Another practice supported herein is to perform pre-GWAS QC on homogenous ancestry groups rather than on the entire cohort. In addition to known QC metrics sensitive to population ancestry, such as heterozygosity rate and IBD, we show by applying QC on ancestry groups rather than on the entire sample there is a reduction in marker loss due to MAF and HWE thresholds. By removing markers that would be retained in subpopulation analyses potential etiologically relevant associations may be missed.
