FastGWA-GLMM: a generalized linear mixed model association tool for biobank-scale data

Abstract Compared to linear mixed model-based genome-wide association (GWA) methods, generalized linear mixed model (GLMM)-based methods have better statistical properties when applied to binary traits but are computationally much slower. Here, leveraging efficient sparse matrix-based algorithms, we developed a GLMM-based GWA tool (called fastGWA-GLMM) that is orders of magnitude faster than the state-of-the-art tool (e.g., ~37 times faster when n=400,000) with more scalable memory usage. We show by simulation that the fastGWA-GLMM test-statistics of both common and rare variants are well-calibrated under the null, even for traits with an extreme case-control ratio (e.g., 0.1%). We applied fastGWA-GLMM to the UK Biobank data of 456,348 individuals, 11,842,647 variants and 2,989 binary traits (full summary statistics available at http://fastgwa.info/ukbimpbin) and identified 259 rare variants associated with 75 traits, demonstrating the use of imputed genotype data in a large cohort to discover rare variants for binary complex traits.