this approach. Here, we applied disease network analysis and gene-based analysis (GBA) to examine genetic variants linked to GC and simultaneously associated with other phenotypes. We conducted a single-nucleotide polymorphism (SNP) level meta-analysis and GBA through a systematic genome-wide association study (GWAS) linked to GC, to integrate published results for the SNP variants and group them into major GC-associated genes. We then performed disease network and expression quantitative trait loci (eQTL) analyses to evaluate cross-phenotype associations and expression levels of GC-related genes. Seven genes (MTX1, GBAP1, MUC1, TRIM46, THBS3, PSCA, and ABO) were associated with GC as well as blood urea nitrogen (BUN), glomerular filtration rate (GFR), and uric acid (UA). In addition, 17 SNPs regulated the expression of genes located on 1q22, 24 SNPs regulated the expression of PSCA on 8q24.3, and rs7849820 regulated the expression of ABO on 9q34.2. Furthermore, rs1057941 and rs2294008 had the highest posterior causal probabilities of being a causal candidate SNP in 1q22, and 8q24.3, respectively. These findings identified seven GC-associated genes exhibiting a cross-association with GFR, BUN, and UA.

Association between the single-nucleotide polymorphism (rs1030868) variant in matrix metallopeptidase 2 gene and the development of lymphedema

BackgroundUnderstanding the genetic and molecular pathophysiology of lymphedema contributes to the identification of the complex interaction of genes associated with lymphedema and provides a key therapeutic opportunity to restore lymphatic function. This study aims to answer whether the single-nucleotide polymorphism (SNP) rs1030868 in the MMP-2 gene could be an associated variant in lymphedema development.MethodsThis study was carried out on 93 lymphedema cases (patients’ group) and 187 healthy individuals (control group). Genotyping of MMP-2 (rs1030868) was done following the protocol of Custom TaqMan® SNP Genotyping Assays. TaqMan™ Fast Advanced Master Mix (Cat# 4448892) was used.ResultsThe risk alleles for MMP-2 SNP rs1030868 were A and G of lymphedema development. The GG genotype was associated with triple the risk of lymphedema (OR 3.2, 95% CI 1.2–6.5, p = 0.019), while the AA genotype was associated with 5.9 times the likelihood of lymphedema (OR 5.9, 95% CI 2.3–11.9, p < 0.001).ConclusionsWe concluded that the single-nucleotide polymorphisms of rs1030868 in the matrix metallopeptidase 2 gene (allele A and allele G) could be associated variants with the development of lymphedema.

A common variant rs2054564 in ADAMTS17 is associated with susceptibility to lumbar spondylosis

The molecular pathophysiology underlying lumbar spondylosis development remains unclear. To identify genetic factors associated with lumbar spondylosis, we conducted a genome-wide association study using 83 severe lumbar spondylosis cases and 182 healthy controls and identified 65 candidate disease-associated single nucleotide polymorphisms (SNPs). Replication analysis in 510 case and 911 control subjects from five independent Japanese cohorts identified rs2054564, located in intron 7 of ADAMTS17, as a disease-associated SNP with a genome-wide significance threshold (P = 1.17 × 10–11, odds ratio = 1.92). This association was significant even after adjustment of age, sex, and body mass index (P = 7.52 × 10–11). A replication study in a Korean cohort, including 123 case and 319 control subjects, also verified the significant association of this SNP with severe lumbar spondylosis. Immunohistochemistry revealed that fibrillin-1 (FBN1) and ADAMTS17 were co-expressed in the annulus fibrosus of intervertebral discs (IVDs). ADAMTS17 overexpression in MG63 cells promoted extracellular microfibrils biogenesis, suggesting the potential role of ADAMTS17 in IVD function through interaction with fibrillin fibers. Finally, we provided evidence of FBN1 involvement in IVD function by showing that lumbar IVDs in patients with Marfan syndrome, caused by heterozygous FBN1 gene mutation, were significantly more degenerated. We identified a common SNP variant, located in ADAMTS17, associated with susceptibility to lumbar spondylosis and demonstrated the potential role of the ADAMTS17-fibrillin network in IVDs in lumbar spondylosis development.

SNP Diversity and Genetic Structure of "Rogosija", an Old Western Balkan Durum Wheat Collection.

Durum wheat landraces represent a genetic resource for the identification and isolation of new valuable genes and alleles, useful to increase the crop adaptability to climate change. Several durum wheat landraces, all denominated "Rogosija", were extensively cultivated in the Western Balkan Peninsula until the first half of the 20th century. Within the conservation program of the Montenegro Plant Gene Bank, these landraces were collected, but without being characterized. The main goal of this study was to estimate the genetic diversity of the "Rogosija collection" consisting of 89 durum accessions, using 17 morphological descriptors and the 25K Illumina single nucleotide polymorphism (SNP) array. The genetic structure analysis of the Rogosija collection showed two distinguished clusters localized in two different Montenegro eco-geographic micro-areas, characterized by continental Mediterranean climate and maritime Mediterranean climate. Data suggest that these clusters could be composed of two different Balkan durum landrace collections evolved in two different eco-geographic micro-areas. Moreover, the origin of Balkan durum landraces is discussed.

Structural variations and environmental specificities of flowering time-related genes in Brassica napus.

We found that the flowering time order of accessions in a genetic population considerably varied across environments, and homolog copies of essential flowering time genes played different roles in different locations. Flowering time plays a critical role in determining the life cycle length, yield, and quality of a crop. However, the allelic polymorphism of flowering time-related genes (FTRGs) in Brassica napus, an important oil crop, remains unclear. Here, we provide high-resolution graphics of FTRGs in B. napus on a pangenome-wide scale based on single nucleotide polymorphism (SNP) and structural variation (SV) analyses. A total of 1337 FTRGs in B. napus were identified by aligning their coding sequences with Arabidopsis orthologs. Overall, 46.07% of FTRGs were core genes and 53.93% were variable genes. Moreover, 1.94%, 0.74%, and 4.49% FTRGs had significant presence-frequency differences (PFDs) between the spring and semi-winter, spring and winter, and winter and semi-winter ecotypes, respectively. SNPs and SVs across 1626 accessions of 39 FTRGs underlying numerous published qualitative trait loci were analyzed. Additionally, to identify FTRGs specific to an eco-condition, genome-wide association studies (GWASs) based on SNP, presence/absence variation (PAV), and SV were performed after growing and observing the flowering time order (FTO) of plants in a collection of 292 accessions at three locations in two successive years. It was discovered that the FTO of plants in a genetic population changed a lot across various environments, and homolog copies of some key FTRGs played different roles in different locations. This study revealed the molecular basis of the genotype-by-environment (G × E) effect on flowering and recommended a pool of candidate genes specific to locations for breeding selection.

Effects of leptin and thyroglobulin gene polymorphisms on beef colour in Holstein bulls for slaughter in Turkey

n the present work, live weight (LW), hot carcass weight (HCW), and beef colour values of Turkish Holstein bull (THBs) samples, and their relationship with single nucleotide polymorphisms (SNPs) variants were determined. E2JW and E2FB variants of leptin (LEP), and C422T variant of thyroglobulin (TG) genes were determined in 100 heads of THBs by polymerase chain reaction fragment length polymorphism (PCR-RFLP). Genotyping was carried out by capillary electrophoresis. The colour of raw and cooked beefs was spectrophotometrically measured before and after cooking. The cooked beefs were significantly brighter in the LEP E2JW AA and AT variants than in the TT genotype (p &lt; 0.05). Based on b* of raw beefs, the yellowish colour density in the LEP E2JW AA genotype variant was significantly higher than in AT and TT (p &lt; 0.05). The most significant correlation was determined between b* and L* (0.695), and b* and a* (0.694) of raw beefs, while the correlation coefficient between LW and HCW was found to be 0.604 (p &lt; 0.01). The LEP E2JW AA marker genotype for cattle with brighter and more intense beef, and the LEP E2JW TT variant genotype to increase beef yield should be selected as a study by using MAS method at an early age. Also, AT / CT / CC marker genotypes of THBs should be selected in LEP E2JW / E2FB / TG C422T marker loci, respectively to generate more income from the increase in LW and HCW.

Estimating inbreeding rate and effective population size in the Finnish Ayrshire population in the era of genomic selection.

Genomic selection has been applied in dairy cattle breeding over the last decade. Using genomic information may speed up genetic gain as breeding values can be predicted reasonably accurately directly after birth. However, genetic diversity may decrease if the inbreeding rate per generation increases and the effective population size decreases. Despite many positive qualities of the Finnish Ayrshire, for example, high average protein yield and fertility, over time the breed has lost its place as the most common dairy breed in Finland. Thus, maintaining the genetic variability of the breed is becoming more important. The aim of our research was to estimate the impact of genomic selection on inbreeding rate and effective population size using both pedigree and genomic data. The genomic data included 46,914 imputed single nucleotide polymorphism (SNP) variants from 75,038 individuals, and the pedigree data included 2,770,025 individuals. All animals in the data were born between 2000 and 2020. Genomic inbreeding coefficients were estimated as the proportion of SNPs in runs of homozygosity (ROH) out of the total number of SNPs. The inbreeding rate was estimated by regressing the mean genomic inbreeding coefficients on birth years. Effective population size was then estimated based on the inbreeding rate. Additionally, effective population size was estimated from the mean increase in individual inbreeding using pedigree data. Introduction of genomic selection was assumed to have taken place gradually; years 2012-2014 were treated as a transition period from the traditional phenotype-based breeding value estimation to genomic-based estimation. The median length of the identified homozygous segments was 5.5Mbp, and a slight increase in the proportion of segments over 10Mbp was observed after 2010. The inbreeding rate decreased from 2000 to 2011 and subsequently increased slightly. The pedigree- and genomic-based estimates of inbreeding rate were similar to each other. The estimates of effective population size based on the regression method were very sensitive to the number of years considered; thus, the estimates were not very reliable. The effective population size estimated from the mean increase in individual inbreeding reached its highest value of 160 in 2011 and decreased to 150 after that. In addition, the generation interval in the sire path has decreased from 5.5 years to 3.5 years after genomic selection was implemented. Based on our results, after the implementation of genomic selection, the proportion of long ROH stretches has increased, the generation interval in the sire path has decreased, the inbreeding rate has increased and the effective population size has decreased. However, the effective population size is still at a good level, allowing for an efficient selection scheme in the Finnish Ayrshire breed.

The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis

Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.

The transcription factor MebHLH18 in cassava functions in decreasing low temperature-induced leaf abscission to promote low-temperature tolerance.

The reactive oxygen species (ROS) signal regulates stress-induced leaf abscission in cassava. The relationship between the function of the cassava transcription factor bHLH gene and low temperature-induced leaf abscission is still unclear. Here, we report that MebHLH18, a transcription factor, involved in regulating low temperature-induced leaf abscission in cassava. The expression of the MebHLH18 gene was significantly related to low temperature-induced leaf abscission and POD level. Under low temperatures, the levels of ROS scavengers in different cassava genotypes were significantly different in the low temperature-induced leaf abscission process. Cassava gene transformation showed that MebHLH18 overexpression significantly decreased the low temperature-induced leaf abscission rate. Simultaneously, interference expression increased the rate of leaf abscission under the same conditions. ROS analysis showed a connection between the decrease in the low temperature-induced leaf abscission rate caused by MebHLH18 expression and the increase in antioxidant activity. A Genome-wide association studies analysis showed a relationship between the natural variation of the promoter region of MebHLH18 and low temperature-induced leaf abscission. Furthermore, studies showed that the change in MebHLH18 expression was caused by a single nucleotide polymorphism variation in the promoter region upstream of the gene. The high expression of MebHLH18 led to a significant increase in POD activity. The increased POD activity decreased the accumulation of ROS at low temperatures and the rate of leaf abscission. It indicates that the natural variation in the promoter region of MebHLH18 increases antioxidant levels under low temperatures and slows down low temperature-induced leaf abscission.

Patient Characteristics and Prevalence of Single Nucleotide Polymorphism (SNP) V16A MnSOD Gene in Diabetic Retinopathy Patients at RSUP Prof. Dr. I.G.N.G. Ngoerah Denpasar Bali

Diabetic Retinopathy (DR) is a microvascular complication of Diabetes Mellitus (DM) caused by hyperglycemia and oxidative stress that is prevalent to the blindness risk. Manganese superoxide dismutase (MnSOD) gene affect the oxidative damage and progression of DR severity. This study aims to determine the association of patient characteristics on the severity and prevalence of Single Nucleotide Polymorphism (SNP) V16A in the MnSOD gene in DR patients at Prof. Dr. I.G.N.G. Ngoerah Denpasar Bali. Twelve (12) subjects with Non-Proliferative DR and 21 subjects with Proliferative DR were enrolled. Patient characteristics (age, T2DM duration, BMI, blood pressure) were associated to the DR severity using cross-sectional analytic study. While to detect the status of the SNP V16A MnSOD gene using descriptive experimental study. DNA segment amplification was performed using the PCR method, sequencing was performed to detect the base pattern at the location of the SNP. A domination of the VV genotype in the SNP V16A MnSOD gene was present in all subjects (100%). The majority of subjects were female (51,5%), age range 40-65 years (84,9%), T2DM duration &lt;10 years (60,6%), normal BMI (60,6%). Blood pressure was dominated with non hypertension 60,6%, with a history of oral anti hypertensive. No significant association was found between patient characteristics and the DR severity (p&lt;0,05). We may conclude that wildtype variant (VV) SNP V16A MnSOD gene was dominated in this finding. There is no significant association between patient characteristics and the severity of DR in Prof. Dr. I.G.N.G. Ngoerah Denpasar Bali. Keywords: Diabetic Retinopathy, MnSOD gene, SNP V16A

Genome-wide association study identifies GhSAL1 affects cold tolerance at the seedling emergence stage in upland cotton (Gossypium hirsutum L.).

Genomic analysis of upland cotton revealed that cold tolerance was associated with ecological distribution. GhSAL1 on chromosome D09 negatively regulated cold tolerance of upland cotton. Cotton can undergo low-temperature stress at the seedling emergence stage, which adversely affects growth and yield; however, the regulatory mechanism underlying cold tolerance remains nebulous. Here, we analyze the phenotypic and physiological parameters in 200 accessions from 5 ecological distributions under constant chilling (CC) and diurnal variation of chilling (DVC) stresses at the seedling emergence stage. All accessions were clustered into four groups, of which Group IV, with most germplasms from the northwest inland region (NIR), had better phenotypes than Groups I-III under the two kinds of chilling stresses. A total of 575 significantly associated single-nucleotide polymorphism (SNP) were identified, and 35 stable genetic quantitative trait loci (QTL) were obtained, of which 5 were associated with traits under CC and DVC stress, respectively, while the remaining 25 were co-associated. The accumulation of dry weight (DW) of seedling was associated with the flavonoid biosynthesis process regulated by Gh_A10G0500. The emergence rate (ER), DW, and total length of seedling (TL) under CC stress were associated with the SNPs variation of Gh_D09G0189 (GhSAL1). GhSAL1HapB was the elite haplotype, which increased ER, DW, and TL by 19.04%, 11.26%, and 7.69%, respectively, compared with that of GhSAL1HapA. The results of virus-induced gene silencing (VIGS) experiment and determination of metabolic substrate content preliminarily illustrated that GhSAL1 negatively regulated cotton cold tolerance through IP3-Ca2+ signaling pathway. The elite haplotypes and candidate genes identified in this study could be used to improve cold tolerance at the seedling emergence stage in future upland cotton breeding.

Genetic variants of glucose metabolism and exposure to smoking in African American breast cancer.

Insulin resistance (IR) is a well-established risk factor for breast cancer (BC) development in African American (AA) postmenopausal women. While obesity and IR are more prevalent in AA than in white women, they are under-represented in genome-wide studies for systemic regulation of IR. By examining 780 genome-wide IR single-nucleotide polymorphisms (SNPs) available in our data, we tested 4689 AA women in a Random Survival Forest framework. With 37 BC-associated lifestyle factors, we conducted a gene-environment interaction analysis to estimate risk prediction for BC with the most influential genetic and behavioral factors and evaluated their combined and joint effects on BC risk. By accounting for variations of individual SNPs in BC in the prediction model, we detected four fasting glucose-associated SNPs in PCSK1, SPC25, ADCY5, and MTNR1B and three lifestyle factors (smoking, oral contraceptive use, and age at menopause) as the most predictive markers for BC risk. Our joint analysis of risk genotypes and lifestyle with smoking revealed a synergistic effect on the increased risk of BC, particularly estrogen/progesterone positive (ER/PR+) BC, in a gene-lifestyle dose-dependent manner. The joint effect of smoking was more substantial in women with prolonged exposure to cigarette smoking and female hormones. The top genome-wide association-SNPs associated with metabolic biomarkers in combination with lifestyles synergistically increase the predictability of invasive ER/PR+ BC risk among AA women. Our findings highlight generically targeted preventive interventions for women who carry particular risk genotypes and lifestyles.

Evaluation of a barley (Hordeum vulgare) chromosome 2 drought tolerance quantitative trait locus in genomic backgrounds of two cultivars

AbstractA barley drought tolerance Quantitatif Trait Locus (QTL) on chromosome 2 was transferred from tolerant cultivar ‘Tadmor’ to susceptible ‘Baronesse’ and ‘Aydanhanım’. Effects of this QTL on drought tolerance and other traits were studied using near‐isogenic lines under controlled environments and field trials for two years. This QTL resulted in 5.0% and 9.1% improvement in leaf relative water content of ‘Baronesse’ and ‘Aydanhanım’ cultivars, respectively, under controlled environments. The QTL accelerated heading and maturity by 2.5 days in ‘Baronesse’ and by 5–6 days in ‘Aydanhanım’. It was associated with shorter stature and more ears. This QTL region increased grain yields by 1.1 and 0.6 t/ha in ‘Baronesse’ and ‘Aydanhanım’, respectively, mainly by increasing the number of tillers. There were previous reports related to yield promoting effects of this region harbouring flowering locus eps2 (barley HvCEN gene). However, sequencing of 1025 bp fragment encompassing HvCEN coding region revealed that our parents and near‐isogenic lines had no Single Nucleotide Polymorphism (SNP) variation, ruling out direct involvement of eps2. These findings pointed to the possible effect of another flowering locus in the QTL region.

Com probe implemented STexS II greatly enhances specificity in SARS-CoV-2 variant detection

The initial introduction of utilizing double helix structural oligonucleotides known as SNP typing with excellent specificity (STexS) in a standard PCR greatly improved the detection of single nucleotide polymorphisms (SNP) by enhancing amplification rates of primer-matching strands and interrupting mismatched strands by constant instability of kinetics regarding alignment attaching and detaching. The model was beneficial overall in detecting SNP variants consisting of large amounts of wildtype strands such as EGFR mutation genotyping for early detection of non-small cell lung cancer. While the STexS PCR is advantageous in detecting SNPs and biomarkers, limitations were yet observed. Despite the ability to detect variants 10 times more effective than a typical amplification-refractory mutation system PCR, it could only perform optimally in DNA concentrations around 101 ~ 105. To further enhance STexS specificity to perform detecting viral-RNA variants such as the infamous SARS-CoV-2, a novel improvement of the regular TaqMan Probe using Com-probes to inhibit high copy wild targets and amplify low copy mutant targets. By introducing the novel STexS II, omicron variants of SARS-CoV-2 were able to be successfully detected in high concentrations of normal genes.

Association between CDKN1A gene rs1801270 polymorphisms and susceptibility to colorectal cancser in an Iranian population

CDKN1A gene is implicated in cell differentiation, development process, repair, apoptosis, senescence, migration, and tumorigenesis. Somatic alterations and polymorphisms may interfere in the function of CDKN1A, and this could affect the individual susceptibility to colorectal cancer (CRC). Here in, we evaluated the importance of single nucleotide polymorphic variants in codon 31 of CDKN1A (rs1801270: C > A) for the development of colorectal cancer in an Iranian population. A total of 150 CRC patients and 150 healthy controls were enrolled in this study. Genomic DNA was extracted from peripheral blood specimens. Genotypes were determined using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) assay. In CRC patients, the genotype frequencies detected were 90%, 8.0% and 2.0%2 for CC, AC and AA genotypes while the genotype frequencies in control group were 78%, 20.7% and 1.35% 1.35% for CC, AC and AA genotype, respectively. There were statistically significant differences in the distribution of CDKN1A rs1801270 genotypes and allele frequencies between colorectal cancer patients and healthy controls (p value = 0.021). Also, results indicated a significant negative association between AC genotype and risk of colorectal cancer occurrence. (Odds ratio (OR)=0.357; 95% confidence interval (CI)=0.168–0.760, p = 0.007). Our data suggest that the AC genotype may have a protective role in the development of CRC in an Iranian population.

A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis.

Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 contigs (614 Mb) combining long- and short-read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC-FISH. Whole genome resequencing of six males and six females enabled the identification of 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) consistent with an XX/XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. The fshr gene displayed differential expression between male and female gonads from 86 days post-fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of amh and cyp19a1a, testis and ovary marker genes, respectively, in males and females. The Y-linked fshr allele, which included 24 nonsynonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X-linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.

Identification of genetic risk loci for depression and migraine comorbidity in Han Chinese residing in Taiwan.

The genetic association between depression and migraine has not been well investigated in Asian populations. Furthermore, the genetic basis of depression and comorbid migraine subtypes remains nebulous. Hence, in the current study we investigate the susceptibility loci associated with depression and migraine comorbidity in the Han Chinese population in Taiwan. We perform a genome-wide association study involving 966 migraine patients, with or without comorbid depression. Genotyping is performed using participant genomic DNA. Association analyses are performed for the entire migraine cohort (subgroups: episodic migraine, chronic migraine, and migraine with or without aura). Results show that the single nucleotide polymorphism variants of the CDH4 intron region (rs78063755), NTRK3-AS1 downstream region (rs57729223), and between LINC01918 and GPR45 (rs2679891) are suggestively associated with depression. Twenty additional susceptibility loci occur within the subgroups. A multivariate association study demonstrated that a variant in the intron region of CDH4 rs78063755 was associated with Beck Depression Inventory and Migraine Disability Assessment scores. The findings of this study identify several genetic loci suggestively associated with depression among migraine patients in the Han Chinese population. Moreover, a potential genetic basis has been characterized for depression and migraine comorbidity, thus providing genetic candidates for further investigation.

Роль генов систем натрийуретических пептидов и антиоксидантной защиты в формировании риска развития инфаркта миокарда (предварительные результаты пилотного исследования)

Aim: to reveal a relationship of single-nucleotide polymorphic variants of the genes of the natriuretic peptides, antioxidant defense systems and the endothelial function with the development of myocardial infarction. Patients and Methods: the study included 146 patients with myocardial infarction (MI) and maintained or moderately decreased left ventricular ejection fraction: 108 males and 38 females with a mean age of 57 (51; 64) years. The control group was composed of Kemerovo city residents without acute MI (n=300, 190 females and 110 males). To make the evaluation, genomic DNA was isolated from the peripheral blood by phenol- chloroform extraction according to the standard protocol. Real-time PCR method was used for genotyping. To conduct the study, 24 polymorphic variants of 14 genes (those of the natriuretic peptides, antioxidant defense systems and the endothelial function) were selected. Results: significant associations with the allelic variants of CBR1 and CBR3 genes (carbonyl reductase 1 and 3 genes) of the antioxidant defense system were found in the sample of studied patients with MI (not divided by gender or age). When the patients were divided by gender, the following associations were found: in males the single-nucleotide polymorphic variant (SNPV) genotypes CBR1 rs9024 and CBR3 rs1056892 had the protective effect against susceptibility to myocardial infarction (dominant inheritance pattern). It was demonstrated that allelic variants in the NPR2 gene (the gene of atrial natriuretic peptide receptor 2) comprised a risk factor for MI development. In females, a relationship between the assessed genetic factors and the MI development (dominant inheritance pattern) could be associated with SNPV genotypes NPR2 rs13288085 and rs7034957, CBR1 rs9024, and CBR3 rs1056892 which are characterized by the protective effect. Conclusion: some polymorphic variants of the genes of the natriuretic peptide and antioxidant defense systems are associated with the risk and the protective effect against MI susceptibility. The preliminary findings indicate that it is necessary to continue investigations of the identified single-nucleotide polymorphic variants and to assess their impact on the MI severity and the risk of recurrent cardiovascular events in the long-term perspective. KEYWORDS: myocardial infarction, gene, natriuretic peptides, antioxidant defense, polymorphic variants. FOR CITATION: Khutornaya M.V., Khryachkova O.N., Sinitskaya A.V. et al. Role of the genes of the natriuretic peptide and antioxidant defense systems in creating the risk of myocardial infarction development (the preliminary results of a pilot study). Russian Medical Inquiry. 2023;7(1):5–12 (in Russ.). DOI: 10.32364/2587-6821-2023-7-1-5-12.

Comparative whole-genome analysis of diphtheria toxin-producing Corynebacterium ulcerans isolates from sheltered cats in Osaka, Japan.

Diphtheria toxin-producing Corynebacterium ulcerans is a zoonotic pathogen that causes human diphtheria-like symptoms. After performing whole-genome analysis of the five isolates from sheltered cats in Osaka, Japan, we compared them with genome sequences of 25 strains of C. ulcerans from a public database. The five isolates from cats harbored 14 genes encoding possible virulence factors in diphtheria-toxin-producing C. ulcerans. These isolates also had diphtheria toxin gene-encoding prophage in their chromosome, although differences were found in other prophages possession. Whole-genome single-nucleotide polymorphism analysis showed that cats' isolates belonged to ST337 branch, as were strains from Japanese human patients, with 41 or more single-nucleotide polymorphisms variations. High-resolution single-nucleotide polymorphism analysis of C. ulcerans was sufficient to distinguish cats' isolates clearly as not different by conventional genotyping methods.

The variation of the androgen receptor single nucleotide polymorphism (rs6152) gene in different stages of endometriosis disease in Iraqi women

The variation of the androgen receptor single nucleotide polymorphism (rs6152) gene in different stages of endometriosis disease in Iraqi women