Q-Q Plot of GWA results, Scoring Index and Heatmap for NECS with Matched and Unmatched Controls. The QQ plot (top left) shows the substantial decrease of the inflation in the GWA results when controls are matched to cases within each cluster with the genomic control factor, λ, decreasing from 1.44 to 1.07. When adjusting for the top 4 PCs in the unmatched analysis, λ decreases to 1.04, however, many of the top associations are missed (Figure 7). The scoring index (bottom left) for the combined analysis of the NECS and controls from the Illumina database maximized and optimized at 8 clusters (SI = 0.919, 95% CI: (0.907, 0.931)). The heatmap displays a pattern for the top 4 PCs.
Solovieff et al. BMC Genetics 2010 11:108 doi:10.1186/1471-2156-11-108