Genetic association study of SOX2 gene polymorphisms with high myopia in a Chinese population

Purpose: The aim of this study is to investigate whether SOX2 gene variants were associated with high myopia in a Chinese population. Methods: This study is conducted using case-control association analysis. This study recruited 83 healthy controls (with binocular spherical equivalent between –0.50 and +0.50 D) and 117 high myopia cases (spherical equivalent > –6.00 D in both eyes). Three single-nucleotide polymorphisms were selected from HapMap database for genotyping by direct sequencing. Statistical software (SPSS 22.0) was used for statistical analysis. The chi-square test was used to examine the difference in the frequency between cases and controls. Results: Genotype distributions in the three single-nucleotide polymorphisms were all in accordance with the Hardy–Weinberg equilibrium. The differences of rs4575941 locus genotype frequency and allele frequency between the case group and the control group were statistically significant (p = .043 and p = .029, respectively). The rs4575941 allele G frequency in the high myopia group was significantly higher than that in the control group with an odds ratio value of 1.579. However, the value of a chi-square test for the trend was 0.029, and after Bonferroni test, the p value was .087. Conclusion: In Chinese population, rs4575941 in SOX2 gene was likely to play some roles in the genetic susceptibility to high myopia; the rs4575941 allele G might be a risk gene for high myopia.

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Association of single nucleotide polymorphisms in CACNA 1A/CACNA 1C/CACNA 1H calcium channel genes with diabetic peripheral neuropathy in Chinese population

Bioscience Reports ◽

10.1042/bsr20171670 ◽

2018 ◽

Vol 38 (3) ◽

Cited By ~ 1

Author(s):

Lin Sun ◽

Jun Ma ◽

Qian Mao ◽

Yun-Long Yang ◽

Lin-Lin Ma ◽

...

Keyword(s):

Peripheral Neuropathy ◽

Single Nucleotide Polymorphisms ◽

Calcium Channel ◽

Diabetic Peripheral Neuropathy ◽

Chinese Population ◽

Control Group ◽

Case Group ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Pcr Rflp

The present study was conducted to explore the correlations between single nucleotide polymorphisms (SNPs) in the calcium channel CACNA 1A, CACNA 1C, and CACNA 1H genes and diabetic peripheral neuropathy (DPN) amongst the Chinese population. In total, 281 patients diagnosed with type 2 diabetes participated in the present study. These patients were divided into the case group, which was subdivided into the DPN (143 cases) and the non-DPN groups (138 cases). Subsequently, 180 healthy individuals that had undergone routine health examinations were also recruited and assigned to the control group. PCR-restriction fragment length polymorphism (PCR-RFLP) was used to detect the genotype and allele frequencies of CACNA 1A, CACNA 1C, and CACNA 1H genes; logistic regression analysis to investigate the association of gene polymorphisms with DNP. Gene–gene interactions were then detected by generalized multifactor dimensionality reduction (GMDR). The results revealed that CACNA 1A rs2248069 and rsl6030, CACNA 1C rs216008 and rs2239050, and CACNA 1H rs3794619, and rs7191246 SNPs were all associated with DPN, while rs2248069, rsl6030, rs2239050, and rs7191246 polymorphisms were attributed to the susceptibility to DPN. It was also observed that the optimal models were three-, four- and five-dimensional models with a prediction accuracy of 61.05% and the greatest consistency of cross-validation was 10/10. In summary, these findings demonstrated that the SNPs in the CACNA 1A, CACNA 1C, and CACNA 1H genes were involved in the pathophysiology of DPN. In addition, polymorphisms in the CACNA 1A, CACNA 1C, and CACNA 1H genes and their interactions also had effects on DPN.

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Association of IGF1 single-nucleotide polymorphisms with myopia in Chinese children

PeerJ ◽

10.7717/peerj.8436 ◽

2020 ◽

Vol 8 ◽

pp. e8436

Author(s):

Tianyu Cheng ◽

Jingjing Wang ◽

Shuyu Xiong ◽

Bo Zhang ◽

Qiangqiang Li ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Chinese Population ◽

Additive Models ◽

Chinese Children ◽

Nucleotide Polymorphisms ◽

Chi Square ◽

Single Nucleotide ◽

Link Type ◽

Polymerase Chain ◽

And Gender

Purpose To investigate the association between insulin-like growth factor 1 (IGF1) single-nucleotide polymorphisms (SNPs) and myopia in a young Chinese population. Methods A total of 654 Chinese children aged 6–13 years from one primary school participated in our study and underwent a series of comprehensive ocular examinations, including cycloplegic refraction and measurements of axial length. Myopia was defined as a spherical equivalence (SE) ≤ −0.5 D in the worse eye. In total, six tagging SNPs of IGF1 were genotyped using the PCR-LDR (Polymerase Chain Reaction-Ligation Detection Reaction) method. We tested four different genetic modes (the allele, dominant, recessive, and additive models) of these SNPs and used multivariate logistic regression to calculate the effect of SNPs on myopia. In addition, we conducted a haplotype analysis with a variable-sized slide-window strategy. Results Overall, 281 myopic children and 373 non-myopic controls were included in the analysis. The SNP rs2162679 showed a statistical difference between the two groups in both the allele (p = 0.0474) and additive (p = 0.0497) models. After adjusting for age and gender, children with the genotype AA in the SNP rs2162679 had a higher risk of myopia than those with the genotype GG (OR = 2.219, 95% CI [1.218–4.039], p = 0.009). All haplotypes that varied significantly between the two groups contained the SNP rs2162679, and the four-SNP window rs5742653–rs2162679 had the lowest p value (Chi square = 5.768, p = 0.0163). However, after permutation tests, none of the associations remained statistically significant. Conclusion The SNP rs2162679 in IGF1 was associated with myopia in a young Chinese population. The G allele in the SNP rs2162679 may protect against myopia.

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CD44, IL-33, and ST2 Gene Polymorphisms on Hepatocellular Carcinoma Susceptibility in the Chinese Population

BioMed Research International ◽

10.1155/2020/2918517 ◽

2020 ◽

Vol 2020 ◽

pp. 1-11

Author(s):

Xiaolan Pan ◽

Meiqin Li ◽

Lei Huang ◽

Dan Mo ◽

Yihua Liang ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Single Nucleotide Polymorphisms ◽

Chinese Population ◽

Haplotype Analysis ◽

Control Group ◽

Case Group ◽

Nucleotide Polymorphisms ◽

Cancer Stemness ◽

Single Nucleotide ◽

The Relationship

The interleukin- (IL-) 33/ST2 axis plays a pivotal role in tumorigenesis through influencing cancer stemness and other mechanisms. CD44 is one of the critical markers of hepatocellular carcinoma (HCC) among the cancer stem cells (CSCs). There is still a lack of CD44 gene single-nucleotide polymorphisms (SNPs) combined with IL-33/ST2 pathway single-nucleotide polymorphisms in HCC susceptibility analysis literature, although CD44 and IL-33/ST2 have been reported separately in human cancers. This study is aimed at investigating the relationship between CD44, IL-33, and ST2 SNPs and HCC susceptibility and clinicopathological features. We analyzed 565 HCC patients and 561 healthy controls in the Chinese population. The genes for CD44rs187115A>G, IL-33 rs1929992A>G, and ST2 rs3821204G>C were typed using the SNaPshot method. We found that the distribution frequencies of CD44 and ST2 alleles and genotypes in both the HCC case group and the control group were statistically significant ( p < 0.05 ). The results showed that individuals carrying at least one G allele of the CD44 rs187115 gene were at a higher risk than the AA genotype carriers ( p = 0.007 , odds ratio OR = 1.429 , 95% confidence interval (CI): 1.102–1.854). Similarly, individuals with at least one C allele of ST2 rs3821204 had a higher risk of HCC than those with GG genes ( p ≤ 0.001 , OR = 1.647 , 95% CI: 1.296-2.093). Combining the haplotype analysis of the 3 loci suggested that CD44 rs187115, IL-33 rs1929992, and ST2 rs3821204 are associated with the risk of HCC and could potentially serve as useful genetic markers for HCC in some populations of China.

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High myopia is not associated with single nucleotide polymorphisms in the COL2A1 gene in the Chinese population

Molecular Medicine Reports ◽

10.3892/mmr.2011.626 ◽

2011 ◽

Author(s):

Qingjiong Zhang

Keyword(s):

Single Nucleotide Polymorphisms ◽

Chinese Population ◽

High Myopia ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Col2a1 Gene

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Study of Dental Caries and PTH Gene

Frontiers in Dental Medicine ◽

10.3389/fdmed.2021.703549 ◽

2021 ◽

Vol 2 ◽

Author(s):

Caio Luiz Bitencourt Reis ◽

Mariane Carolina Faria Barbosa ◽

Daniela Coelho de Lima ◽

Isabela Ribeiro Madalena ◽

Flares Baratto-Filho ◽

...

Keyword(s):

Dental Caries ◽

Single Nucleotide Polymorphisms ◽

International System ◽

Binary Logistic Regression ◽

Nucleotide Polymorphisms ◽

Gene Encoding ◽

Chi Square ◽

Single Nucleotide ◽

Chi Square Test ◽

Brazilian Children

Parathyroid hormone (PTH) is essential for calcium and phosphate homeostasis in odontogenesis-related cells. Therefore, the present study aimed to investigate the association between single nucleotide polymorphisms in the gene encoding PTH, and dental caries in Brazilian children. Three hundred and fifty-three children (170 boys and 183 girls, age ranging from 8 to 11 years old) were included in this study. The International System for Detection and Assessment of Carious Lesions (ICDAS) was used for diagnosis of dental caries. Visible biofilm was also evaluated during the clinical examination. Genomic DNA was extracted from saliva for real-time PCR to evaluate the single nucleotide polymorphisms rs6256, rs307247 and rs694 in PTH gene. Dental caries was classified in ICDAS0 vs. ICDAS1−6 or ICDAS1−2 vs. ICDAS3−6. Chi-square test, binary logistic regression adjusted by biofilm and haplotype analyses were performed (p < 0.05). Biofilm was associated with dental caries (p < 0.05). There were no associations between dental caries and rs6256, rs307247, rs694 in none of the analyses performed (p > 0.05). In conclusion, the present study supports that the single nucleotide polymorphisms rs6256, rs307247, and rs694 in the PTH-encoding gene are not associated with dental caries in Brazilian children.

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An association between tyrosinase gene single nucleotide polymorphisms and melanin distribution in chicken

Chinese Journal of Agricultural Biotechnology ◽

10.1079/cjb200576 ◽

2005 ◽

Vol 2 (3) ◽

pp. 167-171

Author(s):

Chen Zhi-Qiang ◽

Deng Xue-Mei ◽

Zhou Jun ◽

Li Ning ◽

Wu Chang-Xin

Keyword(s):

Single Nucleotide Polymorphisms ◽

Single Strand Conformation Polymorphism ◽

Nucleotide Polymorphisms ◽

Chi Square ◽

Single Nucleotide ◽

Melanin Biosynthesis ◽

Tyrosinase Gene ◽

Key Enzyme ◽

Chi Square Test ◽

Conformation Polymorphism

AbstractTyrosinase (TYR) is a key enzyme of melanin biosynthesis. Single-strand conformation polymorphism (SSCP) analysis was applied to detect the single nucleotide polymorphisms (SNPs) in the upstream regulating region from -641 to -2125 bp of the TYR gene. Three SNPs were found in this region. Correlations were obtained between genotypes of the SNP sites and pigment traits in chicken parental and F2 generations of the Chinese Agricultural University (CAU) resource population. The chi-square test indicated that these mutations were significantly related to shank and body skin colours.

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