Association of SELE genotypes/haplotypes with sE-selectin levels in Taiwanese individuals: interactive effect of MMP9 level.

BACKGROUND: E-selectin is implicated in various inflammatory processes and related disorders. We aimed to investigate the role of SELE-gene genotypes/haplotypes on plasma levels of MMP9 and sE-selectin in Taiwanese individuals. METHODS: Five hundred twenty individuals were enrolled. Seven tagging SELE single nucleotide polymorphisms were analyzed. RESULTS: SELE genotypes were found associated with MMP9 and sE-selectin levels. Multivariate analysis identified that the most significant genetic polymorphism (rs5368 genotype) was independently associated with MMP9 levels (P < 0.001). One haplotype (GGAGAGT) was marginally associated with MMP9 levels (P = 0.0490). One SELE SNP, (rs3917406, P = 0.031) was associated with sE-selectin levels after adjusting for MMP9 and sICAM1 levels. Subgroup and interaction analysis revealed association of SELE SNP rs10800469 with sE-selectin levels only in the highest quartile of MMP9 level (P = 0.002, interaction P = 0.023). Haplotype analysis showed one haplotype (AAAAAGC) borderline associated with sE-selectin level (P = 0.0511). CONCLUSION: SELE genotypes/haplotypes are independently associated with MMP9 and E-selectin levels in Taiwanese individuals. The associations of SELE genotypes/haplotypes with sE-selectin levels are affected by MMP9 levels.

A base-calling algorithm for Tm-shifted melting curve SNP assay.

BACKGROUND: Tm-shifted melting curve SNP assays are a class of homogeneous, low-cost genotyping assays. Alleles manifest themselves as signal peaks in the neighbourhood of theoretical allele-specific melting temperatures. Base calling for these assays has mostly relied on unsupervised algorithm or human visual inspection to date. However, a practical clinical test needs to handle one or few individual samples at a time. This could pose a challenge for unsupervised algorithms which usually require a large number of samples to define alleles-representing signal clusters on the fly. METHODS: We presented a supervised base-calling algorithm and software for Tm-shifted melting curve SNP assays. The algorithm comprises a peak detection procedure and an ordinal regression model. The peak detection procedure is required for building models as well as handling new samples. Ordinal regression is proposed because signal intensities of alleles AA, AB, and BB usually follow an ordinal pattern with the heterozygous allele lie between two distinct homozygous alleles. Coefficients of the ordinal regression model are first trained and then used for base calling. RESULTS: A dataset of 12 SNPs of 44 unrelated persons was used for a demonstration purpose. The call rate is 99.6%. Among the base calls, 99.1% are identical to those made by the sequencing method. A small fraction of the melting curve signals (0.4%) is declared as "no call" for further human inspection. A software was implemented using the Java language, providing a graphical user interface for the visualization and handling of multiple melting curve signals. CONCLUSIONS: Tm-shifted melting curve SNP assays, together with the proposed base calling algorithm and software, provide a practical solution for genetic tests on a clinical setting. The software is available in http://www.bioinformatics.org/mcsnp/wiki/Main/HomePage.

Effect of obesity on the association between common variations in the HNF1A gene region and C-reactive protein level in Taiwanese.

BACKGROUND: The level of C-reactive protein (CRP), an inflammatory biomarker that predicts future cardiovascular events, is a heritable trait that has been associated with variants of CRP and hepatic nuclear factor-1α (HNF1A) genes. Our aim was to test the statistical association between HNF1A genotypes/haplotypes and serum CRP level in Taiwanese. METHODS: A sample population of 617 Taiwanese subjects (all Han-Chinese origin) was enrolled. Five HNF1A single nucleotide polymorphisms (SNPs) rs1920792, rs1169288, rs7310409, rs2464196, rs1169310 were genotyped and analyzed. RESULTS: After adjusting for clinical covariates, minor alleles of all the 5 study SNPs were associated with decreased CRP level (P=0.0078, P=0.0107, P=0.0006, P=0.0004 and P=0.0003, respectively). A common haplotype (TGATA) tagged by the minor alleles of study SNPs was associated with significantly decreased CRP level (P=0.0112). Subgroup analysis revealed that the association between HNF1A genotypes and CRP level occurred only in non-obese subjects. CONCLUSIONS: HNF1A polymorphisms are independently associated with CRP level in Taiwanese. Further, HNF1A genotypes interact with obesity to set CRP level, revealing that genetic determinants for CRP level may be different between obese and non-obese individuals.

Association between functional variants of the ICAM1 and CRP genes and metabolic syndrome in Taiwanese subjects.

Although inflammation has been shown to play an important role in metabolic syndrome (MetS), the association between inflammatory marker gene polymorphisms and the risk of MetS has not been fully elucidated. This study was initiated to investigate the association between functional variants of inflammatory marker genes and the risk of MetS in Taiwanese adults. The sample population comprised 615 unrelated subjects, of which 22% had MetS. The single nucleotide polymorphisms rs5491 on the intercellular adhesive molecule 1 (ICAM1) gene and rs3091244 on C-reactive protein (CRP) were genotyped. The ICAM1 rs5491 polymorphism was significantly associated with the level of soluble intercellular adhesive molecule 1 (P < .001). Both the ICAM1 rs5491 and the CRP rs3091244 were shown to have significant association with MetS after adjustment for age, sex, smoking, and body mass index, but not after adjustment for levels of the respective serum marker. Independent associations between the combined ICAM1-CRP (rs5491 and rs3091244) genotypes and MetS were found by multivariate analysis (P = .005). In subgroup analysis, association of combined genotypes with insulin resistance and MetS mainly occurred in subjects with central obesity. In conclusion, inflammatory marker gene polymorphisms play an important role in modulating the risk of insulin resistance and MetS for subjects with central obesity. These findings will contribute toward a better understanding of the mechanism of association between inflammatory markers and the risk of developing atherosclerotic disease.

Association between an ASIC3 gene variant and insulin resistance in Taiwanese.

BACKGROUND: Acid-sensing ion channel 3 (ASIC3) is a ligand-gated cation channel activated by extracellular protons. ASIC3(-/-) mice exhibit protection against age-dependent glucose intolerance with enhanced insulin sensitivity. METHODS: To determine the association between ASIC3 genetic polymorphisms and insulin resistance in Taiwanese, 606 unrelated subjects with no history of cardiovascular disease were recruited during routine health examinations. RESULTS: Six ASIC3 gene polymorphisms were genotyped and only the rs2288646 polymorphism was found associated with insulin resistance. Significantly lower fasting serum insulin levels and homeostasis model assessment of insulin resistance (HOMA-IR) index and significantly higher quantitative insulin sensitivity check index (QUICKI) were observed in subjects carrying the rs2288646-A allele than in the non-carriers (P=0.028, P=0.047 and P=0.031, respectively) after adjustment for age, gender, and body mass index (BMI). Significantly lower frequencies of the rs2288646-A-containing genotypes were found in insulin resistant subjects (P=0.023). By multivariate analysis, rs2288646 genotypes, age, BMI, fasting plasma glucose level, C-reactive protein level, and soluble intercellular adhesive molecule 1 level, were all independently associated with HOMA-IR index and QUICKI (all, P<0.05). CONCLUSIONS: Our analysis indicated an independent association between an ASIC3 genetic polymorphism and insulin resistance in Taiwanese.

Association of matrix metalloproteinase 9 genotypes and cardiovascular disease risk factors with serum matrix metalloproteinase 9 concentrations in Taiwanese individuals.

BACKGROUND: Circulating concentrations of matrix metalloproteinase 9 (MMP-9) are associated with cardiovascular disease mortality in patients with coronary artery disease. We investigated the determinants of MMP-9 concentrations by analyzing MMP-9 genotypes and risk factors for cardiovascular disease. METHODS: A total of 596 individuals were recruited for this study. Six single nucleotide polymorphisms (SNP) with coverage of the MMP-9 gene region were analyzed; and two genotypes, rs3918242-TT and rs2274756-AA, which were in nearly complete linkage disequilibrium, were associated with higher MMP-9 values (p=0.007 and p=0.008, respectively). In age- and gender-adjusted regression models, MMP-9 concentrations were positively associated with the homeostasis model assessment of insulin resistance (HOMA-IR) index and triglyceride concentrations, fasting serum insulin, fasting plasma glucose, C-reactive protein, fibrinogen, and serum amyloid A. By multivariate analysis, rs2274756 genotypes, age, smoking status, fibrinogen and fasting plasma glucose concentrations were all independently associated with MMP-9 (p=0.007, p=0.033, p=0.003, p=0.013, and p=0.012, respectively). CONCLUSIONS: The rs2274756-AA and rs3918242-TT genotypes, younger age, current smoking status and increased fasting plasma glucose, and fibrinogen concentrations were independently associated with high serum MMP-9 concentrations in Taiwanese individuals.

Association between C-reactive protein gene haplotypes and C-reactive protein levels in Taiwanese: interaction with obesity.

OBJECTIVE: The level of C-reactive protein (CRP), an inflammatory marker that predicts future cardiovascular events, is a heritable trait. Our aim was to test the statistical associations between variations in the CRP gene and serum CRP levels in a Taiwanese population with interaction analysis. METHODS: A sample population of 617 Taiwanese subjects was enrolled. Five CRP single nucleotide polymorphisms (SNPs) previously reported to be associated with CRP level and with reasonable coverage of the CRP gene region were analyzed using polymerase chain reaction and restriction enzyme digestion or by TaqMan SNP Genotyping Assays. RESULTS: After adjusting for clinical covariates, minor alleles of 3 of the 5 SNPs were associated with change in CRP level: rs3091244 and rs1205 were associated with increased CRP level (P=0.001 and P<0.001, respectively) and rs1800947 with decreased CRP level (P=0.003). Two haplotypes inferred from 5 SNPs (GCGCG and AAGCG) were associated with increased CRP level (P=0.017 and P<0.0001, respectively). Interaction analysis revealed interaction of obesity with CRP genotypes associated with high CRP level (interaction P=0.034 and 0.020 for SNPs rs2794521 and rs1800947, respectively). An effect of obesity on CRP level was also noted in haplotype interaction analysis with the association occurring predominantly in obese subjects (P=0.034). CONCLUSION: CRP polymorphisms are independently associated with increased or decreased CRP level in Taiwanese. Further, CRP genotypes/haplotypes interact with obesity to set CRP level. These findings have implications for the prediction of atherosclerotic disease.

Genetic variation in the ASIC3 gene influences blood pressure levels in Taiwanese.

BACKGROUND: The acid-sensing ion channel 3 (ASIC3) is a ligand-gated cation channel activated by extracellular protons, and is associated with an exercise-induced pressor reflex and possibly autonomic imbalance. METHODS: To test the statistical association between genetic polymorphisms of the ASIC3 gene and blood pressure (BP) variations in Taiwanese, 551 unrelated individuals (286 men and 265 women) were recruited from a routine health examination. The participants had no prior history of cardiovascular disease or medication use for hypertension. RESULTS: Six ASIC3 gene polymorphisms were genotyped; three were polymorphic, and only the rs2288646 polymorphism was associated with variations in BP among participants. Significantly higher systolic, diastolic, and mean BP were observed in participants carrying the rs2288646-A allele (P=0.034, 0.023, and 0.010, respectively). Significantly higher frequencies of the rs2288646-A-containing genotype were observed in normotensive, prehypertensive, and hypertensive subgroups (P for trend=0.026); and in those with higher systolic and diastolic BPs (P for trend=0.005 and P for trend=0.002, respectively). The association between the rs2288646-A allele and BP persisted even after adjustment for age, sex, BMI, and other metabolic factors. When a second independent group of 403 individuals was combined with the first group of 551 (n=954), a significantly higher frequency of the rs2288646-A-containing genotype was observed in participants with hypertension (9.7 vs. 4.0%, P=0.003). CONCLUSION: Our data showed an independent association between an ASIC3 genetic polymorphism and BP variations in Taiwanese. These results suggest that the ASIC3 may be involved in BP regulation.