Three novel genetic variants in the FAM110D, CACNA1A and NLRP12 genes are associated with susceptibility to hypertension among Dai people

2021 ◽  
Author(s):  
Lin Zhang ◽  
Yun Sun ◽  
Xiaochao Zhang ◽  
Xiyun Shan ◽  
Jianmei Li ◽  
...  
Keyword(s):  
Logistic Regression ◽  
Multiple Logistic Regression Analysis ◽  
Candidate Snps ◽  
Nucleotide Polymorphisms ◽  
Control Groups ◽  
Single Nucleotide ◽  
Future Studies ◽  
And Control ◽  
The Relationship ◽  
Generation Sequencing

Abstract Background Although the genetic factors associated with hypertension remain unknown, genetic variations in genes related to ion channels, inflammation, and the cell cycle may affect susceptibility to hypertension. In the present study, the association between hypertension and 10 candidate single-nucleotide polymorphisms (SNPs) was evaluated among Chinese Dai people, who have a smaller gene pool than Han individuals. Methods A total of 1193 samples from Dai people were collected, including 488 with hypertension and 705 with normal blood pressure. Based on the preliminary results of whole-genome sequencing among pools of individuals (Pool-seq), ten candidate SNPs in six genes (FAM110D, ADD1, RAG1, CACNA1C, CACNA1A, and NLRP12) were genotyped in the case and control groups by multiplex PCR for SNP genotyping with next-generation sequencing (MultiPCR-NGS). The relationship between hypertension and each candidate SNP was evaluated using the χ2 test and multiple logistic regression analysis. Results The χ2 test showed that the allele frequencies of rs3748856 in FAM110D, rs139118504 in CACNA1A, and rs34436714 in NLRP12 were significantly different between the case and control groups (P < 0.005). After adjusting for age, BMI, TC, TG, and LDL, logistic regression analyses revealed that the association between the three SNPs and hypertension among Dai people remained significant (P = 0.012, 2.71 × 10 -4, and 0.017, respectively). Conclusion These findings indicate that there may be different molecular pathogeneses of hypertension among Dai people, which should be noted in future studies.

scholarly journals Genotyping analysis of the Pax9 Gene in patients with maxillary canine impaction

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 254 ◽  
Author(s):  
Evy Eida Vitria ◽  
Iwan Tofani ◽  
Lindawati Kusdhany ◽  
Endang Winiati Bachtiar
Keyword(s):  
Inclusion Criteria ◽  
Nucleotide Polymorphism ◽  
Chromosome 14 ◽  
Control Groups ◽  
Maxillary Canine ◽  
Single Nucleotide ◽  
Ncbi Dbsnp ◽  
Polymerase Chain ◽  
And Control ◽  
The Relationship

Background: Paired-box gene 9 (PAX9) mutation is potentially associated with impaction in some patient populations. Here, we analyzed the relationship between PAX9 polymorphism and the occurrence of maxillary canine impaction. Methods: Patients with and without maxillary canine impaction were selected based on specific inclusion criteria, and samples of genomic DNA were obtained from a buccal mucosa swab. DNA was amplified by polymerase chain reaction and sequenced for further bioinformatics analysis to identify single nucleotide polymorphism (SNP) genotypes. Genotype and allele counting was performed in both case and control groups prior to conducting statistical analysis. Results: Four SNPs were identified in patients with maxillary canine impaction, with relative confidence determined based on chromatogram-peak assessment. All SNPs were located in exon 3 of PAX9 and in the region sequenced by the primer pair −197Fex3 and +28Rex3. Three of the SNPs (rs375436662, rs12881240, and rs4904210) were reported previously and are annotated in NCBI (dbSNP version 150), whereas another SNP mapped to chromosome 14 has not been reported. Patients with a CC genotype at SNP 3 [odds ratio (OR): 2.61 vs. TT; 1.28 vs. CT] and a CC genotype at SNP 4 [OR: 0.71 vs. GG; 0.79 vs. CG] were more likely to have maxillary canine impaction. Conclusions: These results demonstrated that the presence of SNPs 3 and 4 is associated with increased likelihood of suffering from maxillary canine impaction.

scholarly journals Variations in MHC-DRB1 exon2 and associations with Brucellosis susceptibility in Chinese Merino sheep

2016 ◽  
Author(s):  
Yue’e Chen ◽  
Wanyun Xu ◽  
Chuangfu Chen ◽  
Hugh T Blair ◽  
Jianfeng Gao
Keyword(s):  
Haplotype Analysis ◽  
Nucleotide Polymorphisms ◽  
Control Groups ◽  
Single Nucleotide ◽  
Merino Sheep ◽  
Pcr Products ◽  
Polymerase Chain ◽  
And Control ◽  
Control Samples ◽  
Online Software

MHC-DRB1 exon2 was amplified by polymerase chain reaction (PCR) from 126 healthy and 67 Brucellosis-infected Chinese Merino sheep. PCR products were analyzed using the SSCP technique, and then cloned to allow sequencing of the different alleles. For each SNP, allelic and genotypic frequencies were compared between case and control samples, in addition the association with Brucellosis susceptibility was determined. Haplotypes and their frequencies were established and analyzed by SHEsis online software. There were forty-one single nucleotide polymorphisms (SNPs) in the 270 bp DNA sequence. The distribution of C>T alleles at locus 109 was significantly different between case and control samples. The linkage disequilibrium (LD) analysis showed that there were nine LD blocks in MHC-DRB1 exon2 and strong LD between SNPs existed in every Block. Haplotype analysis identified nine haplotypes with strong LD, but only Hap8 and Hap9 in case-control groups were significantly different (P<0.05); neither haplotype contained the C>T allele at locus 109. In conclusion, genetic variants of MHC-DRB1 gene exon2 demonstrated associations with Brucellosis susceptibility, indicating that further research is warranted.

Estrogen Receptor Alpha Gene Single Nucleotide Polymorphisms, +2464 C/T and -4576A/C, and Breast Cancer Risk, a Hospital-Based Case-Control Study

2019 ◽  
Author(s):  
Ali Akbar Amirzargar ◽  
Maryam Sadr ◽  
Samira Esmaeili Reykande ◽  
Elham Mohebbi ◽  
Mohammad Shirkhoda ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Estrogen Receptor ◽  
Breast Cancer Risk ◽  
Cancer Risk ◽  
Single Nucleotide Polymorphisms ◽  
Estrogen Receptor Alpha ◽  
Nucleotide Polymorphisms ◽  
Control Groups ◽  
Single Nucleotide ◽  
And Control

Background: Estrogen is a risk factor for the development of breast cancer. The effect of estrogen is primarily mediated by estrogen receptor alpha 1 (ESR1). In this study, we investigated the association between breast cancer risk and the frequency of alleles and genotypes for two ESR1 single nucleotide polymorphisms (SNPs) in breast cancer patients and a healthy control group. Methods: A total of 98 female patients with pathologically confirmed breast cancer and 93 age-matched healthy female controls who were selected from the visitors of the general hospital were recruited in the study. Two ESR1 candidate polymorphisms; +2464 C/T (rs3020314) and -4576 A/C (rs1514348) were selected. The frequency of alleles and genotypes was determined using Quantitative Real-Time PCR assay. Linkage disequilibrium (LD) was assessed for each pair of markers. Using logistic regression, genotype frequencies were estimated as odds ratios with 95% confidence intervals. Results: There was no significant difference in the genotype and allele distributions of ESR1 for SNPs +2464 C/T and SNP -4576 A/C between patients and controls. The frequency of the ESR1 +2464 T/T genotype in case and control groups was 31.6% vs 29.0%, (OR TT/TC: 1.13, 95%CI: 0.58, 2.20; P = 0.69). The frequency of the +2464C allele was 33.9% vs 35.2%, (OR C/T: 0.94, 95%CI: 0.60, 1.47; P =0.79). The frequency of the ESR1 -4576C/C genotype in case and control groups was 37.75% vs 33.36%, OR CC/AC: 1.02, 95%CI: 0.51, 1.97; P =0.98). The frequency of the -4576A allele was 36.2% vs 43.6 %, (OR C/A: 0.73, 95%CI: 0.47, 1.13; P =0.14). Conclusion: The results indicated that ESR1 polymorphism does not show any significant association with breast cancer risk among female Iranian adults.

scholarly journals Exploration of CYP21A2 and CYP17A1 polymorphisms and preeclampsia risk among Chinese Han population: a large-scale case-control study based on 5021 subjects

2020 ◽  
Vol 14 (1) ◽  
Author(s):  
Bo Hou ◽  
Xuewen Jia ◽  
Ziwen Deng ◽  
Xin Liu ◽  
Huitang Liu ◽  
...  
Keyword(s):  
Large Scale ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Single Nucleotide ◽  
Allelic Frequencies ◽  
Genome Wide ◽  
And Control ◽  
The Relationship

Abstract Background Several genome-wide association studies have identified single-nucleotide polymorphisms (SNPs), such as rs4409766, rs1004467, and rs3824755 in CYP17A1 and rs2021783 in CYP21A2, as new hypertension susceptibility genetic variants in the Chinese population. This study aimed to look into the relationship between preeclampsia (PE) and these SNPs in Chinese Han women. Methods Overall, 5021 unrelated pregnant women were recruited, including 2002 patients with PE and 3019 normal healthy controls. The real-time PCR (TaqMan) method was applied to genotype these four polymorphisms. Results A statistically obvious difference in the allelic frequencies was observed in CYP21A2 rs2021783 between cases and controls (χ2 = 7.201, Pc = 0.028 by allele), and the T allele was associated with the occurrence and development of PE (OR = 1.151, 95% CI 1.039–1.275). We also found a significant association between rs2021783 and the development of early-onset PE (Pc = 0.008 by genotype, Pc = 0.004 by allele). For rs1004467 and rs3824755, the distribution of allelic frequencies differed markedly between mild PE and control groups (χ2 = 6.843, Pc = 0.036; χ2 = 6.869, Pc = 0.036), and patients with the TT genotype of rs1004467 were less easy to develop mild PE than were those carrying the CT or CC genotype (χ2 = 7.002, Pc = 0.032, OR = 1.306, 95% CI 1.071–1.593). The GG genotype of rs3824755 appeared to a protective effect on the occurrence of mild PE (OR = 0.766, 95% CI 0.629–0.934). Conclusions CYP21A2 rs2021783 appears to be closely related to PE susceptibility, and CYP17A1 rs1004467 and rs3824755 seem to be closely associated with mild PE in Han women.

scholarly journals Single Nucleotide Polymorphism in the Promoter of the Human Interleukin-13 Gene Is Associated with Asthma in Malaysian Adults

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Ammu Kutty Radhakrishnan ◽  
Vijaya Lechimi Raj ◽  
Lee-Keng Tan ◽  
Chong-Kin Liam
Keyword(s):  
Buffy Coat ◽  
Allele Frequencies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Interleukin 13 ◽  
Pcr Rflp ◽  
Chromosome 5Q31 ◽  
And Control ◽  
The Relationship ◽  
Genotype And Allele Frequencies

Asthma susceptibility genes are mapped to a region on human chromosome 5q31-q33, which contains a cluster of proinflammatory cytokine genes such as interleukin-13 (IL-13), which is associated with asthma. This study investigated the allele frequencies of two single nucleotide polymorphisms (SNPs) (−1111C>T and 4257C>A) in theIL-13gene between asthmatics and healthy volunteers as well as the relationship between these SNPs and IL-13 production. DNA extracted from buffy coat of asthmatic and control subjects was genotyped using the PCR-RFLP method. Amount of IL-13 produced by mitogen-stimulated peripheral blood leucocytes PBLs (PBLs) was determined by ELISA. The frequencies of the −1111C and 4257G wild-type alleles were 0.52 and 0.55 in asthmatics and were 0.67 and 0.56 in controls. A significant (P<0.05) association was found between genotype and allele frequencies of SNP at position −1111C>T between asthmatic and control groups (OR, 1.810; 95% CI = 1.184 to 2.767;P<0.05). The mitogen-stimulated PBLs from asthmatics produced higher amounts of IL-13 production (P<0.001). The 4257GA heterozygous and 4257AA homozygous mutant alleles were associated with higher IL-13 production in asthmatics (P<0.05). Our results show that the −1111T mutant allele are associated with asthma and the 4257A mutant alleles are associated with elevated IL-13 production.

scholarly journals The The relationship between NLRP3 rs10159239 and Vaspin rs2236242 gene variants and obstructive sleep apnea

2021 ◽  
Vol 126 (1) ◽  
Author(s):  
Buğra Kerget ◽  
Ferhan Kerget ◽  
Çiğdem Yüce Kahraman ◽  
Alperen Aksakal ◽  
Ömer Araz
Keyword(s):  
Obstructive Sleep Apnea ◽  
Sleep Apnea ◽  
Upper Airway ◽  
Control Group ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Obstructive Sleep ◽  
And Control ◽  
The Relationship ◽  
Increased Susceptibility

Background: In obstructive sleep apnea (OSA), recurrent upper airway obstruction and apnea/hypopnea episodes result in endothelial dysfunction, which leads to the release of many proinflammatory cytokines and reactive oxygen species (ROS). ROS induces NLRP3, a protein involved in the synthesis of interleukin (IL)-1 and IL-18; vaspin is a serine protease inhibitor that has an important role in suppressing the activation of NLRP3 inflammasome. In this study, we aimed to investigate the effect of NLRP3 rs10159239 (rs9239) and vaspin rs2236242 (rs6242) single nucleotide polymorphisms (SNPs) on OSA development. Methods: This study included 220 individuals who underwent polysomnography (118 patients with OSA and 102 healthy controls). NLRP3 rs9239 and vaspin rs6242 mutation frequencies were analyzed. Results: The NLRP3 rs9239 SNP genotype analysis revealed no statistically significant differences between the OSA and control groups. In the vaspin gene analysis, the rs6242 AA genotype was significantly more frequent in the OSA group compared with the control group, while the AT genotype was more frequent in controls (P = 0.004, P = 0.02). Comparison of rs6242 allele levels showed that the A allele was significantly more frequent in OSA patients than in controls (P = 0.03). The AA genotype was significantly more frequent in patients with severe OSA than in patients with mild or moderate OSA and the control group (P = 0.001 for all). Serum vaspin levels were significantly lower in carriers of the AA genotype than those with AT and TT genotypes (P = 0.001). Conclusion: The vaspin rs6242 SNP AA genotype increased susceptibility to OSA, while the AT genotype appeared to be protective. The lower plasma vaspin levels in OSA compared with the control group and in patients with the AA genotype suggest that vaspin may be a protective biomarker for OSA.

scholarly journals Association of Novel Single Nucleotide Polymorphisms of Genes Involved in Cell Functions with Male Infertility: A Study of Male Cases in Northwest Iran

2021 ◽  
Author(s):  
Elham Ghadrkhomi ◽  
Seyed Abdolhamid Angaji ◽  
Maryam Khosravi ◽  
Mohammad Reza Mashayekhi
Keyword(s):  
Male Infertility ◽  
Nucleotide Polymorphisms ◽  
Control Groups ◽  
Single Nucleotide ◽  
Cell Functions ◽  
Infertile Men ◽  
Significant Difference ◽  
And Control ◽  
Strength Of Association ◽  
Global Health Problem

Background: Infertility is a global health problem caused by various environmental and genetic factors. Male infertility accounts for 40–50% of all cases of infertility and approximately half of them are grouped as idiopathic with no definitive causes. Previous studies have suggested an association between some SNPs and infertility in men. In this study, an attempt was made to investigate the association of 7 different SNPs of 4 genes involved in common cell functions with male infertility. Methods: MTHFR rs1801131 (T>G), MTHFR rs2274976 (G>A), FASLG rs80358238 (A>G), FASLG rs12079514 (A>C), GSTM1 rs1192077068 (G>A), BRCA2 rs4987117 (C>T), and BRCA2 rs11571833 (A>T) were genotyped in 120 infertile men with idiopathic azoospermia or severe oligospermia and 120 proven fertile controls using ARMS-PCR methods. Next, 30% of SNPs were regenotyped to confirm the results. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using SPSS statistical software to evaluate the strength of association. The p˂0.05 were considered statistically significant. Results: Statistical analysis revealed significant association between MTHFR rs-2274976 AA variant (OR: 10.00, CI: 3.203-31.225), FASLG rs12079514 AC variant (OR: 0.412, CI: 0.212-0.800), and BRCA2 rs11571833 TT variant OR: 6.233, CI: 3.211-12.101) with male infertility, but there was no significant difference between case and control groups in MTHFR rs1801131 (p= 0.111), GSTM1 rs1192077068 (p=0.272), BRCA2 rs4987117 (p=0.221), and FASLG rs80358238 (p=0.161). Conclusion: Our findings suggested that some novel polymorphisms including MTHFR rs2274976, FASLG rs12079514, and BRCA2 rs11571833 might be the possible predisposing risk factors for male infertility in cases with idiopathic azoospermia. 

Polymorphic variants of MnSOD Val16Ala, CAT-262 C < T and GPx1 Pro198Leu genotypes and the risk of laryngeal cancer in a smoking population

2013 ◽  
Vol 127 (10) ◽  
pp. 997-1000 ◽  
Author(s):  
G Aynali ◽  
M Doğan ◽  
R Sütcü ◽  
Ö Yüksel ◽  
M Yariktaş ◽  
...  
Keyword(s):  
Laryngeal Cancer ◽  
Control Group ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Smoking Intensity ◽  
Cancer Group ◽  
Smoking Duration ◽  
Polymerase Chain ◽  
And Control ◽  
The Relationship

AbstractObjective:To investigate the relationship between development of laryngeal cancer and the presence of polymorphisms of the MnSOD Val16Ala, CAT-262 C < T and GPx1 Pro198Leu genes in a smoking population.Patients and methods:Single nucleotide polymorphisms were determined in DNA from the peripheral blood erythrocytes of 48 heavy smokers (25 patients with laryngeal cancer and 23 cancer-free controls), using polymerase chain reaction.Results:There were no significant differences in age, smoking duration or smoking intensity, comparing the two groups. The homozygous AA genotype of MnSOD Val16Ala was significantly more prevalent in the cancer group than the control group (92vs13 per cent, respectively), while the heterozygous AV genotype of MnSOD Val16Ala was more prevalent in the control group than the cancer group (87vs8 per cent, respectively) (p < 0.001). There were no significant differences between the cancer and control groups regarding GPx1 Pro198Leu or CAT-262 C < T polymorphisms.Conclusion:Polymorphism of the MnSOD Val16Ala gene may contribute to susceptibility to laryngeal cancer among smokers.

scholarly journals Association between Vitamin D Receptor Single-Nucleotide Polymorphisms and Colorectal Cancer in the Thai Population: A Case-Control Study

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Sirinporn Suksawatamnuay ◽  
Supachaya Sriphoosanaphan ◽  
Prapimphan Aumpansub ◽  
Satimai Aniwan ◽  
Kessarin Thanapirom ◽  
...  
Keyword(s):  
Vitamin D ◽  
Single Nucleotide Polymorphisms ◽  
Vitamin D Receptor ◽  
Colorectal Carcinogenesis ◽  
Nucleotide Polymorphisms ◽  
Control Groups ◽  
Thai Population ◽  
Single Nucleotide ◽  
And Control ◽  
Control Study

Vitamin D and its cognate intracellular nuclear receptor, namely, vitamin D receptor (VDR), are involved in the regulation of a variety of body metabolic processes, immune function, and oncogenesis. A large number of studies demonstrated the association of low vitamin D levels and variations in five common single nucleotide polymorphisms (SNPs), FokI, BsmI, Tru9I, ApaI, and TaqI, with the risk of several cancers, including colorectal cancers. However, these associations vary among different populations. This case-control study was aimed at analysing whether common single-nucleotide polymorphisms (SNPs) and haplotypes of the vitamin D receptor (VDR) gene contribute to colorectal carcinogenesis in the Thai population. We enrolled 364 Thai participants from King Chulalongkorn Memorial Hospital between 2014 and 2015. Half of the participants underwent colonoscopy and showed a normal colon without polyps (control group) and another half were newly diagnosed patients with colorectal cancer (CRC) by colonoscopy during the index period, were under treatment, or were followed up at the outpatient clinic (case group). Differences in allele and genotype frequencies of five common VDR SNPs, between the case and control groups, were the primary outcome measures. Differences in haplotype frequencies of the five SNPs between the case and control groups were the secondary outcome measures. Among the 364 participants, baseline characteristics were not significantly different between the case and control groups, except for the higher proportion of males in the CRC group. The mean vitamin D level was also not significantly different between the case and control groups (24.6±9.1 vs. 25.3±10.6 ng/mL, p=0.52). None of the five VDR SNPs was associated with CRC development (p>0.05). However, haplotype analysis of these polymorphisms demonstrated that the AGGT haplotype was associated with a decreased risk of CRC (odds ratio 0.24, 95% confidence interval 0.07-0.81, p=0.01). The AGGT haplotype was associated with a lower risk of CRC in the Thai population. This genetic linkage might support the role of vitamin D in colorectal carcinogenesis. However, this finding requires further study within a larger population and a multivariate analysis of other established risk factors.

scholarly journals Association of the PSRC1 rs599839 Variant with Coronary Artery Disease in a Mexican Population

Medicina ◽  
2020 ◽  
Vol 56 (9) ◽  
pp. 427
Author(s):  
Martha Eunice Rodríguez-Arellano ◽  
Jacqueline Solares-Tlapechco ◽  
Paula Costa-Urrutia ◽  
Helios Cárdenas-Hernández ◽  
Marajael Vallejo-Gómez ◽  
...  
Keyword(s):  
Coronary Artery Disease ◽  
Logistic Regression ◽  
Coronary Artery ◽  
Multiple Logistic Regression Analysis ◽  
Mexican Population ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Major Health Problem ◽  
Logistic Regression Models ◽  
Artery Disease

Background and Objectives: Coronary artery disease (CAD) is a major health problem in México. The identification of modifiable risk factors and genetic biomarkers is crucial for an integrative and personalized CAD risk evaluation. In this work, we aimed to validate in a Mexican population a set of eight selected polymorphisms previously associated with CAD, myocardial infarction (MI), or dyslipidemia. Materials and Methods: A sample of 907 subjects (394 CAD cases and 513 controls) 40–80 years old was genotyped for eight loci: PSRC1 (rs599839), MRAS (rs9818870), BTN2A1 (rs6929846), MTHFD1L (rs6922269), CDKN2B (rs1333049), KIAA1462 (rs3739998), CXCL12 (rs501120), and HNF1A (rs2259816). The association between single nucleotide polymorphisms (SNPs) and CAD was evaluated by logistic regression models. Results: Multiple logistic regression analysis with adjustment by age, gender, and body mass index showed that rs599839 was significantly associated with CAD (ORADD = 0.72, p = 0.009; ORDOM = 0.66, p = 0.007). Conclusions: The PSRC1 rs599839 polymorphism shows a significant protective association with CAD in this sample of the Mexican population.

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