Leveraging omics data to boost the power of genome-wide association studies

Genome-wide association studies (GWASs) have successfully identified many genetic variants and risk loci for complex traits and common diseases in the last 15 years. However, these identified variants, in general, can explain only a small to moderate proportion of the heritability, thus the task of improving GWAS power for more discoveries remains both critical and challenging. In addition to the usual but costly or even infeasible route of continuing to increase the sample size, many approaches have been proposed to incorporate functional annotations to prioritize SNPs but with only limited success. Here, by taking advantage of increasing availability of various types of omics data, we propose a new and orthogonal approach by integrating individual-level omics data with GWASs. The premise is that since omics data reflect both genetic and environmental (such as diet and other lifestyle) effects on individuals, they can be used to account for (otherwise unexplained) variations among individuals in GWAS analysis, leading to more precise/efficient estimation and thus higher power. As a concrete example, we propose boosting GWAS power by adjusting for metabolomics data in GWAS analysis. We applied the method to the UK Biobank subcohort of n = 90,000 individuals with both GWAS and metabolomics data. The analysis of 7 quantitative traits and one binary trait demonstrated clear power gains. For example, the new method (after adjusting for metabolomics data) identified 13 new loci for diastolic blood pressure that were all missed by the standard GWAS, and most or all of the 13 new signals were validated in two much larger GWAS datasets (n = 340,000 and 700,000); the improved estimation efficiency was equivalent to a 38.4% gain of GWAS sample size. The proposed method is both simple and promising and broadly applicable to integrating GWASs with other omics data.