scholarly journals Association of single-nucleotide polymorphisms in RHOB and TXNDC3 with knee osteoarthritis susceptibility: two case-control studies in East Asian populations and a meta-analysis

2008 ◽  
Vol 10 (3) ◽  
pp. R54 ◽  
Author(s):  
Dongquan Shi ◽  
Takahiro Nakamura ◽  
Masahiro Nakajima ◽  
Jin Dai ◽  
Jianghui Qin ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Knee Osteoarthritis ◽  
Meta Analysis ◽  
East Asian ◽  
Case Control ◽  
Nucleotide Polymorphisms ◽  
Case Control Studies ◽  
Single Nucleotide ◽  
Asian Populations

scholarly journals Association of Sex Determining Region Y-Box 17 Gene Polymorphisms and Intracranial Aneurysm: A Case-Control Study and Meta-analysis

Neurosurgery ◽  
2019 ◽  
Vol 66 (Supplement_1) ◽  
Author(s):  
Museung Park ◽  
Yong-Jun Cho ◽  
Jin Sue Jeon
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Confidence Interval ◽  
Odds Ratio ◽  
Gene Polymorphisms ◽  
Meta Analysis ◽  
East Asian ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Unruptured Aneurysms ◽  
Asian Populations

Abstract INTRODUCTION Genome-wide association studies have revealed an association between SRY (Sex Determining Region Y)-box 17 (SOX17) gene and intracranial aneurysm (IA) formation. However, results were mainly derived from European and Japanese populations. We investigated the association between SOX17 gene polymorphisms and IA in a homogeneous Korean population. We performed a meta-analysis to assess these results in East-Asian populations. METHODS This cross-sectional study included 187 age- and sex-matched patients with IA and 372 control subjects. Genetic association analysis was performed in the generalized linear model to identify associations between 4 single nucleotide polymorphisms and IA, including 95 patients with ruptured aneurysms and 92 with unruptured aneurysms. The East-Asian meta-analysis of 5100 IA cases and 7930 control cases was conducted under an inverse variance model. RESULTS Among 4 single nucleotide polymorphisms that passed quality control tests, the minor C allele of rs1072737 was significantly associated with IA (odds ratio 0.69, 95% confidence interval 0.49-0.96, P = .03). None of the 4 single nucleotide polymorphisms showed a significant association between patients with ruptured and unruptured aneurysms. Meta-analysis revealed that G alleles of rs10958409 and rs9298506 were significantly associated with IA in the East-Asian population after removing study heterogeneity (odds ratio 1.11, 95% confidence interval 1.04-1.19, P = .0023 and odds ratio 1.19, 95% confidence interval 1.07-1.32, P = .0016). CONCLUSION Identification of genetic variants located near SOX17 is likely to be clinically significant for IA formation. rs10958409 and rs9298506 may increase risk of IA in East-Asian populations. Our findings may help in the identification of IA pathogenesis.

scholarly journals Meta-analysis reveals significant association between FOXP3 polymorphisms and susceptibility to Graves’ disease

2021 ◽  
Vol 49 (4) ◽  
pp. 030006052110041
Author(s):  
Guiqin Tan ◽  
Xin Wang ◽  
Guangbing Zheng ◽  
Juan Du ◽  
Fangyu Zhou ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Pooled Analysis ◽  
Case Control ◽  
Graves Disease ◽  
Nucleotide Polymorphisms ◽  
Case Control Studies ◽  
China National Knowledge Infrastructure ◽  
Asian Populations ◽  
Knowledge Infrastructure ◽  
Independent Case

Objective This meta-analysis aimed to determine the associations between the rs3761547, rs3761548, and rs3761549 single-nucleotide polymorphisms (SNPs) of the forkhead box P3 ( FOXP3) gene and susceptibility to Graves’ disease (GD). Methods Case–control studies with information on the associations between the rs3761547, rs3761548, and rs3761549 FOXP3 SNPs and GD published before 01 May 2020 were identified in the PubMed, Embase, Web of Science, and China National Knowledge Infrastructure databases. Data from the studies were analyzed using RevMan version 5.3. Results Seven independent case–control studies including 4051 GD patients and 4569 controls were included in the meta-analysis. The overall pooled analysis indicated that FOXP3/rs3761548 and FOXP3/rs3761549 polymorphisms were significantly associated with GD susceptibility (rs3761548: A vs. C, odds ratio [OR] = 1.32, 95% confidence interval [CI] 1.05–1.67; rs3761549: TT vs. CC, OR = 1.98, 95%CI 1.49–2.65; (TT + TC) vs. CC, OR = 1.44, 95%CI 1.11–1.88). In contrast, the FOXP3/rs3761547 polymorphism was not associated with GD susceptibility. Subgroup analysis according to ethnicity showed that rs3761548 was associated with GD in Asians but not in Caucasians, whereas rs3761549 was associated in both Asians and Caucasians. Conclusion This meta-analysis demonstrated that FOXP3/rs3761548 and FOXP3/rs3761549 SNPs were significantly associated with susceptibility to GD, at least in Asian populations.

Investigation of Leptin and its receptor (LEPR) for single nucleotide polymorphisms in colorectal cancer: A case-control study involving 2,306 subjects.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e16100-e16100
Author(s):  
Jing Lin ◽  
Yu Chen ◽  
Bin Lan ◽  
Zeng-qing Guo ◽  
Wei-feng Tang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Single Nucleotide Polymorphisms ◽  
Case Control Study ◽  
Case Control ◽  
Nucleotide Polymorphisms ◽  
Case Control Studies ◽  
Chinese Han ◽  
Single Nucleotide ◽  
Subgroup Analyses ◽  
Control Study

e16100 Background: Colorectal cancer is a leading cause of cancer deaths, with poor prognosis. Some studies have reported that obesity and overweight are risk factor for the development of CRC. Leptin ( LEP) and its receptor ( LEPR) single nucleotide polymorphisms (SNPs) might regulate energy balance and be implicated in the development of CRC. The aim of this case-control study was to assess the association of LEP rs2167270 G > A, rs7799039 A > G, LEPR rs6588147 G > A, rs1137100 G > A and rs1137101 G > A SNPs with susceptibility to CRC in Eastern Chinese Han population. Methods: 1,003 CRC cases and 1,303 matched controls was compared. Five functional SNPs in LEP and LEPR genes were chosen to evaluate the correlation of these chosen SNPs with CRC susceptibility. We used the SNPscan genotyping assay to genotype LEP and LEPR SNPs. Results: A significantly decreased risk of CRC was found to be associated with the LEPR rs6588147 polymorphism (GA vs. GG: crude P= 0.007 and GA/AA vs. GG: crude P= 0.018). With adjustments for risk factors (e.g. age, gender, drinking, BMI and smoking), these associations were not changed. In subgroup analyses, the association of LEP rs2167270 with a decreased risk of CRC was found in the ≥61 years old subgroup. For LEPR rs1137100, the association of this SNP with an increased susceptibility of CRC was found in the BMI < 24 kg/m2 subgroup. In subgroup analyses for LEPR rs6588147, we identified that this locus also decreased the susceptibility of CRC in the male subgroup, < 61 years old subgroup, never smoking subgroup and never drinking subgroup. For LEPR rs1137101, the relationship of this polymorphism with a decreased susceptibility to CRC was found in the never drinking subgroup. Conclusions: The present study highlights that LEPR rs6588147, rs1137101 and LEP rs2167270 may decrease the risk of CRC. However, LEPR rs1137100 is associated with susceptibility to CRC. Further case-control studies with larger sample sizes should be conducted to validate our findings.

scholarly journals SUN-711 Association of Single Nucleotide Polymorphisms of CYP11B2, CYP11B1 and CYP17A1 with Primary Aldosteronism in a Multi-Ethnic Malaysian Cohort

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Afifah Azam ◽  
Mohammad Arif Shahar ◽  
Siti Liyana Saud Gany ◽  
Norlela Sukor ◽  
Nor Azmi Kamaruddin ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Primary Aldosteronism ◽  
East Asian ◽  
Genotype Imputation ◽  
Chinese Patients ◽  
Nucleotide Polymorphisms ◽  
Steroidogenic Enzyme ◽  
Single Nucleotide ◽  
Asian Populations ◽  
Increased Risk

Abstract Primary aldosteronism (PA), also known as Conn’s syndrome, is a common curable cause of hypertension. Family studies of essential hypertensive patients suggest that heritable genetic factors play a role in blood pressure regulation1. Interestingly, single nucleotide polymorphisms (SNP) in genes encoding enzymes involved with adrenal steroidogenesis, CYP11B2, CYP11B1 and CYP17A1, associate with increased risk of hypertension2. Therefore, we analysed whether selected SNPs in these genes are associated with PA. We performed an association study using genotype imputation for selected SNPs of the steroidogenic enzyme genes CYP11B2 (rs4546, rs1799998, rs13268025), CYP11B1 (rs6410, rs149845727), and CYP17A1 (rs1004467, rs138009835, rs2150927) from a pilot genome wide association study of Malaysian PA patients and healthy controls which was merged with the Singapore Genome Variation Project (SGVP) population dataset3. Genotype imputation for minor and major alleles was validated using PCR sequencing (n&gt;10 for each genotype). Further, one SNP from each steroidogenic enzyme (CYP11B2:rs1799998, CYP11B1:rs6410 and CYP17A1:rs1004467) was validated using commercial TaqMan genotyping assays on the ABI 7000 Sequence Detection System which was performed on 149 PA patients and 78 non-hypertensive healthy individuals. Case-control genetic association analysis was performed at http://www.oege.org/software/orcalc.html and the association between genotypes and phenotypes was done using the independent-samples Kruskal-Wallis test on SPSS (version 25). The Minor Allele Frequencies (MAFs) for rs1004467, rs6410 and rs1799998 were similar to East Asian populations but differed significantly different from European, African, American and South Asian populations (rs1004467 MAF: C=0.258/298, rs6410 MAF: A=0.265/298, rs1799998 MAF: C=0.225/298). In Chinese patients matched by gender, heterozygotes for rs6410 had significantly increased risk of PA compared to common homozygotes (OR: 3.15, 95% CI: 1.01–9.8, p=0.04). Across patients of different ethnicity, the distribution of aldosterone levels was significantly different (p=0.039). In summary, only SNP rs6410 in Chinese patients matched by gender showed association with PA in our South East Asian cohort. More functional experiments need to be done to find out whether this is causal for PA or whether the SNP is in linkage disequilibrium with the actual functional causative SNPs. Once the functional SNP is known, identification of these germline variants in asymptomatic family members would allow early screening of PA to be offered and potentially provide novel drug targets to treat the disease. References: 1Timberlake et al., Curr Opin Nephrol Hypertens. 2001 Jan;10(1):71-9. 2MacKenzie et al., Int J Mol Sci. 2017 Mar 7;18(3). pii: E579. 3Teo et al., Genome Res. 2009 Nov;19(11):2154-62.

scholarly journals The Effect of Single Nucleotide Polymorphisms on Depression in Combination With Coronary Diseases: Protocol for a Systematic Review and Meta-analysis

2021 ◽  
Author(s):  
De Zhao Kong ◽  
Lu Gao ◽  
Hang Li ◽  
Yu Wang ◽  
Miao Miao Wang ◽  
...  
Keyword(s):  
Systematic Review ◽  
Coronary Heart Disease ◽  
Heart Disease ◽  
Single Nucleotide Polymorphisms ◽  
Confidence Interval ◽  
Meta Analysis ◽  
Case Control ◽  
Current Evidence ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

Abstract Background: Depression and coronary heart disease (CHD) have common risk mechanisms. Common single nucleotide polymorphisms (SNPs) may be associated with the risk of depression combined with coronary heart disease. Methods: This protocol was designed according to the PRISMA-P guidelines. CENTRAL in the Cochrane Library, MEDLINE Ovid, Embase Ovid, Web of Science, CNKI, CQVIP, SinoMed, Wanfang Data, and ChiCTR will be systematically searched. We will include case-control studies and cohort studies investigating the relationship between gene SNPs and depression and coronary heart disease comorbidities. The Newcastle-Ottawa Scale (NOS) will be used to assess the risk of bias. When measuring dichotomous outcomes, we will use the risk ratio (RR) and 95% confidence interval (95%CIs) in a cohort study and use the odds ratio (OR) and 95% confidence interval (95%CIs) in a case-control study. Five genetic models (allele model, homozygous model, heterozygous model, dominant model, and recessive model) will be evaluated for each included study. Subgroup analysis by ethnicity will be performed. If necessary, post hoc analysis will be made according to different types.Discussion: The purpose of this meta-analysis is to comprehensively study the current evidence and assess the association between single nucleotide polymorphisms and susceptibility of depression in combination with coronary heart disease.Systematic review registration: This protocol was prospectively registered in the PROSPERO (registration number CRD42021229371).

scholarly journals Association of Glutathione S-transferases (GSTT1, GSTM1 and GSTP1) Genes Polymorphisms with Nonalcoholic Fatty Liver Disease Susceptibility: A Meta-analysis of Case-control Studies

2021 ◽  
Author(s):  
Yi Zhu ◽  
Ming Qiao
Keyword(s):  
Liver Disease ◽  
Fatty Liver ◽  
Fatty Liver Disease ◽  
Meta Analysis ◽  
Case Control ◽  
Nucleotide Polymorphisms ◽  
Case Control Studies ◽  
Single Nucleotide ◽  
Nonalcoholic Fatty Liver ◽  
Glutathione S Transferases

Abstract Background: Glutathione S-transferases (GSTs) genes single-nucleotide polymorphisms (SNPs) have been connected with the susceptibility of nonalcoholic fatty liver disease (NAFLD), but with inconsistent results across the current evidences. The present work was schemed to explore the association between GSTs genes polymorphisms and the NAFLD vulnerability via meta-analysis.Methods: PubMed, Web of Science, Cochrane Library, China National Knowledge Infrastructure (CNKI) and Wanfang were retrieved for eligible literatures previous to March 10, 2021. The odds ratio (OR) of the dichotomic variables and the standardized mean difference of quantitative variables with corresponding 95% confidence intervals (95%CIs) were computed to evaluate the strength of the associations. The quality of included studies were assessed via using Newcastle-Ottawa Scale (NOS).Results: In total, 7 case-control studies encompassing 804 NAFLD patients and 1362 disease-free controls in this meta-analysis. Ultimately, this analysis included six, five and five studies for GSTM1, GSTT1 and GSTP1 polymorphisms respectively. The pooled data revealed that the GSTs genes single-nucleotide polymorphisms had conspicuous associations with NAFLD susceptibility: for GSTM1, null vs. present, OR=1.46, 95%CI 1.20-1.79, P=0.0002; for GSTT1, null vs. present, OR=1.34, 95%CI 1.06-1.68, P=0.01; for GSTP1, Ile/Val or Val/Val vs. Ile/Ile, OR=1.60, 95%CI 1.23-2.09, P=0.0005.Conclusion: This work revealed that the GSTM1 null, GSTT1 null and GSTP1-Val genotypes might be related to increased NAFLD susceptibility.

scholarly journals TMEM41B is a pan-flavivirus host factor

2020 ◽  
Author(s):  
H.-Heinrich Hoffmann ◽  
William M Schneider ◽  
Kathryn Rozen-Gagnon ◽  
Linde A Miles ◽  
Felix Schuster ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
East Asian ◽  
Rna Replication ◽  
Membrane Curvature ◽  
Genome Replication ◽  
Nucleotide Polymorphisms ◽  
Mechanistic Studies ◽  
Single Nucleotide ◽  
Asian Populations ◽  
Flavivirus Infection

SUMMARYFlaviviruses pose a constant threat to human health. These RNA viruses are transmitted by the bite of infected mosquitoes and ticks and regularly cause outbreaks. To identify host factors required for flavivirus infection we performed full-genome loss of function CRISPR-Cas9 screens. Based on these results we focused our efforts on characterizing the roles that TMEM41B and VMP1 play in the virus replication cycle. Our mechanistic studies on TMEM41B revealed that all members of the Flaviviridae family that we tested require TMEM41B. We tested 12 additional virus families and found that SARS-CoV-2 of the Coronaviridae also required TMEM41B for infection. Remarkably, single nucleotide polymorphisms (SNPs) present at nearly twenty percent in East Asian populations reduce flavivirus infection. Based on our mechanistic studies we hypothesize that TMEM41B is recruited to flavivirus RNA replication complexes to facilitate membrane curvature, which creates a protected environment for viral genome replication.HIGHLIGHTSTMEM41B and VMP1 are required for both autophagy and flavivirus infection, however, autophagy is not required for flavivirus infection.TMEM41B associates with viral proteins and likely facilitates membrane remodeling to establish viral RNA replication complexes.TMEM41B single nucleotide polymorphisms (SNPs) present at nearly twenty percent in East Asian populations reduce flavivirus infection.TMEM41B-deficient cells display an exaggerated innate immune response upon high multiplicity flavivirus infection.

scholarly journals Prevalence of uncoupling protein one genetic polymorphisms and their relationship with cardiovascular and metabolic health

2021 ◽  
Author(s):  
Petros C. Dinas ◽  
Eleni Nintou ◽  
Maria Vliora ◽  
Anna E. Pravednikova ◽  
Paraskevi Sakellariou ◽  
...  
Keyword(s):  
Risk Factors ◽  
Uncoupling Protein ◽  
Meta Analysis ◽  
Case Control ◽  
Cochrane Library ◽  
Nucleotide Polymorphisms ◽  
Sample Collection ◽  
Case Control Studies ◽  
Single Nucleotide

The contribution of UCP1 single nucleotide polymorphisms (SNPs) to susceptibility for cardiometabolic pathologies (CMP) and their involvement in specific risk factors for these conditions varies across populations. We tested whether UCP1 SNPs A-3826G, A-1766G, Ala64Thr and A-112C are associated with the most common CMP (cardiovascular disease, hypertension, metabolic syndrome, and type-2 diabetes) and CMP risk factors. This case-control study included blood sample collection from 2,283 Caucasians (1,139 healthy; 1,144 CMP) across Armenia, Greece, Poland, Russia and United Kingdom for genotyping of the above-mentioned SNPs. We extended the results via a systematic review and meta-analysis, covering PubMed, Embase, and Cochrane Library databases. In Armenia the GA genotype and A allele of Ala64Thr were associated with ~2-fold higher risk for CMP compared to the GG genotype or G allele, respectively (p<0.05). In Greece, A allele of Ala64Thr SNP decreased the risk of CMP by 39%. Healthy individuals with A-3826G GG genotype and carriers of mutant allele of A-112C and Ala64Thr had higher body mass index compared to those carrying other genotypes. In healthy Polish, higher waist-to-hip ratio (WHR) was observed in heterozygotes A-3826G compared to AA homozygotes. Heterozygosity of the A-112C and Ala64Thr SNPs was related to lower WHR in CMP individuals compared to wild type homozygotes (p<0.05). Meta-analysis in case-control studies showed no statistically significant odds ratios in different alleles across the four studied SNPs (p>0.05). Thus, we conclude that the studied SNPs could be associated with the most common CMP and their risk factors in some populations.

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