Lack of association between delayed tooth emergence and single nucleotide polymorphisms in estrogen receptors

Abstract The purpose of the study was to investigate the association between single nucleotide polymorphisms (SNPs) in genes encoding estrogen receptors (ESR1 and ESR2, respectively) and delayed tooth emergence (DTE). This cross-sectional study was composed of biological unrelated children of both sexes, age ranging from 11 to 13 years old. DTE was defined when the successor primary tooth was still present in the oral cavity after its exfoliation time or the absence of the permanent tooth emergence into the oral cavity. Children were diagnosed with DTE when they had at least one delayed permanent tooth, according to age of exfoliation of each tooth proposed by The American Dental Association. Genomic DNA from saliva was used to evaluate the SNPs in ESR1 (rs9340799 and rs2234693) and ESR2 (rs1256049 and rs4986938) using Real-Time PCR. Chi-square or Fisher exact tests and Logistic Regression adjusted by age and gender were performed. SNP-SNP interaction was accessed by multifactor dimensionality reduction (MDR) analysis also adjusted by gender and age. The established alpha of this study was 5%. Among 537 included children, 296 (55%) were in the “DTE” group and the 241 (45%) were in the “Control” group. Age and gender were not statistically different among the groups (p>0.05). Genotype distribution of the SNPs rs9340799, rs2234693, rs1256049 and rs4986938 were not associated with DTE (p> 0.05). The models elected by MDR were not statistically significant either. Conclusions: The studied SNPs in ESR1 and ESR2 were not associated with permanent DTE.

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The role of IFIH1 gene rs1990760 and rs2111485 single-nucleotide polymorphisms in generalized vitiligo predisposition

TURKISH JOURNAL OF MEDICAL SCIENCES ◽

10.3906/sag-1808-63 ◽

2019 ◽

Author(s):

DURU ONAN ◽

AHU YORULMAZ ◽

FATİH SÜHEYL EZGÜ ◽

KADİR MUTLU HAYRAN ◽

SERAY KÜLCÜ ÇAKMAK ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Gene Locus ◽

Statistical Significance ◽

Additive Models ◽

Nucleotide Polymorphisms ◽

Age And Gender ◽

Single Nucleotide ◽

Hardy Weinberg Equilibrium ◽

And Gender

Background and Aim: Interferon-induced helicase (IFIH1) is a gene locus that has been recently defined as a candidate for susceptibility to generalized vitiligo (GV). The objectives of this study were to assess the association of IFIH1 gene, rs2111485 and rs1990760 single-nucleotide polymorphisms (SNP) with susceptibility to GV and the autoimmune diseases accompanying to GV. Materials and Methods: We prospectively studied GV patients and frequency-matched healthy controls by age and gender. The genotypes of the participants were determined for rs1990760 and rs2111485 SNPs of IFIH1. Dominant, recessive and additive models were evaluated for each SNP adjusted for age and gender. Results: The patients and their controls were demonstrated to be in the Hardy-Weinberg equilibrium for SNP1 (2q24.2, rs1990760, IFIH1, T/C) and SNP2 (2q24.2, rs2111485, IFIH1, G/A) respectively (all p> 0.7). For SNP1 every T allel addition was significantly associated with 1.53 times protectiveness in terms of vitiligo risk (P= 0.033). As for SNP2 every G allel addition was associated with 1.42 times protectiveness, close to statistical significance (P= 0.100). Conclusions: We detected that for SNP1 each T allel and for SNP2 each G allel are protective in terms of vitiligo development. Hereby, we confirmed that IFIH1 gene locus has a role in GV susceptibility. Keywords: Vitiligo, single nucleotide polymorphism, genes

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Susceptibility to Heart Defects in Down Syndrome Is Associated with Single Nucleotide Polymorphisms in HAS 21 Interferon Receptor Cluster and VEGFA Genes

Genes ◽

10.3390/genes11121428 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1428

Author(s):

Carmela Rita Balistreri ◽

Claudia Leonarda Ammoscato ◽

Letizia Scola ◽

Tiziana Fragapane ◽

Rosa Maria Giarratana ◽

...

Keyword(s):

Down Syndrome ◽

Single Nucleotide Polymorphisms ◽

Heart Defects ◽

Chromosome 21 ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Cardiac Defects ◽

Risk Alleles ◽

And Gender ◽

Heart Disorders

Background: Congenital heart defects (CHDs) are present in about 40–60% of newborns with Down syndrome (DS). Patients with DS can also develop acquired cardiac disorders. Mouse models suggest that a critical 3.7 Mb region located on human chromosome 21 (HSA21) could explain the association with CHDs. This region includes a cluster of genes (IFNAR1, IFNAR2, IFNGR2, IL10RB) encoding for interferon receptors (IFN-Rs). Other genes located on different chromosomes, such as the vascular endothelial growth factor A (VEGFA), have been shown to be involved in cardiac defects. So, we investigated the association between single nucleotide polymorphisms (SNPs) in IFNAR2, IFNGR2, IL10RB and VEGFA genes, and the presence of CHDs or acquired cardiac defects in patients with DS. Methods: Individuals (n = 102) with DS, and age- and gender-matched controls (n = 96), were genotyped for four SNPs (rs2229207, rs2834213, rs2834167 and rs3025039) using KASPar assays. Results: We found that the IFNGR2 rs2834213 G homozygous genotype and IL10RB rs2834167G-positive genotypes were more common in patients with DSand significantly associated with heart disorders, while VEGFA rs3025039T-positive genotypes (T/*) were less prevalent in patients with CHDs. Conclusions: We identified some candidate risk SNPs for CHDs and acquired heart defects in DS. Our data suggest that a complex architecture of risk alleles with interplay effects may contribute to the high variability of DS phenotypes.

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ADIPOQ single nucleotide polymorphisms and breast cancer in northeastern Mexican women

BMC Medical Genetics ◽

10.1186/s12881-020-01125-8 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Ricardo M. Cerda-Flores ◽

Karen Paola Camarillo-Cárdenas ◽

Gabriela Gutiérrez-Orozco ◽

Mónica Patricia Villarreal-Vela ◽

Raquel Garza-Guajardo ◽

...

Keyword(s):

Breast Cancer ◽

Single Nucleotide Polymorphisms ◽

Mexican Women ◽

Genotype Distribution ◽

Nucleotide Polymorphisms ◽

Allelic Discrimination Assay ◽

Allelic Discrimination ◽

Single Nucleotide ◽

Significant Difference ◽

Hardy Weinberg Equilibrium

Abstract Background Adiponectin gene (ADIPOQ) polymorphisms have been shown to affect adiponectin serum concentration and some have been associated with breast cancer (BC) risk. The aims of this study were to describe the frequency of single nucleotide polymorphisms (SNPs) of ADIPOQ in Mexican women with BC and to determine if they show an association with it. Methods DNA samples from 397 patients and 355 controls were tested for the ADIPOQ gene SNPs: rs2241766 (GT) and rs1501299 (GT) by TaqMan allelic discrimination assay. Hardy–Weinberg equilibrium (HWE) was tested. Multiple SNP inheritance models adjusted by age and body mass index (BMI) were examined for the SNP rs1501299. Results We found that in the frequency analysis of rs1501299 without adjusting the BMI and age, the genotype distribution had a statistically significant difference (P = 0.003). The T allele was associated with a BC risk (OR, 1.99; 95% CI 1.13–3.51, TT vs. GG; OR, 1.53; 95% CI 1.12–2.09, GT vs. GG). The SNP rs2241766 was in HW disequilibrium in controls. In conclusion, the rs1501299 polymorphism is associated with a BC risk. Conclusions Identification of the genotype of these polymorphisms in patients with BC can contribute to integrate the risk profile in both patients and their relatives as part of a comprehensive approach and increasingly more personalized medicine.

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Single Nucleotide Polymorphisms of Immunity-Related Genes and Their Effects on Immunophenotypes in Different Pig Breeds

Genes ◽

10.3390/genes12091377 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1377

Author(s):

Ann Ying-An Chen ◽

Chao-Wei Huang ◽

Shyh-Hwa Liu ◽

An-Chi Liu ◽

Hso-Chi Chaung

Keyword(s):

Single Nucleotide Polymorphisms ◽

Cell Surface ◽

Interferon Α ◽

Transcriptional Level ◽

Surface Markers ◽

Genotype Distribution ◽

Cell Surface Markers ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Immune Related Genes

Enhancing resistance and tolerance to pathogens remains an important selection objective in the production of livestock animals. Single nucleotide polymorphisms (SNPs) vary gene expression at the transcriptional level, influencing an individual’s immune regulation and susceptibility to diseases. In this study, we investigated the distribution of SNP sites in immune-related genes and their correlations with cell surface markers of immune cells within purebred (Taiwan black, Duroc, Landrace and Yorkshire) and crossbred (Landrace-Yorkshire) pigs. Thirty-nine SNPs of immune-related genes, including 11 cytokines, 5 chemokines and 23 Toll-like receptors (TLRs) (interferon-α and γ (IFN-α, γ), tumor necrosis factor-α (TNF-α), granulocyte-macrophage colony-stimulating factor (GM-CSF), Monocyte chemoattractant protein-1 (MCP-1) and TLR3, TLR4, TLR7, TLR8, and TLR9) were selected, and the percentages of positive cells with five cell surface markers of CD4, CD8, CD80/86, MHCI, and MHCII were analyzed. There were 28 SNPs that were significantly different among breeds, particularly between Landrace and Taiwan black. For instance, the frequency of SNP1 IFN-α -235A/G in Taiwan black and Landrace was 11.11% and 96.15%, respectively. In addition, 18 SNPs significantly correlated with the expression of cell surface markers, including CD4, CD8, CD80/86, and MHCII. The percentage of CD4+ (39.27%) in SNP33 TLR-8 543C/C was significantly higher than those in A/C (24.34%), at p < 0.05. Together, our findings show that Taiwan black pigs had a unique genotype distribution, whereas Landrace and Yorkshire had a more similar genotype distribution. Thus, an understanding of the genetic uniqueness of each breed could help to identify functionally important SNPs in immunoregulation.

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Effects of Ninjurin 2 Polymorphisms on Susceptibility of Coronary Heart Disease

10.21203/rs.3.rs-33439/v2 ◽

2020 ◽

Author(s):

Yuping Yan ◽

Xiaoyan Du ◽

Xiaoxi liu ◽

Jingjie Li ◽

Zichao Xiong ◽

...

Keyword(s):

Coronary Heart Disease ◽

Heart Disease ◽

Case Control Study ◽

Case Control ◽

Nucleotide Polymorphisms ◽

Age And Gender ◽

Single Nucleotide ◽

Chd Risk ◽

And Gender ◽

Control Study

Abstract Objective: The aim of this study was to explore the effects of NINJ2 polymorphisms on susceptibility of coronary heart disease (CHD).Methods: We conducted a case-control study with 499 CHD cases and 505 age- and sex- matched controls. Five single nucleotide polymorphisms (SNP) in NINJ2 (rs118050317, rs75750647, rs7307242, rs10849390 and rs11610368) were genotyped by Agena MassARRAY platform. Odd ratios (OR) and 95% confidence intervals (CI) were calculated using logistic regression to assess the association of NINJ2 polymorphism and CHD risk adjusting for age and gender..Results: NINJ2 rs118050317 significantly increased the risk of CHD in people over 60 years old (allele: P = 0.010; heterozygote: P = 0.016; dominant: P = 0.015; additive: P = 0.021) and women (allele: P = 0.026; heterozygote: P = 0.015; dominant: P = 0.018; additive: P = 0.030). Rs118050317 and rs7307242 were closely related to the risk of hypertension in CHD patients. Additionally, rs75750647 significantly increased diabetes risk in multiple models among CHD cases (allele: P = 0.014; homozygote: P = 0.037; heterozygote: P = 0.044; dominant: P = 0.019; additive: P = 0.013), whereas rs10849390 could protect CHD patients from diabetes in allele (P = 0.035), homozygote (P = 0.047) and additive (P = 0.037) models. We also observed two block (block 1: rs118050317 and rs75750647; block 2: rs7307242, rs10849390 and rs11610368) in NINJ2.Conclusion: Our results suggested that the relationships of NINJ2 polymorphisms and CHD risk were dependent on age, sex or complications.

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Effects of Ninjurin 2 Polymorphisms on Susceptibility of Coronary Heart Disease

10.21203/rs.2.24554/v1 ◽

2020 ◽

Author(s):

Yuping Yan ◽

Xiaoyan Du ◽

Xiaoxi Liu ◽

Jingjie Li ◽

Zichao Xiong ◽

...

Keyword(s):

Coronary Heart Disease ◽

Heart Disease ◽

Case Control Study ◽

Strong Relationship ◽

Nucleotide Polymorphisms ◽

Age And Gender ◽

Single Nucleotide ◽

Chd Risk ◽

And Gender ◽

Control Study

Abstract Objective The aim of this study was to explore the effects of NINJ2 polymorphisms on susceptibility of coronary heart disease (CHD). Methods We conducted a case-control study with 499 CHD cases and 505 age- and sex- matched controls. Five single nucleotide polymorphisms (SNP) in NINJ2 (rs118050317, rs75750647, rs7307242, rs10849390 and rs11610368) were genotyped by Agena MassARRAY platform. Odd ratios (OR) and 95% confidence intervals (CI) were calculated using logistic regression to assess the association of NINJ2 polymorphism and CHD risk adjusting for age and gender.. Results NINJ2 rs118050317 significantly increased CHD risk among people older than 60 years old (allele: P = 0.010; heterozygote: P = 0.016; dominant: P = 0.015; additive: P = 0.021) and women (allele: P = 0.026; heterozygote: P = 0.015; dominant: P = 0.018; additive: P = 0.030). Rs118050317 and rs7307242 had strong relationship with hypertension risk in CHD patients. Additionally, rs75750647 significantly increased diabetes risk in multiple models among cases (allele: P = 0.014; homozygote: P = 0.037; heterozygote: P = 0.044; dominant: P = 0.019; additive: P = 0.013), whereas rs10849390 could protect CHD patients from diabetes in allele ( P = 0.035), homozygote ( P = 0.047) and additive ( P = 0.037) models. We also observed two block (block 1: rs118050317 and rs75750647; block 2: rs7307242, rs10849390 and rs11610368) in NINJ2 . Conclusion Our results suggest that NINJ2 polymorphisms are associated with CHD risk.

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Single Nucleotide Polymorphisms in Carnosinase Genes (CNDP1 and CNDP2) are Associated With Power Athletic Status

International Journal of Sport Nutrition and Exercise Metabolism ◽

10.1123/ijsnem.2017-0098 ◽

2017 ◽

Vol 27 (6) ◽

pp. 533-542 ◽

Cited By ~ 4

Author(s):

João Paulo Limongi França Guilherme ◽

Antonio Herbert Lancha

Keyword(s):

Single Nucleotide Polymorphisms ◽

Endurance Athletes ◽

Genotype Distribution ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Athletic Status ◽

Genotype Frequencies ◽

Significant Difference ◽

Minor Alleles ◽

Representative Cohort

Carnosine (β-alanyl-L-histidine), abundantly found in skeletal muscle, plays an important role during exercise, especially for high-intensity contractions. Variability in muscle carnosine content between individuals exists and may also be explained by different genetic bases, although no study has addressed the association of polymorphisms in genes related to carnosine metabolism in athletes. This study aimed to investigate the frequency of single nucleotide polymorphisms (SNPs) in the carnosinase genes (CNDP1 and CNDP2) in a large Brazilian cohort of athletes and nonathletes. Eight SNPs were compared between a representative cohort of elite athletes from Brazil (n = 908) and a paired group of nonathletes (n = 967). The athletes were stratified into three groups: endurance (n = 328), power (n = 415), and combat (n = 165). The CNDP2 rs6566810 (A/A genotype) is overrepresented in endurance athletes, but only in international-level endurance athletes. Three SNPs (CNDP2 rs3764509, CNDP2-CNDP1 rs2346061, and CNDP1 rs2887) were overrepresented in power athletes compared with nonathletes. Carriers of the minor allele had an increased odds ratio of being a power athlete. For the rs2346061, no significant difference was observed in genotype frequencies between power and combat sports athletes, but for rs2887 the power and combat groups showed an inverse genotype distribution. In conclusion, we found that minor alleles carriers for CNDP2 rs3764509 (G-allele), CNDP2-CNDP1 rs2346061 (C-allele), and CNDP1 rs2887 (A-allele) are more likely to be a power athlete. These polymorphisms may be novel genetic markers for power athletes. Furthermore, these results are suggestive of a distinct CNDP genotype for sporting development.

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Obesity in the Balinese is associated with FTO rs9939609 and rs1421085 single nucleotide polymorphisms

PeerJ ◽

10.7717/peerj.8327 ◽

2020 ◽

Vol 8 ◽

pp. e8327

Author(s):

Lidwina Priliani ◽

Sukma Oktavianthi ◽

Ria Hasnita ◽

Hazrina T. Nussa ◽

Rut C. Inggriani ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Rural Areas ◽

Nucleotide Polymorphisms ◽

Obesity Prevalence ◽

Single Nucleotide ◽

Risk Alleles ◽

Destination Area ◽

And Gender ◽

Urban And Rural Areas ◽

Fto Rs9939609

Obesity prevalence is increasing worldwide, including in the Bali Province, Indonesia, a popular tourism destination area. The common single nucleotide polymorphisms (SNPs) rs9939609 and rs1421085 of the fat mass and obesity-associated (FTO) gene have been repeatedly reported as one of the important obesity genetic risk factors. We have examined the associations of FTO rs9939609 and rs1421085 SNPs with obesity in the 612 unrelated Balinese subjects living in urban and rural areas. Linear and logistic regression analyses with adjustment for age and gender were employed to investigate the association between FTO genotypes, haplotypes and obesity parameters. We found that the FTO SNPs genotypes increased BMI by 1.25 kg/m2 (p = 0.012) for rs9939609 AA and 1.12 kg/m2 (p = 0.022) for rs1421085 CC, particularly in females and in rural population. Subjects carrying these genotypes also showed a tendency to maintain high BMI, regardless of their age. Our result showed that the FTO rs9939609 and rs1421085 risk alleles were associated with increased BMI and obesity in the Balinese.

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Association of IGF1 single-nucleotide polymorphisms with myopia in Chinese children

PeerJ ◽

10.7717/peerj.8436 ◽

2020 ◽

Vol 8 ◽

pp. e8436

Author(s):

Tianyu Cheng ◽

Jingjing Wang ◽

Shuyu Xiong ◽

Bo Zhang ◽

Qiangqiang Li ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Chinese Population ◽

Additive Models ◽

Chinese Children ◽

Nucleotide Polymorphisms ◽

Chi Square ◽

Single Nucleotide ◽

Link Type ◽

Polymerase Chain ◽

And Gender

Purpose To investigate the association between insulin-like growth factor 1 (IGF1) single-nucleotide polymorphisms (SNPs) and myopia in a young Chinese population. Methods A total of 654 Chinese children aged 6–13 years from one primary school participated in our study and underwent a series of comprehensive ocular examinations, including cycloplegic refraction and measurements of axial length. Myopia was defined as a spherical equivalence (SE) ≤ −0.5 D in the worse eye. In total, six tagging SNPs of IGF1 were genotyped using the PCR-LDR (Polymerase Chain Reaction-Ligation Detection Reaction) method. We tested four different genetic modes (the allele, dominant, recessive, and additive models) of these SNPs and used multivariate logistic regression to calculate the effect of SNPs on myopia. In addition, we conducted a haplotype analysis with a variable-sized slide-window strategy. Results Overall, 281 myopic children and 373 non-myopic controls were included in the analysis. The SNP rs2162679 showed a statistical difference between the two groups in both the allele (p = 0.0474) and additive (p = 0.0497) models. After adjusting for age and gender, children with the genotype AA in the SNP rs2162679 had a higher risk of myopia than those with the genotype GG (OR = 2.219, 95% CI [1.218–4.039], p = 0.009). All haplotypes that varied significantly between the two groups contained the SNP rs2162679, and the four-SNP window rs5742653–rs2162679 had the lowest p value (Chi square = 5.768, p = 0.0163). However, after permutation tests, none of the associations remained statistically significant. Conclusion The SNP rs2162679 in IGF1 was associated with myopia in a young Chinese population. The G allele in the SNP rs2162679 may protect against myopia.

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Single Nucleotide Polymorphisms Associated with Methotrexate-induced Nausea in Juvenile Idiopathic Arthritis

10.21203/rs.3.rs-59432/v2 ◽

2021 ◽

Author(s):

Nini Kyvsgaard ◽

Torben Stamm Mikkelsen ◽

Thomas D. Als ◽

Anne Estmann Christensen ◽

Thomas J. Corydon ◽

...

Keyword(s):

Juvenile Idiopathic Arthritis ◽

Single Nucleotide Polymorphisms ◽

Snp Analysis ◽

Genotype Distribution ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Minor Alleles ◽

Genes Encoding ◽

Metabolizing Enzyme ◽

The Impact

Abstract BackgroundContext: Methotrexate (MTX) is a cornerstone in the treatment of juvenile idiopathic arthritis (JIA). MTX treatment is commonly associated with nausea. Large inter-individual variation exists in the level of MTX-induced nausea, possibly due to genetic factors. Purpose: To investigate whether MTX-induced nausea was associated with single nucleotide polymorphisms (SNPs) in genes encoding MTX-transporter proteins, a MTX metabolizing enzyme and a nausea receptor.FindingsMethods: Children aged ≥9 years treated with MTX for JIA were eligible. MTX-induced nausea was registered by the children’s completion of a nausea diary (min. 7 days) and the parents’ completion of the MTX intolerance severity score (MISS). The selected SNPs were: SLCO1B1 (rs4149056; rs4149081), SLCO1B3 (rs2117032), SLC19A1 (rs1051266), ABCC2 (rs2273697; rs3740066; rs717620), ABCB1 (rs2032582; rs1045642), MTHFR (rs1801131, rs1801133), HTR3A (rs1062613; rs1985242; rs1176713) and HTR3B (rs1176744). Results: Enrolled were 121 JIA patients (82 girls: 39 boys) with a median age of 13.3 years (IQR: 11.3-15.1). The median MTX dose was 9.7 mg/m2/week (IQR: 9.0-10.9). The median MTX treatment duration prior to enrolment was 340 days (IQR: 142-766). The SNP analysis was available for 119 patients. MTX intolerance was associated with the genotype distribution of rs1801133 (MTHFR) (p= 0.02). There was no additive effect of the minor alleles for any of the selected SNPs, nor any significant haplotype associations. Conclusion Summary: MTX-induced nausea may be influenced by genetic polymorphisms in a MTX metabolizing enzyme (rs1801133; MTHFR). Implications: Further analyses involving inclusion of larger cohorts are needed to understand the impact of SNPs on MTX-induced nausea in JIA.

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