We used the YFS samples that were assayed for SNPs, phenotype, and expression to assess the consistency of individual-level and summary-based TWAS. We first computed GWAS association statistics between phenotype (height) and SNP and used them in conjunction with the expression data to impute summary-based TWAS statistics. The TWAS statistics were compared to those from the simple regression of (height ~ expression) in the YFS data. We observed a correlation of 0.415 (Supplementary Figure 5), consistent with an average cis-h2g of 0.17 (≈0.415^2) observed for these genes. When restricting to a regression of (height ~ cis component of expression) we observed a correlation of 0.998 to the summary based TWAS, demonstrating the equivalence of the two approaches when using in-sample LD.
