Research Paper Volume 10, Issue 3 pp 492—514

Figure 1. Scheme of univariate and pleiotropic meta-analyses in stage 2. (A) Statistics from stage 1 univariate GWAS of 20 phenotypes in five cohorts denoted PiCj, i∈1,20- and j∈1,5-. (B) Univariate statistics from the meta-analysis across cohorts using the fixed-effects meta-test (PiM) and Fisher test (PiFc). (C) Statistics from the pleiotropic meta-analysis across phenotypes in cohort j for: (i) omnibus tests with correlation matrix for phenotypes ΣjP (OpCj) and effect statistics ΣjB (ObCj) and (ii) Fisher test (FpCj). (D) Meta-statistics from Fisher test across cohorts for the results in (C) (OpFc, ObFc, and FpFc). (E) Meta-statistics across phenotypes for the results in (B) from (i) meta-test across cohorts and omnibus test across phenotypes with correlation matrix for phenotypes ΣmP (MOp), (ii) meta-test across cohorts and omnibus test across phenotypes with correlation matrix for effect statistics ΣmB (MOb), (iii) meta-test across cohorts and Fisher test across phenotypes (MFp), and (iv) Fisher test across cohorts and Fisher test across phenotypes (FcFp). Pathway 1: meta-analysis combining statistics across cohorts (pathway 1a) and pleiotropic meta-analysis across phenotypes (pathway 1b). Pathway 2: meta-analysis combining statistics across phenotypes (pathway 2a) and cohorts (pathway 2b).