In this case, trait i is the "discovery" sample.
The ENIGMA consortium has completed a meta-analysis of site-level GWAS in a discovery sample of 13,171 subjects of European ancestry2, 61.
The CHARGE consortium has completed meta-analysis of site-level GWAS in a discovery sample of 12,803 subjects of European ancestry42.
A genome-wide association study (GWAS) of educational attainment was conducted in a discovery sample of 101,069 individuals and a replication sample of 25,490.
To control for possible biases arising from differential blood sample cellular composition between groups, we used haematology data collected in the discovery sample during the randomized placebo-controlled trial.
In summary, element (i,j) in this figure represents the pi1 statistic when assessing the 0.05 FDR genes (identified in the discovery sample) from trait i (rows) in the replication sample (trait j)(columns).
The discovery sample pools numerous datasets and contains information from participants in 15 different countries.
To construct a PRS, an initial GWAS is done which is considered the discovery sample.
In the discovery sample, 2,731 cases and 10,747 controls passed quality control steps, and 429,912 markers were successfully genotyped.
Primarily, this was an investigation of a single disease (schizophrenia) where the SNPs derived from the discovery sample were tested in an independent schizophrenia replication sample.
For the calculation we used assumptions derived from Gormley et al.: Discovery cohort = 375.000; variance explained in the discovery sample = 0.1463; and a prevalence of 0.158.
