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Gut microbiome sequencing studies have great potential to translate microbial analysis outcomes into human health research. Sequencing strategies of 16S amplicon and whole-metagenome shotgun (WMS) are two main methods in microbiome research with respective advantages. However, how sample heterogeneity, sequencers and library preparation protocols affect the sequencing reproducibility of gut microbiome needs further investigation. This study aims to provide a reference for the selection of sequencing technologies by comparing differences in microbial composition from different sampling sites. The results of three widely adopted sequencers showed that the technical repetition correlation (r= 0. 94) was high in WMS method, while the biological repetition correlation (r = 0. 69) was low. Bray-Curtis distance identified that dissimilarity from biological replicates was larger than that of technical replicates (P<0. 001). In addition, dissimilarity and specific taxonomic profiles were observed between 16S and WMS datasets. Our results imply that homogenization is a necessary step before sample DNA extraction. The sequencers contributed less to taxonomic variation than the library preparation protocols. We developed an empirical Bayes approach that " borrowed information" in calculations and analyzed batch effect parameters using standardized data and prior distributions of (non-) parameters, which may improve population comparability between 16S and WMS and provide a basis for further application to fusion analysis of published 16S and microbial datasets.
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Esophageal squamous cell carcinoma （ESCC） is a malignant tumor caused by both environmental and genetic factors. Epidemiology studies have identified smoking as a major environmental risk factor. In recent years， the advancement of genomics research has led to the recognition of the influence of genetic variation in ESCC. We reviewed the research progress in smoking， genetic polymorphism and their interaction on susceptibility to ESCC. Reducing exposure time to tobacco was found to be the most effective way to reduce the risk. At the genetic level， mutations in DNA repair genes， regulation genes of carcinogen-metabolizing enzymes， cell cycle regulation genes， folate metabolism related genes， and alcohol metabolism related genes were found to significantly increase the risk of ESCC. However， studies on the interaction between smoking and genetic polymorphisms in ESCC risk are still limited， more studies are needed for better screening of the high-risk populations and the prevention.
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Esophageal squamous cell carcinoma （ESCC） is a malignant tumor caused by both environmental and genetic factors. Epidemiology studies have identified smoking as a major environmental risk factor. In recent years， the advancement of genomics research has led to the recognition of the influence of genetic variation in ESCC. We reviewed the research progress in smoking， genetic polymorphism and their interaction on susceptibility to ESCC. Reducing exposure time to tobacco was found to be the most effective way to reduce the risk. At the genetic level， mutations in DNA repair genes， regulation genes of carcinogen-metabolizing enzymes， cell cycle regulation genes， folate metabolism related genes， and alcohol metabolism related genes were found to significantly increase the risk of ESCC. However， studies on the interaction between smoking and genetic polymorphisms in ESCC risk are still limited， more studies are needed for better screening of the high-risk populations and the prevention.
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Hepatitis B virus (HBV) infection is an important global public health concern and a major cause of chronic hepatitis, cirrhosis and liver cancer. Many studies have shown that different genotypes and subtypes have significant differences in pathogenicity, thus affecting the disease progression and prognosis of infected individuals. So far, a total of 10 HBV genotypes and more than 40 subtypes have been reported across the world, and these subtypes have shown distinct distribution characteristics. In the present review, we systematically summarized the current situation on the global distribution of HBV genotypes.
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Objective To investigate whether the mannose-binding-lectin 2 (MBL2) gene was associated with type 2 diabetes in the populations living the northern part of China. Methods The study involved 318 type 2 diabetic patients and 448 normoglycemic controls. The variances of rs1800450, rs1800451 and rs11003125 were determined by the Multiplex SNaPshot method. Fasting blood-glucose, triglyceride and total cholesterol were also measured. All of these results were analyzed by logistic regression method. Linkage disequilibrium and Haplotype measures were computed in all samples using Haploview. Results There seemed no mutation on rs 1800451 while the rs 1800450 and rs11003125 polymorphism was consistent with Hardy-Weinberg expectations in both the case and the control groups. Genotypes and allele frequencies of rs1800450 as well as rs11003125 were observed (P=0.006, P=0.003) and (P=0.010, P=0.004), respectively. Data from logistic regression analysis revealed that factors as overweight, abdominal obesity, hypercholesterolemia, GG genotype frequencies of Exonl rs1800450 polymorphism as well as (GC + CC) genotype frequencies of rs11003125 polymorphism in MBL2 conferred increased risks for type 2 diabetes. Haplotype analyses of the two SNPs (rs1800450, rs11003125) revealed similar effects as compared with the single SNP associations. Only haplotype constructed from GC alleles conferred increased trends for type 2 diabetes (OR=2.21, 95％ CI: 1.47-3.33, P=0.000). Conclusion Our result suggested that the Exonl rs1800450 polymorphism and promoter region rs11003125 polymorphism in MBL2 gene were both associated with type 2 diabetes in the Chinese population living in the northern areas of China. The G allele of rs 1800450 and C allele of rs 11003125 might be the risk factors of type 2 diabetes.
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Objective To investigate whether G1155942T polymorphism in WNK4 gene is associated with essential hypertension in a population with Kazakhs ethnicity,in Xinjiang.Methods This study covered 563 hypertension patients and 346 normotensive controls.The variant of G1155942T was determined by the TaqMan probe real-time PCR method.Some biochemical indices such as glucose (GLU),triglyeeride (TG) and total cholesterol (TC) were also measured.All of these results were under logistic regression analysis.Addictive model was applied to assess the interactive effects between WNK4 gene G1155942T mutation and environmental factors on hypertension. Results The G1155942T polymorphism was consistent with Hardy-Weinberg expectations in both case and control groups.Genotype and allele frequencies of G1155942T were observed (P=0.004,P=0.003).Data through logistic regression analysis showed that factors as age,BMI,total cholesterol as well as the GT + TT genotype frequencies of Exon 8 G1155942T polymorphism in WNK4 were responsible for the increased risks for hypertension.Positive interactions between G1155942T mutation and gender,BMI,GLU,the OR were 3.75 (95% CI:1.19-11.80),5.77 (95% CI:1.93-17.21 ) and 8.67 (95% CI:1.03-72.99),respectively.Conclusion Our result suggested that the Exon 8 G1155942T polymorphism in WNK4 gene was associated with hypertension in the studied Kazakhs ethnic group in Xinjiang and the T allele might be the risk factor for essential hypertension.There were interactive effects between WNK4 gene G1155942T mutation,gender,BMI,and GLU.
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Objective To investigate the association between methylthioadenosine phosphorylase (MTAP) gene single nucleotide polymorphisms (SNP) and myocardial infarction (MI) in the Chinese Han ethnicity. Methods 432 patients suffered from myocardial infarction and 430 controls were involved for case and control groups, respectively. Nine tag SNPs in MTAP gene were selected and genotyped. Results We found no significant association of selected tag SNPs with MI in all of the samples. However, in stratified analysis, significant association was observed at rs7027989 in male subjects. The risk of MI increased by 26% (P=0.005) for male subjects of minor allele carriers in a dominant model. The increased risk of MI at rs7027989 remained significant after adjusting for confounding factors. Conclusion MTAP gene might be involved in the etiology of MI in Chinese Han ethnicity.
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<p><b>OBJECTIVE</b>To investigate whether the WNK lysine deficient protein kinase 4 (WNK4) gene C1155547T polymorphism is associated with essential hypertension (EH) in Xinjiang Kazakhs and to assess the effect of the interaction between this polymorphism and environment factors on EH.</p><p><b>METHODS</b>The study covered 556 hypertension patients and 341 normotensive controls. The C1155547T was determined by Taqman probe real-time PCR method. Some biochemical index such as glucose, triglyceride and total cholesterol were also measured. All of these results were analyzed with Logistic regression analysis. Additive model was applied to assess the effect of interaction between the WNK4 gene C1155547T polymorphism and environment factors on hypertension.</p><p><b>RESULTS</b>The C1155547T polymorphism was consistent with Hardy-Weinberg equilibrium in both the case and control groups. There was significant difference in the genotype frequencies (P=0.003). The T allele frequency was significantly higher in the patient group (P=0.002). Logistic regression analysis revealed that the age, body mass index (BMI), total cholesterol as well as the CT+TT genotype frequency conferred increased risks for EH. Positive interaction between the C1155547T polymorphism and gender, BMI, glucose was observed. The ORs were 3.85 (95%CI:1.23-12.04), 5.91 (95%CI:1.99-17.57) and 8.77 (95%CI:1.04-73.93), respectively.</p><p><b>CONCLUSION</b>The result suggested that the exon 7 C1155547T polymorphism in WNK4 gene might be associated with EH in Xinjiang Kazakhs, the T allele might be the risk factor of essential hypertension. There were interactive effects between the WNK4 gene C1155547T polymorphism and gender, BMI and glucose.</p>
الموضوعات
Adult , Female , Humans , Male , Middle Aged , Asian People , Ethnology , Genetics , China , Hypertension , Ethnology , Genetics , Point Mutation , Polymorphism, Single Nucleotide , Protein Serine-Threonine Kinases , Geneticsالملخص
Objective To analyze the risk factors that associated with survival of postoperative patients with glioma. Methods From 2000 to 2006, 522 patients were enrolled in our hospital and were analyzed related risk factors by using Kaplan-Meier' s Product-Limit Survival Estimates method, log-rank test and Cox' s proportional-hazards model. Analysis of data were performed in SAS 9.1. Results In univariate analysis, age, sex, extent of resection in surgery and pathological grades appeared to be associated with survival rate of the patients (α=0.05). Cox regression analysis showed these four factors were also significant (HR value 0.811, 1.553, 1.634 and 1.429, respectively). Multivariate Cox regression model also showed that age, pathological grades and extent of resection in surgery were main factors affecting the survival of the patients while HR value increased with the ascending class (2.349, 3.826, and 5.062, respectively)with only subtotal excision enter the model (HR=1.459). Other factors had no statistical importance on survival rate. Conclusion Age, extent of resection in surgery, pathological grades, chemotherapy after surgery, and radiotherapy after surgery might associate with the prognosis of the patients with glioma.
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Objective To investigate whether polymorphisms in CYP11B2 gene are associated with nonfamilial structural atrial fibrillation(AF) in Chinese Han population. Methods A free-designed pair-matched hospital based ease-control study was performed in 297 cases and 297 controls. We investigated two tagging single nucleotide polymorphisms (tSNPs)-rs4545, rs3802228 in CYP11B2 gene by using GenomeLab~(TM) SNPstream technique. Results Two tSNPs were consistent with Hardy-Weinberg expectations in case and control groups. Compared with controls, the left atrial diameter of cases was significantly higher(P<0.0001). No significant difference in genotype or allele frequencies of tSNPs in CYP11B2 gene was observed. However, at the site of rs3802228 in 3' UTR of the case group, the left atrial diameter in AF patients with GG genotype was significantly higher than others. After adjusted for covariates age, smoking, Body mass index and hypertension, we did not observe the association of rs4545, rs3802228 with AE Conclusion Our result suggested that polymorphisms of rs4545 in CYP11B2 gene might not be associated with atrial fibrillation but polymorphism of 3' UTR rs3802228 locus in CYP11B2 gone might be associated with atrial structural remodeling.
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<p><b>OBJECTIVE</b>To investigate the association between M235T and G-6A polymorphism of AGT gene, insertion/deletion (I/D) polymorphism of ACE gene, Gly460Trp polymorphism of ADD1 gene, C825T polymorphism of GNB3 gene and essential hypertension in Xinjiang Kazakhs group as well as to identify the interactions of gene-gene and gene-environment.</p><p><b>METHODS</b>A case-control study (n = 441) was performed in 241 cases and 202 controls. Polymerase chain reaction and restrict fragment length polymorphism (PCR-PFLP) technique were used to detect the genotypes polymorphism.</p><p><b>RESULTS</b>Comparing the frequencies of alleles and genotypes, there were no statistical significances except frequency of allele of M235T (P = 0.0483) identified. In logistic regression analysis, there were significant differences in all of the loci. The 4 loci model (AGE/CHO/G-6A/ACE) appeared the best model in MDR analysis.</p><p><b>CONCLUSION</b>Our research data showed that the polymorphisms of all the four genes might be associated with hypertension in the Kazakhs group of Xinjiang while there might be interactions existed in AGT, ACE, AGE and CHO.</p>