LDAK-GBAT: Fast and powerful gene-based association testing using summary statistics

We present LDAK-GBAT, a tool for gene-based association testing using summary statistics from genome-wide association studies that is computationally efficient, produces well-calibrated p values, and is significantly more powerful than existing tools. LDAK-GBAT takes approximately 30 min to analyze imputed data (2.9M common, genic SNPs), requiring less than 10 Gb memory. It shows good control of type 1 error given an appropriate reference panel. Across 109 phenotypes (82 from the UK Biobank, 18 from the Million Veteran Program, and nine from the Psychiatric Genetics Consortium), LDAK-GBAT finds on average 19% (SE: 1%) more significant genes than the existing tool sumFREGAT-ACAT, with even greater gains in comparison with MAGMA, GCTA-fastBAT, sumFREGAT-SKAT-O, and sumFREGAT-PCA.