Computational protocol: Association between the SNPs of the TOB1 gene and gastric cancer risk in the Chinese Han population of northeast China

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Protocol publication

[…] The potentially functional SNPs were selected using the NCBI dbSNP database (http://www.ncbi.nlm.nih.gov/snp) and SNPinfo (http://snpinfo.niehs.nih.gov/snpinfo/snpfuc.htm). The criterion applied on the minor allele frequency (MAF) in the NCBI was greater than 0.05 in the Chinese Han population. Ultimately, thirteen SNPs (rs78420930, rs35220381, rs12950561, rs7221352, rs61482741, rs9303568, rs34700818, rs12949115, rs9903822, rs12601477, rs11656976, rs9898809 and rs4626) were selected in our study. [...] Continuous variables with a normal distribution were described as the mean ± standard deviation and were compared using a Student's t-test. Discrete variables were described as the frequency (percentage) and were compared using the Chi-square (χ2) test. The genotype frequencies for all the TOB1 gene polymorphisms of the controls were tested for Hardy-Weinberg equilibrium by using a Chi-square test. Associations of the genotypes and alleles with the risk of GC were estimated by the odds ratios (ORs) and 95% confidence intervals (CIs). Linkage disequilibrium (LD) and haplotype analyses were performed with Haploview 4.2 software (http://sourceforge.net/projects/haploview/). P values and ORs with 95% CIs were calculated using a logistic regression analysis adjusted for age, gender, smoking status, pack-years, and drinking status. All the statistical analyses were performed using the SAS 9.3 software. All P values in the study were two-sided, and P<0.05 was considered statistically significant. […]

Pipeline specifications

Software tools SNPinfo, Haploview
Databases dbSNP
Application GWAS
Diseases Euthyroid Sick Syndromes, Stomach Neoplasms