Results of the GWAS were then used as part of gene-based tests of association in the Knowledge-based mining system for Genome-wide Genetic studies (KGG) software package Version 3.5.38, 39 This approach uses an extended Simes test that integrates prior functional information and the meta-analysis association results when combining the SNP P-values within a gene to obtain an overall association P-value for each entire gene. We conducted 24 576 gene-based tests of association. The genome-wide significance level according to the Knowledge-based mining system for Genome-wide Genetic studies default setting of Benjamini and Hochberg false discovery rate threshold of 0.05 (ref. 40) was 9.38 × 10−6.
