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

PeerJ ◽  
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.

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

Genes ◽  
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.

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

2021 ◽  
Vol 32 (6) ◽  
pp. 107-114
Author(s):  
Isabela Ribeiro Madalena ◽  
Caio Luiz Bitencourt Reis ◽  
Daniela Silva Barroso de Oliveira ◽  
Giovana Daniela Pecharki ◽  
Paula Cristina Trevilatto ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Oral Cavity ◽  
Estrogen Receptors ◽  
Permanent Tooth ◽  
Genotype Distribution ◽  
Nucleotide Polymorphisms ◽  
Age And Gender ◽  
Single Nucleotide ◽  
And Gender ◽  
Tooth Emergence

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.

scholarly journals Effective Detection of Human Leukocyte Antigen Risk Alleles in Celiac Disease Using Tag Single Nucleotide Polymorphisms

PLoS ONE ◽  
2008 ◽  
Vol 3 (5) ◽  
pp. e2270 ◽  
Author(s):  
Alienke J. Monsuur ◽  
Paul I. W. de Bakker ◽  
Alexandra Zhernakova ◽  
Dalila Pinto ◽  
Willem Verduijn ◽  
...  
Keyword(s):  
Celiac Disease ◽  
Single Nucleotide Polymorphisms ◽  
Human Leukocyte Antigen ◽  
Human Leukocyte ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Leukocyte Antigen ◽  
Risk Alleles

scholarly journals Single Nucleotide Polymorphisms and Thromboembolism in Acute Lymphoblastic Leukemia — a NOPHO ALL2008 Study

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 143-143 ◽  
Author(s):  
Kirsten Brunsvig Jarvis ◽  
Marissa Le Blanc ◽  
Morten Tulstrup ◽  
Ellen Ruud ◽  
Ruta Tuckuviene ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Single Nucleotide Polymorphisms ◽  
Risk Score ◽  
Genetic Risk ◽  
Lymphoblastic Leukemia ◽  
European Ancestry ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Risk Alleles ◽  
All Treatment

Abstract Introduction: Thromboembolism (TE) is a major toxicity of acute lymphoblastic leukemia (ALL) treatment and contributes to substantial morbidity and mortality. Several germline DNA variants have been associated with TE in adults without cancer. A meta-analysis of genome-wide association studies on TE by Germain et al. (Am J Hum Genet 2015) identified single nucleotide polymorphisms (SNPs) in 8 genes that contribute to increased risk of TE in adults (ABO,F2, F5,F11, FGG,PROCR,TSPAN15, and SLC44A2). De Haan et al. (Blood 2012) found that SNPs in 5 of these (F5, F2, F11, FGG, and ABO) predicted TE almost as well as a 31 SNP-based risk score. However, the impact of these SNPs in patients with cancer, particularly in children, remains uncertain. Materials and methods: The Nordic Society of Pediatric Hematology and Oncology (NOPHO) ALL2008 protocol for children and adults (1-45 years) included a 3-drug induction (vincristine, doxorubicin, glucocorticosteroid) followed by exposure to asparaginase (1,000 IU/m.sq. i.m.) from week 5 until week 33 (details of therapy in Toft, Leukemia 2018). We collected germline DNA and prospectively registered TE events on 1482 children and adults diagnosed with ALL and treated according to the ALL2008 protocol in seven Nordic and Baltic countries (7/2008-7/2016) (Rank, Blood 2018). Inclusion criteria for TE were i) symptomatic venous or arterial TE confirmed by imaging or by autopsy for TE diagnosed post mortem or ii) asymptomatic TE confirmed by imaging due to other non-TE symptoms and treated with systemic anticoagulation. Based on previously published data and a priori power calculations, we selected and genotyped 5 SNPs: F5 rs6025 (risk allele frequency (RAF) 0.05), F11 rs2036914 (RAF 0.52), FGG rs2066865 (RAF 0.22), and ABO SNPs rs8176719 (RAF 0.39) and rs2519093 (RAF 0.24). Three SNPs (F5 and the two ABO SNPs) were found by imputation, which was done on a subset of patients with European ancestry and included in the NOPHO ALL2008 protocol (N = 1229). We constructed genetic risk scores using a combination of the SNPs. Results: During the ALL treatment period 107 of 1482 patients developed TE (2.5-year cumulative incidence 7.3%, 95% confidence interval (CI) 5.9-8.5). In multivariate Cox regression analysis controlling for age, gender, presence of mediastinal mass and enlarged lymph nodes (N = 1192, whereof TE events 84), we found statistically significant associations with TE development for SNPs F5 rs6025 (hazard ratio (HR) 2.96, 95% CI 1.59-5.48), F11 rs2036914 (HR 1.62, 95% CI 1.18-2.24), and FGG rs2066865 (HR 1.40 95% CI 1.01-1.95), whereas there were no significant associations with ABO SNPs rs8176719 (HR 0.98, 95% CI 0.64-1.51) or rs2519093 (HR 1.06, 95% CI 0.65-1.73). An unweighted 3 SNP risk score based on SNPs F5, F11, and FGG was associated with TE development (HR 1.59, 95% CI 1.27-1.98) (Figure 1). Twenty-six of 217 patients with ≥3 risk alleles developed TE (12.0%, 95% CI 8.1-17.2), compared to 62 of 1007 patients with <3 risk alleles (6.2%, 95% CI 4.8-7.9). The association was strongest in the adolescent age group (10-18 years; HR 1.88, 95% CI 1.35-2.63). Thirteen of 43 adolescents with ≥3 risk alleles developed TE (30.2%, 95% CI 17.8-46.3), compared to 20 of 182 adolescents with <3 risk alleles (11.0%, 95% CI 7.0-16.7) (Figure 2). In adults (>18 years) the proportion who developed TE was quite high in both the group with ≥3 risk alleles (23.5%, 95% CI 7.8-50.2) and with <3 risk alleles (17.6% 95%CI 11.1-26.3). In children (1-10 years) the proportion who developed TE was low in both the group with ≥3 risk alleles (5.7%, 95% CI 2.8-10.9) and with <3 risk alleles (3.2%, 95% CI 2.1-4.8). A weighted 3 SNP genetic risk score based on estimated odds ratios from literature for SNPs F5, F11 and FGG was also associated with TE development (HR 2.84, 95% CI 1.85-4.36). Again, the association was strongest in adolescents (HR 4.20, 95% CI 2.22-7.94). Conclusion: Based on the strong association between F5 rs6025, F11 rs2036914, and FGG rs2066865 and TE development, not least for adolescents, future preventive measures for TE should target adolescents with ≥3 risk alleles as well as any adults ≥18 years. Disclosures No relevant conflicts of interest to declare.

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

PeerJ ◽  
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.

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

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

scholarly journals DRD2/ANKK1 Taq1A but not COMT single nucleotide polymorphisms contribute to the link between temporal impulsivity and obesity in men

2020 ◽  
Author(s):  
Filip Morys ◽  
Jakob Simmank ◽  
Annette Horstmann
Keyword(s):  
Genetic Variability ◽  
Single Nucleotide Polymorphisms ◽  
The Body ◽  
Nucleotide Polymorphisms ◽  
Cross Sectional ◽  
Single Nucleotide ◽  
Dopaminergic Transmission ◽  
And Gender ◽  
Gender Interactions ◽  
The Brain

AbstractTemporal impulsivity, the tendency to choose a smaller, sooner over a larger, delayed reward, is associated with single nucleotide polymorphisms (SNPs) in COMT and DRD2-related ANKK1 genes, whose products regulate dopaminergic transmission in the brain. Temporal impulsivity is also consistently associated with obesity, sometimes in a genderdependent fashion. Further, there seems to be no direct association between these SNPs and obesity. In this study, we investigated an interaction between BMI, COMT, and DRD2/ANKK1 SNPs, and temporal impulsivity. We tested three plausible models of associations between those variables: (1) genetic variability influencing BMI through temporal impulsivity and gender interactions, (2) genetic variability interacting with temporal impulsivity to influence BMI, (3) interaction of BMI and genetic variability influencing temporal impulsivity. We found evidence for the second model: in men, BMI was dependent on temporal impulsivity and the DRD2/ANKK1 SNP. It shows that increased temporal impulsivity combined with a disadvantageous DRD2/ANKK1 genotype might be a vulnerability factor for the development of obesity. Our study, even though cross-sectional, adds to the body of literature regarding the influence of the dopaminergic system on obesity measures. Our results point to a factor explaining discrepancies in results regarding associations of temporal impulsivity and BMI in women and men.

scholarly journals Association between Vitamin D Deficiency and Single Nucleotide Polymorphisms in the Vitamin D Receptor and GC Genes and Analysis of Their Distribution in Mexican Postmenopausal Women

Nutrients ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 1175 ◽  
Author(s):  
Berenice Rivera-Paredez ◽  
Nayeli Macías ◽  
Mayeli M. Martínez-Aguilar ◽  
Alberto Hidalgo-Bravo ◽  
Mario Flores ◽  
...  
Keyword(s):  
Vitamin D ◽  
Single Nucleotide Polymorphisms ◽  
Postmenopausal Women ◽  
Vitamin D Receptor ◽  
Genetic Variants ◽  
European Ancestry ◽  
Nucleotide Polymorphisms ◽  
The South ◽  
Single Nucleotide ◽  
Risk Alleles

Genome-wide association studies in people with European ancestry suggest that polymorphisms in genes involved in vitamin D (VD) metabolism have an effect on serum concentrations of 25-hydroxyvitamin D. However, nothing is known about these polymorphisms in populations with Amerindian ancestry. Our aim was to evaluate the association between genetic variants on the vitamin D receptor (VDR) and the vitamin D binding protein (GC) genes, involved in the VD pathway, and VD deficiency in 689 unrelated Mexican postmenopausal women. We also described the frequencies of these variants in 355 postmenopausal women from different ethnic groups. Based on our preliminary results of 400 unrelated Mexican postmenopausal women, three single nucleotide polymorphisms (SNPs) were selected for genotyping. The SNPs rs4516035 in VDR and rs2282679 in GC were associated with VD deficiency. Additionally, women who carried three risk alleles had a 3.67 times higher risk of suffering VD deficiency, compared to women with no risk alleles (p = 0.002). The rs4516035-C allele frequency in the Amerindian population was enriched in the South East region of Mexico. In contrast, the highest frequency of the rs2298850-C allele, a proxy for the tag SNP rs2282679, was observed in the South region. Our results indicate that genetic variants in VDR and GC genes are associated with VD deficiency in Mexican postmenopausal women. Moreover, an association was observed for the variants rs3794060 and rs4944957 of the DHCR7/NADSYN1 gene with osteopenia/osteoporosis.

The functional impact of alternative splicing and single nucleotide polymorphisms in rheumatoid arthritis

2020 ◽  
Vol 21 ◽  
Author(s):  
R. Kowshik Aravilli ◽  
S. Laveen Vikram ◽  
V. Kohila
Keyword(s):  
Rheumatoid Arthritis ◽  
Alternative Splicing ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Factors ◽  
Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Risk Alleles ◽  
Multiple Loci ◽  
Genomics And Proteomics

: Advances in genomics and proteomics aid the identification of genes associated with various diseases. Genomewide association studies (GWAS) have identified multiple loci as risk alleles for susceptibility to rheumatoid arthritis (RA). A bisection of RA risk can be attributed to genetic factors. Over 100 associated genetic loci that encompass immune regulatory factors have been found to be linked with RA. Aberrant single nucleotide polymorphisms (SNPs) and alternative splicing mechanisms in such loci induce RA. These aberrations are viewed as potential therapeutic targets due to their association with multitude of diseases. This review presents few imperious genes whose alterations can cause severe bone deformities culminating in RA.

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