scholarly journals An Efficient Gatekeeper Algorithm for Detecting GxE

2010 ◽  
Vol 9 ◽  
pp. CIN.S4731
Author(s):  
Jimmy T. Efird
Keyword(s):  
Public Health ◽  
Interactive Effects ◽  
Design Phase ◽  
Nucleotide Polymorphisms ◽  
False Negatives ◽  
Single Nucleotide ◽  
Public Health Screening ◽  
Gene Environment ◽  
Genetic And Environmental Factors ◽  
Selection Of

The risk for many complex diseases is believed to be a result of the interactive effects of genetic and environmental factors. Developing efficient techniques to identify gene-environment interactions (GxE) is important for unraveling the etiologic basis of many modern day diseases including cancer. The problem of false positives and false negatives continues to pose significant roadblocks to detecting GxE and informing targeted public health screening and intervention. A heuristic gatekeeper method is presented to guide the selection of single nucleotide polymorphisms (SNPs) in the design phase of a GxE study.

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

Nutrients ◽  
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.

scholarly journals Gene-Environment Interactions in Progressive Supranuclear Palsy

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.

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

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.

scholarly journals Selection of X-chromosome Inactivation Model

2017 ◽  
Vol 16 ◽  
pp. 117693511774727 ◽  
Author(s):  
Jian Wang ◽  
Rajesh Talluri ◽  
Sanjay Shete
Keyword(s):  
X Chromosome ◽  
X Chromosome Inactivation ◽  
Association Test ◽  
Chromosome Inactivation ◽  
Simulation Studies ◽  
Nucleotide Polymorphisms ◽  
Unified Approach ◽  
Cancer Genetic ◽  
Single Nucleotide ◽  
Selection Of

To address the complexity of the X-chromosome inactivation (XCI) process, we previously developed a unified approach for the association test for X-chromosomal single-nucleotide polymorphisms (SNPs) and the disease of interest, accounting for different biological possibilities of XCI: random, skewed, and escaping XCI. In the original study, we focused on the SNP-disease association test but did not provide knowledge regarding the underlying XCI models. One can use the highest likelihood ratio (LLR) to select XCI models (max-LLR approach). However, that approach does not formally compare the LLRs corresponding to different XCI models to assess whether the models are distinguishable. Therefore, we propose an LLR comparison procedure (comp-LLR approach), inspired by the Cox test, to formally compare the LLRs of different XCI models to select the most likely XCI model that describes the underlying XCI process. We conduct simulation studies to investigate the max-LLR and comp-LLR approaches. The simulation results show that compared with the max-LLR, the comp-LLR approach has higher probability of identifying the correct underlying XCI model for the scenarios when the underlying XCI process is random XCI, escaping XCI, or skewed XCI to the deleterious allele. We applied both approaches to a head and neck cancer genetic study to investigate the underlying XCI processes for the X-chromosomal genetic variants.

scholarly journals A Novel Test System for Genotyping rs43703016 Single-nucleotide Substitutions in the Bovine CSN3 Gene

2019 ◽  
pp. 1-5
Author(s):  
Svetlana Kovalchuk ◽  
Arina Tagmazyan ◽  
Eugene Klimov
Keyword(s):  
Nucleotide Substitution ◽  
Milk Proteins ◽  
Test System ◽  
Nucleotide Polymorphisms ◽  
Dna Testing ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Allele Specific ◽  
Selection Of

Aims: Caseins are among the main milk proteins that determine many of its properties. Bovine kappa-casein (CSN3) is associated with the qualitative composition of milk, as well as with the quality of cheese obtained from this milk. The rs43703016 single-nucleotide substitution (g.88532332A>C; Asp148Ala) in exon 4 of the bovine CSN3 gene plays an important role in the production of quality hard cheeses. Various methods for the DNA testing of this substitution have been developed in the last three decades. Emergent DNA technologies provide an opportunity to modernize methods of genotyping single-nucleotide polymorphisms. Results: We have developed and verified a method to differentiate A/C alleles of the rs43703016 substitution in the bovine CSN3 gene by real-time PCR using allele-specific fluorescent probes. Conclusion: Our new method allows fast genotyping of animals, and may be used for selection of cows carrying the CC genotype, which determines good cheese-making properties of milk.

scholarly journals Prevalence and Genomic Characterization of Brucella canis Strains Isolated from Kennels, Household, and Stray Dogs in Chile

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2073
Author(s):  
Nicolás Galarce ◽  
Beatriz Escobar ◽  
Eduard Martínez ◽  
Natalia Alvarado ◽  
Gabriela Peralta ◽  
...  
Keyword(s):  
Public Health ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Stray Dogs ◽  
Control Programs ◽  
Official Control ◽  
Brucella Canis ◽  
Genomic Characterization ◽  
Canine Brucellosis

Canine brucellosis caused by Brucella canis is a zoonotic disease that causes reproductive alterations in dogs, such as infertility, abortion, and epididymitis. This pathogen is especially prevalent in South America, and due to the lack of official control programs and the growing trend of adopting dogs it constitutes a public health risk that must be addressed. The aim of this study was to determine the prevalence of B. canis infection in kennel, shelter, and household dogs and to characterize the genomic properties of circulating strains, including ure and virB operons and omp25/31 genes. Samples from 771 dogs were obtained, and the infection was detected by blood culture and/or serology in 7.0% of the animals. The complete ure and virB operons and the omp25/31 genes were detected. Interestingly, we found different single-nucleotide polymorphisms (SNPs) in some of the analyzed genes, which could mean a change in the fitness or virulence of these strains. This study provides further evidence about dogs as a source of B. canis strains that can infect people. This also highlights the need to implement official control programs, including the mandatory testing of dogs, especially stray dogs, before adoption.

scholarly journals 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

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Krisztina Mártha ◽  
Bernadette Kerekes Máthé ◽  
Valeriu George Moldovan ◽  
Claudia Bănescu
Keyword(s):  
Environmental Factors ◽  
Genetic Background ◽  
Orthodontic Treatment ◽  
Statistical Significance ◽  
Nucleotide Polymorphisms ◽  
Inhibitor Protein ◽  
Single Nucleotide ◽  
Variant Genotype ◽  
Genetic And Environmental Factors ◽  
Age And Sex

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.

scholarly journals Genetic Factors of Nitric Oxide’s System in Psychoneurologic Disorders

2020 ◽  
Vol 21 (5) ◽  
pp. 1604 ◽  
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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