scholarly journals A systematic review on papers that study on Single Nucleotide Polymorphism that affects coronavirus 2019 severity

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Siyeon Suh ◽  
Sol Lee ◽  
Ho Gym ◽  
Sanghyuk Yoon ◽  
Seunghwan Park ◽  
...  
Keyword(s):  
Clinical Studies ◽  
Time History ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Common Features ◽  
Newcastle Ottawa Scale ◽  
History Of ◽  
Severity Of The Disease ◽  
Ottawa Scale

Abstract Background COVID-19, caused by SARS-CoV-2 has become the most threatening issue to all populations around the world. It is, directly and indirectly, affecting all of us and thus, is an emerging topic dealt in global health. To avoid the infection, various studies have been done and are still ongoing. COVID-19 cases are reported all over the globe, and among the millions of cases, genetic similarity may be seen. The genetical common features seen within confirmed cases may help outline the tendency of infection and degree severity of the disease. Here, we reviewed multiple papers on SNPs related to SARS-CoV-2 infection and analyzed their results. Methods The PubMed databases were searched for papers discussing SNPs associated with SARS-CoV-2 infection and severity. Clinical studies with human patients and statistically showing the relevance of the SNP with virus infection were included. Quality Assessment of all papers was done with Newcastle Ottawa Scale. Results In the analysis, 21 full-text literature out of 2956 screened titles and abstracts, including 63,496 cases, were included. All were human-based clinical studies, some based on certain regions gathered patient data and some based on big databases obtained online. ACE2, TMPRSS2, and IFITM3 are the genes mentioned most frequently that are related to SARS-CoV-2 infection. 20 out of 21 studies mentioned one or more of those genes. The relevant genes according to SNPs were also analyzed. rs12252-C, rs143936283, rs2285666, rs41303171, and rs35803318 are the SNPs that were mentioned at least twice in two different studies. Conclusions We found that ACE2, TMPRSS2, and IFITM3 are the major genes that are involved in SARS-CoV-2 infection. The mentioned SNPs were all related to one or more of the above-mentioned genes. There were discussions on certain SNPs that increased the infection and severity to certain groups more than the others. However, as there is limited follow-up and data due to a shortage of time history of the disease, studies may be limited.

scholarly journals A Systematic Review on Papers That Study on SNPs That Affect SARS-CoV-2 Infection & COVID-19 Severity

2021 ◽  
Author(s):  
Siyeon Suh ◽  
Sol Lee ◽  
Ho Gym ◽  
Sun Ha Jee ◽  
Sanghyuk Yoon ◽  
...  
Keyword(s):  
Systematic Review ◽  
Virus Infection ◽  
Global Health ◽  
Full Text ◽  
Clinical Studies ◽  
Time History ◽  
The World ◽  
History Of ◽  
Severity Of The Disease

Abstract Background:COVID-19, caused by SARS-CoV-2 has become the most threatening issue to all populations around the world. It is directly and indirectly affecting all of us and thus, is a emergence topic dealt in global health. In order to avoid the infection, various studies have been done and still ongoing. Now having over 141 million cases of COVID19 and causing over 3 million deaths around the world, the tendency of infection and degree severity of the disease shown in different groups of people came up as an issue. Here, we reviewed 21 papers on SNPs related to SARS-CoV-2 infection severity and analyzed the results of them.Methods:The PubMed databases were searched for papers discussing SNPs associated with SARS-CoV-2 infection severity. Clinical studies with human patients and statistically showing relevance of the SNP with virus infection were included. Quality Assessment of all papers were done with Newcastle Ottawa Scale.Results:In the analysis, 21 full-text literatures out of 2956 screened titles and abstracts, including 63496 cases, were included. All were human based clinical studies, some based on certain regions gathered patient data and some based on big databases obtained online. ACE2, TMPRSS2, IFITM3 are the genes mentioned most frequently that are related with SARS-CoV-2 infection. 20 out of 21 studies mentioned one of more of those genes. The relevant genes according to SNPs were also analyzed. rs12252-C, rs143936283, rs2285666, rs41303171, and rs35803318 are the SNPs that were mentioned at least twice in two different studies.Conclusions: We found that ACE2, TMPRSS2, IFITM3 are the major genes that are involved in SARS-CoV-2 infection. The mentioned SNPs were all related to one or more of the above mentioned genes. There were discussions on certain SNPs that increased the infection severity to certain ethinic groups more than the others. However, as there is limited follow up and data due to shortage of time history of the disease, studies may be limited.

scholarly journals The role of single nucleotide polymorphism of val66met (rs6265) of the brain-derived neurotropic factor in formation of endpoints after st-segment elevation myocardial infarction

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
O.V Petyunina ◽  
M.P Kopytsya ◽  
A.E Berezin ◽  
A.A Berezin
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bdnf Gene ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
St Segment Elevation ◽  
Acute Stemi ◽  
End Point ◽  
St Segment ◽  
The Brain

Abstract Background The single nucleotide polymorphism (SNP) Val66Met (rs6265) of the brain-derived neurotrophic factor (BDNF) gene is a possible candidate that is associated with the development of psychopathology and combines it with cardiovascular events. Purpose To research the possible associations of single-nucleotide polymorphism of Val66Met BDNF gene with the occurrence of endpoints after 6 months of follow-up after ST segment elevation myocardial infarction (STEMI). Methods 256 acute STEMI patients after successful primary percutaneous coronary intervention (PCI) were enrolled in the study. TIMI III blood flow restoring through culprit artery was determined. The study of SNP of Val66Met (rs6265) of the BDNF gene was performed by real-time polymerase chain reaction. The emotional state of the patients and its relationship with stress were assessed with the questionnaire “Depression, Anxiety and Stress-21”. All acute STEMI patients received adjuvant treatment due to current ESC recommendations. All procedures performed in the study involving human participants were in accordance with the ethical standards and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards and approved by the local ethics committee. Written inform consent was obtained from each patient. The primary endpoint was combined event (follow-up major adverse cardiac events – MACEs and hospitalization) that occurred within 6-month of the discharge from the hospital. MACEs were defined as the composite of CV death, recurrent angina, newly diagnosed heart failure. Results The frequency of genotypes Val66Met gene for BDNF in STEMI patients (n=256) was the following: 66ValVal=74.2% (n=190), 66ValMet + 66MetMet – 25.8% (n=66). The 66ValMet + 66MetMet polymorphism in the BDNF gene, stress and anxiety on 10–14 days before the event, as well as reduced left ventricular ejection fraction (LVEF), were independently associated with combined 6 months clinical end point after STEMI. Severity of depression according to depression scale was more profound in individuals with 66ValMet+66MetMet polymorphysms in BDNF gene (P=0.045) than in patients with 66ValVal genotype. Univariate and multivariate linear regressions has shown that 66ValMet+66MetMet genotype in BDNF gene, anxiety and stress before event, LVEF had independent power on dependent variable entitled combined end point after 6 month observation for STEMI patients with successful revascularization (P=0.0395). Kaplan-Meier curves demonstrated that STEMI patients with 66ValVal genotype in BDNF gene had a lower accumulation of combined end point compared with acute STEMI patients with 66ValMet+66ValMet polymorphism (Cox-criterion, P=0.019; log-rang criterion, P=0.03). Conclusion The Val66Met polymorphism in BDNF gene was found as an independent predictor for combined 6-month clinical end points after acute STEMI treated primary PCI. Funding Acknowledgement Type of funding source: None

scholarly journals Temporal fluctuations of Y-chromosomal variation in Bos taurus

2008 ◽  
Vol 4 (6) ◽  
pp. 752-754 ◽  
Author(s):  
Emma Svensson ◽  
Anders Götherström
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bos Taurus ◽  
Demographic History ◽  
Northern Europe ◽  
Chromosomal Gene ◽  
Chromosomal Variation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Domestic Species ◽  
History Of

Phylogeography has recently become more abundant in studies of demographic history of both wild and domestic species. A single nucleotide polymorphism (SNP) in the intron of the Y-chromosomal gene UTY19 displays a north–south gradient in modern cattle. Support for this geographical distribution of haplogroups has previously also been seen in ancient cattle from Germany. However, when analysing 38 historic remains of domestic bulls and three aurochs from northern Europe for this SNP we found no such association. Instead, we noted extensive amounts of temporal variation that can be attributed to transportation of cattle and late breed formation.

A vascular endothelial growth factor A genetic variant is associated with improved ventricular function and transplant-free survival after surgery for non-syndromic CHD

2017 ◽  
Vol 28 (1) ◽  
pp. 39-45 ◽  
Author(s):  
Constantine D. Mavroudis ◽  
Daniel Seung Kim ◽  
Nancy Burnham ◽  
Alexandra H. Morss ◽  
Jerry H. Kim ◽  
...  
Keyword(s):  
Vascular Endothelial Growth Factor ◽  
Single Nucleotide Polymorphism ◽  
Growth Factor ◽  
Ventricular Function ◽  
Vascular Endothelial ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Free Survival ◽  
Endothelial Growth Factor

AbstractBackgroundWe have previously shown that the minor alleles of vascular endothelial growth factor A (VEGFA) single-nucleotide polymorphism rs833069 and superoxide dismutase 2 (SOD2) single-nucleotide polymorphism rs2758331 are both associated with improved transplant-free survival after surgery for CHD in infants, but the underlying mechanisms are unknown. We hypothesised that one or both of these minor alleles are associated with better systemic ventricular function, resulting in improved survival.MethodsThis study is a follow-up analysis of 422 non-syndromic CHD patients who underwent neonatal cardiac surgery with cardiopulmonary bypass. Echocardiographic reports were reviewed. Systemic ventricular function was subjectively categorised as normal, or as mildly, moderately, or severely depressed. The change in function was calculated as the change from the preoperative study to the last available study. Stepwise linear regression, adjusting for covariates, was performed for the outcome of change in ventricular function. Model comparison was performed using Akaike’s information criterion. Only variables that improved the model prediction of change in systemic ventricular function were retained in the final model.ResultsGenetic and echocardiographic data were available for 335/422 subjects (79%). Of them, 33 (9.9%) developed worse systemic ventricular function during a mean follow-up period of 13.5 years. After covariate adjustment, the presence of the VEGFA minor allele was associated with preserved ventricular function (p=0.011).ConclusionsThese data support the hypothesis that the mechanism by which the VEGFA single-nucleotide polymorphism rs833069 minor allele improves survival may be the preservation of ventricular function. Further studies are needed to validate this genotype–phenotype association and to determine whether this mechanism is related to increased vascular endothelial growth factor production.

scholarly journals Transmission analysis of a large TB outbreak in London: mathematical modelling study using genomic data

2019 ◽  
Author(s):  
Yuanwei Xu ◽  
Hollie Topliffe ◽  
James Stimson ◽  
Helen R. Stagg ◽  
Ibrahim Abubakar ◽  
...  
Keyword(s):  
Mathematical Modelling ◽  
Disease Transmission ◽  
Machine Learning Techniques ◽  
Reconstruction Method ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Patient Level ◽  
Learning Techniques ◽  
Level Data ◽  
History Of

AbstractOutbreaks of tuberculosis- such as the large isoniazid-resistant outbreak centered on London, United Kingdom, which originated in 1995- provide excellent opportunities to model transmission of this devastating disease. Transmission chains for tuberculosis are notoriously difficult to ascertain, but mathematical modelling approaches, combined with whole-genome sequencing (WGS) data, have strong potential to contribute to transmission analyses. Using such data, we aimed to reconstruct transmission histories for the outbreak using a Bayesian approach, and to use machine learning techniques with patient-level data to identify the key covariates associated with transmission. By using our transmission reconstruction method that accounts for phylogenetic uncertainty, we are able to identify 24 transmission events with reasonable confidence, 11 of which have zero single nucleotide polymorphism (SNP) distance, and as maximum distance of 3. Patient age, alcohol abuse and history of homelessness were found to be the most important predictors of being credible tuberculosis transmitters.

scholarly journals The AGT M235T (RS699, 4072T>C) polymorphism is not associated with elite weightlifting performance

2018 ◽  
Vol 23 ◽  
pp. 34
Author(s):  
Sigal Ben-Zaken ◽  
Yoav Meckel ◽  
Dan Nemet ◽  
Michal Pantanowitz ◽  
Alon Eliakim
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Allele Frequency ◽  
Genetic Background ◽  
Elite Athletes ◽  
National Level ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Common Features ◽  
Genotype Frequencies ◽  
The Common

It is now well established that genetic background influences an athlete’s ability to excel in different sport disciplines. Previous studies have demonstrated that among power athletes, single nucleotide polymorphism (SNP) in the AGT genotype (Thr-Thr), was significantly more prevalent among weightlifters compared to sprinters and jumpers indicating that despite the common features of these sport subtypes (short and very intense), they vary in their strength and speed abilities, as well as in their genetic make-up. The aim of the present study was to assess whether the AGT SNP can be used also to distinguish elite from national levels weightlifters. The AGT M235T genotype frequencies were assessed in 47 weightlifters (30 elite, 17 national level) and 86 non-athletes control. The Thr-Thr genotype was significantly higher among weightlifters (29.8%) compared to controls (12.8%) (p=0.048). Thr allele frequency was significantly higher among weightlifters (55.3%) compared to controls (37.8%) (p=0.021). However, there was no difference in the prevalence of the polymorphism between national level and elite athletes. In conclusion, the results suggest that the AGT polymorphism cannot predict elite competitive weightlifting performance.

scholarly journals Risk of gout among Taiwanese adults with ALDH-2 rs671 polymorphism according to BMI and alcohol intake

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Yu-Ruey Liu ◽  
Disline Manli Tantoh ◽  
Chuan-Chao Lin ◽  
Chih-Hsuan Hsiao ◽  
Yung-Po Liaw
Keyword(s):  
Alcohol Drinking ◽  
Lower Risk ◽  
Alcohol Intake ◽  
Normal Weight ◽  
Nucleotide Polymorphism ◽  
Aldehyde Dehydrogenase 2 ◽  
Single Nucleotide ◽  
Independent Variables ◽  
History Of ◽  
History Of Cancer

Abstract Background Gout stems from both modifiable and genetic sources. We evaluated the risk of gout among Taiwanese adults with aldehyde dehydrogenase-2 (ALDH2) rs671 single nucleotide polymorphism (SNP) according to body mass index (BMI) and alcohol drinking. Methods We obtained information of 9253 individuals having no personal history of cancer from the Taiwan Biobank (2008–2016) and estimated the association between gout and independent variables (e.g., rs671, BMI, and alcohol drinking) using multiple logistic regression. Results Alcohol drinking and abnormal BMI were associated with a higher risk of gout whereas the rs671 GA+AA genotype was associated with a lower risk. The odds ratios (ORs) and 95% confidence intervals (CIs) were 1.297 and 1.098–1.532 for alcohol drinking, 1.550 and 1.368–1.755 for abnormal BMI, and 0.887 and 0.800–0.984 for GA+AA. The interaction between BMI and alcohol on gout was significant for GG (p-value = 0.0102) and GA+AA (p-value = 0.0175). When we stratified genotypes by BMI, alcohol drinking was significantly associated with gout only among individuals with a normal BMI (OR; 95% CI = 1.533; 1.036–2.269 for GG and 2.109; 1.202–3.699 for GA+AA). Concerning the combination of BMI and alcohol drinking among participants stratified by genotypes (reference, GG genotype, normal BMI, and no alcohol drinking), the risk of gout was significantly higher in the following categories: GG, normal BMI, and alcohol drinking (OR, 95% CI = 1.929, 1.385–2.688); GG, abnormal BMI, and no alcohol drinking (OR, 95% CI, = 1.721, 1.442–2.052); GG, abnormal BMI, and alcohol drinking (OR, 95% CI = 1.941, 1.501–2.511); GA+AA, normal BMI, and alcohol drinking (OR, 95% CI = 1.971, 1.167–3.327); GA+AA, abnormal BMI, and no alcohol drinking (OR, 95% CI = 1.498, 1.256–1.586); and GA+AA, abnormal BMI, and alcohol drinking (OR, 95% CI = 1.545, 1.088–2.194). Conclusions Alcohol and abnormal BMI were associated with a higher risk of gout, whereas the rs671 GA+AA genotype was associated with a lower risk. Noteworthy, BMI and alcohol had a significant interaction on gout risk. Stratified analyses revealed that alcohol drinking especially among normal-weight individuals might elevate the risk of gout irrespective of the genotype.

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