GWAS Results of EL for Matched and Unmatched Subjects. The x-axis reports the -log10 p-values for the GWAS in which subjects were matched based on 8 clusters. The y-axis reports the -log10 p-values for the GWAS controlling for the top 4 PCs in which an equal number of subjects were randomly chosen from the Illumina controls. The dotted line is drawn at a value of 7. The SNPs in the bottom right hand rectangle are SNPs which would be selected as the top SNPs in the matched and would be missed in the unmatched PC adjusted analysis. There are 19 SNPs with a p-value less than 10E-07 for the matched analysis for which the p-value is greater than 10E-07 for the unmatched PC adjusted analysis.
Solovieff et al. BMC Genetics 2010 11:108 doi:10.1186/1471-2156-11-108