Computational protocol: Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure

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Protocol publication

[…] Stage 1 was a meta-analysis of directly genotyped and imputed SNPs from population-based or control samples from case-control studies, in the International Consortium of Blood Pressure Genome-wide Association Studies (ICBP-GWAS). The characteristics of the 35 studies, including demographics, genotyping arrays, quality control filters and statistical analysis methods used are listed in . Imputation of allele dosage of ungenotyped SNPs in HapMap CEU v21a or v22 was carried out by each of the studies using MACH, IMPUTE or BIMBAM with parameters and pre-imputation filters as specified in . SNPs were excluded from analysis if the study-specific imputation quality (r2.hat in MACH or .info in IMPUTE) was <0.3. In total, up to 2652054 genotyped or imputed autosomal SNPs were analyzed. Full details of the models, methods, and corrections for antihypertensive treatment are provided in the . All analyses assumed an additive genetic model and were adjusted for sex, age, age, body mass index and ancestry principal components. In related individuals, regression methods that account for relatedness were applied. All study-specific effect estimates and coded alleles were oriented to the forward strand of the HapMap release 22 with the alphabetically higher allele as the coded allele. To capture loss of power due to imperfect imputation, we estimated “N effective” as the sum of the study-specific products of the imputation quality metric and the sample size. No filtering on minor allele frequency was done. Genomic control was carried out on study-level data and inverse variance weighting was used for meta-analysis of Stage 1. The meta-analysis results were subject to genomic control. Lambda estimates are given in . […]

Pipeline specifications

Software tools IMPUTE, BIMBAM
Application GWAS