Objective To review the research progress of bone morphogenetic protein (BMP) and the liability of ossification of the posterior longitudinal ligament (OPLL). Methods Recent literature concerning BMP and the liability of OPLL was reviewed, analysed, and summarized. Results The single nucleotide polymorphisms (SNPs) of BMP gene may produce a minor cumulative effect and increase individual susceptibility to OPLL. A variety of environmental factors can promote the occurrence and development of OPLL by increasing the expression of BMP gene. Conclusion The SNPs of BMP gene may increase individual susceptibility to OPLL. However, interaction of cumulative effect of the SNPs and environmental factors can promote the liability to OPLL.
Objective To explore the correlation between the single nucleotide polymorphism (SNP) in the promotor of hepatic l ipase (HL) gene and untraumatic avascular necrosis of the femoral head (ANFH). Methods Between January 2007 and June 2009, 243 patients with ANFH were treated (case group), including 143 cases of steroid-induced, 79 cases of alchol-induced, and 21 cases of idiopathic. There were 156 males and 87 females with an age ranged from 16 to 64 years. Atotal of 96 normal individuals (matched for age, sex, and nation) served as control group. The blood sample of all subjects were collected to extract DNA. The promotor of HL was sequenced to find the SNP. A statistic on the frequencies of the genotype and the allele of the SNP was made. The frequencies of the genotype and the allele were analyzed with χ2 test according to case-control principle. Results The rs59644784 and rs1800588 were found in the sequenced region. It was accorded with Hardy-Weinbery genetic equil ibrium law in rs59644784 and rs1800588 of the control group and case group. There was no significant difference in the allele and genotype of rs59644784 and rs1800588 between the control group and case group (P gt; 0.05). The two SNPs existed complete l inkage disequil ibrium according to the l inkage disequil ibrium analysis. Conclusion The heterozygosity of the SNP is not consistency, and heterozygosity may be associated with the diversity of the race. ANFH is not associated with rs59644784 and rs1800588 SNPs.
ObjectiveThrough Sequenom iPEX system analyzed the genetic susceptibility in patients with Medial temporal lobe epilepsy (MTLE) which screening hyperpolarization-activated cyclic nucleotide gated channel (HCN) subunit HCN1 and HCN2 single nucleotide polymorphism blood samples. MethodsPatients with epilepsy who were diagnosed MTLE in our epileptic clinic from December 2013 to April 2016 were included in this study, total 143 cases. Healthy volunteers who received annual physical checkups were recruited to serve as controls total 120 cases. The group enter criterion according to a 2004 ILAE report mainly:①12~55 years old; ②attack forms:partial onset seizures or secondary tonic-closure-clonus attack, a common onset symptoms such as stomach gas rise feeling, sense of deja vu, automatism etc.; ③with or without febrile convulsions history; ④EEG displayed unilateral or bilateral temporal spike, sharp slow wave, or their spines slow-wave sample such as epilepsy wave; ⑤head MRI displayed hippocampal sclerosis. Exclusion criteria:①tumors; ②head MRI display focal cortical dysplasia (FCD). Using sequenom iPLEX technology platform to detect all the object of study of gene polymorphism sites total ten sites. All statistical tests were conducted using SPSS version 16.0. Resultsall sites fulfilled Hardy-Weinberg genetic balance. The results showed that HCN1 rs17344896 C/T, rs6451973 A/G and HCN2 rs12977194 A/G three polypeptide sites associated with MTLE, with statistical differences(P < 0.05). ConclusionHCN1 and HCN2 genetic suscepibility is one of possible mechanism of MTLE.
To perform a meta-analysis of single nucleotide polymorphism needs to calculate gene frequency. This paper employs allele model as an example to introduce how to calculate gene frequency and display the process of a meta-analysis of single nucleotide polymorphism data using Review Manager 5.3 software.
The association between single nucleotide polymorphism and disease is a typical representation of genetic association studies. Compared with the traditional dichotomous data, single nucleotide polymorphism data has its own characteristics, and 5 genetic models are commonly performed in meta-analysis. In this paper, we show how to use the " meta” package in R software to conduct meta-analysis of single nucleotide polymorphism research through examples.
Objective To explore whether interleukin-10 ( IL-10 ) gene single nucleotide polymorphisms are associated with asthma. Methods The frequency of three single nucleotide polymorphisms ( rs1800896, rs3024492, and rs3024496) and haplotypes of IL-10 gene were analysed in 302 adult asthmatic subjects and 275 controls of Han Chinese in Guangzhou using MALDI-TOF-MS and MassARRAY-IPLEX. The genotype and allele frequencies were analyzed by Chi-square test in both groups.Logistic regression analysis with adjustment for age and sex was conducted. Odds ratio ( OR) and 95%confidence interval ( 95% CI) were calculated to analyze the associations between the susceptibility of asthma and genotypes. Results ①Three genotypes GG, GA, and AA of rs1800896 were found in Han Chinese inGuangzhou. The frequencies of GG, GA, and AA genotypes were 2. 12% , 39. 65% , and 58. 23% ,respectively. The relative risk of developing asthma in the carriers of GA was significantly higher than that in the carriers of AA ( OR=4. 827, P lt;0. 001) . ②Two genotypes AA and AT of rs3024492 were found in Han Chinese in Guangzhou. The frequencies of AA and AT genotypes were 1. 22% and 98. 78% , respectively.The rs3024492 polymorphism was not related to susceptibility in asthma. ③Two genotypes TT and CT of rs3024496 were found in Han Chinese in Guangzhou. The frequencies of TT and CT genotypes were 90. 59% and 9. 41% , respectively. The rs3024496 polymorphism was not related to susceptibility in asthma. Conclusion In IL-10 gene single nucleotide polymorphisms, rs1800896 but not rs3024492 and rs3024496 isstatistically related with the development of asthma.
ObjectiveTo analyze the causal relationship between SARS-CoV-2 infection and retinal vascular obstruction by mendelian randomization (MR). MethodsA two-sample MR analysis utilizing summary statistics from genome-wide association studies (GWAS) in European populations was conducted. The GWAS data for SARS-CoV-2 infection comprised cases of common infection (2 597 856), hospitalized infection (2 095 324), and severe infection (1 086 211). Data on retinal vascular obstruction were obtained from the FinnGen database, which included 203 269 cases of retinal artery obstruction and 182 945 cases of retinal vein obstruction (RVO). Inverse variance weighting (IVW), random effects models, weighted median (WM), MR-Egger regression, simple models, and weighted models were used to analyze the bidirectional causal relationship between different SARS-CoV-2 infection phenotypes and retinal obstruction. The Q statistic was used to assess heterogeneity among single nucleotide polymorphisms (SNP), while MR-Presso was utilized to detect SNP outliers, and MR-Egger intercept tests were performed to evaluate horizontal pleiotropy. ResultsThe MR analysis, using IVW, random effects models, MR-Egger, WM, and weighted models, indicated no significant association between common SARS-CoV-2 infection, hospitalized infection, severe infection, and retinal vascular obstruction (P＞0.05). Additionally, retinal vascular obstruction did not show a significant association with the various SARS-CoV-2 infection phenotypes (P＞0.05). In the simple model, a significant association was found between severe SARS-CoV-2 infection and RVO (P＜0.05), as well as between RVO and common SARS-CoV-2 infection (P＜0.05). No heterogeneity was observed in the IVW and MR-Egger analyses (P＞0.05). The MR-Egger test provided no evidence of horizontal pleiotropy (P＞0.05), and MR-Presso detected no outlier SNP. ConclusionThe findings of this study do not support a causal relationship between SARS-CoV-2 infection and the occurrence of retinal vascular obstruction.
ObjectiveTo explore the relationship between single nucleotide polymorphisms (SNPs) of the Toll-like receptor 4 (TLR4) gene and the risk of pulmonary tuberculosis (PTB) more comprehensively and objectively through meta-analysis.MethodsWe searched all available articles published before June 13th, 2019 in main Chinese and English databases systematically and comprehensively, including PubMed, Embase, China National Knowledge Infrastructure, Wanfang and CQVIP databases. The literature was screened according to the inclusion and exclusion criteria set in advance. In addition, the basic characteristics and data of the included literature were recorded according to a pre-made data collection form. Statistical analyses were performed using the Stata 15.0 software.ResultsA total of 17 eligible original articles were included in the study eventually. Furthermore, allele and genotype data of the 4 most widely studied SNPs (rs4986790, rs4986791, rs10759932, and rs11536889) in the TLR4 gene were extracted. And their allelic model, dominant model, recessive model, homozygous model, and heterozygous model were separately analyzed by meta-analysis. The results showed that the C allele of rs10759932 increased the risk of PTB [odd ratio (OR)=1.144, 95% confidence interval (CI) (1.043, 1.254), P=0.004]. Compared with the TT genotype, the CC+CT genotype and the CT genotype alone of rs10759932 also increased the risk of PTB [OR=1.218, 95%CI (1.084, 1.369), P=0.001; OR=1.227, 95%CI (1.085, 1.387), P=0.001]. Nevertheless, there was no statistical correlation between the other three SNPs (rs4986790, rs4986791 and rs11536889) and the susceptibility to PTB (P>0.05).ConclusionThe allele model, dominant model (CC+CT vs. TT), and heterozygous model (CT vs. TT) of rs10759932 located on the TLR4 gene are closely related to the risk of PTB.
Objective To reveal the association between the single nucleotide polymorphism (SNP) of v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (MAFB) gene rs17820943 locus and non-syndromic cleft l ip with or without cleft palate (NSCL/P) in the southern Chinese Han population. Methods Genotyping of MAFB gene rs17820943 polymorphism was carried out in 300 patients with NSCL/P, 354 normal controls, and an additional 168 case-parent trios with matrix-assisted laser desorption/ionisation time-of-fl ight (MALDI-TOF) mass spectrometry. Then based on the genotypingresults, both a case-control association study and a case-parent trio association study were performed. Results Significant differences were found in the allele and genotype frequencies of rs17820943 locus between case and control groups (Pallele=0.001 and Pgenotype=0.002, respectively). To be specific, the odds radio (OR) values and 95% confidence interval (95%CI) of allele T (frequencies of cases ∶ controls = 0.358 ∶ 0.448) and genotype TT (frequencies of cases ∶ controls = 0.110 ∶ 0.195) were ORT = 0.69 (95%CI: 0.55-0.86) and ORTT = 0.43 (95%CI: 0.26-0.70), respectively. Subsequent case-parent trio analysis also indicated an association between MAFB rs17820943 variant and the risk of NSCL/P (ORT vs. C = 0.55, 95%CI: 0.41-0.75, P value of transmission disequilibrium test was 0.000). Conclusion Polymorphism of MAFB gene rs17820943 locus is associated with NSCL/P in the southern Chinese Han population; MAFB rs17820943 variant may be a susceptible gene of NSCL/P.
Objective To investigate the relationship of p53 codon 72 polymorphism and susceptibility to gastric cancer in high incidence area of Hexi area of Gansu province. Methods The Arg/Pro polymorphism of p53 gene was detected by real-time PCR in 140 patients with gastric cancer, 110 patients with gastric precancerous lesion and 125 healthy controls; Helicobacter pylori (Hp) infection was detected by Warthin-Starry silver method． Results The Pro allele frequencies of p53 gene in gastric cancer cases (0.543) were higher than those in gastric precancerous lesion (0.482) and controls (0.472). The Pro genotype had a more than 1.846 fold increased risk of gastric cancer 〔OR=1.846; 95% 〗CI (1.006-3.387); P =0.046〕． With statistical analysis， the genotype of p53 gene was correlated with location and Laurens histological type （ P ＜ 0.05）. A significantly higher risk of gastric cancer was also seen in cases with p53 Pro genotype, food, Hp infection, positive mind factor and positive family history． Conclusion There is a b correlation between the p53 gene codon 72 Arg/Pro polymophism and susceptibility to gastric cancer in Hexi area of Gansu province and the Pro/Pro genotype may be one of the major risk factors in patients with gastric cancer.