Figure 3
From: Population structure at different minor allele frequency levels
Attempt to recover the clusters observed for MAF between 0.09 and 0.15 (see Figure 1, panels 7 and 8) by means of a single PCA analysis using all the SNVs (bottom panel) or all the common variants (SNVs with MAF >0.05, top panel). We performed logistic regression using cluster membership as the response, and using the top 10 PCs as the predictors. The separation of the clusters is very poor, indicating that the top 10 PCs commonly used in genome-wide association studies in adjusting for population structure fail to uncover the clustering observed using narrow frequency windows.