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Objective:We selected 48 single nucleotide polymorphisms (SNPs) which were published to be related to metabolism syndrome or its components.The study was aimed to explore whether these SNPs play roles in the pathways in the development of Non-alcoholic fatty liver disease (NAFLD) and select the novel genetic variants.Methods:Case-control study was conducted in the physical examination center of a tertiary hospital from April to May in 2013,enrolling 892 participants aged more than 18 years old.The participants were investigated by questionnaire,anthropometric and biochemical measurements.Forty-eight single nucleotide polymorphisms (SNPs) were genotyped,multi-factor logistic regression was used to adjust for confounding.Genetic risk score was used to estimate the cumulative effects of genes.Results:In FTO gene,SNPs rs1558902 (odds ratio (OR)=1.56,95% confidence interval (CI):1.11-2.20,P=0.01),rs8050136 (OR=1.62,95%CI:1.14-2.28,P=0.01) and rs9939609(OR=1.60,95%CI:1.14-2.25,P=0.01) were all associated with NAFLD at additive genetic model after adjustment for behavioral and dietary factors,which were all independent of BMI,but not WC.Other SNPs relating to NAFLD were PAX5(rs16933812) (OR = 2.10,95 % CI = 1.01-4.37,P=0.05),VEGFA (rs6905288)(OR=1.80,95%CI:1.03-3.14,P=0.04),SPRY2 (rs534870) (OR=1.62,95%CI:0.99-2.63,P=0.05) and FAIM2 (rs7138803) (OR=1.74,95%CI:0.99-3.03,P=0.05).The GRS showed a significant stepwise increase risk in NAFLD as a function of the number of risk genotypes (P = 0.0319).Conclusions:The present study demonstrated that SNPs in FTO,VEGFA,PAX5,SPRY2 and FAIM2 were significantly associated with NAFLD in Chinese population.These genes were susceptibility genes for NAFLD.Additionally,the number of risk genotypes play strongest role in NAFLD risk.