Chunk #18 — Materials and Methods — R2 of a polygenic score under heterogeneity

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Meta-GWAS Accuracy and Power (MetaGAP) Calculator Shows that Hiding Heritability Is Partially Due to Imperfect Genetic Correlations across Studies.

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In S2 Derivations we derive a generic expression for the theoretical R2 of a PGS in a hold-out sample, with SNP weights based on a meta-analysis of GWAS results under imperfect CGRs. We consider a PGS that includes all the SNPs that tag independent haplotype blocks (i.e., there is no SNP selection).