Study of rs12532, rs8670 Polymorphism of Msh Homeobox 1 (MSX1), rs61754301, rs4904155 Polymorphism of Paired Box Gene 9 (PAX9), and rs2240308 Polymorphism of Axis Inhibitor Protein 2 (AXIN2) Genes in Nonsyndromic Hypodontia

The etiology of hypodontia is complex, in which both genetic and environmental factors can be related. The main objective of our study was to contribute to elucidating the genetic background of nonsyndromic hypodontia (NSH). In this order, we selected 97 NSH subjects (70 females and 27 males) from patients referred to orthodontic treatment, and we matched to each NSH subject a control by age and sex. DNA was obtained from epithelial cells from the oral mucosa. Genotyping of the PAX9 (rs4904155 and rs61754301), MSX1 (rs8670 and rs12532), and AXIN2 (rs2240308) SNPs was performed by using TaqMan SNP Genotyping Assays on a real-time PCR system. Single-nucleotide polymorphisms (SNPs) were studied for the whole NSH group and for frontal and lateral agenesis NSH subjects separately. Our results showed that the variant genotype (p=0.0008, OR = 2.9, 95% CI = 1.58–5.3) and variant T allele (p=0.0002, OR = 2.65, 95% CI = 1.6–4.39) of the MSX1 rs8670 SNP increased the risk of hypodontia in the studied population when the whole NSH group was compared with controls. The variant genotype of the MSX1 rs8670 SNP was the most frequent in frontal agenesis; meanwhile in the lateral agenesis NSH group, the AXIN2 rs2240308 SNP showed a higher frequency of the variant genotype, with a trend towards statistical significance. In conclusion, the results of the present study showed that the variant genotype and variant T allele of the MSX1 rs8670 SNP increased the risk of hypodontia in the studied population. The presence of the variant A allele of AXIN2 rs2240308 is associated with frontal agenesis but not with lateral agenesis.

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Association of β-defensin 1 gene Polymorphism and dental caries susceptibility in Tamil Ethnicity

Research Journal of Pharmacy and Technology ◽

10.52711/0974-360x.2021.00823 ◽

2021 ◽

pp. 4731-4735

Author(s):

Harini Venkata Subbiah ◽

Usha Subbiah ◽

Athira Ajith

Keyword(s):

Dental Caries ◽

Odds Ratio ◽

Regulatory Elements ◽

Microbial Colonization ◽

Nucleotide Polymorphisms ◽

First Line ◽

Single Nucleotide ◽

Variant Genotype ◽

Dental Caries Susceptibility ◽

Genetic And Environmental Factors

Dental caries is a multifactorial disease that affects a large proportion of the population with both genetic and environmental factors contributing to the disease. Even in healthy oral environmental conditions, some individuals are susceptible to dental caries due to potential genetic contribution. Antimicrobial peptides are expressed in oral cavity and play an important role against microbial colonization and form an important first line defense against cariogenic bacteria. In the present study, we attempt to identify genetic variants that would cause significant functional impact towards susceptibility to dental caries. We investigated single nucleotide polymorphisms (SNPs) of beta-defensin 1 (DEFB1) as predictors of dental caries in tamil ethnic population. A total of 120 subjects were recruited for this study, which included 60 dental caries patients (DMFT>5) and 60 healthy controls (DMFT=0). Three SNPs of 5’UTR regulatory elements of DEFB1 were genotyped by PCR followed by Sanger sequencing. The genotypes associated with susceptibility to caries were found to be significant between rs11362 (p=.025, odds ratio = 3.72, 95% confidence interval (CI) = 1.289-10.742), rs1799946 (p=.023, odds ratio=4.32, 95% CI = 1.33-14.028) gene polymorphisms and risk of dental caries (DMFT>5) in tamil ethnicity. The variant genotype GG of rs1800972 polymorphism was found to be high in cases than controls but was not significant (p=0.136). Our data suggested that β-defensin 1 polymorphisms play a role in the susceptibility to dental caries.

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Association Study among Comethylation Modules, Genetic Polymorphisms and Clinical Features in Mexican Teenagers with Eating Disorders: Preliminary Results

Nutrients ◽

10.3390/nu13093210 ◽

2021 ◽

Vol 13 (9) ◽

pp. 3210

Author(s):

Germán Alberto Nolasco-Rosales ◽

José Jaime Martínez-Magaña ◽

Isela Esther Juárez-Rojop ◽

Thelma Beatriz González-Castro ◽

Carlos Alfonso Tovilla-Zarate ◽

...

Keyword(s):

Dna Methylation ◽

Eating Disorders ◽

Environmental Factors ◽

Clinical Features ◽

Eating Behaviors ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Gene Environment ◽

Gene Correlation ◽

Genetic And Environmental Factors

Eating disorders are psychiatric disorders characterized by disturbed eating behaviors. They have a complex etiology in which genetic and environmental factors interact. Analyzing gene-environment interactions could help us to identify the mechanisms involved in the etiology of such conditions. For example, comethylation module analysis could detect the small effects of epigenetic interactions, reflecting the influence of environmental factors. We used MethylationEPIC and Psycharray microarrays to determine DNA methylation levels and genotype from 63 teenagers with eating disorders. We identified 11 comethylation modules in WGCNA (Weighted Gene Correlation Network Analysis) and correlated them with single nucleotide polymorphisms (SNP) and clinical features in our subjects. Two comethylation modules correlated with clinical features (BMI and height) in our sample and with SNPs associated with these phenotypes. One of these comethylation modules (yellow) correlated with BMI and rs10494217 polymorphism (associated with waist-hip ratio). Another module (black) was correlated with height, rs9349206, rs11761528, and rs17726787 SNPs; these polymorphisms were associated with height in previous GWAS. Our data suggest that genetic variations could alter epigenetics, and that these perturbations could be reflected as variations in clinical features.

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Gene-Environment Interactions in Progressive Supranuclear Palsy

Frontiers in Neurology ◽

10.3389/fneur.2021.664796 ◽

2021 ◽

Vol 12 ◽

Author(s):

Irene Litvan ◽

James A. Proudfoot ◽

Eden R. Martin ◽

David Standaert ◽

David Riley ◽

...

Keyword(s):

Environmental Factors ◽

Progressive Supranuclear Palsy ◽

Symptom Onset ◽

Nucleotide Polymorphisms ◽

Agricultural Risk ◽

Single Nucleotide ◽

Gene Environment ◽

Minor Alleles ◽

Genetic And Environmental Factors ◽

Potential Interactions

Several genetic and environmental factors have been reported in progressive supranuclear palsy (PSP), although none were identified as a definitive cause. We aimed to explore potential gene-environment interactions in PSP. Two hundred and ninety two PSP cases and 292 controls matched for age, sex, and race from the ENGENE-PSP were analyzed to determine the association between PSP and minor alleles of 5 single nucleotide polymorphisms (SNPs) in 4 genes (MAPT, MOBP, EIF2AK3, and STX6), which were previously associated with PSP risk. Interactions between these SNPs and environmental factors, including previously reported occupational and agricultural risk factors for PSP, were assessed for PSP odds and age of symptom onset. Minor alleles of MAPTrs242557 and EIF2AK3rs7571971 were individually associated with increased odds; MAPTrs8070723 minor alleles were associated with lower PSP odds. There were several gene-environment interactions for PSP odds and age of symptom onset, however, they did not remain significant after FDR-correction. Larger scale studies are required to determine potential interactions.

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Molecular Relationships between Bronchial Asthma and Hypertension as Comorbid Diseases

Journal of Integrative Bioinformatics ◽

10.1515/jib-2018-0052 ◽

2018 ◽

Vol 15 (4) ◽

Cited By ~ 4

Author(s):

Elena Yu. Bragina ◽

Irina A. Goncharova ◽

Anna F. Garaeva ◽

Evgeniy V. Nemerov ◽

Anastasija A. Babovskaya ◽

...

Keyword(s):

Bronchial Asthma ◽

Genetic Background ◽

Regulation Of Gene Expression ◽

Common Phenomenon ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Multiple Factors ◽

Comorbid Diseases ◽

Set Up ◽

Molecular Relationships

AbstractComorbidity, a co-incidence of several disorders in an individual, is a common phenomenon. Their development is governed by multiple factors, including genetic variation. The current study was set up to look at associations between isolated and comorbid diseases of bronchial asthma and hypertension, on one hand, and single nucleotide polymorphisms associated with regulation of gene expression (eQTL), on the other hand. A total of 96 eQTL SNPs were genotyped in 587 Russian individuals. Bronchial asthma alone was found to be associated with rs1927914 (TLR4), rs1928298 (intergenic variant), and rs1980616 (SERPINA1); hypertension alone was found to be associated with rs11065987 (intergenic variant); rs2284033 (IL2RB), rs11191582 (NT5C2), and rs11669386 (CARD8); comorbidity between asthma and hypertension was found to be associated with rs1010461 (ANG/RNASE4), rs7038716, rs7026297 (LOC105376244), rs7025144 (intergenic variant), and rs2022318 (intergenic variant). The results suggest that genetic background of comorbidity of asthma and hypertension is different from genetic backgrounds of both diseases manifesting isolated.

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Association of single-nucleotide polymorphisms in the ESR2 and FSHR genes with poor ovarian response in infertile Jordanian women

Clinical and Experimental Reproductive Medicine ◽

10.5653/cerm.2020.03706 ◽

2021 ◽

Vol 48 (1) ◽

pp. 69-79

Author(s):

Amer Mahmoud Sindiani ◽

Osamah Batiha ◽

Esra’a Al-zoubi ◽

Sara Khadrawi ◽

Ghadeer Alsoukhni ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Statistical Significance ◽

Ovarian Response ◽

Control Group ◽

P Value ◽

Case Group ◽

Nucleotide Polymorphisms ◽

Poor Ovarian Response ◽

Single Nucleotide ◽

Number Of Patients

Objective: Poor ovarian response (POR) refers to a subnormal follicular response that leads to a decrease in the quality and quantity of the eggs retrieved after ovarian stimulation during assisted reproductive treatment (ART). The present study investigated the associations of multiple variants of the estrogen receptor 2 (ESR2) and follicle-stimulating hormone receptor (FSHR) genes with POR in infertile Jordanian women undergoing ART.Methods: Four polymorphisms, namely ESR2 rs1256049, ESR2 rs4986938, FSHR rs6165, and FSHR rs6166, were investigated in 60 infertile Jordanian women undergoing ART (the case group) and 60 age-matched fertile women (the control group), with a mean age of 33.60±6.34 years. Single-nucleotide polymorphisms (SNPs) were detected by restriction fragment length polymorphism and then validated using Sanger sequencing.Results: The p-value of the difference between the case and control groups regarding FSHR rs6166 was very close to 0.05 (p=0.054). However, no significant differences were observed between the two groups in terms of the other three SNPs, namely ESR2 rs1256049, ESR2 rs4986938, and FSHR rs6165 (p=0.561, p=0.433, and p=0.696, respectively).Conclusion: The association between FSHR rs6166 and POR was not statistically meaningful in the present study, but the near-significant result of this experiment suggests that statistical significance might be found in a future study with a larger number of patients.

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Associations of Two Obesity-Related Single-Nucleotide Polymorphisms with Adiponectin in Chinese Children

International Journal of Endocrinology ◽

10.1155/2017/6437542 ◽

2017 ◽

Vol 2017 ◽

pp. 1-5 ◽

Cited By ~ 1

Author(s):

Lijun Wu ◽

Liwang Gao ◽

Xiaoyuan Zhao ◽

Meixian Zhang ◽

Jianxin Wu ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Multiple Testing ◽

Association Studies ◽

Statistical Significance ◽

Additive Model ◽

Recessive Model ◽

Chinese Children ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

Purpose. Genome-wide association studies have found two obesity-related single-nucleotide polymorphisms (SNPs), rs17782313 near the melanocortin-4 receptor (MC4R) gene and rs6265 near the brain-derived neurotrophic factor (BDNF) gene, but the associations of both SNPs with other obesity-related traits are not fully described, especially in children. The aim of the present study is to investigate the associations between the SNPs and adiponectin that has a regulatory role in glucose and lipid metabolism. Methods. We examined the associations of the SNPs with adiponectin in Beijing Child and Adolescent Metabolic Syndrome (BCAMS) study. A total of 3503 children participated in the study. Results. The SNP rs6265 was significantly associated with adiponectin under an additive model (P=0.02 and 0.024, resp.) after adjustment for age, gender, and BMI or obesity statuses. The SNP rs17782313 was significantly associated with low adiponectin under a recessive model. No statistical significance was found between the two SNPs and low adiponectin after correction for multiple testing. Conclusion. We demonstrate for the first time that the SNP rs17782313 near MC4R and the SNP rs6265 near BDNF are associated with adiponectin in Chinese children. These novel findings provide important evidence that adiponectin possibly mediates MC4R and BDNF involved in obesity.

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Association of RETN and TNFRSF1B polymorphisms with TNF-α inhibitor response in rheumatoid arthritis patients

10.21203/rs.2.24442/v1 ◽

2020 ◽

Author(s):

Nga Thi Trinh ◽

Hyun Jeong Kim ◽

Woorim Kim ◽

Sang Oh Kang ◽

Kyung Hyun Min ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Disease Activity ◽

Statistical Significance ◽

Univariate Analysis ◽

Multivariable Logistic Regression Analysis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Final Model ◽

Asian Populations ◽

Tnf Α

Abstract Background: Despite the improvement from the introduction of tumor necrosis factor inhibitors (TNFi) in the rheumatoid arthritis (RA), TNFi therapy fails for more than 30% or results in a partial response. Thus, we aimed to explore treatment marker by examining the association of single nucleotide polymorphisms (SNPs) with response to TNFi therapy.Method: Genes associated with RA or RA treatment were reviewed and fourteen SNPs with minor allele frequency ≥ 20% in the East Asian populations were selected and analyzed. Data were collected from 105 RA patients. Our primary endpoint was the disease activity score using 28-joint count after six months of treatment (DAS28-6month). The secondary outcomes were the subcomponents of DAS28.Results: A total of 88 patients were included in the final analyses. Among the 14 SNPs analyzed, one SNP showed statistical significance in DAS28-6month: patients with the GG allele of RETN rs1862513 had a 4.7 times higher chance of low disease activity at 6-months than GC or CC-carriers (p = 0.033), as indicated by multivariable logistic regression analysis. Rs3397 was marginally significant in univariate analysis (p=0.059), but was significant in the multivariable model (p=0.041). The final model explained 24.5% (Nagelkerke R2) of the variance in DAS28-6month.Conclusion: Our results demonstrated that, among the genes related to RA, SNPs in RETN and TNFRSF1B were associated with the response of TNFi treatment.

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Genetic Factors of Nitric Oxide’s System in Psychoneurologic Disorders

International Journal of Molecular Sciences ◽

10.3390/ijms21051604 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1604 ◽

Cited By ~ 1

Author(s):

Regina F. Nasyrova ◽

Polina V. Moskaleva ◽

Elena E. Vaiman ◽

Natalya A. Shnayder ◽

Nataliya L. Blatt ◽

...

Keyword(s):

Nitric Oxide ◽

Neurological Diseases ◽

Small Sample ◽

Nucleotide Polymorphisms ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Penile Erections ◽

Genetic And Environmental Factors ◽

Small Sample Sizes ◽

Disease Modifying Treatment

According to the recent data, nitric oxide (NO) is a chemical messenger that mediates functions such as vasodilation and neurotransmission, as well as displaying antimicrobial and antitumoral activities. NO has been implicated in the neurotoxicity associated with stroke and neurodegenerative diseases; neural regulation of smooth muscle, including peristalsis; and penile erections. We searched for full-text English publications from the past 15 years in Pubmed and SNPedia databases using keywords and combined word searches (nitric oxide, single nucleotide variants, single nucleotide polymorphisms, genes). In addition, earlier publications of historical interest were included in the review. In our review, we have summarized information regarding all NOS1, NOS2, NOS3, and NOS1AP single nucleotide variants (SNVs) involved in the development of mental disorders and neurological diseases/conditions. The results of the studies we have discussed in this review are contradictory, which might be due to different designs of the studies, small sample sizes in some of them, and different social and geographical characteristics. However, the contribution of genetic and environmental factors has been understudied, which makes this issue increasingly important for researchers as the understanding of these mechanisms can support a search for new approaches to pathogenetic and disease-modifying treatment.

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Genetic diversity and genetic origin of Lanping black-boned sheep investigated by genome-wide single-nucleotide polymorphisms (SNPs)

Archives Animal Breeding ◽

10.5194/aab-63-193-2020 ◽

2020 ◽

Vol 63 (1) ◽

pp. 193-201

Author(s):

Heli Xiong ◽

Xiaoming He ◽

Jing Li ◽

Xingneng Liu ◽

Chaochao Peng ◽

...

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphisms ◽

Structure Analysis ◽

Genetic Background ◽

Nucleotide Polymorphisms ◽

Genetic Origin ◽

Single Nucleotide ◽

Sheep Breeds ◽

Genome Wide ◽

Nj Tree

Abstract. Lanping black-boned sheep was first discovered in the 1950s in Lanping county of China and characterized by black pigmentation on skin and internal organs. Due to the novel and unique trait, the genetic background of Lanping black-boned sheep is of great interest. Here, we genotyped genome-wide SNPs (single nucleotide polymorphisms) of Lanping black-boned sheep and Lanping normal sheep using Illumina OvineSNP50 BeadChip to investigate the genetic diversity and genetic origin of Lanping black-boned sheep. We also downloaded a subset SNP dataset of two Tibet-lineage sheep breeds and four other sheep breeds from the International Sheep Genomics Consortium (ISGC) as a reference for interpreting. Lanping black-boned sheep had a lower genetic diversity level when compared to seven other sheep breeds. Principal component analysis (PCA) showed that Lanping black-boned sheep and Lanping normal sheep were clustered into the Asian group, but there was no clear separation between the two breeds. Structure analysis demonstrated a high ancestry coefficient in Lanping black-boned sheep and Lanping normal sheep. However, the two populations were separated into two distinct branches in a neighbor-joining (NJ) tree. We further evaluated the genetic divergence using population FST, which showed that the genetic differentiation that existed between Lanping black-boned sheep and Lanping normal sheep was higher than that between Tibet sheep and Changthangi sheep, which revealed that Lanping black-boned sheep is a different breed from Lanping normal sheep on the genetic level. In addition, structure analysis and NJ tree showed that Lanping black-boned sheep had a relatively close relation with Tibet sheep. The results reported herein are a first step toward understanding the genetic background of Lanping black-boned sheep, and it will provide informative knowledge on the unique genetic resource conservation and mechanism of novel breed formation.

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Polymorphisms in the cytochrome P450 CYP1A1, CYP1A2, CYP1B1 genes and risk of colorectal cancer in a population from Central Russia

Nauchno-prakticheskii zhurnal «Medicinskaia genetika» ◽

10.25557/2073-7998.2020.06.60-61 ◽

2020 ◽

pp. 60-61

Author(s):

А.С. Москалев ◽

Ф.В. Подольский ◽

С.М. Зайцев ◽

Е.А. Новикова ◽

А.В. Полоников ◽

...

Keyword(s):

Colorectal Cancer ◽

Cytochrome P450 ◽

Single Nucleotide Polymorphisms ◽

Healthy Controls ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Central Russia ◽

Increased Risk ◽

Age And Sex

В исследование были включены 256 пациентов с колоректальным раком (134 мужчины, 122 женщины) и 608 практически здоровых добровольцев (279 мужчин, 329 женщин). Генотипирование однонуклеотидных полиморфизмов I462V (rs1048943) CYP1A1, -154A>C (rs762551) CYP1A2 и L432V (rs1056836) CYP1B1 было проведено методом ПЦР в режиме реального времени. Полиморфизм rs1056836 CYP1B1 (замена L432V) ассоциировался с повышенным риском колоректального рака в популяции Центральной России: OR=1,48, 95%CI=1,07-2,04; р=0,02. A total of 256 patients with colorectal cancer (134 males, 122 females) and 608 age- and sex-matched healthy controls (279 males, 329 females) were recruited for the study. Genotyping of single nucleotide polymorphisms (SNPs) I462V (rs1048943) CYP1A1, -154A>C (rs762551) CYP1A2 and L432V (rs1056836) CYP1B1 were done using Taq-Man-based assays. Polymorphism rs1056836 (substitution L432V) CYP1B1 was associated with increased risk of colorectal cancer in the population from Central Russia: OR=1,48, 95%CI=1,07-2,04; p=0,02.

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