The identified set of 12,898 SNPs with low background LD in European American population and common to both the Illumina and Affymetrix commercial platforms can be used in PCA for evaluation of population structure. We detected similar patterns of population substructure in the original scans even though they were nested within different cohorts. The top three axes from the two independent studies appear to point to similar directions and are likely to be a characteristic of the European American population. Further studies are required to correlate differences along the axes of genetic variation with groups defined by self-described ethnic background, geographic location or specific demographic histories. Based on our present experiences, we believe that this set of SNPs should be sufficient for the inference and correction of population structure in GWAS conducted using either the Illumina or Affymetrix commercial platforms within the European American populations, and enables the comparison of population structure between studies performed on different platforms without relying on genotype imputation. The same search algorithm can be used to identify structure inference SNPs suitable for GWAS in other populations, such as African Americans.
