Objective To review the research progress in relationship between hereditary diffuse gastric cancer (HDGC) and CDH1 gene. Methods Literatures on HDGC which were published in recent years were collected and analyzed. Results Aberrant CDH1 gene is significantly correlated with HDGC: mutations of CDH1 exons play the most important role in pathogenesis of HDGC. Screening CDH1 gene mutation is useful for diagnosis of HDGC as well as the treatments. Alterations of CDH1 other than exon mutation, such as intron mutation, gene promoter methylation and single nucleotide polymorphism may result in downregulation of the gene expression. Further study should be done to confirm the roles of these alterations. Conclusions Alterations of CDH1 gene are significantly associated with the pathogenesis of HDGC. Detecting alterations of CDH1 gene are important for diagnosis and management of HDGC as well as to get insights of the pathogenesis of the disease.
ObjectiveTo understand the genetics associations between low-density lipoprotein receptor-related protein 5 (LRP5) gene polymorphisms and susceptibility of osteoporosis in patients with chronic obstructive pulmonary disease (COPD).MethodsThree hundred and seventy-nine patients with acute exacerbation of COPD were divided into groups of non osteoporosis and osteoporosis. Genomic DNA was extracted from all patients. UCSC genome browser and Haploview 4.2 software were used to screen tag single nucleotide polymorphisms (tagSNP) of LRP5 gene. The tagSNP was genotyped by Sequenom MassARRAY SNP detection method. Logistic regression were used to analysis the odds ratio (OR) values and confidence intervals (CI) of each SNP in different genetic models to assess the association between single nucleotide polymorphisms in LRP5 gene and osteoporosis in COPD patients.ResultsEight tagSNPs of LRP5 gene (rs312016 T/C, rs312017 C/T, rs312018 A/G, rs3736228 C/T, rs901823 T/C, rs589963 G/A, rs638051 A/G, rs671494 C/A) were selected for association analysis. Patients of rs901823 carrying C/C genotype had a higher risk of osteoporosis than those carrying T/T and C/T genotypes in COPD patients (in recessive mode, C/C vs. T/T+C/T, OR=9.42, 95%CI=2.01–44.29), P=0.000 431 8).ConclusionsThere is a significant association between rs901823 of LRP5 gene and osteoporosis in patients with COPD. Further studies are needed to discover the mechanism of LRP5 gene polymorphism in the pathogenesis of osteoporosis in COPD patients.
ObjectiveTo investigate the association between polymorphism of V4,F+1 in ADAM33 (adisintegrin and metalloproteinase 33) gene and COPD in a northwestern Uighur population. MethodsA total of 100 Uighur COPD patients and 140 healthy volunteers were recruited in the study. Genotypes were determined by restriction fragment lengthpolymorphism(PCR-RFLP). All subjects had a epidemiological investigation including modified british medical research council(mMRC),COPD assessment test(CAT),and pulmonary function test. The 100 Uighur COPD patients were assessed by revised GOLD2011. ResultsAssessed by revised GOLD2011,the patients of A,B and C grade accounted for 22%,35% and 30%,respectively. There was no statistical significance in the distributions of the V4,F+1 alleles between the patients and the controls(P>0.05). There was no statistical significance between SNPs in ADAM33(V4 and F+1) with the decreased lung function and the grade of COPD(P>0.05). ConclusionThere was no association between polymorphism of V4,F+1 in ADAM33 gene and COPD in a northwestern Uighur population.
ObjectiveTo explore the relationship between the single nucleotide polymorphisms of interleukin (IL)-23R gene and susceptibility to pulmonary tuberculosis in Southwest Chinese Han population.MethodsA total of 680 pulmonary tuberculosis patients (pulmonary tuberculosis group) and 680 healthy controls (healthy control group) diagnosed or examined between January 2014 and February 2016 were recruited from West China Hospital, Sichuan University. Improved multiplex ligation detection reaction (iMLDR) method was used to detect the polymorphism of rs1495965, rs7518660, rs7532161, rs10889677 and rs11465802 of IL-23R gene. The differences in allele frequency distribution, genotype, and genetic model of these five loci between pulmonary tuberculosis patients and healthy control were conducted by using SPSS20.0 and PLINK 1.07. Linkage disequilibrium and haplotype analysis were also carried out by Haploview 4.2.ResultsFinally, 657 pulmonary tuberculosis patients and 669 healthy controls were enrolled for further analyzed. The difference in the allele frequency distribution A (P=0.048), AA genotype (P=0.048) and additive model AA/GG (P=0.048) in rs1495965 was significant between the pulmonary tuberculosis group and healthy control group when we adjusted the gender and age. However, after correction by Bonferroni, the differences in allele frequency distribution, genotype and additive model of all these five loci between the two groups were not statistically significant (P>0.05). rs7518660, rs10889677 and rs11465802 had strong linkage disequilibrium (LD) with each other (r2>0.80); however, there was no association between haplotype GCA and tuberculosis susceptibility (P=0.343).ConclusionsThere is no association between rs1495965, rs7518660, rs7532161, rs10889677 and rs11465802 of IL-23R gene and genetic pulmonary tuberculosis susceptibility in Southwest Chinese Han population. To add loci in the coding region and analysis in different populations is necessary.
ObjectiveTo investigate the associations of signal transducers and activators of transcription 6 (STAT6) gene polymorphisms with susceptibility to tuberculosis in western Chinese Han population.MethodsA total of 900 tuberculosis patients and 1 534 healthy controls of West China Hospital of Sichuan University were enrolled from January 2014 to February 2016. Improved multiplex ligation detection reaction method was used to detect four polymorphisms (rs1059513, rs73118432, rs841718, and rs10783813) of STAT6 gene. The allelic frequencies, genetic types, and different genetic models were analyzed using the chi-square test and unconditional logistic regression models to evaluate the associations of STAT6 gene with tuberculosis risk.ResultsEventually, a total of 856 cases and 1 511 health controls were recruited in our study. No significant differences were observed in allele frequencies, genotype distributions, or genetic models (additive model, dominant model and recessive model) at rs1059513, rs73118432, rs841718, and rs10783813 in STAT6 gene (P>0.05). We found a strong linkage disequilibrium among rs73118432, rs841718, and rs10783813, but there was no statistical difference in haplotype frequencies between the two groups (P>0.05).ConclusionsSTAT6 gene rs73118432, rs841718, rs10783813, and rs1059513 polymorphisms might have no associations with tuberculosis susceptibility in western Chinese Han population. Further studies with larger sample sizes are needed to comfirm these results.
ObjectiveTo investigate the relationship between the gene polymorphism of autophagy-related gene 3 (ATG3) and the development and clinical symptoms of tuberculosis in tuberculosis patients in western China.MethodsAccording to the inclusion and exclusion criteria, 476 tuberculosis patients (tuberculosis group) who were admitted to West China Hospital of Sichuan University from December 2014 to November 2015 and 475 healthy controls (healthy control group) who underwent health examination during the same period were finally included. High-throughput genotyping technology was used to detect genotypes of three single nucleotide polymorphisms (SNPs) (rs2638029, rs2638037, rs3732817) of ATG3 gene, and relevant clinical data of subjects were collected. The relationship between gene polymorphism and susceptibility to tuberculosis and clinical symptoms was analyzed by statistical methods such as χ2 test and logistic regression model.ResultsExcept for GA genotype [odds ratio (OR) =1.375, 95% confidence interval (CI) (1.048, 1.805), P=0.022] and dominant genetic model GG+GA [OR=1.326, 95%CI (1.024, 1.717), P=0.032] in rs2638037, there was no statistically significant difference in the allele frequency, genotype and genetic patterns of rs2638029, rs3732817 and rs2638037 between the two groups (P>0.05), after the adjustment of the gender and age. But after correction by Bonferroni, GA genotype and dominant genetic patterns GG+GA showed no statistical significance between the two groups (P=0.132, 0.201). Haplotype CGA was associated with tuberculosis susceptibility [OR=1.262, 95%CI (1.001,1.593), P=0.048]. There was a statistically significant difference in weight loss symptoms among rs2638037 genotypes (χ2=8.131, P=0.017).ConclusionsThe haplotype CGA of three SNPs of ATG3 gene may be involved in the development of tuberculosis. The rs2638037 single nucleotide polymorphism may be related to weight loss, and more research is needed in the future.
ObjectiveTo explore the relationship between hexokinase domain-containing protein 1 (HKDC-1) single nucleotide polymorphism (SNP) and first-line anti-tuberculosis drug-induced liver injury (ATDILI) in tuberculosis patients in western China.MethodsFrom November 2016 to April 2018, 746 tuberculosis patients treated in West China Hospital of Sichuan University were collected and divided into ATDILI group and non-ATDILI group according to the liver function indicators. DNA was extracted by QIAamp? DNA Blood Mini Kit (Qiagen, Germany). Seven SNPs of the HKDC-1 gene were genotyped by high-throughput genotyping technique and the differences between the two groups were compared.ResultsThere were 118 ATDILI and 628 non-ATDILI cases enrolled in this study. In clinical symptoms, the differences in incidences of fever and weight loss between the two groups were statistically significant (P=0.004, 0.024). The C allele at rs906219 was associated with low susceptibility to ATDILI [odds ratio (OR)=0.737, 95% confidence interval (CI) (0.556, 0.957), P=0.033], and the additive model and dominant model showed that CC/CA genotype had a lower risk of ATDILI than AA genotype [CC vs. AA: OR=0.563, 95%CI (0.325, 0.976), P=0.039; CC+CA vs. AA: OR=0.533, 95%CI (0.348, 0.817), P=0.004].ConclusionThe SNP of rs906219 in HKDC-1 is correlated with ATDILI occurrence in tuberculosis patients in western China, which provides clues for personalized anti-tuberculosis treatment.
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.
Objective To explore the relationships between the polymorphisms of inhibitor genes WIF1 and DKK1 in WNT signaling pathway and susceptibility to tuberculosis, clinical characteristics and laboratory indexes. Methods From December 2014 to November 2016, 475 tuberculosis patients and 370 healthy controls of West China Hospital of Sichuan University were enrolled in the study, and the clinical data of the subjects were collected. High-throughput genotyping technique was used to detect the polymorphisms of WIF1 rs58635985 and DKK1 rs11001548 in WNT signaling pathway. The allele frequency distribution, genotype, genetic model, clinical features and laboratory indexes of two single nucleotide polymorphisms were analyzed by χ2 test and logistic regression analysis. Results There was no significant difference in the allele frequency distribution (P=0.275, 0.949), genotype (P=0.214, 0.659) or genetic models: additive model (P=0.214, 0.659), dominant model (P=0.414, 0.827), recessive model (P=0.227, 0.658) of rs58635985 and rs11001548 between the tuberculosis group and the healthy control group. Subgroup analysis showed no significant difference in allele and genotype distribution between rs58635985 and rs11001548 (pulmonary tuberculosis group vs. healthy control group: P>0.05; pulmonary tuberculosis groupvs. extra-pulmonary tuberculosis group: P>0.05). There was no significant difference in the clinical features (fever, night sweat, fatigue,etc.) or laboratory indexes (complete blood count, erythrocyte sedimentation rate, TB-DNA, etc.) (P>0.05). Conclusions There is no association between rs58635985 of WIF1 gene or rs11001548 of DKK1 gene and genetic susceptibility, clinical characteristics and laboratory indexes in Han population in Western China. To expand the sample size for verification and analysis in different populations is necessary.
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.