Computational protocol: Meta-analysis of GWAS on both Chinese and European populations identifies GPR173 as a novel X chromosome susceptibility gene for SLE

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Protocol publication

[…] On the basis of genotyping data, we imputed the X chromosome SNPs for all three datasets. First, SHAPEIT [] was used to prephase each of the datasets. Subsequently, in order to obtain genotypes of additional SNPs, imputation on X chromosome SNPs was performed using IMPUTE v2.3.2 [] on the three studies separately, using samples from the 1000 Genomes Project (phase 3, released in October 2014, build 37) as the reference. Both of the programs have a specialized algorithm to deal with X chromosome data. In all the studies, SNPs with an imputation score < 0.9 were removed from further analysis. [...] The X chromosomal SNPs passing quality control were analyzed for association using SNPTEST [], fitting a logistic regression model in males and females separately. The association for European data, which comprise samples derived from different cohorts [], was adjusted using four principal components. The two Asian cohorts were adjusted by the top two principal components. Meta-analysis was conducted using METAL [], which employs a method based on inverse variance and weights the effect size estimates of each SNP by its SE. For each SNP, Cochran’s Q statistic and the I2 index were used to test for any evidence of genetic heterogeneity between the Chinese and European data. […]

Pipeline specifications

Software tools SHAPEIT, IMPUTE, SNPTEST
Application GWAS
Diseases Autoimmune Diseases, Lupus Erythematosus, Systemic