A comparative study of data integration methods, integrating genetic association and functional annotation summary statistics

Functional annotations have the potential to increase the power of genome-wide association studies (GWAS) by prioritizing variants according to their biological function. Focusing on variant-specific annotation meta-scores including CADD (Kircher et al., 2014) and Eigen (Ionita-laza et al., 2016), we broadly examined GWAS summary statistics of 1,132 traits from the UK Biobank (Sudlow et al., 2015) using the weighted p-value approach (Genovese et al., 2006) and stratified false discovery control (sFDR) method (Sun et al., 2006). These 1,132 traits were rated by Benjamin Neales lab from the Broad Institute as having medium to high confidence for their heritability estimates. Averaged across the 1,132 UK Biobank traits, sFDR was more robust to uninformative meta-scores, but the weighted p-value method identified more variants using CADD or Eigen, based on performance measures that included type I error control, recall, precision, and relative efficiency. Our application results were consistent with those from an extensive simulation study using three different designs, including leveraging the real genetic data combined with simulated genomic data and vice versa. We also considered the recent FINDOR method (Kichaev et al., 2019), which leverages a set of individual 75 functional annotations into GWAS. An earlier application of FINDOR to 27 traits selected from the z7 category (SNP-heritability p-value < 1.27 x 10-12 by Nealelab) detected 13%-20% additional genome-wide significant loci as compared to the standard annotation-free GWAS, which we confirmed. Moreover, across all 438 traits in the z7 category, 46,631 out 59,764 (80%) significant loci discovered are common across the three data-integration methods. However, across all the 1,132 UK Biobank traits examined, the median [Q1,Q3] of the total numbers of new, genome-wide significant independent loci were 0 [0, 3] by FINDOR, 0 [0, 2] by weighted p-value, and 0 [0, 0] by sFDR. Notably, 162 traits (89%) in the nonsig trait category (SNP-heritability p-value > 0.05, "likely reflecting limited statistical power rather than a true lack of heritability" by Nealelab) had no new discoveries after data-integration by any of the three methods. Our findings suggest that more informative scores or new data integration methods are warranted to further improve the power of GWAS by leveraging the variant functional annotations.