scholarly journals Single nucleotide polymorphism in Interleukin 1 alpha gene might be involved in the Oral Herpes recurrent episodes in Brazilian Para-Athletes

2021 ◽  
Vol 10 (16) ◽  
pp. e564101624166
Author(s):  
João Armando Brancher ◽  
Luana Mordask Bonetto ◽  
Eugenio Esteves Costa ◽  
Rodrigo Von Held ◽  
Jhenyfer da Silva Tavares ◽  
...  
Keyword(s):  
Association Studies ◽  
Interleukin 1 ◽  
Genetic Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Oral Herpes ◽  
Hardy Weinberg Equilibrium ◽  
Dna Collection ◽  
Alpha Gene

The main goal of this study was to investigate if there is an association between Oral Herpes (OH) recurrent episodes and Single Nucleotide Polymorphisms (SNPs) in IL1A, IL10, and IL1RN genes in a group of Brazilian Para-athletes. This transversal study was prepared according to the STrengthening the REporting of Genetic Association Studies (STREGA) guidelines. Oral examination and DNA collection for genotyping were performed in a non-probabilistic convenience sampling composed of Brazilian para-athletes who participated in a Brazilian selective competition. Data referring to the general characterization of sample were collected through a self-reported questionnaire. Candidate genes were chosen with the UCSC Genome Browser and SNPs in IL1A gene (rs17561, rs1304037), IL10 gene (rs1800871), and IL1RN gene (rs9005) were selected and investigated in allelic, genotypic, dominant, and recessive models. Hardy-Weinberg equilibrium was evaluated in each SNP. The sample was composed of 273 para-athletes (63 (23.4%) practice swimming, 61 (22.3%) powerlifting and 145 (63.7%) athletics). OH recurrent episodes was related by 47 (17.2%) para-athletes and the presence of T allele in the rs1304037 increased chance of OH.  These findings suggest that rs1304037 in IL1A gene is associated with OH recurrent episodes in para-athletes.

scholarly journals MCP-1 −2518 A/G Single Nucleotide Polymorphism in Slovak Patients with Systemic Sclerosis

2008 ◽  
Vol 2008 ◽  
pp. 1-4 ◽  
Author(s):  
Zdenka Navratilova ◽  
Jozef Lukac ◽  
Frantisek Mrazek ◽  
Eva Kriegova ◽  
Maria Bucova ◽  
...  
Keyword(s):  
Healthy Subjects ◽  
Association Studies ◽  
Genetic Association Studies ◽  
German Population ◽  
Nucleotide Polymorphism ◽  
Control Groups ◽  
Single Nucleotide ◽  
Slovak Population ◽  
Healthy Control ◽  
Hardy Weinberg Equilibrium

Recent study in a group of German patients with SSc has implicated the SNP in the MCP-1 gene (−2518 A to G) as a factor of susceptibility to SSc. Reflecting the need for replication of genetic association studies, we investigated if this SNP is associated with SSc in another Caucasian population. MCP-1 −2518 A/G genotypes were determined using PCR-SSP in 46 SSc patients and in 449 healthy subjects, all unrelated and of Slovak (Slavonic) origin. The distribution of MCP-1 −2518 A/G genotypes complied with the Hardy-Weinberg equilibrium both in patient and healthy control groups. There was no difference in MCP-1 −2518∗G allele frequency between SSc patients and healthy subjects (patients: 0.23; controls: 0.24; P>.05). Furthermore, MCP-1 −2518 GG homozygotes were similarly represented among SSc patients and healthy subjects (P>.05). The association of MCP-1 −2518 A/G SNP with SSc observed originally in German population was not replicated in the Slovak population.

scholarly journals Prostate Cancer Risk-Associated Single-Nucleotide Polymorphism Affects Prostate-Specific Antigen Glycosylation and Its Function

2019 ◽  
Vol 65 (1) ◽  
pp. e1-e9 ◽  
Author(s):  
Srilakshmi Srinivasan ◽  
Carson Stephens ◽  
Emily Wilson ◽  
Janaththani Panchadsaram ◽  
Kerry DeVoss ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Prostate Specific Antigen ◽  
Association Studies ◽  
Specific Antigen ◽  
Prostate Cancer Risk ◽  
Genetic Association Studies ◽  
Glycosylation Site ◽  
Nucleotide Polymorphisms ◽  
Serum Samples ◽  
Single Nucleotide

Abstract BACKGROUND Genetic association studies have reported single-nucleotide polymorphisms (SNPs) at chromosome 19q13.3 to be associated with prostate cancer (PCa) risk. Recently, the rs61752561 SNP (Asp84Asn substitution) in exon 3 of the kallikrein-related peptidase 3 (KLK3) gene encoding prostate-specific antigen (PSA) was reported to be strongly associated with PCa risk (P = 2.3 × 10−8). However, the biological contribution of the rs61752561 SNP to PCa risk has not been elucidated. METHODS Recombinant PSA protein variants were generated to assess the SNP-mediated biochemical changes by stability and substrate activity assays. PC3 cell–PSA overexpression models were established to evaluate the effect of the SNP on PCa pathogenesis. Genotype-specific correlation of the SNP with total PSA (tPSA) concentrations and free/total (F/T) PSA ratio were determined from serum samples. RESULTS Functional analysis showed that the rs61752561 SNP affects PSA stability and structural conformation and creates an extra glycosylation site. This PSA variant had reduced enzymatic activity and the ability to stimulate proliferation and migration of PCa cells. Interestingly, the minor allele is associated with lower tPSA concentrations and high F/T PSA ratio in serum samples, indicating that the amino acid substitution may affect PSA immunoreactivity to the antibodies used in the clinical immunoassays. CONCLUSIONS The rs61752561 SNP appears to have a potential role in PCa pathogenesis by changing the glycosylation, protein stability, and PSA activity and may also affect the clinically measured F/T PSA ratio. Accounting for these effects on tPSA concentration and F/T PSA ratio may help to improve the accuracy of the current PSA test.

scholarly journals Meta-Analysis of Allergy Genome-Wide Association Studies

2020 ◽  
Author(s):  
Ronin Sharma
Keyword(s):  
Association Studies ◽  
Meta Analysis ◽  
Genetic Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Significance Level ◽  
Genome Wide ◽  
Linear Regressions

AbstractAllergies are complex conditions involving both environmental and genetic factors. The genetic basis underlying allergic disease is investigated through genetic association studies. Genome-wide association studies (GWAS) leverage sequenced data to identify genetic mutations, such as single-nucleotide polymorphisms (SNPs), associated with phenotypes of interest. Machine learning can be used to analyze large datasets and generate predictive models. In this study, several classification models were created to predict the significance level of SNPs associated with allergies. Summary statistics were obtained from the GWAS Catalog and combined from several studies. Biological features such as chromosomal location, base pair location, effect allele, and odds ratio were used to train the models. The models ranged from simple linear regressions to multi-layer neural networks. The final models reached accuracies of 80% and reflect the features that have the largest impact on a SNP’s association level.

scholarly journals Association of Vitamin D Metabolism Gene Polymorphisms with Autoimmunity: Evidence in Population Genetic Studies

2020 ◽  
Vol 21 (24) ◽  
pp. 9626
Author(s):  
Adolfo I. Ruiz-Ballesteros ◽  
Mónica R. Meza-Meza ◽  
Barbara Vizmanos-Lamotte ◽  
Isela Parra-Rojas ◽  
Ulises de la Cruz-Mosso
Keyword(s):  
Vitamin D ◽  
Vitamin D Receptor ◽  
Lupus Erythematosus ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Serum Levels ◽  
Nucleotide Polymorphisms ◽  
Vitamin D Metabolism ◽  
Single Nucleotide ◽  
High Prevalence

A high prevalence of vitamin D (calcidiol) serum deficiency has been described in several autoimmune diseases, including multiple sclerosis (MS), rheumatoid arthritis (AR), and systemic lupus erythematosus (SLE). Vitamin D is a potent immunonutrient that through its main metabolite calcitriol, regulates the immunomodulation of macrophages, dendritic cells, T and B lymphocytes, which express the vitamin D receptor (VDR), and they produce and respond to calcitriol. Genetic association studies have shown that up to 65% of vitamin D serum variance may be explained due to genetic background. The 90% of genetic variability takes place in the form of single nucleotide polymorphisms (SNPs), and SNPs in genes related to vitamin D metabolism have been linked to influence the calcidiol serum levels, such as in the vitamin D binding protein (VDBP; rs2282679 GC), 25-hydroxylase (rs10751657 CYP2R1), 1α-hydroxylase (rs10877012, CYP27B1) and the vitamin D receptor (FokI (rs2228570), BsmI (rs1544410), ApaI (rs7975232), and TaqI (rs731236) VDR). Therefore, the aim of this comprehensive literature review was to discuss the current findings of functional SNPs in GC, CYP2R1, CYP27B1, and VDR associated to genetic risk, and the most common clinical features of MS, RA, and SLE.

BIOINFORMATIC PRIORITIZATION OF SINGLE NUCLEOTIDE POLYMORPHISMS IN GENETIC ASSOCIATION STUDIES

2002 ◽  
Vol 30 (Supplement) ◽  
pp. A132
Author(s):  
Robert C Barber ◽  
Fernando A Rivera-Chavez ◽  
Herbert T Wheeler ◽  
Gina M Whitney ◽  
Dixie L Peters-Hybki ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Association ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Development and characterization of 57 SNP markers in Misgurnus anguillicaudatus

2021 ◽  
Author(s):  
Guiyun Huang ◽  
Fengying Gao ◽  
Zhigang Liu ◽  
Jianmeng Cao ◽  
Gang Chen ◽  
...  
Keyword(s):  
Snp Markers ◽  
Freshwater Species ◽  
Nucleotide Polymorphisms ◽  
Misgurnus Anguillicaudatus ◽  
Population Genetic Analysis ◽  
Single Nucleotide ◽  
Natural Resource Conservation ◽  
Hardy Weinberg Equilibrium ◽  
Selection Of

Abstract The dojo loach Misgurnus anguillicaudatus is an endemic freshwater species to Asia. The effective conservation and molecular-aided selection of M. anguillicaudatus have been limited without sufficient molecular markers. In this study, 112 novel single nucleotide polymorphisms (SNPs) were screened based on 2b-RAD sequencing database, and 57 SNP markers were developed and characterized by genotyping 40 individuals using SNaPshot method. The observed heterozygosity (Ho) ranged from 0.025 to 0.675, while the expected heterozygosity (He) varied from 0.025 to 0.500. The minor allele frequency (MAF) ranged from 0.013 to 0.500. Among these SNPs, 18 loci were found to deviate significantly from the Hardy–Weinberg equilibrium after Bonferroni correction (P < 0.05). The first set of SNP markers developed from M. anguillicaudatus will provide valuable information in further population genetic analysis and natural resource conservation.

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