Computational protocol: HBV-Related Hepatocellular Carcinoma Susceptibility Gene KIF1B Is Not Associated with Development of Chronic Hepatitis B

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Protocol publication

[…] In addition to the SNP of rs17401966 identified by the GWAS in Chinese population, two other candidate SNPs in the intron of KIF1B gene were identified by bioinformatics analysis. The SNP of rs8019, which may located in the binding site of microRNA, was selected using an integrated bioinformatics tool “SNP Info”(http://manticore.niehs.nih.gov/snpfunc.htm) . And rs17401924 was predicted to influence the gene splicing, which was analyzed by “ESE finder” (http://rulai.cshl.edu/cgi-bin/tools/ESE3/esefinder.cgi?process=home) . [...] The differences in distribution of genotype between CHB cases and controls were tested by χ2 test. Logistic regression was used to evaluate the associations between KIF1B genotypes or haplotypes and the outcome of HBV infection. Odds ratios (ORs) and their 95% confidence intervals (CIs) were calculated after adjustment for age and sex where appropriate. Nonsuperiority test was used to confirm the absence of association between all SNPs detected and progression to CHB . All statistical analyses were conducted by Statistical Analysis System Software (version 9.2; SAS Institute, Cary NC). Linkage disequilibrium (LD) of the three SNPs was estimated using Haploview . Haplotypes were reconstructed and Haplotype frequencies were analyzed using Phase 2.1 . […]

Pipeline specifications

Software tools ESEfinder, Haploview
Applications WGS analysis, GWAS
Organisms Hepatitis B virus, Homo sapiens
Diseases Hepatitis B, Carcinoma, Hepatocellular, Hepatitis B, Chronic