Computational protocol: Association of BANK1 and TNFSF4 with systemic lupus erythematosus in Hong Kong Chinese

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Protocol publication

[…] Preprocessing filters were applied for Illumina Human 610-Quad arrays data. Individuals were left out from further analysis if their relationship test failed, indicated by high proportion (>20% of diploid genome) of shared region identical by decent between two individuals calculated by PLINK. Further, individuals were also discarded because of failed heterozygosity test, probably because of sample mix-up. All together six individuals were filtered out and the final sample number is 314 in SLE cases and 920 in controls. In addition, 1172 SNPs and 73 338 SNPs were discarded because of low-genotyping call rate (<0.95) and low-minor allele frequency (<0.01), respectively. SNPs that failed the Hardy–Weinberg equilibrium test (P<0.01) were also excluded from further analysis. After filtering, 489 851 SNPs remained and the total-genotyping call rate for these SNPs in the remaining individuals was 99.9%. Possible population substructure was evaluated with EIGENSTRAT and no population substructure was observed among local cases and controls. Chi-square test was corrected by an genome inflation factor of 1.03 calculated by PLINK. [...] The genotype frequencies of all SNPs were tested for Hardy–Weinberg equilibrium separately in cases and controls and all attained P>0.05. Disease associations were analyzed by basic allelic test, as well as logistic regression and other inheritance models. SNP effect models were tested by using SNPGWA (URL: http://www.phs.wfubmc.edu/public/bios/gene/downloads.cfm). Testing for deviation from additive model was not significant. Corresponding P-values were adjusted for age and sex by logistic regression. Independence test of SNPs in the same gene was performed by logistic regression, as well as haplotype-based association test. Sub-phenotype stratification analysis was performed by case-only approach, in which basic allelic test was performed by comparing minor allele frequency of patients with a specific sub-phenotype to patients without the specific sub-phenotype. Any interaction between BANK1 and TNFSF4 was tested by conditional analysis.All statistical analyzes were performed by PLINK, version 1.05, unless otherwise specified. Linkage disequilibrium patterns and values were obtained by HaploView. […]

Pipeline specifications

Software tools PLINK, Haploview
Application GWAS
Organisms Homo sapiens
Diseases Autoimmune Diseases, Lupus Erythematosus, Systemic