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.

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.

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 Lack of Association between Polymorphisms of theTLR4Gene and Infection with the Hepatitis B and C Viruses

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Orlando de Souza Pires-Neto ◽  
Keyla Santos Guedes de Sá ◽  
Barbara Brasil Santana ◽  
Samara Tatielle Monteiro Gomes ◽  
Ednelza da Silva Graça Amoras ◽  
...  
Keyword(s):  
Hepatitis B ◽  
Haplotype Analysis ◽  
Early Recognition ◽  
Genetic Profile ◽  
Nucleotide Polymorphisms ◽  
Toll Like Receptor 4 ◽  
Single Nucleotide ◽  
Susceptibility To Infection ◽  
Genotype Frequencies ◽  
Polymerase Chain

Toll-like receptor 4 (TLR4) plays a crucial role in the early recognition of pathogenic microorganisms and provides an ideal model to investigate the consequences of genetic variation and susceptibility to diseases. The present study investigated the occurrence of the single nucleotide polymorphisms (SNPs) rs4986790 (A>G) and rs4986791 (C>T) in theTLR4gene in chronic carriers of the hepatitis B (HBV) and C (HCV) viruses. A total of 420 blood samples were collected (HBV, 49; HCV, 72; and controls, 299) at the liver disease outpatient clinic of Hospital da Fundação Santa Casa de Misericórdia do Pará (FSCMPA). Genomic DNA extracted from leukocytes was subjected to real-time polymerase chain reaction (qPCR) analysis to identify the genetic profile of the participants. No significant differences were found in the allele and genotype frequencies between the infected participants and controls. No significant associations were found between the investigated polymorphisms and inflammatory activity, fibrosis, and the presence of cirrhosis; the same results were obtained in the haplotype analysis. The results showed a lack of association between the rs4986790 and rs4986791 SNPs and susceptibility to infection with HBV and HCV, as well as clinical and laboratory information of the patients.

scholarly journals Association of Interleukin-8 with Cachexia from Patients with Low-Third Gastric Cancer

2009 ◽  
Vol 2009 ◽  
pp. 1-6 ◽  
Author(s):  
Bo Song ◽  
Dianliang Zhang ◽  
Shuchun Wang ◽  
Hongmei Zheng ◽  
Xinxiang Wang
Keyword(s):  
Gastric Cancer ◽  
Cancer Cachexia ◽  
Haplotype Analysis ◽  
Positive Association ◽  
Serum Levels ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Increased Risk ◽  
Pcr Rflp ◽  
Polymerase Chain

Background. Interleukin (IL)-8 has been implicated in the development of cancer cachexia. The polymorphism of IL-8 gene, which may affect the production level of IL-8, may be associated with cancer cachexia.Methods. The serum IL-8 level in our study was examined by radioimmunoassay. We also analyzed single nucleotide polymorphisms (SNPs) −251 A/T and +781 C/T of IL-8 gene, using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).Results. The serum levels of IL-8 were significantly elevated in patients with low-third gastric cancer compared with controls, and were further up-regulated in patients with cachexia than those without (Z=−3.134,P=.002). A significantly increased frequency of +781 T allele was noted in patients with cachexia (OR=2.247, 95% CI: 1.351–3.737,P=.002). The +781 TT genotype was observed to be associated with a significantly increased risk of cachexia (OR=3.167, 95% CI: 1.265–7.929,P=.011), and with odds ratio of 3.033 (95% CI: 1.065–8.639,P=.038) for cachexia after adjusting for potential confounding factors. Meanwhile, haplotype analysis indicated a borderline positive association betweenT251T781haplotype and cachexia as compared with theT251C781haplotype (OR=4.92, 95% CI: 1.00–24.28;,P=.053).Conclusions. IL-8 appears to be associated with cachexia from patients with low-third gastric cancer.

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 Polymorphism and molecular characteristics of the <i>CSN1S2</i> gene in river and swamp buffalo

2020 ◽  
Vol 63 (2) ◽  
pp. 345-354
Author(s):  
Xinyang Fan ◽  
Shanshan Gao ◽  
Lin Fu ◽  
Lihua Qiu ◽  
Yongwang Miao
Keyword(s):  
Direct Sequencing ◽  
Physicochemical Characteristics ◽  
Molecular Characteristics ◽  
Nucleotide Polymorphisms ◽  
Milk Traits ◽  
Single Nucleotide ◽  
Pcr Products ◽  
Variation Characteristics ◽  
Polymerase Chain ◽  
Swamp Buffalo

Abstract. The αS2-casein (αS2-CN) is a member of the casein family associated with milk traits in ruminants, but so far the buffalo CSN1S2 gene has not been well understood. In this work, the polymorphisms of CSN1S2 in river and swamp buffalo were detected using direct sequencing of polymerase chain reaction (PCR) products. As a result, 13 single nucleotide polymorphisms (SNPs) were identified in the coding sequence (CDS) of CSN1S2 in two types of buffalo, of which eight SNPs were non-synonymous. The amino acid changes caused by c.580T>C and c.642C>G may affect the function of buffalo αS2-CN. A total of 11 CSN1S2 CDS haplotypes were defined, and accordingly 11 variants of buffalo αS2-CN were inferred and named. The CSN1S2 CDSs of both types of buffalo were 669 nucleotides, which encoded a precursor of 222 amino acids (AAs), and the first 15 AAs constitute a signal peptide. The composition and physicochemical characteristics of two types of buffalo αS2-CNs were similar but slightly different from those of cattle αS2-CN. The αS2-CN mature peptides of buffalo and the species of Bos genus contained a casein domain, and their secondary structures were highly consistent, indicating that they are functionally similar. The results here provide initial insights into the variation, characteristics and biological function of buffalo CSN1S2.

scholarly journals Genotype Associations with the Different Phenotypes of Atopic Dermatitis in Children

2021 ◽  
Vol 64 (2) ◽  
pp. 96-100
Author(s):  
Volodymyr Dytiatkovskyi ◽  
Tetiana Drevytska ◽  
Tetiana Lapikova-Bryhinska ◽  
Victor Dosenko ◽  
Olexandr Abaturov
Keyword(s):  
Atopic Dermatitis ◽  
Pediatric Patients ◽  
Nucleotide Polymorphisms ◽  
Perennial Allergic Rhinitis ◽  
Control Groups ◽  
Single Nucleotide ◽  
Increased Risk ◽  
Genotype C ◽  
And Control ◽  
Rhino Conjunctivitis

This study deals with detecting the associations of atopic dermatitis’ (AD) phenotypes in children: alone or combined with seasonal allergic rhino-conjunctivitis (SARC) and/or perennial allergic rhinitis (PAR), and/or with bronchial asthma (BA) with single nucleotide polymorphisms (SNP) of filaggrin (FLG), thymic stromal lymphopoietin (TSLP) and orsomucoid-like-1 protein 3 (ORMDL3) genes. Male and female pediatric patients aged from 3 to 18 years old were recruited into the main (AD in different combinations with SARC, PAR, BA) and control groups (disorders of digestives system, neither clinical nor laboratory signs of atopy). Patients were genotyped for SNP of rs_7927894 FLG, rs_11466749 TSLP, rs_7216389 ORMDL3 variants. Statistically significant associations of the increased risk were detected of AD combined with SARC and/or PAR and AD combined with BA (possibly, SARC and/or PAR) with C/T rs_7927894 FLG and T/T rs_7216389 ORMDL3 genotypes. Genotype C/C rs_7927894 FLG significantly decreases the risk of AD combined with SARC and/or PAR by 2.56 fold. Several genotypes’ associations had a trend to significance: C/C rs_7216389 ORMDL3 decreases and C/T rs_7216389 ORMDL3 increases the risk for developing AD alone phenotype; A/G rs_11466749 TSLP decreases the risk of AD combined with BA (possibly, SARC and/or PAR) phenotype development.

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