PCR-ligase Detection Reaction Research Articles

NOTCH4 Single-Nucleotide Polymorphism Is Associated with Brain Arteriovenous Malformation in a Chinese Han Population

Introduction: Brain arteriovenous malformations (BAVMs) are high-flow intracranial vascular malformations characterized by the direct connection of arteries to veins without an intervening capillary bed. They are one of the main causes of intracranial hemorrhage and epilepsy, although morbidity is low. Angiogenesis, heredity, inflammation, and arteriovenous malformation syndromes play important roles in BAVM formation. Animal experiments and previous studies have confirmed that NOTCH4 may be associated with BAVM development. Our study identifies a connection between NOTCH4 gene polymorphisms and BAVM in a Chinese Han population. Methods: We enrolled 150 patients with BAVMs confirmed by digital subtraction angiography (DSA) in the Department of Neurosurgery, Zhujiang Hospital, Southern Medical University from June 2017 to July 2019. Simultaneously, 150 patients without cerebrovascular disease were confirmed by computed tomography angiography/magnetic resonance angiography/DSA. DNA was extracted from peripheral blood and NOTCH4 genotypes were identified by PCR-ligase detection reaction. The χ² test or Fisher’s exact test was used to evaluate the differences in allele and genotype frequencies between the BAVM group, control group, bleeding group, and other complications. Results: Two single-nucleotide polymorphisms (SNPs), rs443198 and rs438475, were significantly associated with BAVM. No SNP genotypes were significantly associated with hemorrhage or epilepsy. SNPs rs443198_AA-SNP and rs438475_AA-SNP may be associated with a lower risk of BAVM (p = 0.011, odds ratio (OR) = 0.459, 95% confidence interval (CI): 0.250–0.845; p = 0.033, OR = 0.759, 95% CI: 0.479–1.204). Conclusion: NOTCH4 gene polymorphisms were associated with BAVM and may be a risk factor in a Chinese Han population.

Association between Dietary Zinc and Selenium Intake, Oxidative Stress-Related Gene Polymorphism, and Colorectal Cancer Risk in Chinese Population - A Case-Control Study

Zinc and selenium may protect against colorectal cancer (CRC) progression through their anti-oxidative effects. This study examined the independent and combined effect of dietary zinc and selenium intake, and polymorphisms of the oxidative stress-related genes (superoxide dismutase 1, superoxide dismutase 2, glutathione peroxidase, and catalase) on CRC risk in a Chinese case-control study. A total of 493 cases and 498 sex and age-matched controls were randomly selected from an ongoing case-control study. Dietary information was assessed through face-to-face interviews using a validated food frequency questionnaire. Multiplex PCR-ligase detection reaction was used for genotyping the target SNPs. Multivariable logistic regression was used to estimate the odds ratios (ORs) and 95% confidence interval (CI). Intake of selenium was found to be inversely associated with CRC risk, while zinc was not associated with CRC risk. The ORs (95% CI) for the highest vs. the lowest quartile were 0.42 (95% CI 0.28, 0.64, P trend < 0.001) for selenium and 0.96 (95% CI 0.63, 1.47, P trend = 0.505) for zinc. Combined effect was observed between zinc and SOD1 rs4998557 on CRC risk (P interaction < 0.05). This study identified a novel diet-gene interaction in the oxidative stress pathway on CRC risk in Chinese population.

Assessment of PPARGC1A, PPARGC1B, and PON1 Genetic Polymorphisms in Esophageal Squamous Cell Carcinoma Susceptibility in the Eastern Chinese Han Population: A Case–Control Study Involving 2351 Subjects

Previous studies suggested that alterations in the energy metabolism might be underlying cancer initiation and progression. Polymorphisms of genes involved in energy metabolism regulation, such as peroxisome proliferator-activated receptor gamma coactivator 1α (PPARGC1A), -β (PPARGC1B), and paraoxonase 1 (PON1), might confer susceptibility to esophageal squamous cell carcinoma (ESCC) and partially explain its pathogenesis. We investigated the effects of several single nucleotide polymorphisms (SNPs) in three metabolic-related genes (e.g., PPARGC1A, PPARGC1B, and PON1) on ESCC susceptibility. In total, 829 patients with sporadic ESCC and 1522 nontumor controls were enrolled in the study. SNPs were genotyped using PCR-ligase detection reaction. Our study revealed that the PPARGC1A rs3736265 G/A SNP significantly increased the risk for ESCC (GA vs. GG: adjusted odds ratio [OR] = 1.25, 95% confidence interval [95% CI] = 1.02-1.54, p = 0.034; GA+AA vs. GG: adjusted OR = 1.25, 95% CI = 1.03-1.52, p = 0.027]. In addition, a stratified analysis revealed that the PPARGC1A rs3736265 SNP was correlated with the development of ESCC in male and nondrinking subgroups. We also confirmed that the PPARGC1B rs17572019 G/A SNP promoted the risk of ESCC in subgroup with high alcohol intake. The PPARGC1A rs8192678 C/T polymorphism decreased the susceptibility of ESCC in men. These findings highlight that polymorphisms in PPARGC1A and PPARGC1B may contribute to ESCC susceptibility. In the future, further well-designed epidemiological studies are needed to confirm our findings.

Application of Multiplex Bisulfite PCR–Ligase Detection Reaction–Real-Time Quantitative PCR Assay in Interrogating Bioinformatically Identified, Blood-Based Methylation Markers for Colorectal Cancer

The analysis of CpG methylation in circulating tumor DNA fragments has emerged as a promising approach for the noninvasive early detection of solid tumors, including colorectal cancer (CRC). The most commonly employed assay involves bisulfite conversion of circulating tumor DNA, followed by targeted PCR, then real-time quantitative PCR (alias methylation-specific PCR). This report demonstrates the ability of a multiplex bisulfite PCR-ligase detection reaction-real-time quantitative PCR assay to detect seven methylated CpG markers (CRC or colon specific), in both simulated (approximately 30 copies of fragmented CRC cell line DNA mixed with approximately 3000 copies of fragmented peripheral blood DNA) and CRC patient-derived cell-free DNAs. This scalable assay is designed for multiplexing and incorporates steps for improved sensitivity and specificity, including the enrichment of methylated CpG fragments, ligase detection reaction, the incorporation of ribose bases in primers, and use of uracil DNA glycosylase. Six of the seven CpG markers (located in promoter regions of PPP1R16B, KCNA3, CLIP4, GDF6, SEPT9, and GSG1L) were identified through integrated analyses of genome-wide methylation data sets for 31 different types of cancer. These markers were mapped to CpG sites at the promoter region of VIM; VIM and SEPT9 are established epigenetic markers of CRC. Additional bioinformatics analyses show that the methylation at these CpG sites negatively correlates with the transcription of their corresponding genes.

Association between ADAMTS7 TagSNPs and the risk of myocardial infarction

Purpose of the studyGenome-wide association studies have revealed an association of ADAMTS7 polymorphisms with the risk of cardiovascular diseases. Nonetheless, the role of ADAMTS7 polymorphisms on myocardial infarction (MI) risk...

Associations for BCO2, PCSK9, and TR1B1 Polymorphism and Lifestyle Factors with Ischemic Stroke: A Nested Case-Control Study.

PurposeTo investigate associations for polymorphisms in β-carotene 9′,10′-oxygenase (BCO2, rs10431036 and rs11214109), proprotein convertase subtilisin kexin type 9 (PCSK9, rs11583680), and tribbles pseudokinase 1 (TRIB1, rs17321515 and rs2954029), as well as lifestyle factors, with ischemic stroke (IS).Materials and MethodsThis nested case-control study included 161 patients with IS and 483 matched control individuals. We collected medical reports, lifestyle details, and blood samples from individuals and used the PCR-ligase detection reaction method to genotype single nucleotide polymorphisms (SNPs).ResultsThe GA+AA genotype of rs10431036 (p<0.001) and rs17321515 (p=0.003), the CT+TT genotype of rs11214109 (p=0.005), and the TA+AA genotype of rs2954029 (p=0.006) in dominant models increased the risk of IS. In additive models, the GG genotype of rs17321515 (p=0.005) and the TT genotype of rs2954029 (p=0.008) increased the risk of IS. Adequate intake of fruits/vegetables reduced the risk of IS (p=0.005). Although there was no interaction between genes and fruits/vegetables, people with inadequate intake of fruits/vegetables who carried a risk genotype had a higher risk of IS than those only having inadequate fruits/vegetables intake or those only carrying a risk genotype. Also, the haplotypes AC, AT, and GT (comprising rs10431036 and rs11214109) and GT (comprising rs2954029 and rs17321515) were found to be associated with an increased risk of IS (p<0.05).ConclusionPolymorphisms in BCO2 and TRIB1 and fruits/vegetables intake were associated with IS. These results provide the theoretical basis for gene screening to prevent chronic cerebrovascular diseases.

The Association Between Vitamin D Binding Protein Polymorphisms and Vitamin D Level on Epilepsy in China.

Accumulating studies suggest the potential association between epilepsy and vitamin D (VD) in recent years. Vitamin D binding protein (VDBP) is the main VD carrier and can affect the availability of VD and its metabolites. Thus, this study aimed to investigate the association between VDBP polymorphisms and VD level on epilepsy. A total of 220 epilepsy patients and 210 health controls were enrolled and polymorphisms of VDBP (rs4588, rs7041, rs2298849, and rs2282679) genotype were detected using the PCR-ligase detection reaction method. The circulating status of VD metabolites, 25(OH)D and 24,25(OH)2D, was detected by a validated high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method, and the VD metabolite ratio (VMR), 24,25(OH)2D:25(OH)D, was then calculated. The frequency of rs4588(C>A) and rs2282679(A>C) genotype with AC was significantly lower among the patients relative to the controls [odds ratio, OR = 0.597, 95% confidence interval, CI = 0.401-0.890, p = 0.011 for rs4588(C>A); OR = 0.611, 95% CI = 0.409-0.912, p = 0.016 for rs2282679(A>C), respectively]. For rs7041 genotype distribution, VMR level was significantly higher in patients with GG genotype than in those carrying TT and TG genotype (p = 0.008). Our study demonstrated that the polymorphisms of VDBP rs4588 and rs2282679 may play a potentially important role in epilepsy susceptibility in Chinese Han population.

Associations of human leukocyte antigen and interleukin-18 gene polymorphisms with viral load in patients with hepatitis B infection.

This study aimed to assess the associations of human leukocyte antigen (HLA)-DR and interleukin (IL)-18 gene polymorphisms with hepatitis B virus (HBV).Clinical data were retrospectively reviewed between December 2006 and December 2015 at Xiangyang Central Hospital. HBV patients were assigned to the high and low viral load groups, respectively, according to HBV copies. HLA-DRB1∗03 polymorphisms and IL-18 polymorphisms were detected by sequence-specific primer-polymerase chain reaction (PCR-SSP) and PCR-ligase detection reaction (PCR-LDR), respectively. T cell subgroups were identified by flow cytometry, and IL-18, IL-12, interferon-γ (IFN-γ), IL-4, and IL-10 expression levels were assessed by ELISA. A total of 630 subjects were included in the analysis.Compared with healthy controls, the chronic HBV group showed significantly lower IL-18 (P < .001), IL-12 (P < .001), and IFN-γ (P < .001) expression levels, and markedly increased IL-4 (P < .001) and IL-10 (P < .001) amounts. Th2 cytokine expression was high in HLA-DRB1∗03 positive (+) HBV patients, with low Th1 cytokine levels. The ratios of CD4+/CD8+ and Th1/Th2 cells decreased with increasing HBV DNA levels. The chronic HBV group showed a relatively high frequency of -137G in the IL-18 gene, while IL-18 expression was low in homozygous GG genotype individuals.Polymorphisms in the HLA-DRB1∗03 and IL-18 genes are associated with viral load in HBV. HLA-DRB1 and IL-18 gene polymorphisms are involved in the regulation of the Th1/Th2 balance and expression of relevant cytokines that influence immune responses in HBV.

Polymorphisms of IKZF3 Gene and Autoimmune Thyroid Diseases: Associated with Graves’ Disease but Not with Hashimoto’s Thyroiditis

Background/Aims: The IKZF3 gene encodes a zinc-finger protein that plays an important role in the proliferation and differentiation of B lymphocytes. Autoimmune thyroid diseases (AITDs), mainly include Graves’ disease (GD) and Hashimoto’s thyroiditis (HT), are probably caused by the aberrant proliferation of B cells. The objective of this study was to explore the association between IKZF3 polymorphisms and AITDs. Methods: We examined 915 AITD patients (604 GD and 311 HT) and 814 healthy controls. IKZF3 variants (rs2941522, rs907091, rs1453559, rs12150079 and rs2872507) were tested by PCR-ligase detection reaction. Results: It was manifested that that the minor alleles of the five loci increased susceptibility to GD (p<0.05 for rs2941522, and p<0.01 for rs907091, rs1453559, rs12150079 and rs2872507) but in HT patients, these loci showed no significant difference compared with controls. Similarly, the genotype distributions of GD patients manifested obvious differences in all these loci compared with the control group, whereas no statistical differences were observed between HT patients and controls. Furthermore, bioinformatics tools were used to analyze rs1453559, rs12150079 and rs907091. These variants were believed to be the transcription regulator. Conclusion: It is the first time we reported the association between the IKZF3 polymorphisms and GD, indicating that IKZF3 gene tends to bean important risk factor for the development of GD.

Correlation of Gemin 3 SNP in the microRNA Biosynthesis Pathway with Risk and Prognosis of Patients with Non-Hodgkin's Lymphoma

To evaluate the correlation of single nucleotide polymorphisms (SNP) of Gemin 3(rs197412) in the miRNA biosynthesis with NHL cancer risk and overall prognosis. miR-SNP were genotyped using PCR-ligase detection reaction(LAR, LCR) in NHL group of 230 non-Hodgkin lymphoma (NHL) patients and in control group of 120 healthy persons. The survival curves were drawn using the Kaplan-Meier method, and comparisons between the curves were made using the log-rank test. Multivariate survival analysis was performed by using a Cox proportional hazards model. The rs197412 genotype distribution difference was not statistically significant, in NHL and control group; the survival time of patients carrying the rs197412 TT genotype was significantly longer than that of the patients carrying the CC+CT genotype (P=0.007). In addition, rs197412 was independent from the survival of NHL patients by multivariate analysis (RR: 2.138,95% CI: 1.303-3.508, P<0.01). The single nucleotide polymorphisms of Gemin 3 (rs197412) in the miRNA processing are not related with NHL risk, but that may affect NHL survival.

A novel system for forensic SNP analysis through PCR–ligase detection reaction

With the advantages of lower mutation rates and improved analysis of the degraded or aged samples, single nucleotide polymorphism (SNP) markers has been considered as supplementary to the STRs. Consequently, a robust, simple and cost effective technique for SNP typing is essential to analyze a large number of SNPs. Ligase detection reaction (LDR) could detect a SNP on CE platform through the ability of DNA ligase which can seal the nick junction formed by oligonucleotides hybridized to the flank region of target SNP. Here we purposed a prestudy to set up a 8 Y-SNPs (M9, M74, M35, M95, M110, M89, M13, M20) multiplex panel for forensic application through PCR–ligase detection reaction (LDR) system. Primers of 8 loci were designed for multiplexed PCR. According to the sequence around the SNP site, three LDR probes were designed for each SNP including one common fluorescent labeled probe and two allele specific probes different in size with mismatching bases at the 3’ end. PCR–LDR products were profiled through ABI3130 Genetic Analyzer. A set of 8 Y-SNP could be profiled through two multiplexed PCR and two multiplexed LDR. Even though the number of markers in the current system is limited, when fully developed, it can easily be multiplied more SNPs and yield a greater power of discrimination. Our study indicated that the PCR-LDR could provide a robust, simple and cost effective multiplexed SNP typing method for forensic cases in the future.

Study of Five Pubertal Transition-Related Gene Polymorphisms as Risk Factors for Premature Coronary Artery Disease in a Chinese Han Population.

BackgroundRecently, single nucleotide polymorphisms (SNPs) (DLK-rs10144321, SIX6-rs1254337, MKRN3-rs12148769, LIN28B-rs7759938, and KCNK9-rs1469039) were found to be strongly associated with age at menarche. Recent studies also suggested that age at menarche is a heritable trait and is associated with risks for obesity, type 2 diabetes mellitus (T2DM), cardiovascular disease, and all-cause mortality. Since an association between these five SNPs and premature coronary artery disease (CAD) has never been reported, we investigated whether these SNPs are associated with premature CAD and its severity in a Chinese Han population.MethodsWe enrolled 432 consecutive patients including 198 with premature CAD (<55 years in men and <65 years in women) and 234 controls. All subjects were genotyped for the five SNPs by the PCR-ligase detection reaction method. The associations between these SNPs and premature CAD and its severity were analyzed.ResultsThe following genotypes were identified: GG, AG, and AA at rs10144321 and rs12148769; TT, AT, and AA at rs1254337; CC, CT, and TT at rs1469039; and TT and CT at rs7759938. Significant differences in genotype distribution frequencies at rs1254337 were found between controls and patients with premature CAD (P<0.05). No associations were found between the five SNPs and the severity of coronary lesions (all P>0.05). Compared with controls, patients with premature CAD had a higher prevalence of T2DM and dyslipidemia, and the proportion of patients with T2DM rose significantly with an increase in the number of stenosed coronary vessels (all P<0.05). After adjustment for the clinical parameters in multivariable analysis, three factors were identified that significantly increased the risk of premature CAD: the AA genotype at rs1254337 (OR: 2.388, 95% CI: 1.190–4.792, P = 0.014), male gender (OR: 1.565, 95% CI: 1.012–2.420, P = 0.044), and T2DM (OR 2.252, 95% CI: 1.233–4.348, P = 0.015).ConclusionsAmong the five pubertal transition-related gene polymorphisms, we identified an association between rs1254337 and premature CAD in a Chinese Han population.

Temporal changes in Plasmodium falciparum anti-malarial drug sensitivity in vitro and resistance-associated genetic mutations in isolates from Papua New Guinea

BackgroundIn northern Papua New Guinea (PNG), most Plasmodium falciparum isolates proved resistant to chloroquine (CQ) in vitro between 2005 and 2007, and there was near-fixation of pfcrt K76T, pfdhfr C59R/S108N and pfmdr1 N86Y. To determine whether the subsequent introduction of artemisinin combination therapy (ACT) and reduced CQ-sulphadoxine-pyrimethamine pressure had attenuated parasite drug susceptibility and resistance-associated mutations, these parameters were re-assessed between 2011 and 2013.MethodsA validated fluorescence-based assay was used to assess growth inhibition of 52 P. falciparum isolates from children in a clinical trial in Madang Province. Responses to CQ, lumefantrine, piperaquine, naphthoquine, pyronaridine, artesunate, dihydroartemisinin, artemether were assessed. Molecular resistance markers were detected using a multiplex PCR ligase detection reaction fluorescent microsphere assay.ResultsCQ resistance (in vitro concentration required for 50% parasite growth inhibition (IC50) >100 nM) was present in 19% of isolates. All piperaquine and naphthoquine IC50s were <100 nM and those for lumefantrine, pyronaridine and the artemisinin derivatives were in low nM ranges. Factor analysis of IC50s showed three groupings (lumefantrine; CQ, piperaquine, naphthoquine; pyronaridine, dihydroartemisinin, artemether, artesunate). Most isolates (96%) were monoclonal pfcrt K76T (SVMNT) mutants and most (86%) contained pfmdr1 N86Y (YYSND). No wild-type pfdhfr was found but most isolates contained wild-type (SAKAA) pfdhps. Compared with 2005–2007, the geometric mean (95% CI) CQ IC50 was lower (87 (71–107) vs 167 (141–197) nM) and there had been no change in the prevalence of pfcrt K76T or pfmdr1 mutations. There were fewer isolates of the pfdhps (SAKAA) wild-type (60 vs 100%) and pfdhfr mutations persisted.ConclusionsReflecting less drug pressure, in vitro CQ sensitivity appears to be improving in Madang Province despite continued near-fixation of pfcrt K76T and pfmdr1 mutations. Temporal changes in IC50s for other anti-malarial drugs were inconsistent but susceptibility was preserved. Retention or increases in pfdhfr and pfdhps mutations reflect continued use of sulphadoxine-pyrimethamine in the study area including through paediatric intermittent preventive treatment. The susceptibility of local isolates to lumefantrine may be unrelated to those of other ACT partner drugs.Trial registrationAustralian New Zealand Clinical Trials Registry ACTRN12610000913077.

Association of MEF2A gene 3'UTR mutations with coronary artery disease.

Association of variants in the myocyte enhancer factor 2A (MEF2A) gene and the risk of coronary artery disease (CAD) has drawn much attention but remains controversial. We hypothesized that the 3'-untranslated region (3'-UTR) of this gene could harbor functionally relevant nucleotide changes. Here, we assessed the association between single nucleotide polymorphisms (SNPs) in the 3'-UTR of MEF2A and CAD in the Chinese Han population. A case-control study of 236 CAD patients and 278 controls was carried out. The four target SNPs were genotyped using a multiplex PCR-ligase detection reaction method. Logistic regression under three genetic models was used to analyze the association between target SNPs and the risk of CAD. Associations were detected between two SNPs (rs325380, rs897074) and CAD; however, after Bonferroni's correction, these associations were not deemed significant. A further haplotype study indicated that a 'TA' haplotype carrier of rs325380-rs325381 was associated with CAD risk. Our study thus indicates that variants in the 3'-UTR of MEF2A are associated with CAD in a Chinese Han population.

Correlation between IGF2BP2 gene polymorphism and the risk of breast cancer in Chinese Han women

ObjectiveTo investigate the correlations between the polymorphism of IGF2BP2, a diabetes predisposing gene, and breast cancer risk in Chinese female with Han nationality. MethodThe genomic DNAs were extracted from the peripheral blood drawn from 564 female breast cancer patients and 394 healthy females of Han nationality. The polymorphism of IGF2BP2 gene rs4402960 was detected by a multiplex PCR-Ligase detection reaction (PCR-LDR) assay from genomic DNA. The correlations between genotype and breast cancer risk as well as clinicopathologic characteristics were compared. ResultsThe differences are significant between genotype distribution of IGF2BP2 gene rs4402960 (P=0.009) and allele gene frequency from both disease and control groups. Both T gene carriers (GT+TT) (OR=1.462; 95% CI, 1.127–1.897) and T allele gene (OR=1.382; 95% CI, 1.116–1.710) significantly increase the risk of breast cancer. No considerable correlations were observed between the polymorphism of rs4402960 and the clinical pathological parameters, such as age at diagnosis, lymphatic metastasis, estrogen and progesterone receptor status, cerb-B2 receptor status, and tumor staging. ConclusionsThe IGF2BP2 gene rs4402960 polymorphism increases the breast cancer risk of Chinese females with Han nationality, and is a breast cancer predisposing gene.

Association of polymorphisms in AGTR1 and AGTR2 genes with primary aldosteronism in the Chinese Han population.

Polymorphisms in angiotensin II type-1/2 receptor genes (AGTR1/AGTR2) may be involved in the pathogenesis of primary aldosteronism. The present study aims to reveal some loci susceptible to the disease on the genes in a group of Chinese Han nationality. A case-control study was conducted in 202 patients and 188 controls. Ten tagging SNPs on AGTR1/AGTR2 were genotyped for all subjects via the method of multiplex PCR-ligase detection reaction. Statistical analysis was performed with chi-square test and logistic regression analysis. rs3772616 on the AGTR1 gene was a factor for susceptibility to primary aldosteronism (p<0.001), and the TT genotype significantly decreased the risk of primary aldosteronism compared with the CC homozygote (p=0.008, adjusted OR=0.13; 95%CI: 0.03-0.59). The rs3772616 polymorphism was associated with primary aldosteronism under the additive and dominant models. The female carriers of the G allele in rs5193 showed a significant difference compared with the T allele. The AGTR1 rs3772616 polymorphism can be considered as a hereditary marker for primary aldosteronism, and in the Chinese Han population the rs5193 G allele seems to predispose to it only in women.

Genetic variants of the matrix metalloproteinase family genes and risk for hypertension: a case-control study among northeastern Han Chinese.

In this study, we sought to examine the association between 10 genetic variants in the matrix metalloproteinase (MMP) family genes and the risk of hypertension among northeastern Han Chinese. This was a hospital-based case-control study involving 1009 sporadic hypertensive patients and 756 age-, gender- and ethnicity-matched normotensive controls. The genotypes of the 10 examined variants were determined by PCR-ligase detection reaction method. The genotype/allele distributions of rs3025058 and rs679620 differed significantly between patients and controls, with a Bonferroni corrected α of 0.05/10. The probability of having hypertension was significant for rs3025058 under the additive (odds ratio; 95% confidence interval; P: 1.33; 1.16-1.53; <0.001) and dominant (1.43; 1.18-1.73; <0.001) models and was significant for rs679620 under the additive (1.27; 1.1-1.46; <0.001) model after adjusting for confounders. In a combined analysis, when compared with the reference group (score<3.5 for unfavorable genotypes), participants in the medium- and high-risk groups had odds ratios that increased to 1.61 (95% CI: 1.25-2.51; P<0.001) and 1.92 (95% CI: 1.54-2.39; P<0.001) after adjustment, respectively. Interaction analysis showed that a three-locus model including rs3025058, rs679620 and rs243865 was the best, with a maximum testing accuracy of 0.6605 and a cross-validation consistency of 10 (P=0.0022). Taken together, our findings suggest that the true association between individual variants and the risk of hypertension may not be revealed until combined analyses of multiple variants from genes involving a specific physiological or cellular function are performed. Moreover, we propose a three-locus model that can best characterize the genetic interactions of the MMP multiple gene family.

Association of the rs11196218 polymorphism in TCF7L2 with type 2 diabetes mellitus in Asian population

ObjectiveTo clarify the association of rs11196218 polymorphism in transcription factor 7-like 2 (TCF7L2) and type 2 diabetes mellitus (T2DM) in Asian population by a case–control study and meta-analysis. MethodsIn the case–control study, 1842 patients with T2DM and 7777 normal glucose-tolerant controls in the Henan province of China were genotyped for rs11196218 in TCF7L2 by PCR–ligase detection reaction. We used allele, co-dominant, dominant and recessive models to evaluate the risk association and performed a meta-analysis of the results of different genetic models in previous studies and the current study. ResultsThe AG genotype of rs11196218 was associated with risk of T2DM in the Henan population (odds ratio 1.37, 95% confidence interval 1.06–1.78), and dominant model showed marginal significant association (1.28, 0.99–1.67). Meta-analysis of 10 studies revealed the dominant model associated with T2DM in the overall population (1.20, 1.05–1.36). When stratified by region (southern and northern China and Japan), both the AG genotype and the dominant model were associated with risk of T2DM in southern Chinese (1.31, 1.03–1.66; 1.27, 1.01–1.60, respectively). ConclusionThe rs11196218 polymorphism in TCF7L2 is associated with risk of T2DM in Asian population.

A variant (rs932335) in the HSD11B1 gene is associated with colorectal cancer in a Chinese population

Glucocorticoid hormones have been reported to contribute to the regulation of cellular proliferation and differentiation and to inhibit the growth of cells in several colon tumors and adenocarcinoma cell lines. As a regulator of glucocorticoid levels, type I isoform HSD11B1 is a bidirectional enzyme but acts predominantly as an oxidoreductase to yield active glucocorticoids, cortisol or corticosterone. To date, studies investigating the associations between the polymorphisms of HSD11B1 and the risk for cancer have shown inconclusive results. In our study, we aimed to investigate whether the polymorphisms of HSD11B1 may influence the genetic susceptibility to colorectal cancer (CRC) in a Chinese population. Four single-nucleotide polymorphisms of HSD11B1 (rs846910 G/A, rs11807619 G/T, rs932335 C/G, and rs13306421 G/A) were detected using a PCR-ligase detection reaction in a case-control study comprising 110 CRC patients and 118 controls. Logistic regression was used to evaluate genetic associations with the occurrence of CRC. Real-time PCR was used to test the mRNA expression of HSD11B1 in 18 CRC tissues. The frequencies of the rs932335 GC genotype were significantly higher among the patients compared with controls (P=0.019). Compared with individuals carrying the GG genotype, individuals with the GC/CC genotype had a significantly increased susceptibility to CRC occurrence (odds ratio=2.23, 95% confidence interval=1.27-3.94, P=0.008). In cancer tissues, patients carrying the GG genotype also displayed an increased mRNA level of HSD11B1 (P=0.019). These results suggested that the HSD11B1 rs932335 G/C polymorphism had an effect on CRC occurrence. These findings also suggest that the functional polymorphism rs932335 in intron4 of HSD11B1 may influence the susceptibility to and progression of CRC in a Chinese population. Large population-based prospective studies are required to validate our findings.

No association of SORT1 gene polymorphism with sporadic Alzheimer’s disease in the Chinese Han population

Increasing evidence shows that sortilin (encoded by SORT1 gene), a member of the vacuolar protein sorting 10 family of sorting receptors, can modulate amyloid-β peptides (Aβ) metabolism and clearance, as well as mediate the neurotoxicity of the Aβ oligomer and proneurotrophins, thus playing diverse roles in the pathogenesis of Alzheimer's disease. To assess the association between single nucleotide polymorphism (SNP) of the SORT1 gene and sporadic Alzheimer's disease (sAD) in the Chinese Han population, a case-control study was carried out including 220 sAD patients and 245 controls. One tag SNP was selected from the entire SORT1 gene through construction of linkage disequilibrium blocks, and three SNPs located in the vicinity of SORT1 that affect its expression were also selected. The four target SNPs were genotyped using a multiplex PCR-ligase detection reaction method, yielding no significant association between them or haplotypes containing three of them, and the risk of sAD. The results of this study indicate that polymorphisms of the SORT1 gene are unlikely to confer the risk of sAD in the Chinese Han population.