Computational protocol: Association of IFNGR2 gene polymorphisms with pulmonary tuberculosis among the Vietnamese

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Protocol publication

[…] Representative SNPs around IFNGR2 were selected from HapMap database (The International HapMap Consortium ). SNP genotype data of Han Chinese in Beijing (CHB) encompassing 350 kb from IL10RB to CRYZL1 were analyzed by Haploview 4.2 (Barrett et al. ), and 27 representative SNPs were chosen based on the method of block-by-block tags in linkage disequilibrium (LD) blocks determined by confidence interval method (Gabriel et al. ). The IFNGR2 SNPs identified as mentioned above and selected SNPs were genotyped in 273 TB patients of panel A and 506 controls. Genotyping was performed by the Digitag2 assay that has previously been described in another study (Nishida et al. ). [...] Disease associations with markers were assessed by Chi-square test or Fisher’s exact test, and P values less than 0.05 were considered significant. Statistical analysis was performed using Stata version 10 (StataCorp, College Station, TX, USA). When necessary, P values were subjected to Bonferroni’s correction for multiple comparisons. To determine whether genotype frequencies in the populations are compatible with Hardy–Weinberg equilibrium, Hardy–Weinberg exact tests were carried out using the program Arlequin version 3.11 (Excoffier et al. ). To assess pairwise LD between polymorphisms, we calculated Lewontin’s D′ and r square (r2) for polymorphisms by Haploview version 4.2 (Barrett et al. ). TB disease associated with genetic variations was assessed by odds ratios unadjusted or adjusted for sex, age at recruitment and its interaction using logistic models. Tendency of having resistant alleles in the order of age at diagnosis was also tested using a similar logistic model within the TB group. Difference in luciferase activity between the haplotype under consideration and the other haplotypes was assessed by Wilcoxon rank sum/Mann–Whitney U test. […]

Pipeline specifications

Software tools Haploview, Arlequin
Applications Population genetic analysis, GWAS
Organisms Homo sapiens
Diseases Infection, Tuberculosis, Tuberculosis, Pulmonary