Computational protocol: Role of HLA-DP Polymorphisms on Chronicity and Disease Activity of Hepatitis B Infection in Southern Chinese

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Protocol publication

[…] Three SNPs within chromosome 6, namely rs3077 (in the 3′ untranslated region of the HLA-DPA1 gene), rs9277378 and rs3128917 (inside and near the HLA-DPB1 gene, respectively), were studied (). rs3077 was selected for this study because rs3077 and rs9277535 (at the 3′ untranslated region of HLA-DPB1) have been identified to be strongly associated with persistent HBV infection . We chose to study rs9277378 instead of rs9277535 because, our previous large scale genotypic analysis revealed that, rs9277378 was more readily detected in DNA extracted from sera than rs9277535 (data not shown). Moreover, linkage disequilibrium (LD) analysis by the Haploview software (version 4.2) revealed that rs9277378 has a strong LD with rs9277535 (D’ = 1.00, R2 = 0.954) in the HapMap Han Chinese in Beijing (CHB) and Japanese in Tokyo (JPT) Populations. We also confirmed, in a small subset of 50 randomly selected samples from the current study, that rs9277535 and rs9277378 genotypes were concordant in 48 (96%) samples with a strong LD (D’ = 1.00, R2 = 0.903). The SNP rs3128917 was also chosen for the present study, as this SNP has the highest odds ratio (OR) among 11 SNPs which influence chronicity of HBV infection .The 3 selected SNPs, rs3077, rs9277378 and rs3128917, were genotyped using the TaqMan SNP genotyping assay (Life Technologies, Carlsbad, CA). Briefly, free circulating DNA was extracted from 200 µl of serum samples, using the Purelink Genomic DNA Mini Kit (Life Technologies). The SNP genotyping reaction was performed in a TaqMan real-time PCR format, using SNP-specific primers and FAM- and VIC-labeled allele-specific probes provided in the TaqMan SNP genotyping kit (Life Technologies) and the real-time PCR enzymes and reagents provided in QuantiFast Probe PCR Kit (QIAGEN, Hilden, Germany). The real-time PCR reaction was performed in a RotorGene-Q real-time PCR System (QIAGEN). [...] Statistical analyses were performed using PLINK v.1.07 (http://pngu.mgh.harvard.edu/purcell/plink/) and SPSS 18.0 (SPSS Inc., Chicago, IL). Logistic regression was performed to compare between case and control groups, and all ORs and p values were adjusted for age and sex. The Student t test was used to test normally distributed variables. Categorical variables were tested by the Chi-square test. Statistical significance was defined by p<0.05. […]

Pipeline specifications

Software tools Haploview, PLINK, SPSS
Applications Miscellaneous, GWAS
Organisms Hepatitis B virus
Diseases Hepatitis B