Table 1 Replication of results in GERA

From: Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

Discovery phenotype

Replication phenotype

# Signif genes in disc set

# Replicated genes

π1(all) in repl

π1(sig) in repl

% Replicated genes

# Replicated coloc or undeterm

Coronary artery disease

Any cardiac event

56

6

0.4%

49.1%

10.7%

6

LDL cholesterol

Dyslipidemia

282

219

5.8%

90.8%

78.5%

184

Triglycerides

Dyslipidemia

233

100

5.8%

73.1%

43.5%

69

Schizophrenia

Any psychiatric event

285

60

1.2%

47.6%

21.1%

51

  1. Significant genes/tissue pairs were replicated using a closely matched phenotype in an independent dataset from the GERA cohort36. The criteria consisted in significance threshold for replication at p < 0.05, concordant directions of effect, and meta analysis p-value less than the Bonferroni threshold in the discovery set. π1 is an estimate of proportion of true positives in the replication set. π1(all) uses all gene–tissue pairs whereas π1(sig) is computed using only gene-tissue pairs that were significant in the discovery set. The column ‘# replicated genes coloc or undeterm’ is the number of replicated genes excluding the ones for which there was strong evidence of independent GWAS and eQTL signals
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