Each of 15 studies (59,380 individuals) used genome-wide SNP information to calculate a genomic relationship matrix (GRM) for all pairs of individuals and used this to correct association statistics for cryptic relatedness and population stratification. Each study used a linear mixed model as implemented in the software EMMAX23. Meta-analysis was performed as described for the standard GWAS and using a single GC correction. Each study additionally repeated the analyses for each chromosome using a GRM generated from the remaining 21 chromosomes, or in the case of the largest study (WGHS) repeating the analysis for all odd numbered chromosomes using a GRM generated from the even numbered chromosomes and vice versa. Each study then combined association results from the 22 or 2 parts of the genome into one set of data and we repeated the single GC meta-analysis.
