Computational protocol: The Impact of tagSNPs in CXCL16 Gene on the Risk of Myocardial Infarction in a Chinese Han Population

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Protocol publication

[…] The Chinese Han population's SNP data of CXCL16 gene were downloaded from the HapMap database (http://www.hapmap.org). Then the SNP data of CXCL16 gene were analyzed using Haploview software version 4.2 [] and obtained four tagSNPs, including rs2304973, rs1050998, rs3744700, and rs8123 (). A minor allele frequency (MAF) > 0.05 and a linkage disequilibrium measure (r2) > 0.8 were prerequisites for tagSNPs selection (r2 values were shown in ). These four tagSNPs would capture the information of the 8 known CXCL16 SNPs with a MAF > 0.05 (). Furthermore, the haplotypic blocks of the four tagSNPs were performed with the SHEsis platform [].The genotyping of the four tagSNPs was performed utilizing polymerase chain reaction-ligase detection reaction (PCR-LDR) method (Shanghai Biowing Applied Biotechnology Company), as described previously []. The sequences of primers and probes were listed in Table S1 in Supplementary Material available online at https://doi.org/10.1155/2017/9463272. [...] All the four tagSNPs of CXCL16 gene were tested for confirmation using Hardy-Weinberg expectations by a goodness-of-fit χ2 test among the control subjects. Quantitative variables were expressed as mean ± standard deviation (SD), and qualitative variables were expressed as percentages. The differences of the demographic characteristics between the cases and controls were estimated by the χ2 test (for categorical variables) and Student's t-test (for continuous variables).For the association analysis of individual tagSNP with MI risk, genotype frequencies were assessed by means of multivariate methods based on logistic regression analysis. And the odds ratios (ORs) and 95% confidence intervals (CIs) for the effect of SNPs on MI risk were adjusted by age, sex, smoking, drinking, hypertension, diabetes, and hyperlipidemia. The statistical analyses were performed using the SPSS software (version 19). The haplotype analysis on the polymorphisms was done using SHEsis software freely available at (http://analysis.bio-x.cn/myAnalysis.php). P value of less than 0.05 was used as the criterion of statistical significance. […]

Pipeline specifications

Software tools Haploview, SNPinfo, SPSS
Applications Miscellaneous, GWAS
Organisms Homo sapiens
Diseases Myocardial Infarction, Atherosclerosis